downloaded from propka.ki.ku.dk
This commit is contained in:
Jimmy Charnley Kromann
323
Source/pdb.py
Normal file
323
Source/pdb.py
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import string, sys, copy, Source.lib
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from Source.atom import Atom
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from Source.conformation_container import Conformation_container
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expected_atom_numbers = {'ALA':5,
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'ARG':11,
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'ASN':8,
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'ASP':8,
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'CYS':6,
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'GLY':4,
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'GLN':9,
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'GLU':9,
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'HIS':10,
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'ILE':8,
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'LEU':8,
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'LYS':9,
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'MET':8,
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'PHE':11,
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'PRO':7,
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'SER':6,
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'THR':7,
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'TRP':14,
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'TYR':12,
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'VAL':7}
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def read_pdb(pdb_file, parameters, molecule):
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conformations = {}
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# read in all atoms in the file
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lines = get_atom_lines_from_pdb(pdb_file, ignore_residues = parameters.ignore_residues, keep_protons = molecule.options.keep_protons, chains=molecule.options.chains)
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for (name, atom) in lines:
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if not name in conformations.keys():
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conformations[name] = Conformation_container(name=name, parameters=parameters, molecular_container=molecule)
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conformations[name].add_atom(atom)
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# make a sorted list of conformation names
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names = sorted(conformations.keys(), key=Source.lib.conformation_sorter)
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return [conformations, names]
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def protein_precheck(conformations, names):
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for name in names:
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atoms = conformations[name].atoms
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res_ids = []
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[res_ids.append(resid_from_atom(a)) for a in atoms if not res_ids.count(resid_from_atom(a))]
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for res_id in res_ids:
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res_atoms = [a for a in atoms if resid_from_atom(a) == res_id and a.element != 'H']
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resname = res_atoms[0].resName
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residue_label = '%3s%5s'%(resname, res_id)
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# ignore ligand residues
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if resname not in expected_atom_numbers:
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continue
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# check for c-terminal
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if 'C-' in [a.terminal for a in res_atoms]:
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if len(res_atoms) != expected_atom_numbers[resname]+1:
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print('Warning: Unexpected number (%d) of atoms in residue %s in conformation %s'%(len(res_atoms),residue_label, name))
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continue
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# check number of atoms in residue
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if len(res_atoms) != expected_atom_numbers[resname]:
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print('Warning: Unexpected number (%d) of atoms in residue %s in conformation %s'%(len(res_atoms),residue_label, name))
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return
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def resid_from_atom(a):
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return '%4d %s %s'%(a.resNumb,a.chainID,a.icode)
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def get_atom_lines_from_pdb(pdb_file, ignore_residues = [], keep_protons=False, tags = ['ATOM ', 'HETATM'], chains=None):
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lines = Source.lib.open_file_for_reading(pdb_file).readlines()
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nterm_residue = 'next_residue'
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old_residue = None
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terminal = None
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model = 1
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for line in lines:
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tag = line[0:6]
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# set the model number
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if tag == 'MODEL ':
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model = int(line[6:])
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nterm_residue = 'next_residue'
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if tag == 'TER ':
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nterm_residue = 'next_residue'
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if tag in tags:
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alt_conf_tag = line[16]
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residue_name = line[12:16]
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residue_number = line[22:26]
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# check if we want this residue
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if line[17:20] in ignore_residues:
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continue
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if chains and line[21] not in chains:
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continue
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# set the Nterm residue number - nessecary because we may need to
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# identify more than one N+ group for structures with alt_conf tags
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if nterm_residue == 'next_residue' and tag == 'ATOM ':
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# make sure that we reached a new residue - nessecary if OXT is not the last atom in
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# the previous residue
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if old_residue != residue_number:
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nterm_residue = residue_number
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old_residue = None
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# Identify the configuration
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# convert digits to letters
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if alt_conf_tag in '123456789':
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alt_conf_tag = chr(ord(alt_conf_tag)+16)
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if alt_conf_tag == ' ':
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alt_conf_tag = 'A'
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conformation = '%d%s'%(model, alt_conf_tag)
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# set the terminal
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if tag == 'ATOM ':
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if residue_name.strip() == 'N' and nterm_residue == residue_number:
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terminal = 'N+'
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if residue_name.strip() in ['OXT','O\'\'']:
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terminal = 'C-'
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nterm_residue = 'next_residue'
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old_residue = residue_number
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# and yield the atom
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atom = Atom(line=line)
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atom.terminal = terminal
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#if keep_protons:
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# atom.is_protonated = True
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if not (atom.element == 'H' and not keep_protons): #ignore hydrogen
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yield (conformation, atom)
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terminal = None
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return
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def write_pdb(conformation, filename):
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write_pdb_for_atoms(conformation.atoms, filename)
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return
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def write_pdb_for_atoms(atoms, filename, make_conect_section=False):
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out = Source.lib.open_file_for_writing(filename)
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for atom in atoms:
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out.write(atom.make_pdb_line())
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if make_conect_section:
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for atom in atoms:
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out.write(atom.make_conect_line())
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out.close()
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return
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def write_mol2_for_atoms(atoms, filename):
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header = '@<TRIPOS>MOLECULE\n\n%d %d\nSMALL\nUSER_CHARGES\n'
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atoms_section = '@<TRIPOS>ATOM\n'
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for i in range(len(atoms)):
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atoms_section += atoms[i].make_mol2_line(i+1)
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bonds_section = '@<TRIPOS>BOND\n'
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id = 1
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for i in range(len(atoms)):
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for j in range(i+1,len(atoms)):
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if atoms[i] in atoms[j].bonded_atoms:
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type = get_bond_order(atoms[i],atoms[j])
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bonds_section += '%7d %7d %7d %7s\n'%(id, i+1, j+1, type)
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id+=1
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substructure_section = '@<TRIPOS>SUBSTRUCTURE\n\n'
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if len(atoms)>0:
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substructure_section = '@<TRIPOS>SUBSTRUCTURE\n%-7d %10s %7d\n'%(atoms[0].resNumb,atoms[0].resName,atoms[0].numb)
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out = Source.lib.open_file_for_writing(filename)
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out.write(header%(len(atoms),id-1))
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out.write(atoms_section)
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out.write(bonds_section)
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out.write(substructure_section)
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out.close()
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return
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def get_bond_order(atom1, atom2):
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type = '1'
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pi_electrons1 = atom1.number_of_pi_electrons_in_double_and_triple_bonds
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pi_electrons2 = atom2.number_of_pi_electrons_in_double_and_triple_bonds
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if '.ar' in atom1.sybyl_type:
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pi_electrons1 -=1
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if '.ar' in atom2.sybyl_type:
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pi_electrons2 -=1
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if pi_electrons1 > 0 and pi_electrons2 > 0:
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type = '%d'%(min(pi_electrons1, pi_electrons2)+1)
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if '.ar' in atom1.sybyl_type and '.ar' in atom2.sybyl_type:
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type = 'ar'
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return type
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def write_input(molecular_container, filename):
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out = Source.lib.open_file_for_writing(filename)
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for conformation_name in molecular_container.conformation_names:
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out.write('MODEL %s\n'%conformation_name)
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# write atoms
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for atom in molecular_container.conformations[conformation_name].atoms:
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out.write(atom.make_input_line())
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# write bonds
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for atom in molecular_container.conformations[conformation_name].atoms:
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out.write(atom.make_conect_line())
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# write covalently coupled groups
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for group in molecular_container.conformations[conformation_name].groups:
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out.write(group.make_covalently_coupled_line())
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# write non-covalently coupled groups
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for group in molecular_container.conformations[conformation_name].groups:
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out.write(group.make_non_covalently_coupled_line())
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out.write('ENDMDL\n')
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out.close()
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return
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def read_input(input_file, parameters,molecule):
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conformations = {}
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# read in all atoms in the input file
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lines = get_atom_lines_from_input(input_file)
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for (name, atom) in lines:
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if not name in conformations.keys():
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conformations[name] = Conformation_container(name=name, parameters=parameters, molecular_container=molecule)
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conformations[name].add_atom(atom)
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# make a sorted list of conformation names
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names = sorted(conformations.keys(), key=Source.lib.conformation_sorter)
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return [conformations, names]
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def get_atom_lines_from_input(input_file, tags = ['ATOM ','HETATM']):
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lines = Source.lib.open_file_for_reading(input_file).readlines()
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conformation = ''
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atoms = {}
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numbers = []
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for line in lines:
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tag = line[0:6]
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# set the conformation
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if tag == 'MODEL ':
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conformation = line[6:].strip()
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# found an atom - save it
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if tag in tags:
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atom = Atom(line=line)
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atom.get_input_parameters()
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atom.groups_extracted = 1
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atom.is_protonated = True
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atoms[atom.numb] = atom
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numbers.append(atom.numb)
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# found bonding information - apply it
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if tag == 'CONECT' and len(line)>14:
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conect_numbers = [line[i:i+5] for i in range(6, len(line)-1, 5)]
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center_atom = atoms[int(conect_numbers[0])]
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for n in conect_numbers[1:]:
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b = atoms[int(n)]
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# remember to check for cysteine bridges
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if center_atom.element == 'S' and b.element == 'S':
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center_atom.cysteine_bridge = True
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b.cysteine_bridge = True
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# set up bonding
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if not b in center_atom.bonded_atoms:
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center_atom.bonded_atoms.append(b)
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if not center_atom in b.bonded_atoms:
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b.bonded_atoms.append(center_atom)
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# found info on covalent coupling
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if tag == 'CCOUPL' and len(line)>14:
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conect_numbers = [line[i:i+5] for i in range(6, len(line)-1, 5)]
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center_atom = atoms[int(conect_numbers[0])]
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for n in conect_numbers[1:]:
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cg = atoms[int(n)]
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center_atom.group.couple_covalently(cg.group)
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# found info on non-covalent coupling
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if tag == 'NCOUPL' and len(line)>14:
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conect_numbers = [line[i:i+5] for i in range(6, len(line)-1, 5)]
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center_atom = atoms[int(conect_numbers[0])]
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for n in conect_numbers[1:]:
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cg = atoms[int(n)]
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center_atom.group.couple_non_covalently(cg.group)
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# this conformation is done - yield the atoms
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if tag == 'ENDMDL':
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for n in numbers:
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yield (conformation, atoms[n])
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# prepare for next conformation
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atoms = {}
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numbers = []
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return
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