| Previous changeset 3:489b25966bb9 (2019-04-03) Next changeset 5:d540ea77b909 (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 distance.xml hbonds.py macros.xml pca_cosine.py 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 489b25966bb9 -r 312f912de69d angle.py --- a/angle.py Wed Apr 03 15:46:56 2019 -0400 +++ b/angle.py Mon Oct 07 12:52:40 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 489b25966bb9 -r 312f912de69d dihedrals.py --- a/dihedrals.py Wed Apr 03 15:46:56 2019 -0400 +++ b/dihedrals.py Mon Oct 07 12:52:40 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 489b25966bb9 -r 312f912de69d distance.py --- a/distance.py Wed Apr 03 15:46:56 2019 -0400 +++ b/distance.py Mon Oct 07 12:52:40 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 489b25966bb9 -r 312f912de69d distance.xml --- a/distance.xml Wed Apr 03 15:46:56 2019 -0400 +++ b/distance.xml Mon Oct 07 12:52:40 2019 -0400 |
| [ |
| @@ -1,5 +1,5 @@ <tool id="mdanalysis_distance" name="Distance Analysis" version="@VERSION@"> - <description>Time series using MDAnalysis</description> + <description>- time series using MDAnalysis</description> <macros> <import>macros.xml</import> </macros> @@ -7,8 +7,10 @@ <command detect_errors="exit_code"> <![CDATA[ python '$__tool_directory__/distance.py' - --idcd '$dcdin' - --ipdb '$pdbin' + --itraj '$trajin' + --istr '$strin' + --itrajext '$trajin.ext' + --istrext '$strin.ext' --isegid1 '$segid1' --iresid1 '$resid1' --iname1 '$name1' @@ -21,11 +23,11 @@ ]]></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"/> </inputs> <outputs> @@ -43,13 +45,29 @@ <param name="name2" value="C1"/> <output name="output" file="Distance_Analysis_raw_data.tabular" /> </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"/> + <output name="output"> + <assert_contents> + <has_n_columns n="2" /> + <has_line_matching expression="0\s+3.8.*" /> + <has_line_matching expression="14\s+3.2.*" /> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[ .. class:: infomark **What it does** -This tool calculates and plot distance between the two atoms. +This tool calculates and plots the distance between the two atoms. _____ @@ -60,8 +78,10 @@ - Trajectory file (DCD). - PDB file. - - Segids, resids and names of two atoms to calculate distances. - + - Segment IDs, Residue IDs and names of two atoms to calculate distances. + +Note that a MDAnalysis 'segment' is a larger organizational unit, for example one protein or all the solvent molecules or simply the whole system. + _____ |
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| diff -r 489b25966bb9 -r 312f912de69d hbonds.py --- a/hbonds.py Wed Apr 03 15:46:56 2019 -0400 +++ b/hbonds.py Mon Oct 07 12:52:40 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 489b25966bb9 -r 312f912de69d macros.xml --- a/macros.xml Wed Apr 03 15:46:56 2019 -0400 +++ b/macros.xml Mon Oct 07 12:52:40 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 489b25966bb9 -r 312f912de69d pca_cosine.py --- a/pca_cosine.py Wed Apr 03 15:46:56 2019 -0400 +++ b/pca_cosine.py Mon Oct 07 12:52:40 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 489b25966bb9 -r 312f912de69d ramachandran_plots.py --- a/ramachandran_plots.py Wed Apr 03 15:46:56 2019 -0400 +++ b/ramachandran_plots.py Mon Oct 07 12:52:40 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 489b25966bb9 -r 312f912de69d rdf.py --- a/rdf.py Wed Apr 03 15:46:56 2019 -0400 +++ b/rdf.py Mon Oct 07 12:52:40 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 489b25966bb9 -r 312f912de69d 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 12:52:40 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 489b25966bb9 -r 312f912de69d test-data/test.gro --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.gro Mon Oct 07 12:52:40 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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SOD61593 3.843 -1.704 1.945\n+ 72SOD SOD61594 -3.065 1.131 -3.142\n+ 73SOD SOD61595 2.911 3.091 3.254\n+ 74SOD SOD61596 -0.146 -3.447 -3.468\n+ 75SOD SOD61597 4.142 1.150 2.128\n+ 1CLA CLA61598 3.723 3.931 -0.432\n+ 2CLA CLA61599 0.598 -3.410 -1.411\n+ 3CLA CLA61600 0.305 -4.033 0.027\n+ 4CLA CLA61601 -2.918 -1.991 -2.129\n+ 5CLA CLA61602 3.212 2.681 -1.461\n+ 6CLA CLA61603 -1.276 3.890 3.970\n+ 7CLA CLA61604 -4.135 -0.631 -2.109\n+ 8CLA CLA61605 -4.010 1.992 2.188\n+ 9CLA CLA61606 -3.787 -1.064 -2.665\n+ 10CLA CLA61607 -2.251 4.155 1.278\n+ 11CLA CLA61608 3.522 3.373 -3.509\n+ 12CLA CLA61609 -4.010 0.565 -0.240\n+ 13CLA CLA61610 3.902 -1.240 -4.037\n+ 14CLA CLA61611 1.826 -3.945 2.374\n+ 15CLA CLA61612 0.618 4.143 -3.510\n+ 16CLA CLA61613 2.436 1.511 3.939\n+ 17CLA CLA61614 0.689 2.163 -1.864\n+ 18CLA CLA61615 2.174 0.614 3.695\n+ 19CLA CLA61616 3.731 -0.836 3.639\n+ 20CLA CLA61617 -0.300 -2.083 2.310\n+ 21CLA CLA61618 0.286 1.863 -2.782\n+ 22CLA CLA61619 0.444 -1.592 4.280\n+ 23CLA CLA61620 -3.682 -0.965 2.751\n+ 24CLA CLA61621 3.059 -2.653 -1.385\n+ 25CLA CLA61622 0.268 1.480 3.096\n+ 26CLA CLA61623 2.985 -1.145 -1.289\n+ 27CLA CLA61624 4.257 -1.638 3.915\n+ 28CLA CLA61625 2.109 2.268 2.707\n+ 29CLA CLA61626 3.148 2.184 -0.946\n+ 30CLA CLA61627 -4.279 3.311 -4.200\n+ 31CLA CLA61628 4.121 2.646 2.804\n+ 32CLA CLA61629 3.133 -2.321 3.087\n+ 33CLA CLA61630 -1.188 2.475 1.768\n+ 34CLA CLA61631 4.251 4.197 2.967\n+ 35CLA CLA61632 -2.115 -2.591 4.099\n+ 36CLA CLA61633 -1.664 3.340 -2.049\n+ 37CLA CLA61634 2.401 1.685 0.376\n+ 38CLA CLA61635 -0.304 -2.623 -0.695\n+ 39CLA CLA61636 -2.524 -2.953 -1.453\n+ 40CLA CLA61637 3.494 -2.888 -3.669\n+ 41CLA CLA61638 -3.591 -0.671 0.327\n+ 42CLA CLA61639 -3.097 0.461 -3.295\n+ 43CLA CLA61640 -0.581 1.524 4.242\n+ 44CLA CLA61641 3.940 1.881 -1.383\n+ 45CLA CLA61642 -1.581 2.921 -3.738\n+ 46CLA CLA61643 0.009 -3.649 -3.486\n+ 47CLA CLA61644 -1.288 -4.010 3.837\n+ 48CLA CLA61645 -2.419 1.919 3.696\n+ 49CLA CLA61646 1.622 -1.819 -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' |
| b |
| diff -r 489b25966bb9 -r 312f912de69d test-data/test.xtc |
| b |
| Binary file test-data/test.xtc has changed |