def structure_to_complex(structure: Structure):
residues = {}
chains = {}
for pqr_atom in structure.atoms:
atom = _Atom._create()
atom._symbol = pqr_atom.atom_name[:1]
atom._serial = pqr_atom.atom_number
atom._name = pqr_atom.atom_name
atom._position = pqr_atom.position
atom._is_het = pqr_atom.is_het
if not pqr_atom.chain_id in chains:
chain = _Chain._create()
chain._name = pqr_atom.chain_id
chains[pqr_atom.chain_id] = chain
if not pqr_atom.residue_number in residues:
residue = _Residue._create()
residue._name = pqr_atom.residue_name
residue._type = pqr_atom.residue_name
residue._serial = pqr_atom.residue_number
residues[pqr_atom.residue_number] = residue
chains[pqr_atom.chain_id]._add_residue(residue)
residues[pqr_atom.residue_number]._add_atom(atom)
mol = _Molecule._create()
for chain in chains:
mol._add_chain(chains[chain])
complex = _Complex._create()
complex._add_molecule(mol)
return complex._convert_to_conformers()
def structure(content):
# type: (Content) -> Complex
complex = _Complex._create()
for model in content.models:
complex._add_molecule(structure_molecule(model))
complex._remarks = {}
return complex._convert_to_conformers()
def __next(self):
# Go to next molecule
complex = self.__complexes[self.__complex_idx]
framed_complex = self.__framed_complexes[self.__complex_idx]
self.__molecule_idx += 1
if self.__molecule_idx >= len(framed_complex._molecules):
self.__complex_idx += 1
if self.__complex_idx >= len(self.__complexes):
self.__done()
return
complex = self.__complexes[self.__complex_idx]
framed_complex = self.__framed_complexes[self.__complex_idx]
self.__molecule_idx = 0
self.__saved_complex = complex
self.__saved_is_conformer = len(complex._molecules) == 1
molecule = framed_complex._molecules[self.__molecule_idx]
single_frame = _Complex._create()
single_frame._add_molecule(molecule)
_pdb.to_file(self.__input.name, single_frame)
self.__proc.start()
def structure(content):
num_molecules = max(content.model_count, 1)
atoms_by_molecule = []
for i in range(num_molecules):
atoms_by_molecule.append([])
for ratom in content.atoms:
atoms_by_molecule[ratom.model_number - 1].append(ratom)
complex = _Complex._create()
complex._remarks = content._remarks
for i in range(num_molecules):
molecule = structure_molecule(atoms_by_molecule[i], content.compnds)
molecule._name = str(i)
complex._add_molecule(molecule)
# Done
return complex._convert_to_conformers()
def structure(content):
remarks = StructureRemarks(content.remarks)
complex = _Complex._create()
complex._remarks = remarks
# All structured infos
all_atoms = {}
all_residues = {}
all_chains = {}
all_molecules = {}
helper = None
if content.cell != None:
helper = UnitCellHelper(content.cell)
# Read all atoms
for c_atom in content.atoms:
chain_name = c_atom.chain
if c_atom.is_het:
chain_name = "H" + chain_name
molecule_id = str(c_atom.model)
chain_id = molecule_id + ":" + chain_name
residue_id = chain_id + ":" + str(c_atom.residue_serial)
atom_id = residue_id + ":" + str(c_atom.atom_serial)
if not atom_id in all_atoms:
if not residue_id in all_residues:
if not chain_id in all_chains:
if not molecule_id in all_molecules:
molecule = _Molecule._create()
molecule._name = str(c_atom.model)
all_molecules[molecule_id] = molecule
complex._add_molecule(molecule)
chain = _Chain._create()
chain._name = chain_name
all_chains[chain_id] = chain
all_molecules[molecule_id]._add_chain(chain)
residue = _Residue._create()
residue._name = c_atom.residue_name
residue._type = residue._name
residue.serial = c_atom.residue_serial
all_residues[residue_id] = residue
all_chains[chain_id]._add_residue(residue)
atom = StructureAtom(c_atom, helper)
all_atoms[atom_id] = None
all_residues[residue_id]._add_atom(atom)
# Done
return complex._convert_to_conformers()
def __next(self):
# Go to next molecule
complex = self.__complexes[self.__complex_idx]
framed_complex = self.__framed_complexes[self.__complex_idx]
self.__molecule_idx += 1
# first frame if conformer, all frames if in frames (may change)
if self.__molecule_idx >= len(complex._molecules):
self.__update_secondary_structure(complex)
self.__current_complex_result.clear()
self.__complex_idx += 1
if self.__complex_idx >= len(self.__complexes):
self.__done()
return
complex = self.__complexes[self.__complex_idx]
framed_complex = self.__framed_complexes[self.__complex_idx]
self.__molecule_idx = 0
molecule = framed_complex._molecules[self.__molecule_idx]
single_frame = _Complex._create()
single_frame._add_molecule(molecule)
_pdb.to_file(self.__input.name, single_frame)
self.__proc.start()