def get_atom_lines_from_input(input_file, tags=['ATOM ', 'HETATM']): lines = propka.lib.open_file_for_reading(input_file).readlines() conformation = '' atoms = {} numbers = [] for line in lines: tag = line[0:6] # set the conformation if tag == 'MODEL ': conformation = line[6:].strip() # found an atom - save it if tag in tags: atom = Atom(line=line) atom.get_input_parameters() atom.groups_extracted = 1 atom.is_protonated = True atoms[atom.numb] = atom numbers.append(atom.numb) # found bonding information - apply it if tag == 'CONECT' and len(line) > 14: conect_numbers = [ line[i:i + 5] for i in range(6, len(line) - 1, 5) ] center_atom = atoms[int(conect_numbers[0])] for n in conect_numbers[1:]: b = atoms[int(n)] # remember to check for cysteine bridges if center_atom.element == 'S' and b.element == 'S': center_atom.cysteine_bridge = True b.cysteine_bridge = True # set up bonding if not b in center_atom.bonded_atoms: center_atom.bonded_atoms.append(b) if not center_atom in b.bonded_atoms: b.bonded_atoms.append(center_atom) # found info on covalent coupling if tag == 'CCOUPL' and len(line) > 14: conect_numbers = [ line[i:i + 5] for i in range(6, len(line) - 1, 5) ] center_atom = atoms[int(conect_numbers[0])] for n in conect_numbers[1:]: cg = atoms[int(n)] center_atom.group.couple_covalently(cg.group) # found info on non-covalent coupling if tag == 'NCOUPL' and len(line) > 14: conect_numbers = [ line[i:i + 5] for i in range(6, len(line) - 1, 5) ] center_atom = atoms[int(conect_numbers[0])] for n in conect_numbers[1:]: cg = atoms[int(n)] center_atom.group.couple_non_covalently(cg.group) # this conformation is done - yield the atoms if tag == 'ENDMDL': for n in numbers: yield (conformation, atoms[n]) # prepare for next conformation atoms = {} numbers = [] return
def get_atom_lines_from_input(input_file, tags = ['ATOM ','HETATM']): lines = propka.lib.open_file_for_reading(input_file).readlines() conformation = '' atoms = {} numbers = [] for line in lines: tag = line[0:6] # set the conformation if tag == 'MODEL ': conformation = line[6:].strip() # found an atom - save it if tag in tags: atom = Atom(line=line) atom.get_input_parameters() atom.groups_extracted = 1 atom.is_protonated = True atoms[atom.numb] = atom numbers.append(atom.numb) # found bonding information - apply it if tag == 'CONECT' and len(line)>14: conect_numbers = [line[i:i+5] for i in range(6, len(line)-1, 5)] center_atom = atoms[int(conect_numbers[0])] for n in conect_numbers[1:]: b = atoms[int(n)] # remember to check for cysteine bridges if center_atom.element == 'S' and b.element == 'S': center_atom.cysteine_bridge = True b.cysteine_bridge = True # set up bonding if not b in center_atom.bonded_atoms: center_atom.bonded_atoms.append(b) if not center_atom in b.bonded_atoms: b.bonded_atoms.append(center_atom) # found info on covalent coupling if tag == 'CCOUPL' and len(line)>14: conect_numbers = [line[i:i+5] for i in range(6, len(line)-1, 5)] center_atom = atoms[int(conect_numbers[0])] for n in conect_numbers[1:]: cg = atoms[int(n)] center_atom.group.couple_covalently(cg.group) # found info on non-covalent coupling if tag == 'NCOUPL' and len(line)>14: conect_numbers = [line[i:i+5] for i in range(6, len(line)-1, 5)] center_atom = atoms[int(conect_numbers[0])] for n in conect_numbers[1:]: cg = atoms[int(n)] center_atom.group.couple_non_covalently(cg.group) # this conformation is done - yield the atoms if tag == 'ENDMDL': for n in numbers: yield (conformation, atoms[n]) # prepare for next conformation atoms = {} numbers = [] return
def get_atom_lines_from_input(input_file, tags=['ATOM ', 'HETATM']): """Get atom lines from a PROPKA input file. Args: input_file: input file tags: tags defining atom lines Yields: conformation container, list of atoms """ lines = open_file_for_reading(input_file).readlines() conformation = '' atoms = {} numbers = [] for line in lines: tag = line[0:6] # set the conformation if tag == 'MODEL ': conformation = line[6:].strip() # found an atom - save it if tag in tags: atom = Atom(line=line) atom.get_input_parameters() initialize_atom_group(atom) atom.groups_extracted = 1 atom.is_protonated = True atoms[atom.numb] = atom numbers.append(atom.numb) # found bonding information - apply it if tag == 'CONECT' and len(line) > 14: conect_numbers = [ line[i:i + 5] for i in range(6, len(line) - 1, 5) ] center_atom = atoms[int(conect_numbers[0])] for num in conect_numbers[1:]: bond_atom = atoms[int(num)] # remember to check for cysteine bridges if center_atom.element == 'S' and bond_atom.element == 'S': center_atom.cysteine_bridge = True bond_atom.cysteine_bridge = True # set up bonding if not bond_atom in center_atom.bonded_atoms: center_atom.bonded_atoms.append(bond_atom) if not center_atom in bond_atom.bonded_atoms: bond_atom.bonded_atoms.append(center_atom) # found info on covalent coupling if tag == 'CCOUPL' and len(line) > 14: conect_numbers = [ line[i:i + 5] for i in range(6, len(line) - 1, 5) ] center_atom = atoms[int(conect_numbers[0])] for num in conect_numbers[1:]: cov_atom = atoms[int(num)] center_atom.group.couple_covalently(cov_atom.group) # found info on non-covalent coupling if tag == 'NCOUPL' and len(line) > 14: conect_numbers = [ line[i:i + 5] for i in range(6, len(line) - 1, 5) ] center_atom = atoms[int(conect_numbers[0])] for num in conect_numbers[1:]: cov_atom = atoms[int(num)] center_atom.group.couple_non_covalently(cov_atom.group) # this conformation is done - yield the atoms if tag == 'ENDMDL': for num in numbers: yield (conformation, atoms[num]) # prepare for next conformation atoms = {} numbers = []