def Loadpdb(pdb=None, hetatm= True, verbose=False):
try:
assert(pdb != None) #Check if filehandle to PDB file is passed
except AssertionError:
sys.exit("**No filehandle passed**. Pass a filehandle (to a pdb file) as an argument to Loadpdb.")
AtomNumber=0 #Keeps track of atom indices (assigned in the order atoms listed in input file)
mol_data={} #Key: molid; Value: Molecule_Type Object; Keep track of different molecules (different chains or molecule type) in input structure
first_res =True #To identify molecule type of every molecule in input structure and accordingly define Molecule object.
Prev_res=0 # to keep track of residue change
Prev_chain='aa' # to keep track of chain change in HETATM section
atmTohet = True #To determine transition from ATOM to HETATM record
frame_tag = '' # To keep track of multi-frame entry (multiple entry for same molecule type with same chain id)
'''Load the PDB structure file'''
for line in pdb:
if line[0:4]=="ATOM" and line[12:16].upper().strip() not in ["OXT"]:
AtomNumber+=1
AtomName, ResName, Chain, ResNo, CordX, CordY, CordZ, Occ, Bfac = Pdbcordsec(line)
atm = Atom(AtomName, AtomNumber, ResName, Chain, ResNo, CordX, CordY, CordZ)
#Check for unrecognized residue and new molecule
if not first_res:
if ResName.lower() not in Mol_types['protein'] + Mol_types['lipid'] + Mol_types['ligand']:
print "*** Unrecognized residue name: "+ ResName+ " ***.\nAdded %s as Ligand." % ResName
sys.exit("In file configstruc.py: Add missing residue name("+ ResName+ ") to appropriate molecule in Mol_types")
if ResNo != Prev_res or (Prev_chain != Chain and mol.molecule_type().lower()=='ligand'):
if mol.molecule_type().lower()=='ligand':
mol_data[Molecule.molid] = deepcopy(mol) #copy mol object into dictionary
first_res = True
elif Prev_chain != Chain or ResName.lower() not in Mol_types[mol.molecule_type().lower()]: #Either Chain is different or New residue doesn't belong to current molecule type
mol_data[Molecule.molid] = deepcopy(mol) #copy mol object into dictionary
first_res = True
elif frame_tag.lower() in ['endmdl', 'ter', 'end'] and Prev_chain == Chain: #Different molecule (of same molecule type) with same chain id; as in trajectory frames
mol_data[Molecule.molid] = deepcopy(mol) #copy mol object into dictionary
first_res = True
if first_res: #Initialize mol for new chain or molecule
if ResName.lower() in Mol_types['protein']:
mol = Protein()
elif ResName.lower() in Mol_types['lipid']:
mol = Lipid()
elif ResName.lower() in Mol_types['ligand']:
mol = Ligand()
else:
print "*** Unrecognized residue name: "+ ResName+ " ***.\n Cannot initialize Molecule object."
sys.exit("In file configstruc.py: Add missing residue name("+ ResName+ ") to appropriate molecule in Mol_types")
first_res = False
frame_tag = ''
mol.AddToResidue(atom=atm, occ=Occ, bfac=Bfac)
mol.atmidx.append(AtomNumber)
Prev_res= ResNo
Prev_chain=Chain
elif line[0:6]=="HETATM" and hetatm == True:
if atmTohet:
mol_data[Molecule.molid] = deepcopy(mol) #copy mol object into dictionary
first_res = True
atmTohet = False
AtomNumber+=1
AtomName, ResName, Chain, ResNo, CordX, CordY, CordZ, Occ, Bfac = Pdbcordsec(line)
atm = Atom(AtomName, AtomNumber, ResName, Chain, ResNo, CordX, CordY, CordZ)
#Check for new ligand molecule
if not first_res and (ResNo != Prev_res or Prev_chain != Chain):
mol_data[Molecule.molid] = deepcopy(mol) #copy mol object into dictionary
first_res = True
#Initialize mol for new chain or molecule
if first_res:
if ResName.lower() in Mol_types['ligand']:
mol = Ligand()
else:
print "*** Unrecognized residue name: "+ ResName+ " ***.\n Cannot initialize Ligand object."
sys.exit("In file configstruc.py: Add missing residue name ("+ ResName+ ") to ligand molecule in Mol_types")
first_res = False
mol.AddToResidue(atom=atm, occ=Occ, bfac=Bfac)
mol.atmidx.append(AtomNumber)
Prev_res= ResNo
Prev_chain=Chain
elif line[0:3].lower() in ["ter", "end"] or line[0:6].lower() == "endmdl":
frame_tag = line[0:3]
#append the last mol object to mol_data
mol_data[Molecule.molid] = deepcopy(mol) #copy mol object into dictionary
if verbose:
print "Number of molecules in input file: ", len(mol_data), "\n"
#Update mol_data[molid].nor, mol_data[molid].resids, and check for chain breaks in non-ligand molecules
for key in sorted(mol_data):
if verbose:
print "Molid:", key,"Molecule_Type:",mol_data[key].molecule_type()
mol_data[key].resids = sorted(mol_data[key].residue)
mol_data[key].nor = len(mol_data[key].resids)
if mol_data[key].molecule_type().lower() != 'ligand':
#Check for chain breaks in non-ligand molecule
resids_diff=numpy.array(mol_data[key].resids[1:]) - numpy.array(mol_data[key].resids[:-1])
if mol_data[key].nor != (numpy.sum(resids_diff)+1):
break_indices = numpy.where(resids_diff > 1)
print "Chain break encountered in molecule",key, "at residue positions: "
for res in break_indices[0]:
print mol_data[key].resids[res],
print "\n"
mol_data[key].chain_break = True
return mol_data
def Loadpdb(pdb=None, hetatm=True, verbose=False):
try:
assert (pdb != None) #Check if filehandle to PDB file is passed
except AssertionError:
sys.exit(
"**No filehandle passed**. Pass a filehandle (to a pdb file) as an argument to Loadpdb. "
)
AtomNumber = 0 #Keeps track of atom indices (assigned in the order atoms listed i input file)
mol_data = {
} #Key: molid; Keep track of different molecules (different chains or molecule type) in input structure
check_het = False #To keep track of new Hetero residue
first_res = True #To identify molecule type of every molecule in input structure and accordingly define Molecule object.
Prev_res = 0 # to keep track of residue change in HETATM section; a new Molecule object is assigned for every residue.
Prev_chain = 'a' # to keep track of chain change in HETATM section
'''Load the PDB structure file'''
for line in pdb:
if line[0:4] == "ATOM" and line[12:16].upper().strip() not in ["OXT"]:
AtomNumber += 1
AtomName, ResName, Chain, ResNo, CordX, CordY, CordZ, Occ, Bfac = Pdbcordsec(
line)
atm = Atom(AtomName, AtomNumber, ResName, Chain, ResNo, CordX,
CordY, CordZ)
if first_res: #Initialize mol for new chain or molecule
if ResName.lower() in Mol_types['protein']:
mol = Protein()
elif ResName.lower() in Mol_types['ligand']:
mol = Ligand()
else:
print "*** Unrecognized residue name: " + ResName + " ***.\n Cannot initialize Molecule object."
sys.exit(
"In file configstruc.py: Add missing residue name(" +
ResName + ") to appropriate molecule in Mol_types")
first_res = False
mol.AddToResidue(atom=atm, occ=Occ, bfac=Bfac)
mol.atmidx.append(AtomNumber)
elif line[0:3] == "TER":
mol_data[Molecule.molid] = deepcopy(
mol) #copy mol object into dictionary
first_res = True # mol object will be initialized to molecule type of next molecule
elif line[0:6] == "HETATM" and hetatm == True:
AtomNumber += 1
AtomName, ResName, Chain, ResNo, CordX, CordY, CordZ, Occ, Bfac = Pdbcordsec(
line)
atm = Atom(AtomName, AtomNumber, ResName, Chain, ResNo, CordX,
CordY, CordZ)
#Check for new molecule
if (
ResNo != Prev_res or Prev_chain != Chain
) and check_het == True: #For first HETATM check_het is always False
mol_data[Molecule.molid] = deepcopy(
mol) #copy mol object into dictionary
first_res = True
#Initialize mol for new chain or molecule
if first_res:
if ResName.lower() in Mol_types['ligand']:
mol = Ligand()
else:
print "*** Unrecognized residue name: " + ResName + " ***.\n Cannot initialize Ligand object."
sys.exit(
"In file configstruc.py: Add missing residue name (" +
ResName + ") to ligand molecule in Mol_types")
first_res = False
mol.AddToResidue(atom=atm, occ=Occ, bfac=Bfac)
mol.atmidx.append(AtomNumber)
if Prev_res == 0:
check_het = True
Prev_res = ResNo
Prev_chain = Chain
if hetatm: #If HETATM record was added; append the last hetero residue object to mol_data
mol_data[Molecule.molid] = deepcopy(
mol) #copy mol object into dictionary
if verbose:
print "Number of molecules in input file: ", len(mol_data), "\n"
#Update mol_data[molid].nor, mol_data[molid].resids, and check for chain breaks in non-ligand molecules
for key in sorted(mol_data):
if verbose:
print "Molid:", key, "Molecule_Type:", mol_data[key].molecule_type(
)
if mol_data[key].molecule_type().lower() != 'ligand':
mol_data[key].resids = sorted(mol_data[key].residue)
mol_data[key].nor = len(mol_data[key].resids)
#Check for chain breaks in protein
resids_diff = numpy.array(mol_data[key].resids[1:]) - numpy.array(
mol_data[key].resids[:-1])
if mol_data[key].nor != (numpy.sum(resids_diff) + 1):
break_indices = numpy.where(resids_diff > 1)
print "Chain break encountered in molecule", key, "at residue positions: "
for res in break_indices[0]:
print mol_data[key].resids[res],
print "\n"
return mol_data