Mercurial > repos > chemteam > mdanalysis_rdf
changeset 4:aabf6858f293 draft
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
| author | chemteam |
|---|---|
| date | Mon, 07 Oct 2019 12:41:24 -0400 |
| parents | fdc0c1615372 |
| children | 62eaf6ecd9eb |
| files | angle.py dihedrals.py distance.py hbonds.py macros.xml pca_cosine.py ramachandran_plots.py rdf.py rdf.xml test-data/Ramachandran_Plot_raw_data_gmx.tabular test-data/test.gro test-data/test.xtc |
| diffstat | 12 files changed, 61762 insertions(+), 41 deletions(-) [+] |
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--- a/angle.py Wed Apr 03 15:41:30 2019 -0400 +++ b/angle.py Mon Oct 07 12:41:24 2019 -0400 @@ -16,8 +16,10 @@ def parse_command_line(argv): parser = argparse.ArgumentParser() - parser.add_argument('--idcd', help='input dcd') - parser.add_argument('--ipdb', help='input pdb') + parser.add_argument('--itraj', help='input traj') + parser.add_argument('--istr', help='input str') + parser.add_argument('--itrajext', help='input traj ext') + parser.add_argument('--istrext', help='input str ext') parser.add_argument('--isegid1', help='segid 1') parser.add_argument('--iresid1', help='resid 1') parser.add_argument('--iname1', help='name 1') @@ -52,7 +54,8 @@ return np.rad2deg(theta) -u = mda.Universe(args.ipdb, args.idcd, topology_format="PDB", format="DCD") +u = mda.Universe(args.istr, args.itraj, + topology_format=args.istrext, format=args.itrajext) data = np.array([(u.trajectory.frame, theta(u)) for ts in u.trajectory]) frame, theta = data.T
--- a/dihedrals.py Wed Apr 03 15:41:30 2019 -0400 +++ b/dihedrals.py Mon Oct 07 12:41:24 2019 -0400 @@ -16,8 +16,10 @@ def parse_command_line(argv): parser = argparse.ArgumentParser() - parser.add_argument('--idcd', help='input dcd') - parser.add_argument('--ipdb', help='input pdb') + parser.add_argument('--itraj', help='input traj') + parser.add_argument('--istr', help='input str') + parser.add_argument('--itrajext', help='input traj ext') + parser.add_argument('--istrext', help='input str ext') parser.add_argument('--isegid1', help='segid 1') parser.add_argument('--iresid1', help='resid 1') parser.add_argument('--iname1', help='name 1') @@ -56,7 +58,8 @@ return np.rad2deg(psi) -u = mda.Universe(args.ipdb, args.idcd, topology_format="PDB", format="DCD") +u = mda.Universe(args.istr, args.itraj, + topology_format=args.istrext, format=args.itrajext) data = np.array([(u.trajectory.frame, psi(u)) for ts in u.trajectory]) frame, psi = data.T PSI = np.concatenate(psi, axis=0)
--- a/distance.py Wed Apr 03 15:41:30 2019 -0400 +++ b/distance.py Mon Oct 07 12:41:24 2019 -0400 @@ -14,8 +14,10 @@ def parse_command_line(argv): parser = argparse.ArgumentParser() - parser.add_argument('--idcd', help='input dcd') - parser.add_argument('--ipdb', help='input pdb') + parser.add_argument('--itraj', help='input traj') + parser.add_argument('--istr', help='input str') + parser.add_argument('--itrajext', help='input traj ext') + parser.add_argument('--istrext', help='input str ext') parser.add_argument('--isegid1', help='segid 1') parser.add_argument('--iresid1', help='resid 1') parser.add_argument('--iname1', help='name 1') @@ -34,7 +36,8 @@ atom2 = "(segid %s and resid %s and name %s)" % \ (args.isegid2, args.iresid2, args.iname2) -u = mda.Universe(args.ipdb, args.idcd, topology_format="PDB", format="DCD") +u = mda.Universe(args.istr, args.itraj, + topology_format=args.istrext, format=args.itrajext) x = u.select_atoms(atom1) y = u.select_atoms(atom2)
--- a/hbonds.py Wed Apr 03 15:41:30 2019 -0400 +++ b/hbonds.py Mon Oct 07 12:41:24 2019 -0400 @@ -4,6 +4,7 @@ import csv import sys +import MDAnalysis as mda import MDAnalysis.analysis.hbonds import pandas as pd @@ -11,8 +12,10 @@ def parse_command_line(argv): parser = argparse.ArgumentParser() - parser.add_argument('--idcd', help='input dcd') - parser.add_argument('--ipdb', help='input pdb') + parser.add_argument('--itraj', help='input traj') + parser.add_argument('--istr', help='input str') + parser.add_argument('--itrajext', help='input traj ext') + parser.add_argument('--istrext', help='input str ext') parser.add_argument('--isegid1', help='segid 1') parser.add_argument('--isegid2', help='segid 2') parser.add_argument('--idistance', help='cutoff distance') @@ -31,8 +34,8 @@ distance = float(args.idistance) angle = float(args.iangle) -u = MDAnalysis.Universe( - args.ipdb, args.idcd, topology_format="PDB", format="DCD") +u = mda.Universe(args.istr, args.itraj, + topology_format=args.istrext, format=args.itrajext) h = MDAnalysis.analysis.hbonds.HydrogenBondAnalysis( u, selection1, selection2, distance=distance, angle=angle)
--- a/macros.xml Wed Apr 03 15:41:30 2019 -0400 +++ b/macros.xml Mon Oct 07 12:41:24 2019 -0400 @@ -1,14 +1,14 @@ <macros> - <token name="@VERSION@">0.19</token> + <token name="@VERSION@">0.20</token> <xml name="requirements"> <requirements> - <requirement type="package" version="0.19.2">mdanalysis</requirement> + <requirement type="package" version="0.20.1">mdanalysis</requirement> <yield/> </requirements> </xml> <xml name="analysis_inputs"> - <param format="dcd" name="dcdin" type="data" label="dcd trajectory input"/> - <param format="pdb" name="pdbin" type="data" label="pdb input"/> + <param format="dcd,xtc" name="trajin" type="data" label="DCD/XTC trajectory input"/> + <param format="pdb,gro" name="strin" type="data" label="PDB/GRO input"/> <yield/> </xml> <xml name="sanitizer"> @@ -24,8 +24,13 @@ <yield/> </xml> <xml name="tests_inputs"> - <param name="dcdin" value="test.dcd" /> - <param name="pdbin" value="test.pdb" /> + <param name="trajin" value="test.dcd" ftype="dcd"/> + <param name="strin" value="test.pdb" ftype="pdb"/> + <yield/> + </xml> + <xml name="tests_inputs_gmx"> + <param name="trajin" value="test.xtc" ftype="xtc"/> + <param name="strin" value="test.gro" ftype="gro"/> <yield/> </xml> <xml name="citations">
--- a/pca_cosine.py Wed Apr 03 15:41:30 2019 -0400 +++ b/pca_cosine.py Mon Oct 07 12:41:24 2019 -0400 @@ -12,8 +12,10 @@ def parse_command_line(argv): parser = argparse.ArgumentParser() - parser.add_argument('--idcd', help='input dcd') - parser.add_argument('--ipdb', help='input pdb') + parser.add_argument('--itraj', help='input traj') + parser.add_argument('--istr', help='input str') + parser.add_argument('--itrajext', help='input traj ext') + parser.add_argument('--istrext', help='input str ext') parser.add_argument('--icomponents', help='number of principle components') parser.add_argument('--iindex', help='index of the PC') parser.add_argument('--output', help='output') @@ -23,7 +25,8 @@ args = parse_command_line(sys.argv) -u = mda.Universe(args.ipdb, args.idcd, topology_format="PDB", format="DCD") +u = mda.Universe(args.istr, args.itraj, + topology_format=args.istrext, format=args.itrajext) components = int(args.icomponents) pca_index = int(args.iindex)
--- a/ramachandran_plots.py Wed Apr 03 15:41:30 2019 -0400 +++ b/ramachandran_plots.py Mon Oct 07 12:41:24 2019 -0400 @@ -19,8 +19,10 @@ def parse_command_line(argv): parser = argparse.ArgumentParser() - parser.add_argument('--idcd', help='input dcd') - parser.add_argument('--ipdb', help='input pdb') + parser.add_argument('--itraj', help='input traj') + parser.add_argument('--istr', help='input str') + parser.add_argument('--itrajext', help='input traj ext') + parser.add_argument('--istrext', help='input str ext') parser.add_argument('--isegid1', help='segid 1') parser.add_argument('--iresid1', help='resid 1') parser.add_argument('--iname1', help='name 1') @@ -94,13 +96,16 @@ return np.rad2deg(dihe) -u = mda.Universe(args.ipdb, args.idcd, topology_format="PDB", format="DCD") +u = mda.Universe(args.istr, args.itraj, + topology_format=args.istrext, format=args.itrajext) phi_trajdata = np.array( [(u.trajectory.frame, calc_torsion(dihe_phi)) for ts in u.trajectory]) psi_trajdata = np.array( [(u.trajectory.frame, calc_torsion(dihe_psi)) for ts in u.trajectory]) +print(phi_trajdata, psi_trajdata) + phi_frame, phi_series = phi_trajdata.T psi_frame, psi_series = psi_trajdata.T
--- a/rdf.py Wed Apr 03 15:41:30 2019 -0400 +++ b/rdf.py Mon Oct 07 12:41:24 2019 -0400 @@ -16,8 +16,10 @@ def parse_command_line(argv): parser = argparse.ArgumentParser() - parser.add_argument('--idcd', help='input dcd') - parser.add_argument('--ipdb', help='input pdb') + parser.add_argument('--itraj', help='input traj') + parser.add_argument('--istr', help='input str') + parser.add_argument('--itrajext', help='input traj ext') + parser.add_argument('--istrext', help='input str ext') parser.add_argument('--isegid1', help='segid 1') parser.add_argument('--iresid1', help='resid 1') parser.add_argument('--iname1', help='name 1') @@ -42,7 +44,8 @@ start = float(args.istart) end = float(args.iend) -u = mda.Universe(args.ipdb, args.idcd, topology_format="PDB", format="DCD") +u = mda.Universe(args.istr, args.itraj, + topology_format=args.istrext, format=args.itrajext) x = u.select_atoms(atom1) y = u.select_atoms(atom2)
--- a/rdf.xml Wed Apr 03 15:41:30 2019 -0400 +++ b/rdf.xml Mon Oct 07 12:41:24 2019 -0400 @@ -1,5 +1,5 @@ <tool id="mdanalysis_rdf" name="RDF Analysis" version="@VERSION@"> - <description>Radial Distribution Function between two atoms</description> + <description>- Radial Distribution Function between two atoms</description> <macros> <import>macros.xml</import> </macros> @@ -7,8 +7,10 @@ <command detect_errors="exit_code"> <![CDATA[ python '$__tool_directory__/rdf.py' - --idcd '$dcdin' - --ipdb '$pdbin' + --itraj '$trajin' + --istr '$strin' + --itrajext '$trajin.ext' + --istrext '$strin.ext' --isegid1 '$segid1' --iresid1 '$resid1' --iname1 '$name1' @@ -24,15 +26,17 @@ ]]></command> <inputs> <expand macro="analysis_inputs"/> - <param name="segid1" type="text" value="PRO" label="Segid of atom 1"/> - <param name="resid1" type="text" value="212" label="Resid of atom 1"/> + <param name="segid1" type="text" value="PRO" label="Segment ID of atom 1"/> + <param name="resid1" type="text" value="212" label="Residue ID of atom 1"/> <param name="name1" type="text" value="OE2" label="Atom name of atom 1"/> - <param name="segid2" type="text" value="HET" label="Segid of atom 2"/> - <param name="resid2" type="text" value="3" label="Resid of atom 2"/> + <param name="segid2" type="text" value="HET" label="Segment ID of atom 2"/> + <param name="resid2" type="text" value="3" label="Residue ID of atom 2"/> <param name="name2" type="text" value="C1" label="Atom name of atom 2"/> <param name="nbins" type="text" value="100" label="Number of bins in the histogram"/> - <param name="start" type="text" value="0.0" label="Starting Point"/> - <param name="end" type="text" value="5.0" label="End Point"/> + <param name="start" type="text" min="0.0" value="0.0" label="Starting point (angstroms)" + help="Minimum value of r to calculate RDF for"/> + <param name="end" type="text" value="15.0" label="End point (angstroms)" + help="Maximum value of r to calculate RDF for"/> </inputs> <outputs> <data format="tabular" name="output" label="RDF raw data"/> @@ -58,13 +62,32 @@ </assert_contents> </output> </test> + <test> + <expand macro="tests_inputs_gmx"/> + <param name="segid1" value="SYSTEM"/> + <param name="resid1" value="212"/> + <param name="name1" value="OE2"/> + <param name="segid2" value="SYSTEM"/> + <param name="resid2" value="3"/> + <param name="name2" value="C1"/> + <param name="nbins" value="100"/> + <param name="start" value="0.0"/> + <param name="end" value="5.0"/> + <output name="output"> + <assert_contents> + <has_n_columns n="2" /> + <not_has_text text="nan" /> + <has_line_matching expression="3.275\s+6336.*" /> + </assert_contents> + </output> + </test> </tests> <help><