calculate_diameter: calculate_pore_diameter

annotate calculate_pore_diameter_aqp.py @ 3:b120a98cf623 draft

"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"

author	agpetit
date	Fri, 27 May 2022 07:36:52 +0000
parents	e227d80e53be
children	a4097272ade0

rev	line source
0 e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	1 #!/usr/bin/env python3
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	2
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	3 # coding: utf-8
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	4 """
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	5 This script allows to launch a calculation of the pore diameter of an aquaporin
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	6 as a function of time from a .gro file and an .xtc file.
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	7 At the end of the script, a table containing the evolution of the distance over
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	8 time is created.
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	9 # USAGE : calculate_pore_diameter_aqp.py -xtc xtc_file -gro gro_file
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	10 -npao npa1 Pattern (optional) -npas npa2 Pattern (optional)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	11 -arro arR1 Pattern on H5 (optional) -arrs arR2 Pattern on HE (optional)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	12 -v verbose (optional) -w work_directory (optional)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	13 -o output_directory (optional) --gro_file_ext extension of gro file
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	14 (optional) --xtc_file_ext extension of xtc file (optional)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	15 -log name of log file (optional) -o name of output file (optional).
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	16 """
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	17
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	18
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	19 __all__ = [
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	20 "calculate_length_proto",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	21 "search_pattern",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	22 "run_one_frame_npa_arr",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	23 "run_one_frame_arr",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	24 "run_all_frames_npa_arr",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	25 "run_all_frames_arr",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	26 "create_config_file",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	27 ]
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	28 __author__ = "Agnès-Elisabeth Petit"
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	29 __date__ = "29/04/2021"
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	30 __version__ = "1.0"
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	31 __copyright__ = "(c) 2022 CC-BY-NC-SA"
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	32
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	33 # Library import
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	34 import argparse
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	35 import configparser
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	36 import logging
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	37 import os
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	38 import re
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	39 import sys
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	40
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	41 import MDAnalysis as Mda
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	42
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	43 import numpy as np
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	44
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	45 import pandas as pd
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	46
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	47 # Global variables
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	48
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	49 # Functions
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	50
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	51
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	52 def test_setup():
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	53 global args
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	54 args = parse_arguments()
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	55 args.verbose = True
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	56
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	57
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	58 def parse_arguments():
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	59 parser = argparse.ArgumentParser(
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	60 description="This script allows to launch a calculation of the pore"
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	61 + " diameter of an aquaporin as a function of time from"
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	62 + " a .gro file and an .xtc file.",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	63 formatter_class=argparse.ArgumentDefaultsHelpFormatter,
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	64 prefix_chars="-",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	65 add_help=True,
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	66 )
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	67 parser.add_argument(
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	68 "-v",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	69 "--verbose",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	70 action="store_true",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	71 help="""Information messages to stderr""",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	72 )
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	73 parser.add_argument(
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	74 "-gro", "--gro_file", type=str, nargs=1, help="""My input .gro file"""
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	75 )
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	76 parser.add_argument(
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	77 "-xtc", "--xtc_file", type=str, nargs=1, help="""My input .xtc file"""
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	78 )
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	79 parser.add_argument(
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	80 "--gro_file_ext", type=str, nargs=1, help="""My input .gro file"""
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	81 )
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	82 parser.add_argument(
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	83 "--xtc_file_ext", type=str, nargs=1, help="""My input .xtc file"""
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	84 )
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	85 parser.add_argument(
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	86 "-w", "--work_directory", type=str, nargs=1,
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	87 help="""It's work Directory"""
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	88 )
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	89 parser.add_argument(
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	90 "-od",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	91 "--output_directory",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	92 default="stdout",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	93 type=str,
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	94 nargs=1,
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	95 help="""It's output Directory""",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	96 )
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	97 parser.add_argument(
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	98 "-npao",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	99 "--npa_one",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	100 type=str,
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	101 nargs=1,
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	102 help="""3-letter pattern of the 3 amino acids of npa1""",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	103 )
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	104 parser.add_argument(
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	105 "-npas",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	106 "--npa_second",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	107 type=str,
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	108 nargs=1,
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	109 help="""3-letter pattern of the 3 amino acids of npa2""",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	110 )
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	111 parser.add_argument(
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	112 "-arro",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	113 "--arr_one",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	114 type=str,
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	115 default="",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	116 nargs=1,
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	117 help="""3-letter pattern of the 4 amino acids of first ArR on H5""",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	118 )
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	119 parser.add_argument(
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	120 "-arrs",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	121 "--arr_second",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	122 type=str,
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	123 default="",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	124 nargs=1,
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	125 help="""3-letter pattern of the 4 amino acids of second ArR on HE""",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	126 )
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	127 parser.add_argument("-o", "--output", help="""Output for files""")
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	128 parser.add_argument("-log", "--log_output", help="""Output for files""")
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	129 return parser.parse_args()
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	130
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	131
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	132 def search_amino_acids_pattern(list_pattern, uni):
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	133 """
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	134 Description:Creates a list that contains two lists.
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	135 The first one contains the residue numbers and the second one the residue
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	136 names for each amino acid in the pattern.
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	137 param list_pattern: list of the names of each amino acid of the pattern.
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	138 param uni: MDAnalysis universe.
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	139 return: list containing two lists. One containing residue numbers
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	140 and the other containing residue names.
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	141 """
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	142 if args.verbose:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	143 logging.info("\nFunction search_amino_acids_pattern")
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	144 logging.info("The input list is " + str(list_pattern))
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	145 logging.info("The input universe is " + str(uni))
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	146 if len(list_pattern) == 3:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	147 slct_pattern = (
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	148 "(resname "
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	149 + list_pattern[0]
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	150 + " or resname "
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	151 + list_pattern[1]
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	152 + " or resname "
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	153 + list_pattern[2]
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	154 + ") and name CA"
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	155 )
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	156 else:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	157 slct_pattern = (
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	158 "(resname "
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	159 + list_pattern[0]
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	160 + " or resname "
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	161 + list_pattern[1]
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	162 + " or resname "
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	163 + list_pattern[2]
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	164 + " or resname "
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	165 + list_pattern[3]
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	166 + ") and name CA"
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	167 )
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	168 if args.verbose:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	169 logging.info("The selected pattern is : " + slct_pattern)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	170 list_atm_npa = uni.select_atoms(slct_pattern).residues
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	171 list_all_num_resid = list_atm_npa.resids
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	172 if args.verbose:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	173 logging.info(
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	174 "The list containing all the residue numbers associated"
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	175 + " with the pattern is : " + str(list_all_num_resid)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	176 )
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	177 list_all_name_resid = list_atm_npa.resnames
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	178 if args.verbose:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	179 logging.info(
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	180 "The list containing all the residue names associated with the "
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	181 + "pattern is : " + str(list_all_name_resid)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	182 )
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	183 list_all_resid = [list_all_num_resid, list_all_name_resid]
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	184 if args.verbose:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	185 logging.info(
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	186 "The list containing the lists of numbers and names of residues"
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	187 + " associated with the pattern is : " + str(list_all_resid)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	188 )
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	189 return list_all_resid
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	190
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	191
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	192 def calculate_length_proto(list_num_resid):
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	193 """
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	194 Description : calculate the length of each protomer according to the number
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	195 of amino acids corresponding to the pattern.
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	196 param list_num_resid: list of amino acid numbers corresponding to the
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	197 pattern in the protein.
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	198 return: list of the length of each protomer.
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	199 """
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	200 if args.verbose:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	201 logging.info("\nFunction calculate_length_proto")
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	202 logging.info("The input list is " + str(list_num_resid))
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	203 list_length_proto = [1, 0, 0, 0, 0, 0, 0, 0]
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	204 ind_list_length_proto = 0
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	205 for i, v in enumerate(list_num_resid[1:]):
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	206 if int(v) < int(list_num_resid[i]):
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	207 ind_list_length_proto += 1
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	208 list_length_proto[ind_list_length_proto] += 1
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	209 else:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	210 list_length_proto[ind_list_length_proto] += 1
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	211 if args.verbose:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	212 for i, v in enumerate(list_length_proto):
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	213 logging.info(
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	214 "The length of the protomer "
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	215 + str(i + 1)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	216 + " is "
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	217 + str(v)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	218 + " residues"
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	219 )
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	220 return list_length_proto
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	221
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	222
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	223 def create_config_file(list_length_proto):
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	224 """
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	225 Description : creates a Configparser object that describes the start and
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	226 end indices of each protomer.
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	227 param list_length_proto: list of the length of each protomer.
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	228 return: Configparser object that describes the start and end indices
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	229 of each protomer.
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	230 """
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	231 if args.verbose:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	232 logging.info("\nFunction create_config_file")
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	233 logging.info("The input list is " + str(list_length_proto))
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	234 config = configparser.ConfigParser()
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	235 proto_prev = ""
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	236 for aqp in range(1, 3):
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	237 for p in range(1, 5):
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	238 if aqp == 1 and p == 1:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	239 proto_current = "AQP" + str(aqp) + ",P" + str(p)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	240 config[proto_current] = {}
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	241 config.set(proto_current, "start", str(0))
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	242 config.set(proto_current, "end", str(list_length_proto[0] - 1))
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	243 proto_prev = proto_current
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	244 if args.verbose:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	245 logging.info(proto_current + " starts at index "
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	246 + str(config["AQP1,P1"]["start"])
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	247 + " and finish at index "
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	248 + str(config["AQP1,P1"]["end"]))
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	249 else:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	250 proto_current = "AQP" + str(aqp) + ",P" + str(p)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	251 config[proto_current] = {}
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	252 if aqp == 1 and p == 2:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	253 config.set(proto_current, "start",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	254 str(int(config[proto_prev]["start"]) +
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	255 list_length_proto[p-2] - 1))
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	256 else:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	257 config.set(proto_current, "start",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	258 str(int(config[proto_prev]["start"])
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	259 + list_length_proto[p-2]))
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	260 config.set(proto_current, "end",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	261 str(int(config[proto_prev]["end"])
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	262 + list_length_proto[p-1]))
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	263 proto_prev = proto_current
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	264 if args.verbose:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	265 logging.info(
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	266 proto_current
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	267 + " starts at index "
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	268 + config[proto_current]["start"]
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	269 + " and finish at index "
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	270 + config[proto_current]["end"]
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	271 )
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	272 if args.verbose:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	273 logging.info(
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	274 "The sections of the settings object are : "
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	275 + str(config.sections())
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	276 )
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	277 logging.info(
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	278 "The keys for each section of the settings object are: "
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	279 + str(list(config["AQP1,P3"].keys()))
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	280 )
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	281 return config
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	282
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	283
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	284 def search_pattern(list_all_resid, config, list_pattern, pattern_resid, uni):
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	285 """
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	286 Description : creates the dictionary that contains the name, number and
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	287 position of the residue and the key for the following dictionary.
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	288 param list_all_resid: list containing two lists. One containing residue
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	289 numbers and the other containing residue names.
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	290 param config: Configparser object that describes the start and end indices
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	291 of each protomer.
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	292 param list_pattern: list of the names of each amino acid of the pattern.
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	293 param pattern_resid: string that gives the pattern (NPA1,NPA2,ArR1 ou ArR2)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	294 in which we are.
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	295 param uni: MDAnalysis universe
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	296 return: dictionary which contains as key the name of the
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	297 aquaporin, the protomer and the residue, as well as the residue number.
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	298 The value contains the name, the number and the position of the residue,
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	299 as well as the key of the next dictionary.
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	300 """
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	301 if args.verbose:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	302 logging.info("\nFunction search_pattern")
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	303 logging.info("The first input argument is " + str(list_all_resid))
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	304 logging.info("The second input argument is a configParser object")
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	305 logging.info("The third input argument is " + str(list_pattern))
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	306 logging.info("The fourth input argument is " + str(pattern_resid))
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	307 logging.info("The fourth input argument is " + str(uni))
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	308 num_ca_npa = 0
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	309 num_ca_arr = 0
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	310 dict_resid_pattern = {}
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	311 str_pattern = "".join(list_pattern)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	312 for aqp in range(1, 3):
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	313 for p in range(1, 5):
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	314 list_ind_temp_resid = []
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	315 list_ind_final_resid = []
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	316 proto = "AQP" + str(aqp) + ",P" + str(p)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	317 ss_name_list = list(
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	318 list_all_resid[1][
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	319 int(config[proto]["start"]): int(config[proto]["end"])
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	320 ]
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	321 )
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	322 ss_name_str = "".join(ss_name_list)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	323 pattern = re.compile(str_pattern)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	324 for v in pattern.finditer(ss_name_str):
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	325 if args.verbose:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	326 logging.info(
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	327 "The pattern " + str(pattern) + " is searched in "
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	328 + ss_name_str
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	329 )
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	330 if aqp == 1 and p == 1:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	331 list_ind_temp_resid.append(int(v.start() / 3))
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	332 else:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	333 list_ind_temp_resid.append(
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	334 int(v.start() / 3) + int(config[proto]["start"])
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	335 )
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	336 if args.verbose:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	337 logging.info("The temporary index list is "
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	338 + str(list_ind_temp_resid))
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	339 for ind_current in list_ind_temp_resid:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	340 val_one = list_all_resid[0][ind_current]
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	341 val_two = list_all_resid[0][ind_current + 1]
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	342 val_three = list_all_resid[0][ind_current + 2]
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	343 if val_one + 1 == val_two and val_one + 2 == val_three:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	344 if pattern_resid == "ArR1" or pattern_resid == "ArR2":
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	345 val_four = list_all_resid[0][ind_current + 3]
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	346 if val_one + 3 == val_four:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	347 list_ind_final_resid.append(ind_current)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	348 else:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	349 list_ind_final_resid.append(ind_current)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	350 list_ind_final_resid.append(ind_current + 1)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	351 list_ind_final_resid.append(ind_current + 2)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	352 if len(list_ind_final_resid) == 0:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	353 if args.verbose:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	354 logging.critical("The pattern is not found "
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	355 + "in the protein sequence")
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	356 print("The pattern is not found in the protein sequence")
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	357 sys.exit(1)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	358 if args.verbose:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	359 logging.info("The final index list is "
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	360 + str(list_ind_final_resid))
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	361 ind_list = []
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	362 for ind, val_ind in enumerate(list_ind_final_resid):
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	363 ind_list.append(ind)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	364 key = (
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	365 proto
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	366 + ","
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	367 + list_all_resid[1][val_ind]
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	368 + ","
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	369 + str(list_all_resid[0][val_ind])
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	370 )
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	371 if args.verbose:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	372 logging.info("The key of dictionary is " + key)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	373 slct_resid = (
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	374 "(resid " + str(list_all_resid[0][val_ind])
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	375 + ") and name CA"
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	376 )
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	377 if args.verbose:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	378 logging.info("The selected residue is : " + slct_resid)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	379 resid = uni.select_atoms(slct_resid)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	380 if args.verbose:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	381 logging.info("The AtomGroup is " + str(resid))
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	382 if pattern_resid == "ArR1":
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	383 new_key = "ArR1," + proto
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	384 if args.verbose:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	385 logging.info("The key of next dictionary is "
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	386 + new_key)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	387 position_ca = resid.positions[num_ca_arr]
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	388 num_ca_arr += 1
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	389 elif pattern_resid == "ArR2":
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	390 new_key = "ArR2," + proto
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	391 if args.verbose:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	392 logging.info("The key of next dictionary is "
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	393 + new_key)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	394 position_ca = resid.positions[num_ca_arr]
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	395 num_ca_arr += 1
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	396 else:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	397 if (ind - 3) in ind_list or pattern_resid == "NPA2":
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	398 new_key = "NPA2," + proto
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	399 if args.verbose:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	400 logging.info("The key of next dictionary is "
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	401 + new_key)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	402 position_ca = resid.positions[num_ca_npa]
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	403 else:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	404 new_key = "NPA1," + proto
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	405 if args.verbose:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	406 logging.info("The key of next dictionary is "
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	407 + new_key)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	408 position_ca = resid.positions[num_ca_npa]
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	409 dict_resid_pattern[key] = [
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	410 list_all_resid[1][val_ind],
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	411 list_all_resid[0][val_ind],
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	412 position_ca,
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	413 new_key,
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	414 ]
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	415 if args.verbose:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	416 logging.info(
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	417 "The value associated at the key "
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	418 + key
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	419 + " is "
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	420 + str(dict_resid_pattern[key])
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	421 )
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	422 if len(list_ind_final_resid) > 1:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	423 num_ca_npa += 1
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	424 if args.verbose:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	425 logging.info("The dictionary contains" + str(dict_resid_pattern))
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	426 return dict_resid_pattern
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	427
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	428
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	429 def search_resid_positions(dict_resid_pattern, uni):
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	430 """
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	431 Description : creates the dictionary that contains the position of the
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	432 barycenter of the alpha carbons of NPA and ArR.
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	433 param dict_resid_pattern: dictionary which contains as key the name of the
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	434 aquaporin, the protomer and the residue, as well as the residue number.
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	435 The value contains the name, the number and the position of the residue,
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	436 as well as the key of the next dictionary.
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	437 param uni: MDAnalysis universe.
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	438 return: dictionary which contains as key the name of the pattern,
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	439 the aquaporin and the protomer. The value associated with the key contain
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	440 the position of the barycenter of the pattern.
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	441 """
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	442 if args.verbose:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	443 logging.info("\nFunction search_resid_positions")
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	444 logging.info("The input dictionary is " + str(dict_resid_pattern))
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	445 logging.info("The input universe is " + str(uni))
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	446 dict_pos_resid = {}
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	447 for npa in range(1, 3):
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	448 num_proto = 0
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	449 for aqp in range(1, 3):
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	450 for p in range(1, 5):
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	451 list_atm_npa = []
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	452 key_npa = "NPA" + str(npa) + ",AQP" + str(aqp) + ",P" + str(p)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	453 key_arr1 = "ArR1,AQP" + str(aqp) + ",P" + str(p)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	454 key_arr2 = "ArR2,AQP" + str(aqp) + ",P" + str(p)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	455 for k, v in dict_resid_pattern.items():
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	456 if key_npa == v[3]:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	457 list_atm_npa.append(v[1])
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	458 elif key_arr1 == v[3]:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	459 dict_pos_resid[key_arr1] = v[2]
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	460 elif key_arr2 == v[3]:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	461 dict_pos_resid[key_arr2] = v[2]
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	462 if len(list_atm_npa) > 0:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	463 slct_pattern = (
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	464 "(resid "
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	465 + str(list_atm_npa[0])
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	466 + " or resid "
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	467 + str(list_atm_npa[1])
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	468 + " or resid "
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	469 + str(list_atm_npa[2])
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	470 + ") and name CA"
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	471 )
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	472 if args.verbose:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	473 logging.info("The selected pattern is " + slct_pattern)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	474 atom_group_pattern = uni.select_atoms(slct_pattern)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	475 if args.verbose:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	476 logging.info(str(atom_group_pattern))
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	477 deb = 0 + 3 * num_proto
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	478 fin = +3 + 3 * num_proto
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	479 atm_proto_aqp = atom_group_pattern[deb:fin]
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	480 if args.verbose:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	481 logging.info("deb : " + str(deb) + " fin : "
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	482 + str(fin))
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	483 logging.info("The selected AtomGroup is "
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	484 + str(atm_proto_aqp))
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	485 dict_pos_resid[key_npa] = atm_proto_aqp.centroid()
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	486 num_proto += 1
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	487 if args.verbose:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	488 logging.info("The dictionary contains " + str(dict_pos_resid))
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	489 return dict_pos_resid
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	490
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	491
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	492 def calculate_euclidean_distance(dict_pos_resid, choice_measure):
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	493 """
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	494 Description : creates the dictionary that contains the Euclidean distance
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	495 between ArR and NPA1 or NPA2.
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	496 param dict_pos_resid: dictionary which contains as key the name of the
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	497 pattern, the aquaporin and the protomer.
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	498 The value contains the position of the barycenter of the pattern.
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	499 param choice_measure: variable that contains ArR-ArR or NPA-ArR.
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	500 return: dictionary which contains as key the name of the couple,
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	501 the aquaporin and the protomer.
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	502 The value contains the euclidean distance between the barycenters of
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	503 the two motifs of the couple.
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	504 """
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	505 if args.verbose:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	506 logging.info("\nFunction calculate_euclidean_distance")
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	507 logging.info("The input dictionary is " + str(dict_pos_resid))
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	508 logging.info("The distance will be calculated between"
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	509 + choice_measure)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	510 dict_pair_dist = {}
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	511 if choice_measure == "NPA-ArR":
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	512 for npa in range(1, 3):
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	513 for aqp in range(1, 3):
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	514 for p in range(1, 5):
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	515 key_npa = "NPA" + str(npa) + ",AQP" + str(aqp) \
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	516 + ",P" + str(p)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	517 key_arr1 = "ArR1,AQP" + str(aqp) + ",P" + str(p)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	518 new_key = "ArR-NPA" + str(npa) + ",AQP" + str(aqp) \
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	519 + ",P" + str(p)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	520 dict_pair_dist[new_key] = np.linalg.norm(
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	521 dict_pos_resid[key_npa] - dict_pos_resid[key_arr1]
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	522 )
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	523 if args.verbose:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	524 logging.info(
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	525 "Key NPA : "
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	526 + key_npa
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	527 + " value : "
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	528 + str(dict_pos_resid[key_npa])
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	529 )
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	530 logging.info(
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	531 "Key ArR : "
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	532 + key_arr1
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	533 + " value : "
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	534 + str(dict_pos_resid[key_arr1])
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	535 )
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	536 logging.info(
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	537 "The value associated at the key "
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	538 + new_key
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	539 + " is "
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	540 + str(dict_pair_dist[new_key])
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	541 )
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	542 else:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	543 for aqp in range(1, 3):
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	544 for p in range(1, 5):
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	545 key_arr1 = "ArR1,AQP" + str(aqp) + ",P" + str(p)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	546 key_arr2 = "ArR2,AQP" + str(aqp) + ",P" + str(p)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	547 new_key = "ArR1-ArR2,AQP" + str(aqp) + ",P" + str(p)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	548 dict_pair_dist[new_key] = np.linalg.norm(
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	549 dict_pos_resid[key_arr1] - dict_pos_resid[key_arr2]
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	550 )
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	551 if args.verbose:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	552 logging.info(
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	553 "Key ArR1 : "
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	554 + key_arr1
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	555 + " value : "
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	556 + str(dict_pos_resid[key_arr1])
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	557 )
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	558 logging.info(
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	559 "Key ArR2 : "
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	560 + key_arr2
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	561 + " value : "
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	562 + str(dict_pos_resid[key_arr2])
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	563 )
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	564 logging.info(
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	565 "The value associated at the key "
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	566 + new_key
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	567 + " is "
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	568 + str(dict_pair_dist[new_key])
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	569 )
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	570 if args.verbose:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	571 logging.info("The dictionary contains " + str(dict_pair_dist))
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	572 return dict_pair_dist
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	573
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	574
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	575 def run_one_frame_npa_arr(list_resid_npa1, list_resid_npa2, list_resid_arr,
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	576 uni):
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	577 """
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	578 Description: compiles the different functions to create the dict_pair_dist
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	579 dictionary for one frame.
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	580 param list_resid_npa1: list containing the names of the residues
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	581 constituting the NPA1.
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	582 param list_resid_npa2: list containing the names of the residues
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	583 constituting the NPA2.
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	584 param list_resid_arr: list containing the names of the residues
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	585 constituting the ArR.
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	586 param uni: MDAnalysis universe.
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	587 return: dictionary which contains as key the name of the couple,
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	588 the aquaporin and the protomer.
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	589 The value contains the euclidean distance between the barycenters of
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	590 the two motifs of the couple.
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	591 """
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	592 if args.verbose:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	593 logging.info("\nFunction runForOneFrame")
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	594 logging.info("The first input parameter is " + str(list_resid_npa1))
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	595 logging.info("The second input parameter is " + str(list_resid_npa2))
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	596 logging.info("The third input parameter is " + str(list_resid_arr))
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	597 logging.info("The fourth input parameter is " + str(uni))
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	598 choice_measure = "NPA-ArR"
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	599 if list_resid_npa1 == list_resid_npa2:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	600 if args.verbose:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	601 logging.info("Pattern NPA1 identical to pattern NPA2")
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	602 pattern = "NPA1"
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	603 list_all_resid_npa = search_amino_acids_pattern(list_resid_npa1, uni)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	604 list_length_proto_npa = \
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	605 calculate_length_proto(list(list_all_resid_npa[0]))
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	606 config_npa = create_config_file(list_length_proto_npa)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	607 dict_resid_pattern = search_pattern(
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	608 list_all_resid_npa, config_npa, list_resid_npa1, pattern, uni
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	609 )
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	610 else:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	611 if args.verbose:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	612 logging.info("Pattern NPA1 different from the NPA2 pattern")
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	613 # NPA1
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	614 pattern = "NPA1"
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	615 list_all_resid_npa = search_amino_acids_pattern(list_resid_npa1, uni)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	616 list_length_proto_npa = \
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	617 calculate_length_proto(list(list_all_resid_npa[0]))
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	618 config_npa1 = create_config_file(list_length_proto_npa)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	619 dict_resid_pattern = search_pattern(
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	620 list_all_resid_npa, config_npa1, list_resid_npa1, pattern, uni
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	621 )
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	622 # NPA2
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	623 pattern = "NPA2"
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	624 list_all_resid_npa = search_amino_acids_pattern(list_resid_npa2, uni)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	625 list_length_proto_npa = \
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	626 calculate_length_proto(list(list_all_resid_npa[0]))
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	627 config_npa2 = create_config_file(list_length_proto_npa)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	628 dict_resid_pattern.update(
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	629 search_pattern(
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	630 list_all_resid_npa, config_npa2, list_resid_npa2, pattern, uni
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	631 )
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	632 )
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	633 # ArR
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	634 pattern = "ArR1"
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	635 list_all_resid_arr = search_amino_acids_pattern(list_resid_arr, uni)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	636 list_length_proto_arr = \
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	637 calculate_length_proto(list(list_all_resid_arr[0]))
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	638 config_arr = create_config_file(list_length_proto_arr)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	639 dict_resid_pattern.update(
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	640 search_pattern(list_all_resid_arr, config_arr, list_resid_arr,
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	641 pattern, uni)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	642 )
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	643 # dict position
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	644 dict_pos_resid = search_resid_positions(dict_resid_pattern, uni)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	645 # dict distance
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	646 dict_pair_dist = \
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	647 calculate_euclidean_distance(dict_pos_resid, choice_measure)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	648 return dict_pair_dist
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	649
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	650
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	651 def run_one_frame_arr(list_resid_arr1, list_resid_arr2, uni):
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	652 """
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	653 Description: compiles the different functions to create the dict_pair_dist
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	654 dictionary for one frame.
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	655 param list_resid_arr1: list containing the names of the residues
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	656 constituting the ArR1.
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	657 param list_resid_arr2: list_resid_arr2, list containing the names of
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	658 the residues constituting the ArR2.
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	659 param uni: MDAnalysis universe.
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	660 return: dictionary which contains as key the name of the couple,
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	661 the aquaporin and the protomer.
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	662 The value contains the euclidean distance between the barycenters of
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	663 the two motifs of the couple.
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	664 """
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	665 if args.verbose:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	666 logging.info("\nFunction runForOneFrame")
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	667 logging.info("The first input parameter is " + str(list_resid_arr1))
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	668 logging.info("The second input parameter is " + str(list_resid_arr2))
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	669 logging.info("The third input parameter is " + str(uni))
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	670 dict_resid_pattern = {}
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	671 # ArR1
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	672 pattern = "ArR1"
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	673 list_all_resid_arr1 = search_amino_acids_pattern(list_resid_arr1, uni)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	674 list_length_proto_arr1 = \
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	675 calculate_length_proto(list(list_all_resid_arr1[0]))
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	676 config_arr1 = create_config_file(list_length_proto_arr1)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	677 dict_resid_pattern.update(
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	678 search_pattern(list_all_resid_arr1, config_arr1, list_resid_arr1,
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	679 pattern, uni)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	680 )
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	681 # ArR2
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	682 pattern = "ArR2"
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	683 list_all_resid_arr2 = search_amino_acids_pattern(list_resid_arr2, uni)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	684 list_length_proto_arr2 = \
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	685 calculate_length_proto(list(list_all_resid_arr2[0]))
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	686 config_arr2 = create_config_file(list_length_proto_arr2)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	687 dict_resid_pattern.update(
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	688 search_pattern(list_all_resid_arr2, config_arr2, list_resid_arr2,
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	689 pattern, uni)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	690 )
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	691 # dict position
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	692 dict_pos_resid = search_resid_positions(dict_resid_pattern, uni)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	693 # dict distance
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	694 choice_measure = "ArR-ArR"
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	695 dict_pair_dist = \
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	696 calculate_euclidean_distance(dict_pos_resid, choice_measure)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	697 return dict_pair_dist
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	698
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	699
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	700 def run_all_frames_npa_arr(
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	701 list_resid_npa1, list_resid_npa2, list_resid_arr, col_number, uni
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	702 ):
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	703 """
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	704 Description: creates the table containing the pore diameter of an aquaporin
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	705 over time.
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	706 param list_resid_npa1: list containing the names of the residues
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	707 constituting the NPA1.
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	708 param list_resid_npa2: list containing the names of the residues
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	709 constituting the NPA2.
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	710 param list_resid_arr: list containing the names of the residues
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	711 constituting the ArR.
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	712 param col_number: number of columns in the table
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	713 param uni: MDAnalysis universe.
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	714 return: list containing an array and a key list. The table containing the
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	715 pore diameter of an aquaporin over time.
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	716 """
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	717 if args.verbose:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	718 logging.info("\nFunction runForAllFrame")
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	719 logging.info("The first input parameter is " + str(list_resid_npa1))
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	720 logging.info("The second input parameter is " + str(list_resid_npa2))
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	721 logging.info("The third input parameter is " + str(list_resid_arr))
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	722 logging.info("The fourth input parameter is " + str(col_number))
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	723 logging.info("The fifth input parameter is " + str(uni))
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	724 nbr_frame = len(uni.trajectory)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	725 if args.verbose:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	726 logging.info("The number of frame is " + str(nbr_frame))
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	727 tab_pair_dist = np.empty((nbr_frame, col_number))
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	728 if args.verbose:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	729 logging.info(
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	730 "The dimensions of the table of means and standard deviation are"
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	731 + " as follows " + str(tab_pair_dist.shape)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	732 )
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	733 list_key = []
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	734 pattern_arr = ""
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	735 pattern_npa1 = ""
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	736 pattern_npa2 = ""
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	737 dict_prot = {
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	738 "ALA": "A",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	739 "CYS": "C",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	740 "ASP": "D",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	741 "GLU": "E",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	742 "PHE": "F",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	743 "GLY": "G",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	744 "HIS": "H",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	745 "ILE": "I",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	746 "LYS": "K",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	747 "LEU": "L",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	748 "MET": "M",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	749 "ASN": "N",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	750 "PRO": "P",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	751 "GLN": "Q",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	752 "ARG": "R",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	753 "SER": "S",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	754 "THR": "T",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	755 "VAL": "V",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	756 "TRP": "W",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	757 "TYR": "Y",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	758 "HSD": "H",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	759 "HSP": "H",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	760 }
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	761 for aa in list_resid_arr:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	762 pattern_arr += dict_prot[aa]
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	763 for aa in list_resid_npa1:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	764 pattern_npa1 += dict_prot[aa]
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	765 for aa in list_resid_npa2:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	766 pattern_npa2 += dict_prot[aa]
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	767 for ts in uni.trajectory:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	768 if args.verbose:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	769 logging.info("Frame " + str(uni.trajectory.frame))
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	770 logging.info(str(ts))
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	771 dict_pair_dist = run_one_frame_npa_arr(
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	772 list_resid_npa1, list_resid_npa2, list_resid_arr, uni
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	773 )
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	774 tab_pair_dist[uni.trajectory.frame][0] = uni.trajectory.time
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	775 list_key = ["Time in ps"]
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	776 num_npa_proto = 0
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	777 for npa in range(1, 3):
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	778 if npa == 1:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	779 pattern_complete = "," + pattern_arr + "-" + pattern_npa1 + "1"
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	780 else:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	781 pattern_complete = "," + pattern_arr + "-" + pattern_npa2 + "2"
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	782 for aqp in range(1, 3):
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	783 for p in range(1, 5):
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	784 num_npa_proto += 1
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	785 key1 = "ArR-NPA" + str(npa) + ",AQP" + str(aqp)\
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	786 + ",P" + str(p)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	787 key2 = "AQP" + str(aqp) + ",P" + str(p) + pattern_complete\
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	788 + " (Angstroms)"
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	789 tab_pair_dist[uni.trajectory.frame][num_npa_proto] = \
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	790 dict_pair_dist[key1]
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	791 list_key.append(key2)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	792 list_out = [tab_pair_dist, list_key]
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	793 return list_out
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	794
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	795
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	796 def run_all_frames_arr(list_resid_arr1, list_resid_arr2, col_number, uni):
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	797 """
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	798 Description: creates the table containing the pore diameter of an aquaporin
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	799 over time.
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	800 param list_resid_arr1: list containing the names of the residues
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	801 constituting the ArR1.
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	802 param list_resid_arr2: list containing the names of the residues
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	803 constituting the ArR2.
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	804 param col_number: number of columns in the table
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	805 param uni: MDAnalysis universe.
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	806 return: list containing an array and a key list. The table containing the
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	807 pore diameter of an aquaporin over time.
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	808 """
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	809 if args.verbose:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	810 logging.info("\nFunction runForAllFrame")
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	811 logging.info("The first input parameter is " + str(list_resid_arr1))
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	812 logging.info("The second input parameter is " + str(list_resid_arr2))
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	813 logging.info("The third input parameter is " + str(col_number))
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	814 logging.info("The fourth input parameter is " + str(uni))
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	815 nbr_frame = len(uni.trajectory)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	816 if args.verbose:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	817 logging.info("The number of frame is " + str(nbr_frame))
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	818 tab_pair_dist = np.empty((nbr_frame, col_number))
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	819 if args.verbose:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	820 logging.info(
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	821 "The dimensions of the table of means and standard deviation"
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	822 + " are as follows " + str(tab_pair_dist.shape)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	823 )
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	824 list_key = []
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	825 pattern1 = ""
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	826 pattern2 = ""
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	827 dict_prot = {
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	828 "ALA": "A",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	829 "CYS": "C",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	830 "ASP": "D",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	831 "GLU": "E",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	832 "PHE": "F",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	833 "GLY": "G",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	834 "HIS": "H",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	835 "ILE": "I",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	836 "LYS": "K",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	837 "LEU": "L",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	838 "MET": "M",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	839 "ASN": "N",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	840 "PRO": "P",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	841 "GLN": "Q",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	842 "ARG": "R",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	843 "SER": "S",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	844 "THR": "T",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	845 "VAL": "V",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	846 "TRP": "W",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	847 "TYR": "Y",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	848 "HSD": "H",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	849 "HSP": "H",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	850 }
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	851 for aa in list_resid_arr1:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	852 pattern1 += dict_prot[aa]
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	853 for aa in list_resid_arr2:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	854 pattern2 += dict_prot[aa]
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	855 for ts in uni.trajectory:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	856 if args.verbose:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	857 logging.info("Frame " + str(uni.trajectory.frame))
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	858 logging.info(str(ts))
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	859 dict_pair_dist = run_one_frame_arr(list_resid_arr1, list_resid_arr2,
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	860 uni)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	861 tab_pair_dist[uni.trajectory.frame][0] = uni.trajectory.time
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	862 list_key = ["Time (ps)"]
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	863 num_proto = 0
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	864 for aqp in range(1, 3):
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	865 for p in range(1, 5):
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	866 num_proto += 1
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	867 key1 = "ArR1-ArR2,AQP" + str(aqp) + ",P" + str(p)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	868 key2 = (
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	869 "AQP" + str(aqp) + ",P" + str(p) + "," + pattern1 +
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	870 "-" + pattern2 + " (Angstroms)"
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	871 )
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	872 tab_pair_dist[uni.trajectory.frame][num_proto] = \
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	873 dict_pair_dist[key1]
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	874 list_key.append(key2)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	875 list_out = [tab_pair_dist, list_key]
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	876 return list_out
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	877
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	878
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	879 def create_final_dataframe(
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	880 list_resid_arr1, list_resid_arr2, list_resid_npa1, list_resid_npa2, uni
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	881 ):
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	882 """
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	883 Description: creates the final dataframe.
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	884 param list_resid_arr1: list containing the arr1 pattern
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	885 param list_resid_arr2: list containing the arr2 pattern
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	886 param list_resid_npa1: list containing the npa1 pattern
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	887 param list_resid_npa2: list containing the npa2 pattern
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	888 param uni: MDAnalysis universe
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	889 return: final dataframe
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	890 """
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	891 if args.verbose:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	892 logging.info("\nFunction runForAllFrame")
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	893 logging.info("The first input parameter is " + str(list_resid_arr1))
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	894 logging.info("The second input parameter is " + str(list_resid_arr2))
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	895 logging.info("The third input parameter is " + str(list_resid_npa1))
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	896 logging.info("The fourth input parameter is " + str(list_resid_npa2))
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	897 logging.info("The fifth input parameter is " + str(uni))
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	898 if list_resid_npa1 is None and list_resid_npa2 is None:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	899 if len(list_resid_arr1) >= 4 and len(list_resid_arr2) >= 4:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	900 columns_number = 9
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	901 list_out = run_all_frames_arr(
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	902 list_resid_arr1, list_resid_arr2, columns_number, uni
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	903 )
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	904 else:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	905 if args.verbose:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	906 if len(list_resid_arr1) < 4 <= len(list_resid_arr2):
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	907 logging.critical("Pattern1 must be provided")
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	908 elif len(list_resid_arr1) < 4 and len(list_resid_arr2) < 4:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	909 logging.critical("Pattern1 and Pattern2 must be provided")
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	910 elif len(list_resid_arr1) >= 4 > len(list_resid_arr2):
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	911 logging.critical("Pattern2 must be provided")
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	912 print("Pattern error : please read the log file or help")
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	913 sys.exit(2)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	914 elif list_resid_npa1 is None and list_resid_npa2 is not None:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	915 if args.verbose:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	916 if len(list_resid_arr1) < 4 <= len(list_resid_arr2):
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	917 logging.critical("PatternArr1 must be provided")
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	918 logging.critical("Please, do not put patternArr2")
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	919 logging.critical("PatternNPA1 must be provided")
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	920 elif len(list_resid_arr1) < 4 and len(list_resid_arr2) < 4:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	921 logging.critical("PatternArr1 must be provided")
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	922 logging.critical("PatternNPA1 must be provided")
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	923 elif len(list_resid_arr1) >= 4 > len(list_resid_arr2):
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	924 logging.critical("PatternNPA1 must be provided")
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	925 else:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	926 logging.critical("Please, do not put patternArr2")
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	927 logging.critical("PatternNPA1 must be provided")
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	928 print("Pattern error : please read the log file or help")
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	929 sys.exit(2)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	930 elif list_resid_npa1 is not None and list_resid_npa2 is None:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	931 if args.verbose:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	932 if len(list_resid_arr1) < 4 <= len(list_resid_arr2):
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	933 logging.critical("PatternArr1 must be provided")
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	934 logging.critical("Please, do not put patternArr2")
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	935 logging.critical("PatternNPA2 must be provided")
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	936 elif len(list_resid_arr1) < 4 and len(list_resid_arr2) < 4:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	937 logging.critical("PatternArr1 must be provided")
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	938 logging.critical("PatternNPA2 must be provided")
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	939 elif len(list_resid_arr1) >= 4 > len(list_resid_arr2):
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	940 logging.critical("PatternNPA1 must be provided")
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	941 else:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	942 logging.critical("Please, do not put patternArr2")
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	943 logging.critical("PatternNPA2 must be provided")
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	944 print("Pattern error : please read the log file or help")
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	945 sys.exit(2)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	946 else:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	947 if (
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	948 list_resid_npa1 is not None
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	949 and list_resid_npa2 is not None
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	950 and len(list_resid_arr1) >= 4 > len(list_resid_arr2)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	951 ):
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	952 columns_number = 17
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	953 list_out = run_all_frames_npa_arr(
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	954 list_resid_npa1, list_resid_npa2, list_resid_arr1,
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	955 columns_number, uni
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	956 )
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	957 else:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	958 if len(list_resid_arr1) < 4 <= len(list_resid_arr2):
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	959 logging.critical("PatternArr1 must be provided")
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	960 logging.critical("Please, do not put patternArr2")
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	961 elif len(list_resid_arr1) < 4 and len(list_resid_arr2) < 4:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	962 logging.critical("Pattern1 must be provided")
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	963 print("Pattern error : please read the log file or help")
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	964 sys.exit(2)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	965 list_std = list(np.std(list_out[0], axis=0))
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	966 list_mean = list(np.mean(list_out[0], axis=0))
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	967 np_mean_around = list(np.around(list_mean, decimals=3))
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	968 np_std_around = list(np.around(list_std, decimals=3))
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	969 np_mean_around[0] = "Mean"
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	970 np_std_around[0] = "Std"
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	971 np_mean_around = np.array([np_mean_around])
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	972 np_std_around = np.array([np_std_around])
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	973 np_mean_std_around = np.concatenate((np_mean_around, np_std_around),
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	974 axis=0)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	975 tab_pair_dist = np.concatenate((np_mean_std_around, list_out[0]), axis=0)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	976 df_dist = pd.DataFrame(tab_pair_dist, columns=list_out[1])
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	977 return df_dist
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	978
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	979
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	980 # Class
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	981
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	982
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	983 if __name__ == "__main__":
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	984 args = parse_arguments()
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	985 out_file_name = "test"
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	986 file_name_log = out_file_name + ".log"
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	987 if args.verbose:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	988 if args.log_output:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	989 if os.path.isfile(args.log_output):
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	990 os.remove(args.log_output)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	991 logging.basicConfig(
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	992 filename=args.log_output,
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	993 format="%(levelname)s - %(message)s",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	994 level=logging.INFO,
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	995 )
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	996 else:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	997 if os.path.isfile(file_name_log):
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	998 os.remove(file_name_log)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	999 logging.basicConfig(
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	1000 filename=file_name_log,
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	1001 format="%(levelname)s - %(message)s",
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	1002 level=logging.INFO,
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	1003 )
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	1004 logging.info("verbose mode on")
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	1005 gro_file = ''
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	1006 xtc_file = ''
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	1007 if args.gro_file:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	1008 gro_file = os.path.basename(args.gro_file[0])
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	1009 else:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	1010 logging.critical("A .gro file must be provided")
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	1011 if args.xtc_file:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	1012 xtc_file = os.path.basename(args.xtc_file[0])
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	1013 else:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	1014 logging.critical("A .xtc file must be provided")
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	1015 if args.work_directory:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	1016 work_directory = args.work_directory[0]
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	1017 else:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	1018 work_directory = os.path.dirname(args.gro_file[0])
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	1019 if not work_directory.endswith("/"):
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	1020 work_directory += "/"
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	1021 output_directory = args.output_directory[0]
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	1022 if args.output:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	1023 output = args.output
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	1024 else:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	1025 output = ""
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	1026 os.chdir(work_directory)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	1027 if args.gro_file_ext and args.xtc_file_ext:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	1028 u = Mda.Universe(
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	1029 args.gro_file[0],
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	1030 args.xtc_file[0],
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	1031 topology_format=args.gro_file_ext[0],
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	1032 format=args.xtc_file_ext[0],
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	1033 )
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	1034 else:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	1035 u = Mda.Universe(args.gro_file[0], args.xtc_file[0])
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	1036 if args.verbose:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	1037 logging.info("Load universe : " + str(u))
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	1038 if args.npa_one:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	1039 resid_npa1 = args.npa_one[0].split()
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	1040 else:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	1041 resid_npa1 = args.npa_one
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	1042 if args.npa_second:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	1043 resid_npa2 = args.npa_second[0].split()
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	1044 else:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	1045 resid_npa2 = args.npa_second
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	1046 if args.arr_one:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	1047 resid_arr1 = args.arr_one[0].split()
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	1048 else:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	1049 resid_arr1 = args.arr_one
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	1050 if args.arr_second:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	1051 resid_arr2 = args.arr_second[0].split()
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	1052 else:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	1053 resid_arr2 = args.arr_second
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	1054 df_final = create_final_dataframe(resid_arr1, resid_arr2,
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	1055 resid_npa1, resid_npa2, u)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	1056 if len(output_directory) > 2:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	1057 if not os.path.exists(output_directory):
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	1058 os.makedirs(output_directory)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	1059 os.chdir(output_directory)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	1060 if len(output) > 2:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	1061 df_final.to_csv(output, sep="\t", index=False)
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	1062 else:
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	1063 file_name_tabular = out_file_name + "PairDist.tabular"
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty" agpetit parents: diff changeset	1064 df_final.to_csv(file_name_tabular, sep="\t", index=False)

Mercurial > repos > agpetit > calculate_diameter

annotate calculate_pore_diameter_aqp.py @ 3:b120a98cf623 draft