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