def add_image(self, complex):
complex.thumbnail = tempfile.NamedTemporaryFile(
delete=False, suffix='.png', dir=self.temp_dir.name).name
complex.image = tempfile.NamedTemporaryFile(
delete=False, suffix='.png', dir=self.temp_dir.name).name
mol = complex.rdmol
Chem.AssignStereochemistryFrom3D(mol)
Chem.rdCoordGen.AddCoords(mol)
mol = Draw.rdMolDraw2D.PrepareMolForDrawing(mol)
drawer = Draw.rdMolDraw2D.MolDraw2DSVG(256, 192)
drawer.drawOptions().additionalAtomLabelPadding = 0.3
drawer.DrawMolecule(mol)
drawer.FinishDrawing()
svg = drawer.GetDrawingText()
svg = svg.replace('stroke-linecap:butt', 'stroke-linecap:round')
svg2png(bytestring=svg,
write_to=complex.thumbnail,
output_width=256,
output_height=192)
svg2png(bytestring=svg,
write_to=complex.image,
output_width=1024,
output_height=768)
def file_to_rdkit_mol(file_path: Path) -> Chem.Mol:
"""
Args:
file_path:
Path of the file used to generate the rdkit molecule.
return:
RDKit molecule object generated from its file (or None if incorrect file type is provided).
"""
# Read the file
if file_path.suffix == ".pdb":
mol = Chem.MolFromPDBFile(file_path.as_posix(),
removeHs=False,
sanitize=False)
elif file_path.suffix == ".mol2":
mol = Chem.MolFromMol2File(file_path.as_posix(),
removeHs=False,
sanitize=False)
elif file_path.suffix == ".mol" or file_path.suffix == ".sdf":
mol = Chem.MolFromMolFile(file_path.as_posix(),
removeHs=False,
sanitize=False,
strictParsing=True)
else:
raise FileTypeError(
f"The file type {file_path.suffix} is not supported.")
# run some sanitation
Chem.SanitizeMol(
mol,
(Chem.SANITIZE_ALL ^ Chem.SANITIZE_SETAROMATICITY
^ Chem.SANITIZE_ADJUSTHS),
)
Chem.SetAromaticity(mol, Chem.AromaticityModel.AROMATICITY_MDL)
Chem.AssignStereochemistryFrom3D(mol)
# set the name of the input file
mol.SetProp("_Name", file_path.stem)
return mol
def to_rdmol(plams_mol, sanitize=True, properties=True, assignChirality=False):
"""
Translate a PLAMS molecule into an RDKit molecule type.
PLAMS |Molecule|, |Atom| or |Bond| properties are pickled if they are neither booleans, floats,
integers, floats nor strings, the resulting property names are appended with '_pickled'.
:parameter plams_mol: A PLAMS molecule
:parameter bool sanitize: Kekulize, check valencies, set aromaticity, conjugation and hybridization
:parameter bool properties: If all |Molecule|, |Atom| and |Bond| properties should be converted from PLAMS to RDKit format.
:parameter bool assignChirality: Assign R/S and cis/trans information, insofar as this was not yet present in the PLAMS molecule.
:type plams_mol: |Molecule|
:return: an RDKit molecule
:rtype: rdkit.Chem.Mol
"""
if isinstance(plams_mol, Chem.Mol):
return plams_mol
# Create rdkit molecule
e = Chem.EditableMol(Chem.Mol())
# Add atoms and assign properties to the RDKit atom if *properties* = True
for pl_atom in plams_mol.atoms:
rd_atom = Chem.Atom(pl_atom.atnum)
if 'charge' in pl_atom.properties:
rd_atom.SetFormalCharge(pl_atom.properties.charge)
if properties:
if 'pdb_info' in pl_atom.properties:
set_PDBresidueInfo(rd_atom, pl_atom.properties.pdb_info)
for prop in pl_atom.properties:
if prop not in ('charge', 'pdb_info', 'stereo'):
prop_to_rdmol(pl_atom, rd_atom, prop)
# Check for R/S information
if pl_atom.properties.stereo:
stereo = pl_atom.properties.stereo.lower()
if stereo == 'counter-clockwise':
rd_atom.SetChiralTag(
Chem.rdchem.ChiralType.CHI_TETRAHEDRAL_CCW)
elif stereo == 'clockwise':
rd_atom.SetChiralTag(Chem.rdchem.ChiralType.CHI_TETRAHEDRAL_CW)
e.AddAtom(rd_atom)
# Mapping of PLAMS bond orders to RDKit bond types:
def plams_to_rd_bonds(bo):
if bo > 1.4 and bo < 1.6:
return 12 # bond type for aromatic bond
else:
return int(bo)
# Add bonds to the RDKit molecule
for bond in plams_mol.bonds:
a1 = plams_mol.atoms.index(bond.atom1)
a2 = plams_mol.atoms.index(bond.atom2)
e.AddBond(a1, a2, Chem.BondType(plams_to_rd_bonds(bond.order)))
rdmol = e.GetMol()
# Check for cis/trans information
for pl_bond, rd_bond in zip(plams_mol.bonds, rdmol.GetBonds()):
if pl_bond.properties.stereo:
stereo = pl_bond.properties.stereo.lower()
if stereo == 'e' or stereo == 'trans':
rd_bond.SetStereo(Chem.rdchem.BondStereo.STEREOE)
elif stereo == 'z' or stereo == 'cis':
rd_bond.SetStereo(Chem.rdchem.BondStereo.STEREOZ)
elif stereo == 'up':
rd_bond.SetBondDir(Chem.rdchem.BondDir.ENDUPRIGHT)
elif stereo == 'down':
rd_bond.SetBondDir(Chem.rdchem.BondDir.ENDDOWNRIGHT)
# Assign properties to RDKit molecule and bonds if *properties* = True
if properties:
for prop in plams_mol.properties:
prop_to_rdmol(plams_mol, rdmol, prop)
for pl_bond, rd_bond in zip(plams_mol.bonds, rdmol.GetBonds()):
for prop in pl_bond.properties:
if prop != 'stereo':
prop_to_rdmol(pl_bond, rd_bond, prop)
if sanitize:
Chem.SanitizeMol(rdmol)
conf = Chem.Conformer()
for i, atom in enumerate(plams_mol.atoms):
xyz = Geometry.Point3D(atom._getx(), atom._gety(), atom._getz())
conf.SetAtomPosition(i, xyz)
rdmol.AddConformer(conf)
# REB: Assign all stereochemistry, if it wasn't already there
if assignChirality:
Chem.rdmolops.AssignAtomChiralTagsFromStructure(
rdmol, confId=conf.GetId(), replaceExistingTags=False)
try:
Chem.AssignStereochemistryFrom3D(rdmol,
confId=conf.GetId(),
replaceExistingTags=False)
except AttributeError:
pass
return rdmol
def cap_unit(self, unit, n_neighbors=3):
indices = sorted(unit.atoms.indices)
capped = Chem.rdchem.RWMol()
n_indices = len(indices)
if not n_indices:
return capped
neighbor_ints = rdutils.get_neighbor_ints(self.rdmol, indices,
n_neighbors)
new_conf = Chem.rdchem.Conformer(n_indices + len(neighbor_ints))
conf = self.rdmol.GetConformer(0)
only_on_atoms = []
# add unit atoms
indices = list(map(int, indices))
for ix in indices:
at = self.rdmol.GetAtomWithIdx(ix)
new = capped.AddAtom(at)
new_conf.SetAtomPosition(new, list(conf.GetAtomPosition(ix)))
# add neighbor atoms with AltLoc "+"
for ix in neighbor_ints:
at = self.rdmol.GetAtomWithIdx(ix)
new = capped.AddAtom(at)
at = capped.GetAtomWithIdx(new)
old_info = at.GetPDBResidueInfo()
info = rdutils.copy_pdbinfo(old_info)
# info.SetAltLoc("+")
at.SetMonomerInfo(info)
at.SetNoImplicit(False)
new_conf.SetAtomPosition(new, list(conf.GetAtomPosition(ix)))
only_on_atoms.append(new)
# add bonds
all_ints = indices + neighbor_ints
# things RDKit complains about: np.uint, np.uint32, np.uintp, np.uintc
# capped_ints = np.arange(len(all_ints), dtype=np.uintc)
capped_ints = list(map(int, range(len(all_ints)))) # omg
for i, j in itertools.combinations(capped_ints, 2):
bond = self.rdmol.GetBondBetweenAtoms(all_ints[i], all_ints[j])
if bond is not None:
capped.AddBond(i, j, bond.GetBondType())
capped.AddConformer(new_conf)
# add Hs
Chem.SanitizeMol(
capped,
(Chem.SANITIZE_ALL ^ Chem.SANITIZE_SETAROMATICITY
^ Chem.SANITIZE_ADJUSTHS ^ Chem.SANITIZE_CLEANUPCHIRALITY
^ Chem.SANITIZE_KEKULIZE),
)
hcapped = Chem.AddHs(capped,
explicitOnly=False,
addCoords=True,
onlyOnAtoms=only_on_atoms)
# info_template = hcapped.GetAtomWithIdx(0).GetPDBResidueInfo()
# for i in range(capped_ints[-1], hcapped.GetNumAtoms()):
# at = hcapped.GetAtomWithIdx(i)
# new_info = rdutils.copy_pdbinfo(info_template)
# new_info.SetName("H")
# new_info.SetAltLoc("-")
# at.SetMonomerInfo(new_info)
# Chem.AssignStereochemistry(hcapped)
# Chem.SanitizeMol(hcapped)
# Chem.SanitizeMol(hcapped,
# (
# Chem.SANITIZE_ALL
# ^ Chem.SANITIZE_SETAROMATICITY
# ^ Chem.SANITIZE_ADJUSTHS
# ^ Chem.SANITIZE_CLEANUPCHIRALITY
# ^ Chem.SANITIZE_KEKULIZE
# ),)
Chem.AssignStereochemistryFrom3D(hcapped, 0)
return hcapped
def assign_stereochemistry(rdmol):
if rdmol.GetNumConformers():
Chem.AssignStereochemistryFrom3D(rdmol)
else:
Chem.AssignStereochemistry(rdmol, cleanIt=True)
