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_molecule(model):
# type: (Content.Model) -> Molecule
molecule = _Molecule._create()
molecule._name = model.name
chain = _Chain._create()
chain._name = "S"
molecule._add_chain(chain)
residue = _Residue._create()
residue._name = "SDF"
residue._type = residue._name
residue.serial = 1
chain._add_residue(residue)
atoms_by_serial = {}
for catom in model.atoms:
atom = _Atom._create()
atom._symbol = catom.symbol
atom._serial = catom.serial
atom._position = Vector3(catom.x, catom.y, catom.z)
atom._name = catom.symbol
atom._is_het = True
atom._formal_charge = catom.charge
residue._add_atom(atom)
atoms_by_serial[atom._serial] = atom
for cbond in model.bonds:
if cbond.serial_atom1 in atoms_by_serial and cbond.serial_atom2 in atoms_by_serial:
bond = _Bond._create()
bond._atom1 = atoms_by_serial[cbond.serial_atom1]
bond._atom2 = atoms_by_serial[cbond.serial_atom2]
bond._kind = enums.Kind.safe_cast(cbond.bond_order)
residue._add_bond(bond)
molecule._associated = model._associated
return molecule
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 structure_molecule(atoms, compnds):
# All structured infos
all_residues = {} #<string, Residue>
all_chains = {} #<string, Chain>
all_atoms = {} #<string, Atom>
# Read all atoms
for ratom in atoms:
atom = _Atom._create()
atom._symbol = ratom.element_symbol
atom._serial = ratom.atom_serial_number
atom._name = ratom.atom_name
#atom.alts = ratom.atom_alternate_location
atom._occupancy = ratom.occupancy
atom._bfactor = ratom.bfactor
#atom.charge = ratom.atom_charge
atom._position = Vector3(ratom.atom_x, ratom.atom_y, ratom.atom_z)
atom._is_het = ratom.is_het_atom
atom_id = ratom.chain_identifier + ":" + str(
ratom.residue_serial_number) + ":" + ratom.atom_name + ":" + str(
ratom.atom_serial_number)
if not atom_id in all_atoms:
residue_id = ratom.chain_identifier + ":" + str(
ratom.residue_serial_number) + ":" + ratom.segment_identifier
if not residue_id in all_residues:
residue = _Residue._create()
residue._name = ratom.residue_name
residue._type = residue._name
residue._serial = ratom.residue_serial_number
# residue.insertion_code = ratom.residue_insertion_code
all_residues[residue_id] = residue
chain_id = ratom.chain_identifier
if ratom.is_het_atom:
chain_id = "H" + chain_id
if not chain_id in all_chains:
chain = _Chain._create()
chain._name = chain_id
all_chains[chain_id] = chain
all_chains[chain_id]._add_residue(residue)
all_residues[residue_id]._add_atom(atom)
all_atoms[atom_id] = atom
# Final molecule
molecule = _Molecule._create()
# Assemble molecule contents
for chain in all_chains:
molecule._add_chain(all_chains[chain])
# Done
return molecule