def _parseatoms(self, pdb):
atoms = []
# translate Bio.PDB atom objects to MDAnalysis Atom.
for iatom, atom in enumerate(pdb.get_atoms()):
residue = atom.parent
chain_id = residue.parent.id
atomname = atom.name
atomtype = guess_atom_type(atomname)
resname = residue.resname
resid = int(residue.id[1])
# no empty segids (or Universe throws IndexError)
segid = residue.get_segid().strip() or chain_id or "SYSTEM"
mass = guess_atom_mass(atomname)
charge = guess_atom_charge(atomname)
bfactor = atom.bfactor
# occupancy = atom.occupancy
atoms.append(
Atom(iatom,
atomname,
atomtype,
resname,
resid,
segid,
mass,
charge,
bfactor=bfactor))
return atoms
def _parseatoms(self, pdb):
atoms = []
# translate list of atoms to MDAnalysis Atom.
for iatom, atom in enumerate(pdb._atoms):
# ATOM
if len(atom.__dict__) == 10:
atomname = atom.name
atomtype = atom.element or guess_atom_type(atomname)
resname = atom.resName
resid = int(atom.resSeq)
chain = atom.chainID.strip()
# no empty segids (or Universe throws IndexError)
segid = atom.segID.strip() or chain or "SYSTEM"
mass = guess_atom_mass(atomname)
charge = guess_atom_charge(atomname)
bfactor = atom.tempFactor
# occupancy = atom.occupancy
altLoc = atom.altLoc
atoms.append(Atom(iatom, atomname, atomtype, resname, resid,
segid, mass, charge,
bfactor=bfactor, serial=atom.serial,
altLoc=altLoc))
# TER atoms
#elif len(atom.__dict__) == 5:
# pass
# #atoms.append(None)
self.structure["_atoms"] = atoms
def parse(self):
"""Parse CRD file *filename* and return the dict `structure`.
Only reads the list of atoms.
:Returns: MDAnalysis internal *structure* dict
.. SeeAlso:: The *structure* dict is defined in
`MDAnalysis.topology`
"""
extformat = FORTRANReader(
'2I10,2X,A8,2X,A8,3F20.10,2X,A8,2X,A8,F20.10')
stdformat = FORTRANReader('2I5,1X,A4,1X,A4,3F10.5,1X,A4,1X,A4,F10.5')
atoms = []
atom_serial = 0
with openany(self.filename) as crd:
for linenum, line in enumerate(crd):
# reading header
if line.split()[0] == '*':
continue
elif line.split()[-1] == 'EXT' and bool(int(
line.split()[0])) is True:
r = extformat
continue
elif line.split()[0] == line.split(
)[-1] and line.split()[0] != '*':
r = stdformat
continue
# anything else should be an atom
try:
serial, TotRes, resName, name, x, y, z, chainID, resSeq, tempFactor = r.read(
line)
except:
raise ValueError("Check CRD format at line {}: {}".format(
linenum, line.rstrip()))
atomtype = guess_atom_type(name)
mass = guess_atom_mass(name)
charge = guess_atom_charge(name)
atoms.append(
Atom(atom_serial, name, atomtype, resName, TotRes, chainID,
mass, charge))
atom_serial += 1
structure = {}
structure["_atoms"] = atoms
return structure
def parse(self):
"""Parse CRD file *filename* and return the dict `structure`.
Only reads the list of atoms.
:Returns: MDAnalysis internal *structure* dict
.. SeeAlso:: The *structure* dict is defined in
`MDAnalysis.topology`
"""
extformat = FORTRANReader('2I10,2X,A8,2X,A8,3F20.10,2X,A8,2X,A8,F20.10')
stdformat = FORTRANReader('2I5,1X,A4,1X,A4,3F10.5,1X,A4,1X,A4,F10.5')
atoms = []
atom_serial = 0
with openany(self.filename) as crd:
for linenum, line in enumerate(crd):
# reading header
if line.split()[0] == '*':
continue
elif line.split()[-1] == 'EXT' and bool(int(line.split()[0])) is True:
r = extformat
continue
elif line.split()[0] == line.split()[-1] and line.split()[0] != '*':
r = stdformat
continue
# anything else should be an atom
try:
serial, TotRes, resName, name, x, y, z, chainID, resSeq, tempFactor = r.read(line)
except:
raise ValueError("Check CRD format at line {}: {}".format(
linenum, line.rstrip()))
atomtype = guess_atom_type(name)
mass = guess_atom_mass(name)
charge = guess_atom_charge(name)
atoms.append(Atom(atom_serial, name, atomtype, resName, TotRes, chainID, mass, charge))
atom_serial += 1
structure = {}
structure["_atoms"] = atoms
return structure
def _parseatoms(self, pdb):
atoms = []
# translate Bio.PDB atom objects to MDAnalysis Atom.
for iatom, atom in enumerate(pdb.get_atoms()):
residue = atom.parent
chain_id = residue.parent.id
atomname = atom.name
atomtype = guess_atom_type(atomname)
resname = residue.resname
resid = int(residue.id[1])
# no empty segids (or Universe throws IndexError)
segid = residue.get_segid().strip() or chain_id or "SYSTEM"
mass = guess_atom_mass(atomname)
charge = guess_atom_charge(atomname)
bfactor = atom.bfactor
# occupancy = atom.occupancy
atoms.append(Atom(iatom, atomname, atomtype, resname, resid, segid,
mass, charge, bfactor=bfactor))
return atoms
def _parseatoms(self, pdb):
atoms = []
# translate list of atoms to MDAnalysis Atom.
for iatom, atom in enumerate(pdb._atoms):
# ATOM
if len(atom.__dict__) == 10:
atomname = atom.name
atomtype = atom.element or guess_atom_type(atomname)
resname = atom.resName
resid = int(atom.resSeq)
chain = atom.chainID.strip()
# no empty segids (or Universe throws IndexError)
segid = atom.segID.strip() or chain or "SYSTEM"
mass = guess_atom_mass(atomname)
charge = guess_atom_charge(atomname)
bfactor = atom.tempFactor
# occupancy = atom.occupancy
altLoc = atom.altLoc
atoms.append(
Atom(iatom,
atomname,
atomtype,
resname,
resid,
segid,
mass,
charge,
bfactor=bfactor,
serial=atom.serial,
altLoc=altLoc))
# TER atoms
#elif len(atom.__dict__) == 5:
# pass
# #atoms.append(None)
self.structure["_atoms"] = atoms
