def writeVecStartStopToPDBFile(self,
mainNegCentroid=[],
outputPDBname='Dshift-vectors.pdb',
weightedVectors=[]):
# write located density shift vector start and stop
# xyz positions to a pdb file so that they can then be
# visualised in pymol (or otherwise). 'densMapObj' is
# taken from readAtomMap.py (self.densmap).
from classHolder import singlePDB
from PDBFileManipulation import writePDBline
vecStart = self.densMapObj.abc2xyz(
asymIndices=mainNegCentroid[:3], fracInput=True)
# append vector positions to a pdb file if it exists
lineCount = 0
if os.path.isfile(outputPDBname):
try:
with open(outputPDBname) as f:
i = -1
for i, l in enumerate(f):
pass
lineCount = i + 1
except IOError:
pass
vectorPDBfile = open(outputPDBname, 'a')
atmIDparts = self.atmId.split('-')
vecPosAsAtom = singlePDB(
atomnum=lineCount, residuenum=atmIDparts[1],
atomtype=atmIDparts[3], basetype='V0',
chaintype=atmIDparts[0], X_coord=vecStart[0],
Y_coord=vecStart[1], Z_coord=vecStart[2])
pdbLine = writePDBline(vecPosAsAtom, 1)
vectorPDBfile.write(pdbLine + '\n')
for i, vec in enumerate(weightedVectors):
vecEnd = self.densMapObj.abc2xyz(
asymIndices=np.array(mainNegCentroid[:3]) + vec,
fracInput=True)
vecPosAsAtom = singlePDB(
atomnum=lineCount + i + 1, residuenum=atmIDparts[1],
atomtype=atmIDparts[3], basetype='V' + str(i+1),
chaintype=atmIDparts[0], X_coord=vecEnd[0],
Y_coord=vecEnd[1], Z_coord=vecEnd[2])
pdbLine = writePDBline(vecPosAsAtom, 1)
vectorPDBfile.write(pdbLine + '\n')
vectorPDBfile.close()
def PDBtoList(pdbfilename,PDBarray):
# this function inputs a pdb file name and returns an list of pdb objects,
# organised following the StructurePDB class
pdbin = open(str(pdbfilename), "r")
lines = pdbin.readlines()
print 'Reading PDB file and converting to list of objects'
for line in lines:
if ('ATOM' in str(line[0:6])) or ('HETATM' in str(line[0:6])):
y = singlePDB(StructurePDB)
y.atomnum = int(line[6:11].strip())
y.atomtype = str(line[12:16].strip())
y.basetype = str(line[17:20].strip())
y.chaintype = str(line[21])
y.residuenum = int(line[22:26].strip())
y.X_coord = float(line[30:38].strip())
y.Y_coord = float(line[38:46].strip())
y.Z_coord = float(line[46:54].strip())
y.Occupancy = str(line[54:60].strip())
y.Bfactor = float(line[60:66].strip())
y.atomID = str(line[76:78].strip())
y.atomOrHetatm = str(line[0:6].strip())
PDBarray.append(y)
else:
pass
pdbin.close()
return PDBarray
def writeVecStartStopToPDBFile(
self, mainNegCentroid=[], outputPDBname="Dshift-vectors.pdb", densMapObj=[], weightedVectors=[]
):
# write located density shift vector start and stop xyz positions
# to a pdb file so that they can then be visualised in pymol (or otherwise).
# 'densMapObj' is taken from readAtomMap.py (self.densmap).
from classHolder import singlePDB
from PDBFileManipulation import writePDBline
vecStart = densMapObj.abc2xyz(asymIndices=mainNegCentroid[:3], fracInput=True)
# append vector positions to a pdb file if it exists
lineCount = 0
if os.path.isfile(outputPDBname):
try:
with open(outputPDBname) as f:
i = -1
for i, l in enumerate(f):
pass
lineCount = i + 1
except IOError:
pass
vectorPDBfile = open(outputPDBname, "a")
atmIDparts = self.atmId.split("-")
vecPosAsAtom = singlePDB(
atomnum=lineCount,
residuenum=atmIDparts[1],
atomtype=atmIDparts[3],
basetype="V0",
chaintype=atmIDparts[0],
X_coord=vecStart[0],
Y_coord=vecStart[1],
Z_coord=vecStart[2],
)
pdbLine = writePDBline(vecPosAsAtom, 1)
vectorPDBfile.write(pdbLine + "\n")
for i, vec in enumerate(weightedVectors):
vecEnd = densMapObj.abc2xyz(asymIndices=np.array(mainNegCentroid[:3]) + vec, fracInput=True)
# NOTE THAT PYMOL ARROWS SHOULD BE OF THE FORM BELOW
# print 'cgo_arrow [{}],[{}],hlength=0.25,radius=0.05,hradius=0.075'.
# format(','.join([str(round(v,2)) for v in vecStart]),','.join([str(round(v,2)) for v in vecEnd]))
vecPosAsAtom = singlePDB(
atomnum=lineCount + i + 1,
residuenum=atmIDparts[1],
atomtype=atmIDparts[3],
basetype="V" + str(i + 1),
chaintype=atmIDparts[0],
X_coord=vecEnd[0],
Y_coord=vecEnd[1],
Z_coord=vecEnd[2],
)
pdbLine = writePDBline(vecPosAsAtom, 1)
vectorPDBfile.write(pdbLine + "\n")
vectorPDBfile.close()