def delAtom(self,index):
"""
delAtom(self,index):
deletes one atom from self, and updates all x2i information """
if index < 0 or index >= self.natoms: # if atom doesn't exist:
cu.die('BgfFile.delAtom: Atom at index "%d" does not exist' % index)
del self.a2i[self.a[index].aNo] # delete the a2i record
delaNo = self.a[index].aNo
del self.a[index] # delete the atom
self.natoms -= 1 # update no.of atoms
for i in range(index, self.natoms): # decrement/update all the a2i
atom = self.a[i] # records that come after this
self.a2i[atom.aNo] = i # index number
"""
for i in range(0, len(self.a)):
atom = self.a[i]
ano = index + 1
if delaNo in atom.CONECT:
atom.CONECT.remove(delaNo)
"""
self.max_aNo = max( self.a2i.keys() ) # ... update constants ...
self.min_aNo = min( self.a2i.keys() ) #
def disconnect(self,other,strict=False):
"""
disconnect(self, other, strict=False):
removes the bond between the atoms 'self' and 'other'
if strict is True, dies when no bond is found between the atoms"""
# remove other from self's list
for n in range(len(self.CONECT)):
if self.CONECT[n] == other.aNo:
del self.CONECT[n]
if self.ORDER:
del self.ORDER[n]
break
else:
if strict:
cu.die("atoms %d is not connected to %d"%(self.aNo,other.aNo))
# remove self from other's list
for n in range(len(other.CONECT)):
if other.CONECT[n] == self.aNo:
del other.CONECT[n]
if other.ORDER:
del other.ORDER[n]
break
else:
if strict:
cu.die("atoms %d is not connected to %d"%(other.aNo,self.aNo))
def rmsd(myBGF1,myBGF2,safe=1,noH=0,scOnly=0):
"""
rmsd(myBGF1,myBGF2,safe=1,noH=0,scOnly=0):
returns the RMSD (in A) between the two BgfFile objects, myBGF1 and myBGF2,
that share the same structure.
if 'safe' is set to 0, atom-by-atom similarity comparison will not be carried
out between myBGF1 and myBGF2.
if 'noH' is set to 1, hydrogens will not be included in the RMSD calculation
if 'scOnly' is set to 1, sidechain-only RMSD will be returned
"""
natoms = myBGF1.natoms
if natoms != myBGF2.natoms: # check natoms
cu.die("BGF: rmsd: BgfFile objects don't contain the same number of atoms: %d =/= %d"%(natoms,myBGF2.natoms))
atomCount = 0
sumOfSqrDist = 0.0
for i in range(natoms):
atom1 = myBGF1.a[i]
atom2 = myBGF2.a[i]
if safe and (atom1 != atom2): # check atoms
cu.die("BGF: rmsd: Atom number %d refers to different atoms in the BgfFile objects provided."%i)
if noH and atom1.is_hydrogen():
continue
if scOnly and atom1.is_sidechain():
continue
atomCount += 1
sumOfSqrDist += sqrDistance(atom1, atom2)
myRMSD = math.sqrt(sumOfSqrDist / atomCount)
return myRMSD
def __radd__(self,other):
"""
__radd__(self,other):
reverse __add__
works only if the second object is a BgfFile """
if isinstance(other,BgfFile): # execute if second object is a BgfFile
return BgfFile.__add__(other,self)
elif isinstance(other,BgfAtom): # die if second object is a BgfAtom
cu.die("Cannot add a BgfFile to a BgfAtom object")
def readBgfLine(self,line):
"""
readBgfLine(self,line):
enters info from ATOM/HETATM, CONECT and ORDER lines into a BgfAtom object """
line = line.strip()
line = line.replace("-", " -")
if line[0:6] == 'ATOM ' or line[0:6] == 'HETATM':
if line[0:6] == 'HETATM': self.aTag = 1
l_line = line.split()
try:
self.aNo = int(l_line[1])
self.aName = l_line[2]
self.rName = l_line[3]
self.chain = l_line[4]
self.rNo = int(l_line[5])
self.x = float(l_line[6])
self.y = float(l_line[7])
self.z = float(l_line[8])
self.ffType = l_line[9]
self.bonds = int(l_line[10])
self.lpair = int(l_line[11])
self.charge = float(l_line[12])
except:
print("Error occured while reading the line: " + line)
sys.exit(0)
elif line[0:6] == 'CONECT' or line[0:6] == 'ORDER ':
if not self.aNo:
cu.die('readBgfLine: Cannot read CONECT/ORDER data prior to ATOM data!')
elif int(line[7:12]) != self.aNo:
cu.die('readBgfLine: The line read does not refer to the atom, "%d":\n%s' % (self.aNo, line))
else: # using re.split is OK in the following lines since aNo cannot be 6 digits
if line[0:6] == 'CONECT':
conectInfoString = line[12:].strip()
if conectInfoString:
self.CONECT = cu.list2intList( re.split(r'\s+', conectInfoString) )
else: #elif line[0:6] == 'ORDER ':
if not self.CONECT:
cu.die('readBgfLine: Cannot read ORDER data prior to CONECT data!')
else:
self.ORDER = cu.list2intList( re.split(r'\s+', line[12:].strip()) )
if len(self.CONECT) != len(self.ORDER):
cu.die('readBgfLine: CONECT and ORDER line elements do not match:\n%s%s' % \
(self.CONECTline(), line) )
else:
cu.die('readBgfLine: Line provided does not carry any atom information:\n%s' % (line,))
def getAtom(self, atomNo):
"""
getAtom(self, atomNo):
returns the BgfAtom specified by the atom number (internal index)"""
index = self.a2i.get(atomNo, (-1))
# return:
if index < 0:
cu.die("getAtom: No such atom number, %s, in BgfFile object!" % atomNo)
else:
return self.a[index]
def readBgfFromLines(self,lines,safe=0):
"""
readBgfFromLines(self,lines,safe=0):
reads a list of BGF lines and populates basic fields
if 'safe' is set, data after the charges are not read """
aCount = 0 # counts atoms
for line in lines:
tag = re.split(r'\s+', line)[0]
parse = line.split()
if tag == 'ATOM' or tag == 'HETATM':
# REMARK: maybe safe mode won't work since line is parsed
if safe:
line = line[:80] # do not read anything after 80 chars
atom = BgfAtom()
atom.readBgfLine(line.strip())
self.format = max(self.format, guessBGFformat(atom))
self.a.append(atom)
self.a2i[atom.aNo] = aCount
self.max_aNo = max(atom.aNo, self.max_aNo)
self.min_aNo = min(atom.aNo, self.min_aNo)
aCount += 1
elif tag == 'PERIOD':
if len(parse) == 2:
self.PERIOD = parse[1]
else:
self.PERIOD = ""
elif tag == 'CRYSTX':
if len(parse) > 2:
self.CRYSTX = [ float(parse[1]), float(parse[2]), float(parse[3]), float(parse[4]), float(parse[5]), float(parse[6]) ]
else:
self.CRYSTX = []
elif tag == 'FORCEFIELD':
if len(parse) == 2:
self.FF = str.strip(parse[1])
else:
self.FF = ''
elif tag == 'AXES':
if len(parse) == 2:
self.AXES = str.strip(parse[1])
elif tag == 'SGNAME':
if len(line) > 8:
self.SGNAME = line[7:]
elif tag == 'CELLS':
if len(parse) > 2:
self.CELLS = parse[1:]
elif tag == 'CONECT' or tag == 'ORDER':
aNo = getAtomNumberFromLine(line)
self.a[ self.a2i[aNo] ].readBgfLine(line)
elif tag == 'REMARK':
self.REMARK.append( line.strip()[7:] )
elif tag == 'FORMAT':
if re.search(r'^FORMAT ATOM', line):
self.FORMAT['ATOM'] = line.strip()
elif re.search(r'^FORMAT CONECT', line):
self.FORMAT['CONECT'] = line.strip()
elif re.search(r'^FORMAT ORDER', line):
self.FORMAT['ORDER'] = line.strip()
else:
cu.die("readBgfFromLines: Unkown FORMAT line:\n%s" % line)
elif tag == 'DESCRP':
self.DESCRP = line[7:].strip()
elif tag == 'BIOGRF':
self.BIOGRF = line[7:].strip()
# appended to prevent the errors from XTLGRP keyword. @ 110808
elif tag == 'XTLGRF':
self.BIOGRF = line[7:].strip()
elif tag == 'FORCEFIELD':
self.FF = line.strip()
elif tag == 'REM' or \
tag == 'PHI' or \
tag == 'PSI': # these are fields in the rotamer library
self.OTHER.append(line)
elif tag == 'END':
break
elif parse == []:
continue;
else:
cu.warn("readBgfFromLines: Encountered unknown field:\n%s" % line)
line = line.strip()
if line:
self.OTHER.append(line)
self.natoms = aCount