def __init__(self, routines, outfile, options):
self.pairEnergyResults = {}
self.combinationCount = 0
self.totalCombinations = 0
self.options = options
self.output = extensions.extOutputHelper(routines, outfile)
self.routines = routines
def __init__(self, routines, outfile, options):
self.pairEnergyResults = {}
self.combinationCount = 0
self.totalCombinations = 0
self.options = options
self.output = extensions.extOutputHelper(routines, outfile)
self.routines = routines
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 create_summary_output(routines, outfile):
"""
Output the interaction energy between each possible residue pair.
"""
routines.write("Printing protein summary...\n")
output = extensions.extOutputHelper(routines, outfile)
output.write(routines.protein.getSummary() + '\n')
for residue in routines.protein.getResidues():
output.write(str(residue) + '\n')
def create_summary_output(routines, outfile):
"""
Output the interaction energy between each possible residue pair.
"""
routines.write("Printing protein summary...\n")
output = extensions.extOutputHelper(routines, outfile)
output.write(routines.protein.getSummary() + '\n')
for residue in routines.protein.getResidues():
output.write(str(residue)+'\n')
def create_resinter_output(routines, outfile, options,
residue_combinations=False,
all_residue_combinations=False):
"""
Output the interaction energy between each possible residue pair.
"""
routines.write("Printing residue interaction energies...\n")
output = extensions.extOutputHelper(routines, outfile)
if residue_combinations or all_residue_combinations:
write_all_residue_interaction_energies_combinations(routines, output, options,
all_residue_combinations=all_residue_combinations)
else:
save_residue_interaction_energies(routines.protein.getResidues(), output)
def create_resinter_output(routines,
outfile,
options,
residue_combinations=False,
all_residue_combinations=False):
"""
Output the interaction energy between each possible residue pair.
"""
routines.write("Printing residue interaction energies...\n")
output = extensions.extOutputHelper(routines, outfile)
if residue_combinations or all_residue_combinations:
write_all_residue_interaction_energies_combinations(
routines,
output,
options,
all_residue_combinations=all_residue_combinations)
else:
save_residue_interaction_energies(routines.protein.getResidues(),
output)
def create_hbond_output(routines, outfile, whatif=False,
angleCutoff=ANGLE_CUTOFF,
distanceCutoff=DIST_CUTOFF,
oldDistanceMethod=False):
routines.write("Printing hydrogen bond list...\n")
output = extensions.extOutputHelper(routines, outfile)
cellsize = int(distanceCutoff + 1.0 + 1.0)
protein = routines.protein
routines.setDonorsAndAcceptors()
routines.cells = Cells(cellsize)
routines.cells.assignCells(protein)
for donor in protein.getAtoms():
# Grab the list of donors
if not donor.hdonor:
continue
donorhs = []
for bond in donor.bonds:
if bond.isHydrogen():
donorhs.append(bond)
if donorhs == []:
continue
# For each donor, grab all acceptors
closeatoms = routines.cells.getNearCells(donor)
for acc in closeatoms:
if not acc.hacceptor:
continue
if donor.residue == acc.residue:
continue
#TODO: do we need to do this for plain hbond stuff?
if whatif and (donor.residue.chainID == acc.residue.chainID):
continue
# Do new style distance check
if not oldDistanceMethod:
dist = distance(donor.getCoords(), acc.getCoords())
if dist > distanceCutoff:
continue
for donorh in donorhs:
# Do old style distance check
if oldDistanceMethod:
dist = distance(donorh.getCoords(), acc.getCoords())
if dist > distanceCutoff:
continue
# Do angle check
angle = getAngle(acc.getCoords(), donor.getCoords(), donorh.getCoords())
if angle > angleCutoff:
continue
if whatif:
if (donor.tempFactor > 60.0):
continue
if (acc.tempFactor > 60.0):
continue
thisBstring='B' if donor.isBackbone() else 'S'
thatBstring='B' if acc.isBackbone() else 'S'
score= (1.7/dist) * cos(angle * 3.142 / 180.0)
output.write(_residueString(donor.residue, donor.name))
output.write('-> ')
output.write(_residueString(acc.residue, acc.name))
output.write('Sym= 1 Val= %6.3lf DA=%6.2f DHA=%6.2f (%s-%s)\n' %
(score, dist, angle, thisBstring, thatBstring))
# outfile.write("%4d %-4s (%4d ) %s %-4s-> %4d %-4s (%4d ) %s %-4sSym= 1 Val= %6.3lf DA=%6.2f DHA=%6.2f (%s-%s)\n" % \
# (donor.residue.resSeq,donor.residue.name,donor.residue.resSeq, donor.residue.chainID,donor.name,acc.residue.resSeq,acc.residue.name,acc.residue.resSeq, acc.residue.chainID,acc.name, score, dist, angle, thisBstring, thatBstring))
else:
s = "Donor: %s %s\tAcceptor: %s %s\tdist: %.2f\tAngle: %.2f\n" % \
(donor.residue, donor.name, acc.residue, acc.name, dist, angle)
output.write(s)
routines.write("\n")