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 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 psi angles
Parameters
routines: A link to the routines object
outroot: The root of the output name
options: options object
"""
outname = outroot + ".chi"
outfile = open(outname, "w")
routines.write("\nPrinting chi angles for each residue...\n")
routines.write("Residue chi\n")
routines.write("----------------\n")
# 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("CB"):
cbcoords = residue.getAtom("CB").getCoords()
else:
continue
if residue.hasAtom("CG"):
gcoords = residue.getAtom("CG").getCoords()
elif residue.hasAtom("OG"):
gcoords = residue.getAtom("OG").getCoords()
elif residue.hasAtom("SG"):
gcoords = residue.getAtom("SG").getCoords()
else:
continue
chi = getDihedral(ncoords, cacoords, cbcoords, gcoords)
routines.write("%s\t%.4f\n" % (residue, chi))
outfile.write("%s\t%.4f\n" % (residue, chi))
routines.write("\n")
outfile.close()
def run_extension(routines, outroot, options):
"""
Print the list of psi angles
Parameters
routines: A link to the routines object
outroot: The root of the output name
options: options object
"""
outname = outroot + ".chi"
outfile = open(outname, "w")
routines.write("\nPrinting chi angles for each residue...\n")
routines.write("Residue chi\n")
routines.write("----------------\n")
# 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("CB"):
cbcoords = residue.getAtom("CB").getCoords()
else:
continue
if residue.hasAtom("CG"):
gcoords = residue.getAtom("CG").getCoords()
elif residue.hasAtom("OG"):
gcoords = residue.getAtom("OG").getCoords()
elif residue.hasAtom("SG"):
gcoords = residue.getAtom("SG").getCoords()
else:
continue
chi = getDihedral(ncoords, cacoords, cbcoords, gcoords)
routines.write("%s\t%.4f\n" % (residue, chi))
outfile.write("%s\t%.4f\n" % (residue, chi))
routines.write("\n")
outfile.close()
