| Previous changeset 0:ebeb72aa39a8 (2019-04-03) Next changeset 2:e39bc1f90d8f (2020-02-06) |
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Commit message:
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" |
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modified:
angle.py dihedrals.py distance.py hbonds.py macros.xml pca_cosine.py pca_cosine.xml ramachandran_plots.py rdf.py |
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added:
test-data/Ramachandran_Plot_raw_data_gmx.tabular test-data/test.gro test-data/test.xtc |
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| diff -r ebeb72aa39a8 -r d18e7db42633 angle.py --- a/angle.py Wed Apr 03 15:48:45 2019 -0400 +++ b/angle.py Mon Oct 07 12:50:44 2019 -0400 |
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| @@ -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 |
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| diff -r ebeb72aa39a8 -r d18e7db42633 dihedrals.py --- a/dihedrals.py Wed Apr 03 15:48:45 2019 -0400 +++ b/dihedrals.py Mon Oct 07 12:50:44 2019 -0400 |
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| @@ -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) |
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| diff -r ebeb72aa39a8 -r d18e7db42633 distance.py --- a/distance.py Wed Apr 03 15:48:45 2019 -0400 +++ b/distance.py Mon Oct 07 12:50:44 2019 -0400 |
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| @@ -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) |
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| diff -r ebeb72aa39a8 -r d18e7db42633 hbonds.py --- a/hbonds.py Wed Apr 03 15:48:45 2019 -0400 +++ b/hbonds.py Mon Oct 07 12:50:44 2019 -0400 |
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| @@ -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) |
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| diff -r ebeb72aa39a8 -r d18e7db42633 macros.xml --- a/macros.xml Wed Apr 03 15:48:45 2019 -0400 +++ b/macros.xml Mon Oct 07 12:50:44 2019 -0400 |
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| @@ -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"> |
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| diff -r ebeb72aa39a8 -r d18e7db42633 pca_cosine.py --- a/pca_cosine.py Wed Apr 03 15:48:45 2019 -0400 +++ b/pca_cosine.py Mon Oct 07 12:50:44 2019 -0400 |
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| @@ -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) |
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| diff -r ebeb72aa39a8 -r d18e7db42633 pca_cosine.xml --- a/pca_cosine.xml Wed Apr 03 15:48:45 2019 -0400 +++ b/pca_cosine.xml Mon Oct 07 12:50:44 2019 -0400 |
| [ |
| @@ -1,5 +1,5 @@ <tool id="mdanalysis_cosine_analysis" name="Cosine Content" version="@VERSION@"> - <description>Measure the cosine content of the PCA projection</description> + <description>- measure the cosine content of the PCA projection</description> <macros> <import>macros.xml</import> </macros> @@ -7,8 +7,10 @@ <command detect_errors="exit_code"> <![CDATA[ python '$__tool_directory__/pca_cosine.py' - --idcd '$dcdin' - --ipdb '$pdbin' + --itraj '$trajin' + --istr '$strin' + --itrajext '$trajin.ext' + --istrext '$strin.ext' --icomponents '$components' --iindex '$index' --output '$output' @@ -35,16 +37,25 @@ </assert_contents> </output> </test> + <test> + <expand macro="tests_inputs_gmx"/> + <param name="components" value="3"/> + <param name="index" value="0"/> + <output name="cosout"> + <assert_contents> + <has_text text="0.583" /> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[ .. class:: infomark **What it does** -The cosine content of the principal components is a good indicator for determine good or bad sampling and can be use to determine the convergence of the MD simulation. -This tool can calculate the cosine content of a user define PCA projection. -This tool use zero based indexes (0 is PC1). - +The cosine content of the principal components is a good indicator for determining the quality of the sampling and can be used to determine the convergence of the MD simulation. +This tool can calculate the cosine content of a user-defined PCA projection. Note: it uses zero-based indexes (i.e. 0 is the first principal component). + _____ @@ -63,7 +74,7 @@ **Output** - The cosine content value. - - Tab-separated file of raw data of first three principle component. + - Tab-separated file of raw data of the first three principal components. ]]></help> <expand macro="citations"> |
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| diff -r ebeb72aa39a8 -r d18e7db42633 ramachandran_plots.py --- a/ramachandran_plots.py Wed Apr 03 15:48:45 2019 -0400 +++ b/ramachandran_plots.py Mon Oct 07 12:50:44 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 |
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| diff -r ebeb72aa39a8 -r d18e7db42633 rdf.py --- a/rdf.py Wed Apr 03 15:48:45 2019 -0400 +++ b/rdf.py Mon Oct 07 12:50:44 2019 -0400 |
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| @@ -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) |
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| diff -r ebeb72aa39a8 -r d18e7db42633 test-data/Ramachandran_Plot_raw_data_gmx.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Ramachandran_Plot_raw_data_gmx.tabular Mon Oct 07 12:50:44 2019 -0400 |
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| @@ -0,0 +1,15 @@ +0 -144.6049403672638 97.68547741778757 +1 -141.28378752267525 97.77436430526272 +2 -140.5507581701893 96.64897577753301 +3 -139.80360840706982 96.77167935748881 +4 -134.73236008867292 95.35031471736332 +5 -133.2788812847167 97.90764978970712 +6 -132.85758534848696 97.74270020478778 +7 -132.92861986639113 98.03936669749623 +8 -132.36160579612704 97.75307833579126 +9 -133.24942867028537 98.47767719548273 +10 -129.07281864740457 93.50325320406353 +11 -138.52555276641212 98.65922847590556 +12 -134.17197735904452 86.3334209333448 +13 -135.7743412592041 89.34890663035344 +14 -151.15173106037906 101.47282449338631 |
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| diff -r ebeb72aa39a8 -r d18e7db42633 test-data/test.gro --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.gro Mon Oct 07 12:50:44 2019 -0400 |
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| b'@@ -0,0 +1,61652 @@\n+Glycine aRginine prOline Methionine Alanine Cystine Serine\n+61649\n+ 2SER N 1 2.371 0.440 0.529\n+ 2SER HT1 2 2.277 0.401 0.505\n+ 2SER HT2 3 2.399 0.406 0.623\n+ 2SER HT3 4 2.441 0.402 0.461\n+ 2SER CA 5 2.369 0.591 0.523\n+ 2SER HA 6 2.305 0.626 0.603\n+ 2SER CB 7 2.513 0.648 0.547\n+ 2SER HB1 8 2.550 0.611 0.645\n+ 2SER HB2 9 2.511 0.759 0.552\n+ 2SER OG 10 2.603 0.606 0.444\n+ 2SER HG1 11 2.693 0.638 0.465\n+ 2SER C 12 2.309 0.645 0.394\n+ 2SER O 13 2.229 0.574 0.331\n+ 3ALA N 14 2.342 0.767 0.352\n+ 3ALA HN 15 2.411 0.824 0.396\n+ 3ALA CA 16 2.294 0.828 0.229\n+ 3ALA HA 17 2.242 0.755 0.168\n+ 3ALA CB 18 2.201 0.948 0.258\n+ 3ALA HB1 19 2.251 1.022 0.324\n+ 3ALA HB2 20 2.109 0.913 0.308\n+ 3ALA HB3 21 2.172 0.998 0.164\n+ 3ALA C 22 2.415 0.875 0.151\n+ 3ALA O 23 2.517 0.908 0.207\n+ 4CYS N 24 2.401 0.875 0.017\n+ 4CYS HN 25 2.314 0.848 -0.026\n+ 4CYS CA 26 2.503 0.915 -0.077\n+ 4CYS HA 27 2.577 0.976 -0.027\n+ 4CYS CB 28 2.570 0.795 -0.148\n+ 4CYS HB1 29 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-2.941\n+ 50CLA CLA61647 3.465 -0.771 -3.287\n+ 51CLA CLA61648 -2.032 -3.900 0.685\n+ 52CLA CLA61649 -2.845 0.061 -2.584\n+ 0.00000 0.00000 0.00000\n' |
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| diff -r ebeb72aa39a8 -r d18e7db42633 test-data/test.xtc |
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| Binary file test-data/test.xtc has changed |