| Previous changeset 3:ad135cf42274 (2019-04-03) Next changeset 5:62ce73c9d737 (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 angle.xml dihedrals.py distance.py 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 ad135cf42274 -r e7d0075052c9 angle.py --- a/angle.py Wed Apr 03 15:47:56 2019 -0400 +++ b/angle.py Mon Oct 07 12:51:05 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 |
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| diff -r ad135cf42274 -r e7d0075052c9 angle.xml --- a/angle.xml Wed Apr 03 15:47:56 2019 -0400 +++ b/angle.xml Mon Oct 07 12:51:05 2019 -0400 |
| [ |
| @@ -1,5 +1,5 @@ <tool id="mdanalysis_angle" name="Angle Analysis" version="@VERSION@"> - <description>Time series of Angles</description> + <description>- time series of Angles</description> <macros> <import>macros.xml</import> </macros> @@ -7,8 +7,10 @@ <command detect_errors="exit_code"> <![CDATA[ python '$__tool_directory__/angle.py' - --idcd '$dcdin' - --ipdb '$pdbin' + --itraj '$trajin' + --istr '$strin' + --itrajext '$trajin.ext' + --istrext '$strin.ext' --isegid1 '$segid1' --iresid1 '$resid1' --iname1 '$name1' @@ -24,14 +26,14 @@ ]]></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="segid3" type="text" value="HET" label="Segid of atom 3"/> - <param name="resid3" type="text" value="3" label="Resid of atom 3"/> + <param name="segid3" type="text" value="HET" label="Segment ID of atom 3"/> + <param name="resid3" type="text" value="3" label="Residue ID of atom 3"/> <param name="name3" type="text" value="C2" label="Atom name of atom 3"/> </inputs> <outputs> @@ -52,13 +54,33 @@ <param name="name3" value="C2"/> <output name="output" file="Angle_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"/> + <param name="segid3" value="SYSTEM"/> + <param name="resid3" value="3"/> + <param name="name3" value="C2"/> + <output name="output"> + <assert_contents> + <has_n_columns n="2" /> + <has_line_matching expression="0.0\t70.*" /> + <has_line_matching expression="10.0\t71.*" /> + <has_line_matching expression="11.0\t81.*" /> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[ .. class:: infomark **What it does** -This tool calculates and plot angle between three atoms. +This tool calculates and plots the angle between three atoms. _____ @@ -69,8 +91,10 @@ - Trajectory file (DCD). - PDB file. - - Segids, resids and names of the three atoms to calculate angles. - + - Segment IDs, residue IDs and names of the three atoms for calculating angles. + +Note that a MDAnalysis 'segment' is a larger organizational unit, for example one protein or all the solvent molecules or simply the whole system. + _____ @@ -78,10 +102,9 @@ **Output** - - Tab-separated file of raw data of angle between three atoms calculated for each frame. + - Tab-separated file of raw data of the angle between three atoms calculated for each frame. - Image (as png) of the time series graph. - ]]></help> <expand macro="citations" /> </tool> |
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| diff -r ad135cf42274 -r e7d0075052c9 dihedrals.py --- a/dihedrals.py Wed Apr 03 15:47:56 2019 -0400 +++ b/dihedrals.py Mon Oct 07 12:51:05 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) |
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| diff -r ad135cf42274 -r e7d0075052c9 distance.py --- a/distance.py Wed Apr 03 15:47:56 2019 -0400 +++ b/distance.py Mon Oct 07 12:51:05 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 ad135cf42274 -r e7d0075052c9 hbonds.py --- a/hbonds.py Wed Apr 03 15:47:56 2019 -0400 +++ b/hbonds.py Mon Oct 07 12:51:05 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 ad135cf42274 -r e7d0075052c9 macros.xml --- a/macros.xml Wed Apr 03 15:47:56 2019 -0400 +++ b/macros.xml Mon Oct 07 12:51:05 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 ad135cf42274 -r e7d0075052c9 pca_cosine.py --- a/pca_cosine.py Wed Apr 03 15:47:56 2019 -0400 +++ b/pca_cosine.py Mon Oct 07 12:51:05 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 ad135cf42274 -r e7d0075052c9 ramachandran_plots.py --- a/ramachandran_plots.py Wed Apr 03 15:47:56 2019 -0400 +++ b/ramachandran_plots.py Mon Oct 07 12:51:05 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 ad135cf42274 -r e7d0075052c9 rdf.py --- a/rdf.py Wed Apr 03 15:47:56 2019 -0400 +++ b/rdf.py Mon Oct 07 12:51:05 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 ad135cf42274 -r e7d0075052c9 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 12:51:05 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 ad135cf42274 -r e7d0075052c9 test-data/test.gro --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.gro Mon Oct 07 12:51:05 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 2.626 0.829 -0.238\n+ 4CYS HB2 30 2.491 0.726 -0.185\n+ 4CYS SG 31 2.689 0.708 -0.041\n+ 4CYS C 32 2.434 1.003 -0.177\n+ 4CYS O 33 2.310 1.011 -0.185\n+ 5THR N 34 2.513 1.082 -0.251\n+ 5THR HN 35 2.612 1.073 -0.243\n+ 5THR CA 36 2.463 1.189 -0.334\n+ 5THR HA 37 2.359 1.168 -0.361\n+ 5THR CB 38 2.471 1.327 -0.267\n+ 5THR HB 39 2.436 1.406 -0.337\n+ 5THR OG1 40 2.605 1.358 -0.227\n+ 5THR HG1 41 2.654 1.352 -0.310\n+ 5THR CG2 42 2.379 1.330 -0.145\n+ 5THR HG21 43 2.413 1.259 -0.066\n+ 5THR HG22 44 2.276 1.300 -0.175\n+ 5THR HG23 45 2.375 1.431 -0.100\n+ 5THR C 46 2.539 1.190 -0.465\n+ 5THR O 47 2.581 1.296 -0.511\n+ 6LEU N 48 2.559 1.072 -0.527\n+ 6LEU HN 49 2.522 0.985 -0.489\n+ 6LEU CA 50 2.613 1.064 -0.662\n+ 6LEU HA 51 2.693 1.135 -0.673\n+ 6LEU CB 52 2.664 0.921 -0.694\n+ 6LEU HB1 53 2.704 0.919 -0.798\n+ 6LEU HB2 54 2.578 0.850 -0.687\n+ 6LEU CG 55 2.774 0.867 -0.600\n+ 6LEU HG 56 2.733 0.865 -0.496\n+ 6LEU CD1 57 2.810 0.722 -0.638\n+ 6LEU HD11 58 2.849 0.716 -0.741\n+ 6LEU HD12 59 2.718 0.658 -0.631\n+ 6LEU HD13 60 2.885 0.680 -0.568\n+ 6LEU CD2 61 2.900 0.954 -0.602\n+ 6LEU HD21 62 2.877 1.056 -0.564\n+ 6LEU HD22 63 2.939 0.964 -0.705\n+ 6LEU HD23 64 2.979 0.910 -0.538\n+ 6LEU C 65 2.505 1.102 -0.763\n+ 6LEU O 66 2.529 1.158 -0.868\n+ 7GLN N 67 2.378 1.075 -0.725\n+ 7GLN HN 68 2.357 1.024 -0.641\n+ 7GLN CA 69 2.262 1.113 -0.801\n+ 7GLN HA 70 2.291 1.166 -0.890\n+ 7GLN CB 71 2.178 0.990 -0.840\n+ 7GLN HB1 72 2.098 1.021 -0.910\n+ 7GLN HB2 73 2.128 0.948 -0.749\n+ 7GLN CG 74 2.265 0.878 -0.901\n+ 7GLN HG1 75 2.333 0.834 -0.825\n+ 7GLN HG2 76 2.327 0.921 -0.984\n+ 7GLN CD 77 2.181 0.767 -0.962\n+ 7GLN OE1 78 2.190 0.744 -1.082\n+ 7GLN NE2 79 2.097 0.701 -0.879\n+ 7GLN HE21 80 2.085 0.731 -0.785\n+ 7GLN HE22 81 2.035 0.634 -0.921\n+ 7GLN C 82 2.183 1.207 -0.712\n+ 7GLN O 83 2.176 1.194 -0.590\n+ 8SER N 84 2.125 1.313 -0.770\n+ 8SER HN 85 2.120 1.326 -0.868\n+ '..b'68 1.454\n+ 42SOD SOD61564 -0.047 2.795 -1.594\n+ 43SOD SOD61565 -3.119 1.785 -0.175\n+ 44SOD SOD61566 3.692 3.565 2.568\n+ 45SOD SOD61567 1.160 -2.677 0.405\n+ 46SOD SOD61568 2.182 2.098 -4.358\n+ 47SOD SOD61569 2.499 -3.552 3.622\n+ 48SOD SOD61570 -3.150 2.637 2.545\n+ 49SOD SOD61571 -3.611 -1.369 -0.304\n+ 50SOD SOD61572 3.179 4.217 -1.914\n+ 51SOD SOD61573 -1.544 3.385 3.985\n+ 52SOD SOD61574 3.906 3.226 3.286\n+ 53SOD SOD61575 -1.400 1.258 -2.542\n+ 54SOD SOD61576 0.624 4.043 2.421\n+ 55SOD SOD61577 -0.572 -3.952 2.807\n+ 56SOD SOD61578 -2.287 2.496 -1.486\n+ 57SOD SOD61579 -4.296 -1.353 4.117\n+ 58SOD SOD61580 4.009 2.333 -1.543\n+ 59SOD SOD61581 3.981 3.781 -3.393\n+ 60SOD SOD61582 -2.801 -0.902 2.131\n+ 61SOD SOD61583 0.054 2.141 -3.123\n+ 62SOD SOD61584 1.742 -1.695 -3.684\n+ 63SOD SOD61585 -1.328 3.677 3.172\n+ 64SOD SOD61586 2.023 -1.550 1.871\n+ 65SOD SOD61587 -3.781 1.811 2.706\n+ 66SOD SOD61588 -1.564 0.724 2.624\n+ 67SOD SOD61589 -1.457 -1.438 1.916\n+ 68SOD SOD61590 3.938 -1.495 -0.104\n+ 69SOD SOD61591 -4.177 0.685 -3.156\n+ 70SOD SOD61592 -3.475 -2.557 3.364\n+ 71SOD 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 ad135cf42274 -r e7d0075052c9 test-data/test.xtc |
| b |
| Binary file test-data/test.xtc has changed |