| Next changeset 1:d18e7db42633 (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 pca_cosine.xml ramachandran_plots.py 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 ebeb72aa39a8 angle.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/angle.py Wed Apr 03 15:48:45 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 ebeb72aa39a8 dihedrals.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dihedrals.py Wed Apr 03 15:48:45 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 ebeb72aa39a8 distance.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/distance.py Wed Apr 03 15:48:45 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 ebeb72aa39a8 hbonds.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/hbonds.py Wed Apr 03 15:48:45 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 ebeb72aa39a8 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Apr 03 15:48:45 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 ebeb72aa39a8 pca_cosine.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pca_cosine.py Wed Apr 03 15:48:45 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 ebeb72aa39a8 pca_cosine.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pca_cosine.xml Wed Apr 03 15:48:45 2019 -0400 |
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| @@ -0,0 +1,72 @@ +<tool id="mdanalysis_cosine_analysis" name="Cosine Content" version="@VERSION@"> + <description>Measure the cosine content of the PCA projection</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"> +<![CDATA[ + python '$__tool_directory__/pca_cosine.py' + --idcd '$dcdin' + --ipdb '$pdbin' + --icomponents '$components' + --iindex '$index' + --output '$output' + --cosout '$cosout' + 2>&1 +]]></command> + <inputs> + <expand macro="analysis_inputs"/> + <param name="components" type="integer" value="3" label="Number of components"/> + <param name="index" type="integer" value="0" label="The index of the PCA component projection to be analyzed"/> + </inputs> + <outputs> + <data format="tabular" name="output" label="PCA Analysis raw data"/> + <data format="txt" name="cosout" label="Cosine content of the PCA projection"/> + </outputs> + <tests> + <test> + <expand macro="tests_inputs"/> + <param name="components" value="3"/> + <param name="index" value="0"/> + <output name="cosout"> + <assert_contents> + <has_text text="0.5832533" /> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ +.. class:: infomark + +**What it does** + +The cosine content of the principal components is a good indicator for determine good or bad sampling and can be use to determine the convergence of the MD simulation. +This tool can calculate the cosine content of a user define PCA projection. +This tool use zero based indexes (0 is PC1). + +_____ + + +.. class:: infomark + +**Input** + + - Trajectory file (DCD). + - PDB file. + +_____ + + +.. class:: infomark + +**Output** + + - The cosine content value. + - Tab-separated file of raw data of first three principle component. + + ]]></help> + <expand macro="citations"> + <citation type="doi">10.1103/PhysRevE.65.031910</citation> + </expand> +</tool> |
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| diff -r 000000000000 -r ebeb72aa39a8 ramachandran_plots.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ramachandran_plots.py Wed Apr 03 15:48:45 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 ebeb72aa39a8 rdf.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rdf.py Wed Apr 03 15:48:45 2019 -0400 |
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| @@ -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 ebeb72aa39a8 test-data/Angle_Analysis_Plot.png |
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| Binary file test-data/Angle_Analysis_Plot.png has changed |
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| diff -r 000000000000 -r ebeb72aa39a8 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 15:48:45 2019 -0400 |
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| diff -r 000000000000 -r ebeb72aa39a8 test-data/Dihedral_analysis_raw_data.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Dihedral_analysis_raw_data.tabular Wed Apr 03 15:48:45 2019 -0400 |
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| diff -r 000000000000 -r ebeb72aa39a8 test-data/Distance_Analysis_raw_data.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Distance_Analysis_raw_data.tabular Wed Apr 03 15:48:45 2019 -0400 |
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| diff -r 000000000000 -r ebeb72aa39a8 test-data/RDF_raw_data.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/RDF_raw_data.tabular Wed Apr 03 15:48:45 2019 -0400 |
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| diff -r 000000000000 -r ebeb72aa39a8 test-data/test.dcd |
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| diff -r 000000000000 -r ebeb72aa39a8 test-data/test.pdb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.pdb Wed Apr 03 15:48:45 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 38.902 39.703 1.00 0.00 CLA \n+ATOM 61604 CLA CLA 7 -41.352 -6.310 -21.092 1.00 0.00 CLA \n+ATOM 61605 CLA CLA 8 -40.105 19.915 21.883 1.00 0.00 CLA \n+ATOM 61606 CLA CLA 9 -37.875 -10.640 -26.651 1.00 0.00 CLA \n+ATOM 61607 CLA CLA 10 -22.511 41.548 12.784 1.00 0.00 CLA \n+ATOM 61608 CLA CLA 11 35.216 33.731 -35.093 1.00 0.00 CLA \n+ATOM 61609 CLA CLA 12 -40.102 5.647 -2.397 1.00 0.00 CLA \n+ATOM 61610 CLA CLA 13 39.024 -12.398 -40.371 1.00 0.00 CLA \n+ATOM 61611 CLA CLA 14 18.261 -39.450 23.742 1.00 0.00 CLA \n+ATOM 61612 CLA CLA 15 6.178 41.435 -35.101 1.00 0.00 CLA \n+ATOM 61613 CLA CLA 16 24.358 15.109 39.388 1.00 0.00 CLA \n+ATOM 61614 CLA CLA 17 6.888 21.632 -18.643 1.00 0.00 CLA \n+ATOM 61615 CLA CLA 18 21.744 6.136 36.952 1.00 0.00 CLA \n+ATOM 61616 CLA CLA 19 37.313 -8.363 36.386 1.00 0.00 CLA \n+ATOM 61617 CLA CLA 20 -2.999 -20.832 23.104 1.00 0.00 CLA \n+ATOM 61618 CLA CLA 21 2.857 18.626 -27.815 1.00 0.00 CLA \n+ATOM 61619 CLA CLA 22 4.436 -15.917 42.798 1.00 0.00 CLA \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 -25.242 -29.525 -14.531 1.00 0.00 CLA \n+ATOM 61637 CLA CLA 40 34.942 -28.883 -36.691 1.00 0.00 CLA \n+ATOM 61638 CLA CLA 41 -35.913 -6.707 3.266 1.00 0.00 CLA \n+ATOM 61639 CLA CLA 42 -30.968 4.607 -32.953 1.00 0.00 CLA \n+ATOM 61640 CLA CLA 43 -5.809 15.242 42.418 1.00 0.00 CLA \n+ATOM 61641 CLA CLA 44 39.399 18.809 -13.827 1.00 0.00 CLA \n+ATOM 61642 CLA CLA 45 -15.805 29.210 -37.376 1.00 0.00 CLA \n+ATOM 61643 CLA CLA 46 0.091 -36.491 -34.859 1.00 0.00 CLA \n+ATOM 61644 CLA CLA 47 -12.875 -40.099 38.366 1.00 0.00 CLA \n+ATOM 61645 CLA CLA 48 -24.191 19.188 36.959 1.00 0.00 CLA \n+ATOM 61646 CLA CLA 49 16.215 -18.186 -29.406 1.00 0.00 CLA \n+ATOM 61647 CLA CLA 50 34.647 -7.708 -32.869 1.00 0.00 CLA \n+ATOM 61648 CLA CLA 51 -20.320 -38.996 6.847 1.00 0.00 CLA \n+ATOM 61649 CLA CLA 52 -28.453 0.614 -25.838 1.00 0.00 CLA \n+TER 61650 CLA 52\n+END\n' |
