def run_extension(routines, outroot, options):
"""
Print a list of contacts.
Parameters
routines: A link to the routines object
outroot: The root of the output name
options: options object
"""
outname = outroot + ".con"
outfile = open(outname, "w")
# Initialize - set nearby cells, donors/acceptors
cellsize = int(DIST_CUTOFF + 1.0 + 1.0)
protein = routines.protein
routines.setDonorsAndAcceptors()
routines.cells = Cells(cellsize)
routines.cells.assignCells(protein)
for thisatom in protein.getAtoms():
# Grab the list of thisatoms
if not thisatom.hdonor:
continue
thisatomhs = []
for bond in thisatom.bonds:
if bond.isHydrogen():
thisatomhs.append(bond)
if thisatomhs == []:
continue
# For each thisatom, grab all thatatomeptors
count = 0
closeatoms = routines.cells.getNearCells(thisatom)
for thatatom in closeatoms:
if (thisatom.residue == thatatom.residue):
continue # comment this out to include interresidue contacts
if (thatatom.isHydrogen()):
continue
thisdist = distance(thisatom.getCoords(), thatatom.getCoords())
if (thisdist <= DIST_CUTOFF):
count = count + 1
thisBstring = 'S'
thatBstring = 'S'
hscore = 0.0
if (thisatom.hdonor & thatatom.hacceptor):
hscore = 1.0
if (thisatom.hacceptor & thatatom.hdonor):
hscore = 1.0
if (thisatom.isBackbone()):
thisBstring = 'B'
if (thatatom.isBackbone()):
thatBstring = 'B'
outfile.write("%4d %4d %-4s (%4d ) %s %-4s<>%4d %-4s (%4d ) %s %-4s D=%6.2f H-ene=%6.2f Sym= (%s-%s)\n" % \
(count, thisatom.residue.resSeq,thisatom.residue.name,thisatom.residue.resSeq, thisatom.residue.chainID,thisatom.name,thatatom.residue.resSeq,thatatom.residue.name,thatatom.residue.resSeq, thatatom.residue.chainID,thatatom.name, thisdist, hscore, thisBstring, thatBstring))
routines.write("\n")
outfile.close()
def run_extension(routines, outroot, options):
"""
Print a list of contacts.
Parameters
routines: A link to the routines object
outroot: The root of the output name
options: options object
"""
outname = outroot + ".con"
outfile = open(outname, "w")
# Initialize - set nearby cells, donors/acceptors
cellsize = int(DIST_CUTOFF + 1.0 + 1.0)
protein = routines.protein
routines.setDonorsAndAcceptors()
routines.cells = Cells(cellsize)
routines.cells.assignCells(protein)
for thisatom in protein.getAtoms():
# Grab the list of thisatoms
if not thisatom.hdonor:
continue
thisatomhs = []
for bond in thisatom.bonds:
if bond.isHydrogen():
thisatomhs.append(bond)
if thisatomhs == []:
continue
# For each thisatom, grab all thatatomeptors
count = 0
closeatoms = routines.cells.getNearCells(thisatom)
for thatatom in closeatoms:
if (thisatom.residue == thatatom.residue):
continue # comment this out to include interresidue contacts
if (thatatom.isHydrogen()):
continue
thisdist = distance(thisatom.getCoords(), thatatom.getCoords())
if (thisdist <= DIST_CUTOFF):
count = count+1
thisBstring='S'
thatBstring='S'
hscore= 0.0
if (thisatom.hdonor & thatatom.hacceptor):
hscore = 1.0
if (thisatom.hacceptor & thatatom.hdonor):
hscore = 1.0
if (thisatom.isBackbone()):
thisBstring='B'
if (thatatom.isBackbone()):
thatBstring='B'
outfile.write("%4d %4d %-4s (%4d ) %s %-4s<>%4d %-4s (%4d ) %s %-4s D=%6.2f H-ene=%6.2f Sym= (%s-%s)\n" % \
(count, thisatom.residue.resSeq,thisatom.residue.name,thisatom.residue.resSeq, thisatom.residue.chainID,thisatom.name,thatatom.residue.resSeq,thatatom.residue.name,thatatom.residue.resSeq, thatatom.residue.chainID,thatatom.name, thisdist, hscore, thisBstring, thatBstring))
routines.write("\n")
outfile.close()
def run_extension(routines, outroot, options):
"""
Print a list of salt bridges.
Parameters
routines: A link to the routines object
outroot: The root of the output name
options: options object
"""
outname = outroot + ".salt"
outfile = open(outname, "w")
routines.write("Printing salt bridge list...\n")
# Define the potential salt bridge atoms here (the current lists are for the AMBER
# forcefield and are not necessarily exhaustive).
posresList = ["LYS","ARG","HIP"]
negresList = ["GLU","ASP","CYM"]
posatomList = ["NE","NH1","NH2","NZ","ND1","NE2",]
negatomList = ["SG","OE1","OE2","OD1","OD2"]
# Initialize - set nearby cells
# The cell size adds one for the salt bridge distance, and rounds up
cellsize = int(DIST_CUTOFF + 1.0 + 1.0)
protein = routines.protein
routines.cells = Cells(cellsize)
routines.cells.assignCells(protein)
# Loop over all the atoms
for cation in protein.getAtoms():
# check that we've found a cation
if cation.residue.name == "NMET":
print "YES NMET"
if cation.residue.name not in posresList:
continue
elif cation.name not in posatomList:
continue
# For each cation, grab all potential anions in nearby cells
closeatoms = routines.cells.getNearCells(cation)
for anion in closeatoms:
if cation.residue.name == anion.residue.name:
continue
if anion.residue.name not in negresList:
continue
elif anion.name not in negatomList:
continue
# Do distance check
dist = distance(cation.getCoords(), anion.getCoords())
if dist > DIST_CUTOFF:
continue
#routines.write("Cation: %s %s\tAnion: %s %s\tsaltdist: %.2f\n" % \
# (cation.residue, cation.name, anion.residue, anion.name, dist))
outfile.write("Cation: %s %s\tAnion: %s %s\tsaltdist: %.2f\n" % \
(cation.residue, cation.name, anion.residue, anion.name, dist))
#routines.write("\n")
outfile.close()
def run_extension(routines, outroot, options):
"""
Print a list of salt bridges.
Parameters
routines: A link to the routines object
outroot: The root of the output name
options: options object
"""
outname = outroot + ".salt"
outfile = open(outname, "w")
routines.write("Printing salt bridge list...\n")
# Define the potential salt bridge atoms here (the current lists are for the AMBER
# forcefield and are not necessarily exhaustive).
posresList = ["LYS", "ARG", "HIP"]
negresList = ["GLU", "ASP", "CYM"]
posatomList = [
"NE",
"NH1",
"NH2",
"NZ",
"ND1",
"NE2",
]
negatomList = ["SG", "OE1", "OE2", "OD1", "OD2"]
# Initialize - set nearby cells
# The cell size adds one for the salt bridge distance, and rounds up
cellsize = int(DIST_CUTOFF + 1.0 + 1.0)
protein = routines.protein
routines.cells = Cells(cellsize)
routines.cells.assignCells(protein)
# Loop over all the atoms
for cation in protein.getAtoms():
# check that we've found a cation
if cation.residue.name == "NMET":
print("YES NMET")
if cation.residue.name not in posresList:
continue
elif cation.name not in posatomList:
continue
# For each cation, grab all potential anions in nearby cells
closeatoms = routines.cells.getNearCells(cation)
for anion in closeatoms:
if cation.residue.name == anion.residue.name:
continue
if anion.residue.name not in negresList:
continue
elif anion.name not in negatomList:
continue
# Do distance check
dist = distance(cation.getCoords(), anion.getCoords())
if dist > DIST_CUTOFF:
continue
#routines.write("Cation: %s %s\tAnion: %s %s\tsaltdist: %.2f\n" % \
# (cation.residue, cation.name, anion.residue, anion.name, dist))
outfile.write("Cation: %s %s\tAnion: %s %s\tsaltdist: %.2f\n" % \
(cation.residue, cation.name, anion.residue, anion.name, dist))
#routines.write("\n")
outfile.close()
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")