| Previous changeset 0:d710c7f00ae6 (2019-04-03) Next changeset 2:b348dfa55e0a (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 ramachandran_plots.py ramachandran_plots.xml 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 d710c7f00ae6 -r ce0728b92289 angle.py --- a/angle.py Wed Apr 03 15:46:32 2019 -0400 +++ b/angle.py Mon Oct 07 12:50:22 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 d710c7f00ae6 -r ce0728b92289 dihedrals.py --- a/dihedrals.py Wed Apr 03 15:46:32 2019 -0400 +++ b/dihedrals.py Mon Oct 07 12:50:22 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 d710c7f00ae6 -r ce0728b92289 distance.py --- a/distance.py Wed Apr 03 15:46:32 2019 -0400 +++ b/distance.py Mon Oct 07 12:50:22 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 d710c7f00ae6 -r ce0728b92289 hbonds.py --- a/hbonds.py Wed Apr 03 15:46:32 2019 -0400 +++ b/hbonds.py Mon Oct 07 12:50:22 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 d710c7f00ae6 -r ce0728b92289 macros.xml --- a/macros.xml Wed Apr 03 15:46:32 2019 -0400 +++ b/macros.xml Mon Oct 07 12:50:22 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 d710c7f00ae6 -r ce0728b92289 pca_cosine.py --- a/pca_cosine.py Wed Apr 03 15:46:32 2019 -0400 +++ b/pca_cosine.py Mon Oct 07 12:50:22 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 d710c7f00ae6 -r ce0728b92289 ramachandran_plots.py --- a/ramachandran_plots.py Wed Apr 03 15:46:32 2019 -0400 +++ b/ramachandran_plots.py Mon Oct 07 12:50:22 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 d710c7f00ae6 -r ce0728b92289 ramachandran_plots.xml --- a/ramachandran_plots.xml Wed Apr 03 15:46:32 2019 -0400 +++ b/ramachandran_plots.xml Mon Oct 07 12:50:22 2019 -0400 |
| [ |
| b'@@ -1,42 +1,44 @@\n-<tool id="mdanalysis_ramachandran_plot" name="Ramachandran Plots" version="0.1.3">\n- <description>Calculate and plot the distribution of two diheadrals in a trajectory</description>\n+<tool id="mdanalysis_ramachandran_plot" name="Ramachandran Plots" version="@VERSION@">\n+ <description>- calculate and plot the distribution of two dihedrals in a trajectory</description>\n <macros>\n <import>macros.xml</import>\n </macros>\n <expand macro="requirements">\n- <requirement type="package" version="1.2.1">scipy</requirement>\n+ <requirement type="package" version="1.3.1">scipy</requirement>\n <requirement type="package" version="0.9.0">seaborn</requirement>\n- <requirement type="package" version="1.0.5">nbdime</requirement>\n+ <requirement type="package" version="1.1.0">nbdime</requirement>\n </expand>\n <command detect_errors="exit_code">\n <![CDATA[\n python \'$__tool_directory__/ramachandran_plots.py\'\n- --idcd \'$dcdin\' \n- --ipdb \'$pdbin\'\n- --isegid1 \'$phi.segid1\'\n- --iresid1 \'$phi.resid1\' \n- --iname1 \'$phi.name1\'\n- --isegid2 \'$phi.segid2\'\n- --iresid2 \'$phi.resid2\' \n- --iname2 \'$phi.name2\'\n- --isegid3 \'$phi.segid3\'\n- --iresid3 \'$phi.resid3\' \n- --iname3 \'$phi.name3\'\n- --isegid4 \'$phi.segid4\'\n- --iresid4 \'$phi.resid4\' \n- --iname4 \'$phi.name4\'\n- --isegid5 \'$psi.segid1\'\n- --iresid5 \'$psi.resid1\' \n- --iname5 \'$psi.name1\'\n- --isegid6 \'$psi.segid2\'\n- --iresid6 \'$psi.resid2\' \n- --iname6 \'$psi.name2\' \n- --isegid7 \'$psi.segid3\' \n- --iresid7 \'$psi.resid3\' \n- --iname7 \'$psi.name3\' \n- --isegid8 \'$psi.segid4\' \n- --iresid8 \'$psi.resid4\' \n- --iname8 \'$psi.name4\' \n+ --itraj \'$trajin\' \n+ --istr \'$strin\'\n+ --itrajext \'$trajin.ext\'\n+ --istrext \'$strin.ext\'\n+ --isegid1 \'$phi.phi_segid1\'\n+ --iresid1 \'$phi.phi_resid1\' \n+ --iname1 \'$phi.phi_name1\'\n+ --isegid2 \'$phi.phi_segid2\'\n+ --iresid2 \'$phi.phi_resid2\' \n+ --iname2 \'$phi.phi_name2\'\n+ --isegid3 \'$phi.phi_segid3\'\n+ --iresid3 \'$phi.phi_resid3\' \n+ --iname3 \'$phi.phi_name3\'\n+ --isegid4 \'$phi.phi_segid4\'\n+ --iresid4 \'$phi.phi_resid4\' \n+ --iname4 \'$phi.phi_name4\'\n+ --isegid5 \'$psi.psi_segid1\'\n+ --iresid5 \'$psi.psi_resid1\' \n+ --iname5 \'$psi.psi_name1\'\n+ --isegid6 \'$psi.psi_segid2\'\n+ --iresid6 \'$psi.psi_resid2\' \n+ --iname6 \'$psi.psi_name2\' \n+ --isegid7 \'$psi.psi_segid3\' \n+ --iresid7 \'$psi.psi_resid3\' \n+ --iname7 \'$psi.psi_name3\' \n+ --isegid8 \'$psi.psi_segid4\' \n+ --iresid8 \'$psi.psi_resid4\' \n+ --iname8 \'$psi.psi_name4\' \n --output \'$output\' \n --oramachandran_plot \'$ramachandran_plot\'\n 2>&1\n@@ -44,78 +46,78 @@\n <inputs>\n <expand macro="analysis_inputs"/>\n <section name="phi" title="Phi" expanded="False">\n- <param name="segid1" type="text" value="HET" label="Segid of atom 1">\n+ <param name="phi_segid1" type="text" value="HET" label="Segment ID of atom 1">\n <expand macro="sanitizer"/>\n </param>\n- <param name="resid1" type="text" value="3" label="Resid of atom 1">\n+ <param name="phi_resid1" type="text" value="3" label="Residue ID of atom 1">\n <expand macro="sanitizer_resids"/>\n </param>\n- <param name="name1" type="text" value="O5" label="Atom name of atom 1">\n+ <param name="phi_name1" type="text" value="O5" label="Atom name of atom 1">\n <expand macro="sanitizer"/>\n </param>\n- <param name="segid2" type="text" value="HET" label="Segid of atom 2">\n+ <param name="phi_segid2" type="text" value="HET" label="Segment ID of atom 2'..b' name="psi_name1" value="C1"/>\n+ <param name="psi_segid2" value="HET"/>\n+ <param name="psi_resid2" value="2"/>\n+ <param name="psi_name2" value="O4"/>\n+ <param name="psi_segid3" value="HET"/>\n+ <param name="psi_resid3" value="2"/>\n+ <param name="psi_name3" value="C4"/>\n+ <param name="psi_segid4" value="HET"/>\n+ <param name="psi_resid4" value="2"/>\n+ <param name="psi_name4" value="C3"/>\n <output name="output" file="Ramachandran_Plot_raw_data.tabular" />\n </test>\n+ <test>\n+ <expand macro="tests_inputs_gmx"/>\n+ <param name="phi_segid1" value="SYSTEM"/>\n+ <param name="phi_resid1" value="3"/>\n+ <param name="phi_name1" value="O5"/>\n+ <param name="phi_segid2" value="SYSTEM"/>\n+ <param name="phi_resid2" value="3"/>\n+ <param name="phi_name2" value="C1"/>\n+ <param name="phi_segid3" value="SYSTEM"/>\n+ <param name="phi_resid3" value="2"/>\n+ <param name="phi_name3" value="O4"/>\n+ <param name="phi_segid4" value="SYSTEM"/>\n+ <param name="phi_resid4" value="2"/>\n+ <param name="phi_name4" value="C4"/>\n+ <param name="psi_segid1" value="SYSTEM"/>\n+ <param name="psi_resid1" value="3"/>\n+ <param name="psi_name1" value="C1"/>\n+ <param name="psi_segid2" value="SYSTEM"/>\n+ <param name="psi_resid2" value="2"/>\n+ <param name="psi_name2" value="O4"/>\n+ <param name="psi_segid3" value="SYSTEM"/>\n+ <param name="psi_resid3" value="2"/>\n+ <param name="psi_name3" value="C4"/>\n+ <param name="psi_segid4" value="SYSTEM"/>\n+ <param name="psi_resid4" value="2"/>\n+ <param name="psi_name4" value="C3"/>\n+ <output name="output" file="Ramachandran_Plot_raw_data_gmx.tabular" />\n+ </test>\n </tests>\n <help><![CDATA[\n .. class:: infomark\n \n **What it does**\n \n-A Ramachandran plot ([\xcf\x86,\xcf\x88] plot), originally developed as a way to visualize energetically allowed regions for backbone dihedral angles \xcf\x88 against \xcf\x86 of amino acid.\n-This can be also used to calculate glycosidic \xcf\x86 and \xcf\x88 angles formed between carbohydrates. This tool can calculate and plot the histogram (ramachandran plot) of user define \xcf\x86 and \xcf\x88 angles of a trajectory. \n+A Ramachandran plot ([\xcf\x86,\xcf\x88] plot) was originally developed as a way to visualize the energetically allowed regions for backbone dihedral angles \xcf\x88 and \xcf\x86 of an amino acid.\n+It can be also used to calculate glycosidic \xcf\x86 and \xcf\x88 angles formed between carbohydrates. This tool can calculate and plot the histogram (Ramachandran plot) of user-defined \xcf\x86 and \xcf\x88 angles of a trajectory. \n \n- - For protien \xcf\x86 and \xcf\x88 diheadral definitions see https://proteinstructures.com/Structure/Structure/Ramachandran-plot.html.\n- \n- - For glycan \xcf\x86 and \xcf\x88 diheadral definitions see http://www.glycanstructure.org/\n+ - For protein \xcf\x86 and \xcf\x88 dihedral definitions see https://proteinstructures.com/Structure/Structure/Ramachandran-plot.html. \n+ - For glycan \xcf\x86 and \xcf\x88 dihedral definitions see http://www.glycanstructure.org/\n \n _____\n \n@@ -175,8 +204,10 @@\n \n - Trajectory file (DCD).\n - PDB file.\n- - Segids, resids and names of the four atoms to calculate diheadrals.\n- \n+ - Segment IDs, residue IDs and names of the four atoms to calculate dihedrals.\n+\n+Note that a MDAnalysis \'segment\' is a larger organizational unit, for example one protein or all the solvent molecules or simply the whole system.\n+\n _____\n \n \n@@ -184,8 +215,8 @@\n \n **Output**\n \n- - Tab-separated file of raw data of the \xcf\x86,\xcf\x88 angles time series.\n- - Image (as png) of the Ramachandran Plot.\n+ - Tab-separated file of raw data of the \xcf\x86,\xcf\x88 angles over time.\n+ - Image (as png) of the Ramachandran plot.\n \n \n ]]></help>\n' |
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| diff -r d710c7f00ae6 -r ce0728b92289 rdf.py --- a/rdf.py Wed Apr 03 15:46:32 2019 -0400 +++ b/rdf.py Mon Oct 07 12:50:22 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 d710c7f00ae6 -r ce0728b92289 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 12:50:22 2019 -0400 |
| b |
| @@ -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 d710c7f00ae6 -r ce0728b92289 test-data/test.gro --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.gro Mon Oct 07 12:50:22 2019 -0400 |
| b |
| 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 d710c7f00ae6 -r ce0728b92289 test-data/test.xtc |
| b |
| Binary file test-data/test.xtc has changed |