"""Perform GNM calculations and output the results in plain text NMD, and
graphical formats."""
from ..apptools import *
from .nmaoptions import *
from . import nmaoptions
__all__ = ['prody_gnm']
DEFAULTS = {}
HELPTEXT = {}
for key, txt, val in [
('model', 'index of model that will be used in the calculations', 1),
('altloc', 'alternative location identifiers for residues used in the calculations', "A"),
('cutoff', 'cutoff distance (A)', 10.),
('gamma', 'spring constant', '1.'),
('zeros', 'calculate zero modes', False),
('outbeta', 'write beta-factors calculated from GNM modes', False),
('kirchhoff', 'write Kirchhoff matrix', False),
('figcmap', 'save contact map (Kirchhoff matrix) figure', False),
('figbeta', 'save beta-factors figure', False),
('figmode', 'save mode shape figures for specified modes, '
'e.g. "1-3 5" for modes 1, 2, 3 and 5', '')]:
DEFAULTS[key] = val
HELPTEXT[key] = txt
DEFAULTS.update(nmaoptions.DEFAULTS)
HELPTEXT.update(nmaoptions.HELPTEXT)
DEFAULTS['prefix'] = '_gnm'
[docs]def prody_gnm(pdb, **kwargs):
"""Perform GNM calculations for *pdb*.
"""
for key in DEFAULTS:
if not key in kwargs:
kwargs[key] = DEFAULTS[key]
from os.path import isdir, join, exists
outdir = kwargs.get('outdir')
if not isdir(outdir):
raise IOError('{0} is not a valid path'.format(repr(outdir)))
import numpy as np
import prody
LOGGER = prody.LOGGER
selstr = kwargs.get('select')
prefix = kwargs.get('prefix')
cutoff = kwargs.get('cutoff')
nmodes = kwargs.get('nmodes')
selstr = kwargs.get('select')
model = kwargs.get('model')
altloc = kwargs.get('altloc')
zeros = kwargs.get('zeros')
membrane = kwargs.get('membrane')
if membrane and not exists(pdb):
pdb = prody.fetchPDBfromOPM(pdb)
pdb = prody.parsePDB(pdb, model=model, altloc=altloc)
if prefix == '_gnm':
prefix = pdb.getTitle() + '_gnm'
select = pdb.select(selstr)
if select is None:
raise ValueError('selection {0} do not match any atoms'
.format(repr(selstr)))
LOGGER.info('{0} atoms will be used for GNM calculations.'
.format(len(select)))
if membrane:
gnm = prody.exGNM(pdb.getTitle())
else:
gnm = prody.GNM(pdb.getTitle())
try:
gamma = float(kwargs.get('gamma'))
LOGGER.info("Using gamma {0}".format(gamma))
except ValueError:
try:
Gamma = eval('prody.' + kwargs.get('gamma'))
gamma = Gamma(select)
LOGGER.info("Using gamma {0}".format(Gamma))
except NameError:
raise NameError("Please provide gamma as a float or ProDy Gamma class")
except TypeError:
raise TypeError("Please provide gamma as a float or ProDy Gamma class")
nproc = kwargs.get('nproc')
gnm.buildKirchhoff(select, cutoff, gamma)
gnm.calcModes(nmodes, zeros=zeros, nproc=nproc)
LOGGER.info('Writing numerical output.')
if kwargs.get('outnpz'):
prody.saveModel(gnm, join(outdir, prefix),
matrices=kwargs.get('npzmatrices'))
if kwargs.get('outscipion'):
prody.writeScipionModes(outdir, gnm)
prody.writeNMD(join(outdir, prefix + '.nmd'), gnm, select)
extend = kwargs.get('extend')
if extend:
if extend == 'all':
extended = prody.extendModel(gnm, select, pdb)
else:
extended = prody.extendModel(gnm, select, select | pdb.bb)
prody.writeNMD(join(outdir, prefix + '_extended_' +
extend + '.nmd'), *extended)
outall = kwargs.get('outall')
delim = kwargs.get('numdelim')
ext = kwargs.get('numext')
format = kwargs.get('numformat')
if outall or kwargs.get('outeig'):
prody.writeArray(join(outdir, prefix + '_evectors'+ext),
gnm.getArray(), delimiter=delim, format=format)
prody.writeArray(join(outdir, prefix + '_evalues'+ext),
gnm.getEigvals(), delimiter=delim, format=format)
if outall or kwargs.get('outbeta'):
from prody.utilities import openFile
fout = openFile(prefix + '_beta'+ext, 'w', folder=outdir)
fout.write('{0[0]:1s} {0[1]:4s} {0[2]:4s} {0[3]:5s} {0[4]:5s}\n'
.format(['C', 'RES', '####', 'Exp.', 'The.']))
for data in zip(select.getChids(), select.getResnames(),
select.getResnums(), select.getBetas(),
prody.calcTempFactors(gnm, select)):
fout.write('{0[0]:1s} {0[1]:4s} {0[2]:4d} {0[3]:5.2f} {0[4]:5.2f}\n'
.format(data))
fout.close()
if outall or kwargs.get('outcov'):
prody.writeArray(join(outdir, prefix + '_covariance'+ext),
gnm.getCovariance(), delimiter=delim, format=format)
if outall or kwargs.get('outcc') or kwargs.get('outhm'):
cc = prody.calcCrossCorr(gnm)
if outall or kwargs.get('outcc'):
prody.writeArray(join(outdir, prefix + '_cross-correlations' +
ext), cc, delimiter=delim, format=format)
if outall or kwargs.get('outhm'):
prody.writeHeatmap(join(outdir, prefix + '_cross-correlations.hm'),
cc, resnum=select.getResnums(),
xlabel='Residue', ylabel='Residue',
title=gnm.getTitle() + ' cross-correlations')
if outall or kwargs.get('kirchhoff'):
prody.writeArray(join(outdir, prefix + '_kirchhoff'+ext),
gnm.getKirchhoff(), delimiter=delim, format=format)
if outall or kwargs.get('outsf'):
prody.writeArray(join(outdir, prefix + '_sqfluct'+ext),
prody.calcSqFlucts(gnm), delimiter=delim,
format=format)
figall = kwargs.get('figall')
cc = kwargs.get('figcc')
sf = kwargs.get('figsf')
bf = kwargs.get('figbeta')
cm = kwargs.get('figcmap')
modes = kwargs.get('figmode')
if figall or cc or sf or bf or cm or modes:
try:
import matplotlib.pyplot as plt
except ImportError:
LOGGER.warning('Matplotlib could not be imported. '
'Figures are not saved.')
else:
prody.SETTINGS['auto_show'] = False
LOGGER.info('Saving graphical output.')
format = kwargs.get('figformat')
width = kwargs.get('figwidth')
height = kwargs.get('figheight')
dpi = kwargs.get('figdpi')
format = format.lower()
if figall or cc:
plt.figure(figsize=(width, height))
prody.showCrossCorr(gnm, interactive=False)
plt.savefig(join(outdir, prefix + '_cc.'+format),
dpi=dpi, format=format)
plt.close('all')
if figall or cm:
plt.figure(figsize=(width, height))
prody.showContactMap(gnm, interactive=False)
plt.savefig(join(outdir, prefix + '_cm.'+format),
dpi=dpi, format=format)
plt.close('all')
if figall or sf:
plt.figure(figsize=(width, height))
prody.showSqFlucts(gnm)
plt.savefig(join(outdir, prefix + '_sf.'+format),
dpi=dpi, format=format)
plt.close('all')
if figall or bf:
plt.figure(figsize=(width, height))
bexp = select.getBetas()
bcal = prody.calcTempFactors(gnm, select)
plt.plot(bexp, label='Experimental')
plt.plot(bcal, label=('Theoretical (corr coef = {0:.2f})'
.format(np.corrcoef(bcal, bexp)[0,1])))
plt.legend(prop={'size': 10})
plt.xlabel('Node index')
plt.ylabel('Experimental B-factors')
plt.title(pdb.getTitle() + ' B-factors')
plt.savefig(join(outdir, prefix + '_bf.'+format),
dpi=dpi, format=format)
plt.close('all')
if modes:
indices = []
items = modes.split()
items = sum([item.split(',') for item in items], [])
for item in items:
try:
item = item.split('-')
if len(item) == 1:
indices.append(int(item[0])-1)
elif len(item) == 2:
indices.extend(list(range(int(item[0])-1, int(item[1]))))
except:
pass
for index in indices:
try:
mode = gnm[index]
except:
pass
else:
plt.figure(figsize=(width, height))
prody.showMode(mode)
plt.grid()
plt.savefig(join(outdir, prefix + '_mode_' +
str(mode.getIndex()+1) + '.' + format),
dpi=dpi, format=format)
plt.close('all')
_ = list(HELPTEXT)
_.sort()
for key in _:
prody_gnm.__doc__ += """
:arg {0}: {1}, default is ``{2!r}``""".format(key, HELPTEXT[key],
DEFAULTS[key])
def addCommand(commands):
subparser = commands.add_parser('gnm',
help='perform Gaussian network model calculations')
subparser.add_argument('--quiet', help="suppress info messages to stderr",
action=Quiet, nargs=0)
subparser.add_argument('--examples', action=UsageExample, nargs=0,
help='show usage examples and exit')
subparser.set_defaults(usage_example=
"""This command performs GNM calculations for given PDB structure and \
outputs results in NMD format. If an identifier is passed, structure file \
will be downloaded from the PDB FTP server.
Fetch PDB 1p38, run GNM calculations using default parameters, and results:
$ prody gnm 1p38
Fetch PDB 1aar, run GNM calculations with cutoff distance 7 angstrom for \
chain A carbon alpha atoms with residue numbers less than 70, and \
save all of the graphical output files:
$ prody gnm 1aar -c 7 -s "calpha and chain A and resnum < 70" -A""",
test_examples=[0, 1])
group = addNMAParameters(subparser)
group.add_argument('-c', '--cutoff', dest='cutoff', type=float,
default=DEFAULTS['cutoff'], metavar='FLOAT',
help=HELPTEXT['cutoff'] + ' (default: %(default)s)')
group.add_argument('-g', '--gamma', dest='gamma', type=str,
default=DEFAULTS['gamma'], metavar='STR',
help=HELPTEXT['gamma'] + ' (default: %(default)s)')
group.add_argument('-m', '--model', dest='model', type=int,
metavar='INT', default=DEFAULTS['model'], help=HELPTEXT['model'])
group.add_argument('-L', '--altloc', dest='altloc', type=str,
metavar='INT', default=DEFAULTS['altloc'], help=HELPTEXT['altloc'])
group.add_argument('-w', '--zero-modes', dest='zeros', action='store_true',
default=DEFAULTS['zeros'], help=HELPTEXT['zeros'])
group = addNMAOutput(subparser)
group.add_argument('-b', '--beta-factors', dest='outbeta',
action='store_true', default=DEFAULTS['outbeta'],
help=HELPTEXT['outbeta'])
group.add_argument('-k', '--kirchhoff', dest='kirchhoff',
action='store_true',
default=DEFAULTS['kirchhoff'], help=HELPTEXT['kirchhoff'])
group = addNMAOutputOptions(subparser, '_gnm')
group = addNMAFigures(subparser)
group.add_argument('-B', '--beta-factors-figure', dest='figbeta',
action='store_true',
default=DEFAULTS['figbeta'], help=HELPTEXT['figbeta'])
group.add_argument('-K', '--contact-map', dest='figcmap',
action='store_true',
default=DEFAULTS['figcmap'], help=HELPTEXT['figcmap'])
group.add_argument('-M', '--mode-shape-figure', dest='figmode', type=str,
default=DEFAULTS['figmode'], help=HELPTEXT['figmode'], metavar='STR')
group = addNMAFigureOptions(subparser)
subparser.add_argument('pdb', help='PDB identifier or filename')
subparser.set_defaults(func=lambda ns: prody_gnm(ns.__dict__.pop('pdb'),
**ns.__dict__))
subparser.set_defaults(subparser=subparser)
