| Next changeset 1:ce0728b92289 (2019-10-07) |
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Commit message:
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1 |
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added:
angle.py dihedrals.py distance.py hbonds.py macros.xml pca_cosine.py ramachandran_plots.py ramachandran_plots.xml rdf.py test-data/Angle_Analysis_Plot.png test-data/Angle_Analysis_raw_data.tabular test-data/Dihedral_Analysis_Plot.png test-data/Dihedral_analysis_raw_data.tabular test-data/Distance_Analysis_Plot.png test-data/Distance_Analysis_raw_data.tabular test-data/RDF_Analysis_Plot.png test-data/RDF_raw_data.tabular test-data/Ramachandran_Plot_raw_data.tabular test-data/test.dcd test-data/test.pdb |
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| diff -r 000000000000 -r d710c7f00ae6 angle.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/angle.py Wed Apr 03 15:46:32 2019 -0400 |
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| @@ -0,0 +1,71 @@ +#!/usr/bin/env python + +import argparse +import csv +import sys + +import MDAnalysis as mda + +import matplotlib +matplotlib.use('Agg') # noqa +import matplotlib.pyplot as plt + +import numpy as np +from numpy.linalg import norm + + +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('--isegid1', help='segid 1') + parser.add_argument('--iresid1', help='resid 1') + parser.add_argument('--iname1', help='name 1') + parser.add_argument('--isegid2', help='segid 2') + parser.add_argument('--iresid2', help='resid 2') + parser.add_argument('--iname2', help='name 2') + parser.add_argument('--isegid3', help='segid 3') + parser.add_argument('--iresid3', help='resid 3') + parser.add_argument('--iname3', help='name 3') + parser.add_argument('--output', help='output') + parser.add_argument('--oangle_plot', help='angle plot') + return parser.parse_args() + + +args = parse_command_line(sys.argv) + +atom1 = "(segid %s and resid %s and name %s)" % \ + (args.isegid1, args.iresid1, args.iname1) +atom2 = "(segid %s and resid %s and name %s)" % \ + (args.isegid2, args.iresid2, args.iname2) +atom3 = "(segid %s and resid %s and name %s)" % \ + (args.isegid3, args.iresid3, args.iname3) + + +def theta(u): + A = u.select_atoms(atom1).center_of_geometry() + B = u.select_atoms(atom2).center_of_geometry() + C = u.select_atoms(atom3).center_of_geometry() + BA = A - B + BC = C - B + theta = np.arccos(np.dot(BA, BC)/(norm(BA)*norm(BC))) + return np.rad2deg(theta) + + +u = mda.Universe(args.ipdb, args.idcd, topology_format="PDB", format="DCD") +data = np.array([(u.trajectory.frame, theta(u)) for ts in u.trajectory]) +frame, theta = data.T + +with open(args.output, 'w') as f: + writer = csv.writer(f, delimiter='\t') + writer.writerows(zip(frame, theta)) + +with open(args.output) as f: + g = [xtmp.strip() for xtmp in f] + data = [tuple(map(float, xtmp.split())) for xtmp in g[0:]] + time = [xtmp[0] for xtmp in data] + angle = [xtmp[1] for xtmp in data] + plt.plot(time, angle) + plt.xlabel('Frame No.') + plt.ylabel('Angle (degrees)') + plt.savefig(args.oangle_plot, format='png') |
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| diff -r 000000000000 -r d710c7f00ae6 dihedrals.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dihedrals.py Wed Apr 03 15:46:32 2019 -0400 |
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| @@ -0,0 +1,78 @@ +#!/usr/bin/env python + +import argparse +import csv +import sys + +import MDAnalysis as mda +from MDAnalysis.lib.distances import calc_dihedrals + +import matplotlib +matplotlib.use('Agg') # noqa +import matplotlib.pyplot as plt + +import numpy as np + + +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('--isegid1', help='segid 1') + parser.add_argument('--iresid1', help='resid 1') + parser.add_argument('--iname1', help='name 1') + parser.add_argument('--isegid2', help='segid 2') + parser.add_argument('--iresid2', help='resid 2') + parser.add_argument('--iname2', help='name 2') + parser.add_argument('--isegid3', help='segid 3') + parser.add_argument('--iresid3', help='resid 3') + parser.add_argument('--iname3', help='name 3') + parser.add_argument('--isegid4', help='segid 4') + parser.add_argument('--iresid4', help='resid 4') + parser.add_argument('--iname4', help='name 4') + parser.add_argument('--output', help='output') + parser.add_argument('--odihedral_plot', help='dihedral plot') + return parser.parse_args() + + +args = parse_command_line(sys.argv) + +atom1 = "(segid %s and resid %s and name %s)" % \ + (args.isegid1, args.iresid1, args.iname1) +atom2 = "(segid %s and resid %s and name %s)" % \ + (args.isegid2, args.iresid2, args.iname2) +atom3 = "(segid %s and resid %s and name %s)" % \ + (args.isegid3, args.iresid3, args.iname3) +atom4 = "(segid %s and resid %s and name %s)" % \ + (args.isegid4, args.iresid4, args.iname4) + + +def psi(u): + A = u.select_atoms(atom1).positions + B = u.select_atoms(atom2).positions + C = u.select_atoms(atom3).positions + D = u.select_atoms(atom4).positions + psi = calc_dihedrals(A, B, C, D) + return np.rad2deg(psi) + + +u = mda.Universe(args.ipdb, args.idcd, topology_format="PDB", format="DCD") +data = np.array([(u.trajectory.frame, psi(u)) for ts in u.trajectory]) +frame, psi = data.T +PSI = np.concatenate(psi, axis=0) + +zip(frame, PSI) + +with open(args.output, 'w') as f: + writer = csv.writer(f, delimiter='\t') + writer.writerows(zip(frame, PSI)) + +with open(args.output) as f: + g = [xtmp.strip() for xtmp in f] + data = [tuple(map(float, xtmp.split())) for xtmp in g[0:]] + time = [xtmp[0] for xtmp in data] + dihedral = [xtmp[1] for xtmp in data] + plt.plot(time, dihedral) + plt.xlabel('Frame No.') + plt.ylabel('Dihedral (degrees)') + plt.savefig(args.odihedral_plot, format='png') |
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| diff -r 000000000000 -r d710c7f00ae6 distance.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/distance.py Wed Apr 03 15:46:32 2019 -0400 |
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| @@ -0,0 +1,56 @@ +#!/usr/bin/env python + +import argparse +import sys + +import MDAnalysis as mda + +import matplotlib +matplotlib.use('Agg') # noqa +import matplotlib.pyplot as plt + +import numpy as np + + +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('--isegid1', help='segid 1') + parser.add_argument('--iresid1', help='resid 1') + parser.add_argument('--iname1', help='name 1') + parser.add_argument('--isegid2', help='segid 2') + parser.add_argument('--iresid2', help='resid 2') + parser.add_argument('--iname2', help='name 2') + parser.add_argument('--output', help='output') + parser.add_argument('--odistance_plot', help='odistance plot') + return parser.parse_args() + + +args = parse_command_line(sys.argv) + +atom1 = "(segid %s and resid %s and name %s)" % \ + (args.isegid1, args.iresid1, args.iname1) +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") +x = u.select_atoms(atom1) +y = u.select_atoms(atom2) + +with open(args.output, 'w') as f: + for t in u.trajectory: + r = x.positions - y.positions + d = np.linalg.norm(r) + f.write(str(t.frame) + '\t ') + f.write(str(d) + '\n') + +with open(args.output) as f: + g = [xtmp.strip() for xtmp in f] + data = [tuple(map(float, xtmp.split())) for xtmp in g[0:]] + time = [xtmp[0] for xtmp in data] + distance = [xtmp[1] for xtmp in data] + plt.plot(time, distance) + plt.xlabel('Frame No.') + plt.ylabel(r'Distance ($\AA$)') + plt.savefig(args.odistance_plot, format='png') |
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| diff -r 000000000000 -r d710c7f00ae6 hbonds.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/hbonds.py Wed Apr 03 15:46:32 2019 -0400 |
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| @@ -0,0 +1,69 @@ +#!/usr/bin/env python + +import argparse +import csv +import sys + +import MDAnalysis.analysis.hbonds + +import pandas as pd + + +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('--isegid1', help='segid 1') + parser.add_argument('--isegid2', help='segid 2') + parser.add_argument('--idistance', help='cutoff distance') + parser.add_argument('--iangle', help='ctoff angle') + parser.add_argument('--output', help='output') + parser.add_argument('--ofreq_output', help='frequency output') + parser.add_argument('--onumber_output', help='number of hbond output') + parser.add_argument('--otime_output', help='time steps output') + return parser.parse_args() + + +args = parse_command_line(sys.argv) + +selection1 = "segid %s" % args.isegid1 +selection2 = "segid %s" % args.isegid2 +distance = float(args.idistance) +angle = float(args.iangle) + +u = MDAnalysis.Universe( + args.ipdb, args.idcd, topology_format="PDB", format="DCD") + +h = MDAnalysis.analysis.hbonds.HydrogenBondAnalysis( + u, selection1, selection2, distance=distance, angle=angle) +h.run() +h.generate_table() + +df = pd.DataFrame.from_records(h.table) +df.to_csv(args.output, sep='\t') + +t1 = list(h.count_by_type()) +t2 = list(h.count_by_time()) +t3 = list(h.timesteps_by_type()) + +with open(args.ofreq_output, 'w') as f: + f.write("donor_index\tacceptor_index\t\ + donor_resname\tdonor_resid\tdonor_atom\t\ + hydrogen_atom\tacceptor_reansme\tacceptor_resid\t\ + acceptor_atom\tfrequency\n") + writer = csv.writer(f, delimiter='\t') + writer.writerows(t1) + + +with open(args.onumber_output, 'w') as f1: + f1.write("time_step\tno_of_h_bonds\n") + writer = csv.writer(f1, delimiter='\t') + writer.writerows(t2) + +with open(args.otime_output, 'w') as f2: + f2.write("donor_index\tacceptor_index\t\ + donor_resname\tdonor_resid\tdonor_atom\t\ + hydrogen_atom\tacceptor_reansme\tacceptor_resid\t\ + acceptor_atom\ttime_step\n") + writer = csv.writer(f2, delimiter='\t') + writer.writerows(t3) |
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| diff -r 000000000000 -r d710c7f00ae6 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Apr 03 15:46:32 2019 -0400 |
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| @@ -0,0 +1,38 @@ +<macros> + <token name="@VERSION@">0.19</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="0.19.2">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"/> + <yield/> + </xml> + <xml name="sanitizer"> + <sanitizer invalid_char=""> + <valid initial="string.ascii_letters,string.digits"/> + </sanitizer> + <yield/> + </xml> + <xml name="sanitizer_resids"> + <sanitizer invalid_char=""> + <valid initial="string.digits"/> + </sanitizer> + <yield/> + </xml> + <xml name="tests_inputs"> + <param name="dcdin" value="test.dcd" /> + <param name="pdbin" value="test.pdb" /> + <yield/> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1093/bioinformatics/btz107</citation> + <citation type="doi">10.1002/jcc.21787</citation> + <yield/> + </citations> + </xml> +</macros> |
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| diff -r 000000000000 -r d710c7f00ae6 pca_cosine.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pca_cosine.py Wed Apr 03 15:46:32 2019 -0400 |
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| @@ -0,0 +1,46 @@ +#!/usr/bin/env python + +import argparse +import csv +import sys + +import MDAnalysis as mda +import MDAnalysis.analysis.pca as pca + +import numpy as np + + +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('--icomponents', help='number of principle components') + parser.add_argument('--iindex', help='index of the PC') + parser.add_argument('--output', help='output') + parser.add_argument('--cosout', help='cosine output') + return parser.parse_args() + + +args = parse_command_line(sys.argv) + +u = mda.Universe(args.ipdb, args.idcd, topology_format="PDB", format="DCD") + +components = int(args.icomponents) +pca_index = int(args.iindex) + +PSF_pca = pca.PCA(u, select='backbone') +PSF_pca.run() +n_pcs = np.where(PSF_pca.cumulated_variance > 0.95)[0][0] +atomgroup = u.select_atoms('backbone') + +pca_space = PSF_pca.transform(atomgroup, n_components=components) +cosine = mda.analysis.pca.cosine_content(pca_space, pca_index) + +PCA = list(pca_space) + +with open(args.output, 'w') as f: + writer = csv.writer(f, delimiter='\t') + writer.writerows(PCA) + +with open(args.cosout, 'w') as f1: + f1.write(str(cosine)) |
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| diff -r 000000000000 -r d710c7f00ae6 ramachandran_plots.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ramachandran_plots.py Wed Apr 03 15:46:32 2019 -0400 |
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| @@ -0,0 +1,121 @@ +#!/usr/bin/env python + +import argparse +import csv +import sys +from collections import namedtuple + +import MDAnalysis as mda +from MDAnalysis.lib.distances import calc_dihedrals + +import matplotlib +matplotlib.use('Agg') # noqa +import matplotlib.pyplot as plt + +import numpy as np + +import seaborn as sns + + +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('--isegid1', help='segid 1') + parser.add_argument('--iresid1', help='resid 1') + parser.add_argument('--iname1', help='name 1') + parser.add_argument('--isegid2', help='segid 2') + parser.add_argument('--iresid2', help='resid 2') + parser.add_argument('--iname2', help='name 2') + parser.add_argument('--isegid3', help='segid 3') + parser.add_argument('--iresid3', help='resid 3') + parser.add_argument('--iname3', help='name 3') + parser.add_argument('--isegid4', help='segid 4') + parser.add_argument('--iresid4', help='resid 4') + parser.add_argument('--iname4', help='name 4') + parser.add_argument('--isegid5', help='segid 1') + parser.add_argument('--iresid5', help='resid 1') + parser.add_argument('--iname5', help='name 1') + parser.add_argument('--isegid6', help='segid 2') + parser.add_argument('--iresid6', help='resid 2') + parser.add_argument('--iname6', help='name 2') + parser.add_argument('--isegid7', help='segid 3') + parser.add_argument('--iresid7', help='resid 3') + parser.add_argument('--iname7', help='name 3') + parser.add_argument('--isegid8', help='segid 4') + parser.add_argument('--iresid8', help='resid 4') + parser.add_argument('--iname8', help='name 4') + parser.add_argument('--output', help='output') + parser.add_argument('--oramachandran_plot', help='dihedral plot') + return parser.parse_args() + + +args = parse_command_line(sys.argv) + +Dihedral = namedtuple( + 'Dihedral', ['atom1', 'atom2', 'atom3', 'atom4']) + +# order of dihedral atom is the crystallographic definition +# (see glycanstructure.org) + +# phi +atom1 = "(segid %s and resid %s and name %s)" % \ + (args.isegid1, args.iresid1, args.iname1) +atom2 = "(segid %s and resid %s and name %s)" % \ + (args.isegid2, args.iresid2, args.iname2) +atom3 = "(segid %s and resid %s and name %s)" % \ + (args.isegid3, args.iresid3, args.iname3) +atom4 = "(segid %s and resid %s and name %s)" % \ + (args.isegid4, args.iresid4, args.iname4) + +dihe_phi = Dihedral(atom1, atom2, atom3, atom4) + +# psi +atom1 = "(segid %s and resid %s and name %s)" % \ + (args.isegid5, args.iresid5, args.iname5) +atom2 = "(segid %s and resid %s and name %s)" % \ + (args.isegid6, args.iresid6, args.iname6) +atom3 = "(segid %s and resid %s and name %s)" % \ + (args.isegid7, args.iresid7, args.iname7) +atom4 = "(segid %s and resid %s and name %s)" % \ + (args.isegid8, args.iresid8, args.iname8) + +dihe_psi = Dihedral(atom1, atom2, atom3, atom4) + + +def calc_torsion(dihedral): + """atom 1 -4 are valid atom selections. torsion in degrees is returned""" + A = u.select_atoms(dihedral.atom1).positions + B = u.select_atoms(dihedral.atom2).positions + C = u.select_atoms(dihedral.atom3).positions + D = u.select_atoms(dihedral.atom4).positions + + dihe = calc_dihedrals(A, B, C, D) + return np.rad2deg(dihe) + + +u = mda.Universe(args.ipdb, args.idcd, topology_format="PDB", format="DCD") + +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]) + +phi_frame, phi_series = phi_trajdata.T +psi_frame, psi_series = psi_trajdata.T + +phi_series = np.concatenate(phi_series, axis=0) +psi_series = np.concatenate(psi_series, axis=0) + +zip(phi_frame, phi_series, psi_series) + +with open(args.output, 'w') as f: + writer = csv.writer(f, delimiter='\t') + writer.writerows(zip(phi_frame, phi_series, psi_series)) + +with sns.axes_style("white"): + h = sns.jointplot(x=phi_series, y=psi_series, kind="kde", legend=True) + h.set_axis_labels(r'$\Phi$ (degrees)', r'$\Psi$ (degrees)') + h.ax_joint.set_xlim(-180, 180) + h.ax_joint.set_ylim(-180, 180) + plt.savefig(args.oramachandran_plot, format='png') |
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| diff -r 000000000000 -r d710c7f00ae6 ramachandran_plots.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ramachandran_plots.xml Wed Apr 03 15:46:32 2019 -0400 |
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| b'@@ -0,0 +1,193 @@\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+ <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="0.9.0">seaborn</requirement>\n+ <requirement type="package" version="1.0.5">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 \'$psi.name4\' \n+ --output \'$output\' \n+ --oramachandran_plot \'$ramachandran_plot\'\n+ 2>&1\n+]]></command>\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+ <expand macro="sanitizer"/>\n+ </param>\n+ <param name="resid1" type="text" value="3" label="Resid 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+ <expand macro="sanitizer"/>\n+ </param>\n+ <param name="segid2" type="text" value="HET" label="Segid of atom 2">\n+ <expand macro="sanitizer"/>\n+ </param>\n+ <param name="resid2" type="text" value="3" label="Resid of atom 2">\n+ <expand macro="sanitizer_resids"/>\n+ </param>\n+ <param name="name2" type="text" value="C1" label="Atom name of atom 2">\n+ <expand macro="sanitizer"/>\n+ </param>\n+ <param name="segid3" type="text" value="HET" label="Segid of atom 3">\n+ <expand macro="sanitizer"/>\n+ </param>\n+ <param name="resid3" type="text" value="2" label="Resid of atom 3">\n+ <expand macro="sanitizer_resids"/>\n+ </param>\n+ <param name="name3" type="text" value="O4" label="Atom name of atom 3">\n+ <expand macro="sanitizer"/>\n+ </param>\n+ <param name="segid4" type="text" value="HET" label="Segid of atom 4">\n+ <expand macro="sanitizer"/>\n+ </param>\n+ <param name="resid4" type="text" value="2" label="Resid of atom 4">\n+ <expand macro="sanitizer_resids"/>\n+ </param>\n+ <param name="name4" type="text" value="C4" label="Atom name of atom 4">\n+ <expand macro="sanitizer"/>\n+ </param>\n+ </section>\n+ <section name="psi" title="Psi" expanded="False">\n+ <param name="segid1" type="text" value="HET" label="Segid of atom 1">\n+ <expand macro="sanitizer"/>\n+ </param>\n+ <param name="resid1" type="text" value="3" label="Resid of atom 1">\n+ <expand macro="sanitizer_resids"/>\n+ </param>\n+ <param name="name1" type="text" value="C1" label="Atom name of atom 1">\n+ <expand macro="sanitizer"/>\n+ </p'..b'"text" value="HET" label="Segid of atom 2">\n+ <expand macro="sanitizer"/>\n+ </param>\n+ <param name="resid2" type="text" value="2" label="Resid of atom 2">\n+ <expand macro="sanitizer_resids"/>\n+ </param>\n+ <param name="name2" type="text" value="O4" label="Atom name of atom 2">\n+ <expand macro="sanitizer"/>\n+ </param>\n+ <param name="segid3" type="text" value="HET" label="Segid of atom 3">\n+ <expand macro="sanitizer"/>\n+ </param>\n+ <param name="resid3" type="text" value="2" label="Resid of atom 3">\n+ <expand macro="sanitizer_resids"/>\n+ </param>\n+ <param name="name3" type="text" value="C4" label="Atom name of atom 3">\n+ <expand macro="sanitizer"/>\n+ </param>\n+ <param name="segid4" type="text" value="HET" label="Segid of atom 4">\n+ <expand macro="sanitizer"/>\n+ </param>\n+ <param name="resid4" type="text" value="2" label="Resid of atom 4">\n+ <expand macro="sanitizer_resids"/>\n+ </param>\n+ <param name="name4" type="text" value="C3" label="Atom name of atom 4">\n+ <expand macro="sanitizer"/>\n+ </param>\n+ </section>\n+ </inputs>\n+ <outputs>\n+ <data format="tabular" name="output" label="Ramachandran Plot raw data"/>\n+ <data format="png" name="ramachandran_plot" label="Ramachandran Plot"/>\n+ </outputs>\n+ <tests>\n+ <test>\n+ <expand macro="tests_inputs"/>\n+ <param name="phi.segid1" value="HET"/>\n+ <param name="phi.resid1" value="3"/>\n+ <param name="phi.name1" value="O5"/>\n+ <param name="phi.segid2" value="HET"/>\n+ <param name="phi.resid2" value="3"/>\n+ <param name="phi.name2" value="C1"/>\n+ <param name="phi.segid3" value="HET"/>\n+ <param name="phi.resid3" value="2"/>\n+ <param name="phi.name3" value="O4"/>\n+ <param name="phi.segid4" value="HET"/>\n+ <param name="phi.resid4" value="2"/>\n+ <param name="phi.name4" value="C4"/>\n+ <param name="psi.segid1" value="HET"/>\n+ <param name="psi.resid1" value="3"/>\n+ <param 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+ </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+\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+\n+_____\n+\n+\n+.. class:: infomark\n+\n+**Input**\n+\n+ - Trajectory file (DCD).\n+ - PDB file.\n+ - Segids, resids and names of the four atoms to calculate diheadrals.\n+ \n+_____\n+\n+ \n+.. class:: infomark\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+\n+\n+ ]]></help>\n+ <expand macro="citations" />\n+</tool>\n' |
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| diff -r 000000000000 -r d710c7f00ae6 rdf.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rdf.py Wed Apr 03 15:46:32 2019 -0400 |
| [ |
| @@ -0,0 +1,68 @@ +#!/usr/bin/env python + +import argparse +import csv +import sys + +import MDAnalysis as mda +from MDAnalysis.analysis.rdf import InterRDF + +import matplotlib +matplotlib.use('Agg') # noqa +import matplotlib.pyplot as plt + +import numpy as np + + +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('--isegid1', help='segid 1') + parser.add_argument('--iresid1', help='resid 1') + parser.add_argument('--iname1', help='name 1') + parser.add_argument('--isegid2', help='segid 2') + parser.add_argument('--iresid2', help='resid 2') + parser.add_argument('--iname2', help='name 2') + parser.add_argument('--inbins', help='Number of bins in the histogram') + parser.add_argument('--istart', help='Starting Point') + parser.add_argument('--iend', help='End point') + parser.add_argument('--output', help='output') + parser.add_argument('--ordf_plot', help='RDF plot') + return parser.parse_args() + + +args = parse_command_line(sys.argv) + +atom1 = "(segid %s and resid %s and name %s)" % \ + (args.isegid1, args.iresid1, args.iname1) +atom2 = "(segid %s and resid %s and name %s)" % \ + (args.isegid2, args.iresid2, args.iname2) +bins = int(args.inbins) +start = float(args.istart) +end = float(args.iend) + +u = mda.Universe(args.ipdb, args.idcd, topology_format="PDB", format="DCD") +x = u.select_atoms(atom1) +y = u.select_atoms(atom2) + +rdf = InterRDF(x, y, nbins=bins, range=(start, end)) +rdf.run() +bins = rdf.bins +bins = np.around(bins, decimals=3) +RDF = rdf.rdf +zip(bins, RDF) + +with open(args.output, 'w') as f: + writer = csv.writer(f, delimiter='\t') + writer.writerows(zip(bins, RDF)) + +with open(args.output) as f: + g = [xtmp.strip() for xtmp in f] + data = [tuple(map(float, xtmp.split())) for xtmp in g[0:]] + time = [xtmp[0] for xtmp in data] + rdf = [xtmp[1] for xtmp in data] + plt.plot(time, rdf) + plt.xlabel(r'r ($\AA$)') + plt.ylabel('g(r)') + plt.savefig(args.ordf_plot, format='png') |
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| diff -r 000000000000 -r d710c7f00ae6 test-data/Angle_Analysis_raw_data.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Angle_Analysis_raw_data.tabular Wed Apr 03 15:46:32 2019 -0400 |
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| @@ -0,0 +1,15 @@ +0.0 70.84919180880273 +1.0 70.97155495136695 +2.0 70.37097279938007 +3.0 70.12692388497567 +4.0 71.15946406922332 +5.0 71.91362565497833 +6.0 71.91268728348935 +7.0 71.97418402125982 +8.0 72.1521609490865 +9.0 72.3083065219282 +10.0 71.5291313235259 +11.0 81.56576116363512 +12.0 73.46330915394758 +13.0 67.04185741201445 +14.0 70.0710549275429 |
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| diff -r 000000000000 -r d710c7f00ae6 test-data/Ramachandran_Plot_raw_data.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Ramachandran_Plot_raw_data.tabular Wed Apr 03 15:46:32 2019 -0400 |
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| diff -r 000000000000 -r d710c7f00ae6 test-data/test.dcd |
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| diff -r 000000000000 -r d710c7f00ae6 test-data/test.pdb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.pdb Wed Apr 03 15:46:32 2019 -0400 |
| b |
| b'@@ -0,0 +1,61655 @@\n+REMARK FILENAME: MINIMIZE.INP \n+REMARK PURPOSE: SETUP PERIODIC BOUNDARY CONDITIONS AND ENERGY MINIMIZATION \n+REMARK AUTHOR: THARINDU SENAPATHI \n+REMARK DATE: 9/25/18 11:16:58 CREATED BY USER: galaxy \n+ATOM 1 N SER 2 23.711 4.396 5.292 1.00 0.00 PRO \n+ATOM 2 HT1 SER 2 22.774 4.012 5.048 1.00 0.00 PRO \n+ATOM 3 HT2 SER 2 23.993 4.056 6.233 1.00 0.00 PRO \n+ATOM 4 HT3 SER 2 24.412 4.016 4.606 1.00 0.00 PRO \n+ATOM 5 CA SER 2 23.692 5.909 5.232 1.00 0.00 PRO \n+ATOM 6 HA SER 2 23.045 6.255 6.026 1.00 0.00 PRO \n+ATOM 7 CB SER 2 25.129 6.479 5.468 1.00 0.00 PRO \n+ATOM 8 HB1 SER 2 25.502 6.112 6.451 1.00 0.00 PRO \n+ATOM 9 HB2 SER 2 25.108 7.590 5.522 1.00 0.00 PRO \n+ATOM 10 OG SER 2 26.032 6.062 4.445 1.00 0.00 PRO \n+ATOM 11 HG1 SER 2 26.928 6.382 4.649 1.00 0.00 PRO \n+ATOM 12 C SER 2 23.087 6.445 3.945 1.00 0.00 PRO \n+ATOM 13 O SER 2 22.287 5.741 3.315 1.00 0.00 PRO \n+ATOM 14 N ALA 3 23.417 7.674 3.515 1.00 0.00 PRO \n+ATOM 15 HN ALA 3 24.112 8.236 3.961 1.00 0.00 PRO \n+ATOM 16 CA ALA 3 22.937 8.280 2.293 1.00 0.00 PRO \n+ATOM 17 HA ALA 3 22.421 7.554 1.681 1.00 0.00 PRO \n+ATOM 18 CB ALA 3 22.012 9.476 2.583 1.00 0.00 PRO \n+ATOM 19 HB1 ALA 3 22.509 10.220 3.241 1.00 0.00 PRO \n+ATOM 20 HB2 ALA 3 21.086 9.125 3.082 1.00 0.00 PRO \n+ATOM 21 HB3 ALA 3 21.718 9.984 1.638 1.00 0.00 PRO \n+ATOM 22 C ALA 3 24.147 8.753 1.509 1.00 0.00 PRO \n+ATOM 23 O ALA 3 25.174 9.077 2.073 1.00 0.00 PRO \n+ATOM 24 N CYS 4 24.005 8.749 0.169 1.00 0.00 PRO \n+ATOM 25 HN CYS 4 23.142 8.478 -0.258 1.00 0.00 PRO \n+ATOM 26 CA CYS 4 25.025 9.149 -0.766 1.00 0.00 PRO \n+ATOM 27 HA CYS 4 25.769 9.761 -0.272 1.00 0.00 PRO \n+ATOM 28 CB CYS 4 25.700 7.948 -1.484 1.00 0.00 PRO \n+ATOM 29 HB1 CYS 4 26.256 8.290 -2.382 1.00 0.00 PRO \n+ATOM 30 HB2 CYS 4 24.907 7.257 -1.851 1.00 0.00 PRO \n+ATOM 31 SG CYS 4 26.887 7.076 -0.411 1.00 0.00 PRO \n+ATOM 32 C CYS 4 24.341 10.034 -1.774 1.00 0.00 PRO \n+ATOM 33 O CYS 4 23.104 10.106 -1.853 1.00 0.00 PRO \n+ATOM 34 N THR 5 25.135 10.817 -2.507 1.00 0.00 PRO \n+ATOM 35 HN THR 5 26.125 10.731 -2.426 1.00 0.00 PRO \n+ATOM 36 CA THR 5 24.625 11.886 -3.343 1.00 0.00 PRO \n+ATOM 37 HA THR 5 23.595 11.683 -3.608 1.00 0.00 PRO \n+ATOM 38 CB THR 5 24.715 13.266 -2.674 1.00 0.00 PRO \n+ATOM 39 HB THR 5 24.358 14.060 -3.371 1.00 0.00 PRO \n+ATOM 40 OG1 THR 5 26.051 13.580 -2.272 1.00 0.00 PRO \n+ATOM 41 HG1 THR 5 26.535 13.523 -3.104 1.00 0.00 PRO \n+ATOM 42 CG2 THR 5 23.787 13.298 -1.447 1.00 0.00 PRO \n+ATOM 43 HG21 THR 5 24.126 12.589 -0.663 1.00 0.00 PRO \n+ATOM 44 HG22 THR 5 22.759 13.003 -1.749 1.00 0.00 PRO \n+ATOM 45 HG23 THR 5 23.752 14.313 -1.003 1.00 0.00 PRO \n+ATOM 46 C THR 5 25.385 11.902 -4.645 1.00 0.00 PRO \n+ATOM 47 O THR 5 25.810'..b' CLA CLA 2 5.975 -34.097 -14.115 1.00 0.00 CLA \n+ATOM 61600 CLA CLA 3 3.049 -40.330 0.268 1.00 0.00 CLA \n+ATOM 61601 CLA CLA 4 -29.182 -19.908 -21.287 1.00 0.00 CLA \n+ATOM 61602 CLA CLA 5 32.119 26.809 -14.613 1.00 0.00 CLA \n+ATOM 61603 CLA CLA 6 -12.762 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\n+ATOM 61620 CLA CLA 23 -36.824 -9.651 27.515 1.00 0.00 CLA \n+ATOM 61621 CLA CLA 24 30.595 -26.534 -13.854 1.00 0.00 CLA \n+ATOM 61622 CLA CLA 25 2.683 14.798 30.965 1.00 0.00 CLA \n+ATOM 61623 CLA CLA 26 29.848 -11.446 -12.895 1.00 0.00 CLA \n+ATOM 61624 CLA CLA 27 42.574 -16.385 39.148 1.00 0.00 CLA \n+ATOM 61625 CLA CLA 28 21.090 22.680 27.072 1.00 0.00 CLA \n+ATOM 61626 CLA CLA 29 31.477 21.841 -9.460 1.00 0.00 CLA \n+ATOM 61627 CLA CLA 30 -42.789 33.106 -42.003 1.00 0.00 CLA \n+ATOM 61628 CLA CLA 31 41.212 26.460 28.038 1.00 0.00 CLA \n+ATOM 61629 CLA CLA 32 31.330 -23.211 30.873 1.00 0.00 CLA \n+ATOM 61630 CLA CLA 33 -11.882 24.746 17.676 1.00 0.00 CLA \n+ATOM 61631 CLA CLA 34 42.509 41.966 29.673 1.00 0.00 CLA \n+ATOM 61632 CLA CLA 35 -21.155 -25.909 40.988 1.00 0.00 CLA \n+ATOM 61633 CLA CLA 36 -16.645 33.397 -20.493 1.00 0.00 CLA \n+ATOM 61634 CLA CLA 37 24.008 16.848 3.761 1.00 0.00 CLA \n+ATOM 61635 CLA CLA 38 -3.042 -26.229 -6.954 1.00 0.00 CLA \n+ATOM 61636 CLA CLA 39 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