# HG changeset patch # User bgruening # Date 1595937583 0 # Node ID 9a08f0d1b3058045ae65fbbac47462e6470f6fa3 # Parent 449c3def61ccdd437496a451a18d6e302e19e13b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0" diff -r 449c3def61cc -r 9a08f0d1b305 change_title_to_metadata_value.py --- a/change_title_to_metadata_value.py Thu Apr 09 13:53:21 2020 +0000 +++ b/change_title_to_metadata_value.py Tue Jul 28 11:59:43 2020 +0000 @@ -9,13 +9,13 @@ import os import sys import argparse -import openbabel -openbabel.obErrorLog.StopLogging() -import pybel import random import string +from openbabel import openbabel, pybel +openbabel.obErrorLog.StopLogging() + def main(): parser = argparse.ArgumentParser( description="Change the title from a molecule file to metadata \ diff -r 449c3def61cc -r 9a08f0d1b305 cheminfolib.py --- a/cheminfolib.py Thu Apr 09 13:53:21 2020 +0000 +++ b/cheminfolib.py Tue Jul 28 11:59:43 2020 +0000 @@ -13,8 +13,8 @@ print('psycopg2 is not available. It is currently used in the pgchem wrappers, that are not shipped with default CTB') try: - import pybel - import openbabel + from openbabel import openbabel, pybel + openbabel.obErrorLog.StopLogging() except: print('OpenBabel could not be found. A few functions are not available without OpenBabel.') diff -r 449c3def61cc -r 9a08f0d1b305 distance_finder.py --- a/distance_finder.py Thu Apr 09 13:53:21 2020 +0000 +++ b/distance_finder.py Tue Jul 28 11:59:43 2020 +0000 @@ -12,10 +12,10 @@ # there would be properties for distance1, distance2 and distance3. import argparse, os, sys, math + from openbabel import pybel - def log(*args, **kwargs): """Log output to STDERR """ diff -r 449c3def61cc -r 9a08f0d1b305 macros.xml --- a/macros.xml Thu Apr 09 13:53:21 2020 +0000 +++ b/macros.xml Tue Jul 28 11:59:43 2020 +0000 @@ -1,9 +1,9 @@ - 2.4.2.2 + 3.1.1 - openbabel + openbabel python diff -r 449c3def61cc -r 9a08f0d1b305 multi_obgrep.py --- a/multi_obgrep.py Thu Apr 09 13:53:21 2020 +0000 +++ b/multi_obgrep.py Tue Jul 28 11:59:43 2020 +0000 @@ -6,15 +6,14 @@ """ import sys, os import argparse -import openbabel -openbabel.obErrorLog.StopLogging() -import pybel import multiprocessing import tempfile import subprocess import shutil import shlex +from openbabel import openbabel, pybel +openbabel.obErrorLog.StopLogging() def parse_command_line(): parser = argparse.ArgumentParser() parser.add_argument('-i', '--infile', required=True, help='Molecule file.') diff -r 449c3def61cc -r 9a08f0d1b305 ob_addh.py --- a/ob_addh.py Thu Apr 09 13:53:21 2020 +0000 +++ b/ob_addh.py Tue Jul 28 11:59:43 2020 +0000 @@ -5,9 +5,9 @@ """ import sys, os import argparse -import openbabel + +from openbabel import openbabel, pybel openbabel.obErrorLog.StopLogging() -import pybel def parse_command_line(argv): parser = argparse.ArgumentParser() diff -r 449c3def61cc -r 9a08f0d1b305 ob_addh.xml --- a/ob_addh.xml Thu Apr 09 13:53:21 2020 +0000 +++ b/ob_addh.xml Tue Jul 28 11:59:43 2020 +0000 @@ -1,8 +1,9 @@ - + at a certain pH value macros.xml + 0 diff -r 449c3def61cc -r 9a08f0d1b305 ob_filter.py --- a/ob_filter.py Thu Apr 09 13:53:21 2020 +0000 +++ b/ob_filter.py Tue Jul 28 11:59:43 2020 +0000 @@ -10,9 +10,9 @@ import argparse import cheminfolib import json -import pybel import shlex, subprocess +from openbabel import pybel cheminfolib.pybel_stop_logging() def parse_command_line(): diff -r 449c3def61cc -r 9a08f0d1b305 ob_genProp.py --- a/ob_genProp.py Thu Apr 09 13:53:21 2020 +0000 +++ b/ob_genProp.py Tue Jul 28 11:59:43 2020 +0000 @@ -8,9 +8,9 @@ import argparse import openbabel openbabel.obErrorLog.StopLogging() -import pybel import cheminfolib +from openbabel import pybel def parse_command_line(argv): parser = argparse.ArgumentParser() diff -r 449c3def61cc -r 9a08f0d1b305 ob_remIons.py --- a/ob_remIons.py Thu Apr 09 13:53:21 2020 +0000 +++ b/ob_remIons.py Tue Jul 28 11:59:43 2020 +0000 @@ -6,9 +6,9 @@ """ import sys, os import argparse -import openbabel + +from openbabel import openbabel, pybel openbabel.obErrorLog.StopLogging() -import pybel def parse_command_line(): parser = argparse.ArgumentParser() diff -r 449c3def61cc -r 9a08f0d1b305 ob_spectrophore_search.py --- a/ob_spectrophore_search.py Thu Apr 09 13:53:21 2020 +0000 +++ b/ob_spectrophore_search.py Tue Jul 28 11:59:43 2020 +0000 @@ -6,12 +6,11 @@ """ import sys, os import argparse -import openbabel -openbabel.obErrorLog.StopLogging() -import pybel import math import numpy as np +from openbabel import openbabel, pybel +openbabel.obErrorLog.StopLogging() #TODO get rid of eval() global spectrophore diff -r 449c3def61cc -r 9a08f0d1b305 remove_protonation_state.py --- a/remove_protonation_state.py Thu Apr 09 13:53:21 2020 +0000 +++ b/remove_protonation_state.py Tue Jul 28 11:59:43 2020 +0000 @@ -6,9 +6,9 @@ """ import sys, os import argparse -import openbabel + +from openbabel import openbabel, pybel openbabel.obErrorLog.StopLogging() -import pybel def parse_command_line(): parser = argparse.ArgumentParser() diff -r 449c3def61cc -r 9a08f0d1b305 subsearch.py --- a/subsearch.py Thu Apr 09 13:53:21 2020 +0000 +++ b/subsearch.py Tue Jul 28 11:59:43 2020 +0000 @@ -6,14 +6,14 @@ """ import sys, os import argparse -import openbabel -openbabel.obErrorLog.StopLogging() -import pybel import multiprocessing import tempfile import subprocess import shutil +from openbabel import openbabel, pybel +openbabel.obErrorLog.StopLogging() + def parse_command_line(): parser = argparse.ArgumentParser() parser.add_argument('-i', '--infile', required=True, help='Molecule file.') diff -r 449c3def61cc -r 9a08f0d1b305 test-data/ob_convert_on_CID2244.cml --- a/test-data/ob_convert_on_CID2244.cml Thu Apr 09 13:53:21 2020 +0000 +++ b/test-data/ob_convert_on_CID2244.cml Tue Jul 28 11:59:43 2020 +0000 @@ -1,27 +1,27 @@ - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + diff -r 449c3def61cc -r 9a08f0d1b305 test-data/ob_convert_on_CID2244.pdb --- a/test-data/ob_convert_on_CID2244.pdb Thu Apr 09 13:53:21 2020 +0000 +++ b/test-data/ob_convert_on_CID2244.pdb Tue Jul 28 11:59:43 2020 +0000 @@ -1,5 +1,5 @@ COMPND 2244 -AUTHOR GENERATED BY OPEN BABEL 2.3.90 +AUTHOR GENERATED BY OPEN BABEL 3.1.0 HETATM 1 O UNL 1 3.732 -0.060 0.000 1.00 0.00 O HETATM 2 O UNL 1 6.330 1.440 0.000 1.00 0.00 O HETATM 3 O UNL 1 4.598 1.440 0.000 1.00 0.00 O @@ -23,16 +23,16 @@ HETATM 21 H UNL 1 6.330 2.060 0.000 1.00 0.00 H CONECT 1 5 12 CONECT 2 11 21 -CONECT 3 11 -CONECT 4 12 -CONECT 5 1 6 7 -CONECT 6 5 8 11 -CONECT 7 5 9 14 -CONECT 8 6 10 15 -CONECT 9 7 10 16 -CONECT 10 8 9 17 -CONECT 11 2 3 6 -CONECT 12 1 4 13 +CONECT 3 11 11 +CONECT 4 12 12 +CONECT 5 1 6 7 7 +CONECT 6 5 8 8 11 +CONECT 7 5 5 9 14 +CONECT 8 6 6 10 15 +CONECT 9 7 10 10 16 +CONECT 10 8 9 9 17 +CONECT 11 2 3 3 6 +CONECT 12 1 4 4 13 CONECT 13 12 18 19 20 CONECT 14 7 CONECT 15 8 diff -r 449c3def61cc -r 9a08f0d1b305 test-data/ob_depiction_svg_on_8_mol.svg --- a/test-data/ob_depiction_svg_on_8_mol.svg Thu Apr 09 13:53:21 2020 +0000 +++ b/test-data/ob_depiction_svg_on_8_mol.svg Tue Jul 28 11:59:43 2020 +0000 @@ -7,44 +7,44 @@ - -