def toMolecule(self, formalcharges=False, ids=None):
"""
Return the moleculekit.molecule.Molecule
Parameters
----------
formalcharges: bool
If True,the formal charges are used instead of partial ones
ids: list
The list of conformer ids to store in the moleculekit Molecule object- If None, all are returned
Default: None
Returns
-------
mol: moleculekit.molecule.Molecule
The moleculekit Molecule object
"""
from moleculekit.molecule import Molecule
class NoConformerError(Exception):
pass
if ids is None:
ids = np.arange(self.numFrames)
if self.numFrames == 0:
raise NoConformerError(
"No Conformers are found in the molecule. Generate at least one conformer."
)
elif not isinstance(ids, list) and not isinstance(ids, np.ndarray):
raise ValueError(
'The argument ids should be a list of confomer ids')
mol = Molecule()
mol.empty(self.numAtoms)
mol.record[:] = 'HETATM'
mol.resname[:] = self.ligname[:3]
mol.resid[:] = self._resid
mol.coords = self._coords[:, :, ids]
mol.name[:] = self._name
mol.element[:] = self._element
if formalcharges:
mol.charge[:] = self._formalcharge
else:
mol.charge[:] = self._charge
mol.box = np.zeros((3, self.numFrames), dtype=np.float32)
mol.viewname = self.ligname
mol.bonds = self._bonds
mol.bondtype = self._bondtype
mol.atomtype = self._atomtype
return mol
def test_mcs_atom_matching(self):
from moleculekit.home import home
from moleculekit.molecule import Molecule
import numpy as np
path = home(dataDir="test-molecule-graphalignment")
mol1 = Molecule(os.path.join(path, "OIC.cif"))
mol1.atomtype = mol1.element
idx = np.random.permutation(np.arange(mol1.numAtoms))
mol1.reorderAtoms(idx)
mol2 = Molecule("5VBL")
mol2.filter("resname OIC")
atm1, atm2 = mcsAtomMatching(mol1, mol2, bondCompare="order")
assert len(atm1) == 11
assert np.array_equal(mol1.name[atm1], mol2.name[atm2])
atm1, atm2 = mcsAtomMatching(mol1, mol2, bondCompare="any")
assert len(atm1) == 11
# Compare elements here since it can match O to OXT when ignoring bond type
assert np.array_equal(mol1.element[atm1], mol2.element[atm2])
def pdb2psf_CA(pdb_name_in, psf_name_out, bonds=True, angles=True):
mol = Molecule(pdb_name_in)
mol.filter("name CA")
n = mol.numAtoms
atom_types = []
for i in range(n):
atom_types.append(CA_MAP[(mol.resname[i], mol.name[i])])
if bonds:
bonds = np.concatenate(
(
np.arange(n - 1).reshape([n - 1, 1]),
(np.arange(1, n).reshape([n - 1, 1])),
),
axis=1,
)
else:
bonds = np.empty([0, 2], dtype=np.int32)
if angles:
angles = np.concatenate(
(
np.arange(n - 2).reshape([n - 2, 1]),
(np.arange(1, n - 1).reshape([n - 2, 1])),
(np.arange(2, n).reshape([n - 2, 1])),
),
axis=1,
)
else:
angles = np.empty([0, 3], dtype=np.int32)
mol.atomtype = np.array(atom_types)
mol.bonds = bonds
mol.angles = angles
mol.write(psf_name_out)
def pdb2psf_CACB(pdb_name_in, psf_name_out, bonds=True, angles=True):
mol = Molecule(pdb_name_in)
mol.filter("name CA CB")
n = mol.numAtoms
atom_types = []
for i in range(n):
atom_types.append(CACB_MAP[(mol.resname[i], mol.name[i])])
CA_idx = []
CB_idx = []
for i, name in enumerate(mol.name):
if name[:2] == "CA":
CA_idx.append(i)
else:
CB_idx.append(i)
if bonds:
CA_bonds = np.concatenate(
(
np.array(CA_idx)[:-1].reshape([len(CA_idx) - 1, 1]),
np.array(CA_idx)[1:].reshape([len(CA_idx) - 1, 1]),
),
axis=1,
)
CB_bonds = np.concatenate(
(
np.array(CB_idx).reshape(len(CB_idx), 1) - 1,
np.array(CB_idx).reshape(len(CB_idx), 1),
),
axis=1,
)
bonds = np.concatenate((CA_bonds, CB_bonds))
else:
bonds = np.empty([0, 2], dtype=np.int32)
if angles:
CA_angles = np.concatenate(
(
np.array(CA_idx)[:-2].reshape([len(CA_idx) - 2, 1]),
np.array(CA_idx)[1:-1].reshape([len(CA_idx) - 2, 1]),
np.array(CA_idx)[2:].reshape([len(CA_idx) - 2, 1]),
),
axis=1,
)
CB_angles = []
cbn = 0
for i in CA_idx:
if mol.resname[i] != "GLY":
if i != 0:
CB_angles.append(
[CA_idx[CA_idx.index(i) - 1], i, CB_idx[cbn]])
if i != CA_idx[-1]:
CB_angles.append(
[CA_idx[CA_idx.index(i) + 1], i, CB_idx[cbn]])
cbn += 1
CB_angles = np.array(CB_angles)
angles = np.concatenate((CA_angles, CB_angles))
else:
angles = np.empty([0, 3], dtype=np.int32)
mol.atomtype = np.array(atom_types)
mol.bonds = bonds
mol.angles = angles
mol.write(psf_name_out)