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"""
Ramachandran extension
Print both the phi and psi angles to standard out. See the individual
functions for more info.
Author: Mike Bradley and Todd Dolinsky
"""
__date__ = "17 February 2006"
__author__ = "Mike Bradley, Todd Dolinsky"
from src.utilities import getDihedral
import extensions
def addExtensionOptions(extensionGroup):
"""
Add options to set output type.
"""
extensionGroup.parser.set_defaults(rama_output='rama')
extensionGroup.add_option('--phi_only', dest='rama_output', action='store_const', const = 'phi',
help='Only include phi angles in output. '+
'Rename output file {output-path}.phi')
extensionGroup.add_option('--psi_only', dest='rama_output', action='store_const', const = 'psi',
help='Only include psi angles in output. '+
'Rename output file {output-path}.psi')
def usage():
return 'Print the per-residue phi and psi angles to {output-path}.rama for Ramachandran plots'
def create_rama_output(routines, outfile, outputtype='rama'):
routines.write("\nPrinting %s angles for each residue...\n" % (outputtype if outputtype != 'rama' else 'phi and psi'))
verboseHeader = "Residue %s\n" % (outputtype.capitalize() if outputtype != 'rama' else 'Phi Psi')
routines.write(verboseHeader)
routines.write('-' * len(verboseHeader) + '\n')
output = extensions.extOutputHelper(routines, outfile)
# Initialize some variables
protein = routines.protein
for residue in protein.getResidues():
if residue.hasAtom("N"):
ncoords = residue.getAtom("N").getCoords()
else:
continue
if residue.hasAtom("CA"):
cacoords = residue.getAtom("CA").getCoords()
else:
continue
if residue.hasAtom("C"):
ccoords = residue.getAtom("C").getCoords()
else:
continue
try:
if residue.peptideN != None:
pepncoords = residue.peptideN.getCoords()
else:
continue
if residue.peptideC != None:
pepccoords = residue.peptideC.getCoords()
else:
continue
except AttributeError: # Non amino acids
continue
output.write(str(residue))
if outputtype in ('rama', 'phi'):
phi = getDihedral(pepccoords, ncoords, cacoords, ccoords)
output.write("\t%.4f" % phi)
if outputtype in ('rama', 'psi'):
psi = getDihedral(ncoords, cacoords, ccoords, pepncoords)
output.write("\t%.4f" % psi)
output.write('\n')
routines.write("\n")
def run_extension(routines, outroot, options):
"""
Print the list of phi and psi angles for use in a Ramachandran plot.
Parameters
routines: A link to the routines object
outroot: The root of the output name
options: options object
"""
outputType = options.rama_output
outname = outroot + '.' + outputType
with open(outname, "w") as outfile:
create_rama_output(routines, outfile, outputtype=outputType)
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