RDKit interface¶

RDKit is a collection of cheminformatics and machine-learning software written in C++ and Python. PLAMS interface to RDKit originates from QMFlows project and features functions for generating PLAMS molecules from string representations (SMARTS, SMILES) as well as a handful of tools for dealing with proteins and PDB files.

from_rdmol(rdkit_mol, confid=-1, properties=True)[source]¶

Translate an RDKit molecule into a PLAMS molecule type. RDKit properties will be unpickled if their name ends with ‘_pickled’.

Parameters:	rdkit_mol (rdkit.Chem.Mol) – RDKit molecule confid (int) – conformer identifier from which to take coordinates properties (bool) – If all Chem.Mol, Chem.Atom and Chem.Bond properties should be converted from RDKit to PLAMS format.
Returns:	a PLAMS molecule
Return type:	Molecule

to_rdmol(plams_mol, sanitize=True, properties=True, assignChirality=False)[source]¶

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’.

Parameters:	plams_mol (Molecule) – A PLAMS molecule sanitize (bool) – Kekulize, check valencies, set aromaticity, conjugation and hybridization properties (bool) – If all Molecule, Atom and Bond properties should be converted from PLAMS to RDKit format. assignChirality (bool) – Assign R/S and cis/trans information, insofar as this was not yet present in the PLAMS molecule.
Returns:	an RDKit molecule
Return type:	rdkit.Chem.Mol

from_smiles(smiles, nconfs=1, name=None, forcefield=None, rms=0.1)[source]¶

Generates PLAMS molecule(s) from a smiles strings.

Parameters:	smiles (str) – A smiles string nconfs (int) – Number of conformers to be generated name (str) – A name for the molecule forcefield (str) – Choose ‘uff’ or ‘mmff’ forcefield for geometry optimization and ranking of comformations. The default value None results in skipping of the geometry optimization step. rms (float) – Root Mean Square deviation threshold for removing similar/equivalent conformations
Returns:	A molecule with hydrogens and 3D coordinates or a list of molecules if nconfs > 1
Return type:	Molecule or list of PLAMS Molecules

from_smarts(smarts, nconfs=1, name=None, forcefield=None, rms=0.1)[source]¶

Generates PLAMS molecule(s) from a smarts strings. This allows for example to define hydrogens explicitly. However it is less suitable for aromatic molecules (use from_smiles in that case).

Parameters:	smarts (str) – A smarts string nconfs (int) – Number of conformers to be generated name (str) – A name for the molecule forcefield (str) – Choose ‘uff’ or ‘mmff’ forcefield for geometry optimization and ranking of comformations. The default value None results in skipping of the geometry optimization step. rms (float) – Root Mean Square deviation threshold for removing similar/equivalent conformations.
Returns:	A molecule with hydrogens and 3D coordinates or a list of molecules if nconfs > 1
Return type:	Molecule or list of PLAMS Molecules

get_conformations(mol, nconfs=1, name=None, forcefield=None, rms=-1, enforceChirality=False)[source]¶

Generates 3D conformation(s) for an rdkit_mol or a PLAMS Molecule

Parameters:	mol (rdkit.Chem.Mol or Molecule) – RDKit or PLAMS Molecule nconfs (int) – Number of conformers to be generated name (str) – A name for the molecule forcefield (str) – Choose ‘uff’ or ‘mmff’ forcefield for geometry optimization and ranking of comformations. The default value None results in skipping of the geometry optimization step rms (float) – Root Mean Square deviation threshold for removing similar/equivalent conformations. enforceChirality (bool) – Enforce the correct chirality if chiral centers are present
Returns:	A molecule with hydrogens and 3D coordinates or a list of molecules if nconfs > 1
Return type:	Molecule or list of PLAMS Molecules

from_sequence(sequence, nconfs=1, name=None, forcefield=None, rms=0.1)[source]¶

Generates PLAMS molecule from a peptide sequence. Includes explicit hydrogens and 3D coordinates.

Parameters:	sequence (str) – A peptide sequence, e.g. ‘HAG’ nconfs (int) – Number of conformers to be generated name (str) – A name for the molecule forcefield (str) – Choose ‘uff’ or ‘mmff’ forcefield for geometry optimization and ranking of comformations. The default value None results in skipping of the geometry optimization step. rms (float) – Root Mean Square deviation threshold for removing similar/equivalent conformations.
Returns:	A peptide molecule with hydrogens and 3D coordinates or a list of molecules if nconfs > 1
Return type:	Molecule or list of PLAMS Molecules

modify_atom(mol, idx, element)[source]¶

Change atom “idx” in molecule “mol” to “element” and add or remove hydrogens accordingly

Parameters:	mol (Molecule or rdkit.Chem.Mol) – molecule to be modified idx (int) – index of the atom to be modified element (str) –
Returns:	Molecule with new element and possibly added or removed hydrogens
Return type:	Molecule

apply_template(mol, template)[source]¶

Modifies bond orders in PLAMS molecule according template smiles structure.

Parameters:	mol (Molecule or rdkit.Chem.Mol) – molecule to be modified template (str) – smiles string defining the correct chemical structure
Returns:	Molecule with correct chemical structure and provided 3D coordinates
Return type:	Molecule

apply_reaction_smarts(mol, reaction_smarts, complete=False, forcefield=None, return_rdmol=False)[source]¶

Applies reaction smirks and returns product. If returned as a PLAMS molecule, thismolecule.properties.orig_atoms is a list of indices of atoms that have not been changed (which can for example be used partially optimize new atoms only with the freeze keyword)

Parameters:	mol (Molecule or rdkit.Chem.Mol) – molecule to be modified reactions_smarts (str) – Reactions smarts to be applied to molecule complete (bool or float (value between 0 and 1)) – Apply reaction until no further changes occur or given fraction of reaction centers have been modified forcefield (str) – Specify ‘uff’ or ‘mmff’ to apply forcefield based geometry optimization of product structures. return_rdmol (bool) – return a RDKit molecule if true, otherwise a PLAMS molecule
Returns:	(product molecule, list of unchanged atoms)
Return type:	(Molecule, list of int)

readpdb(pdb_file, removeHs=False, proximityBonding=False, return_rdmol=False)[source]¶

Generate a molecule from a PDB file

Parameters:	pdb_file (path- or file-like) – The PDB file to read removeHs (bool) – Hydrogens are removed if True proximityBonding (bool) – Enables automatic proximity bonding return_rdmol (bool) – return a RDKit molecule if true, otherwise a PLAMS molecule
Returns:	The molecule
Return type:	Molecule or rdkit.Chem.Mol

writepdb(mol, pdb_file=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='UTF-8'>)[source]¶

Write a PDB file from a molecule

Parameters:	mol (Molecule or rdkit.Chem.Mol) – molecule to be exported to PDB pdb_file (path- or file-like) – The PDB file to write to, or a filename

add_Hs(mol, forcefield=None, return_rdmol=False)[source]¶

Add hydrogens to protein molecules read from PDB. Makes sure that the hydrogens get the correct PDBResidue info.

Parameters:	mol (Molecule or rdkit.Chem.Mol) – Molecule to be protonated forcefield (str) – Specify ‘uff’ or ‘mmff’ to apply forcefield based geometry optimization on new atoms. return_rdmol (bool) – return a RDKit molecule if true, otherwise a PLAMS molecule
Returns:	A molecule with explicit hydrogens added
Return type:	Molecule or rdkit.Chem.Mol

partition_protein(mol, residue_bonds=None, split_heteroatoms=True, return_rdmol=False)[source]¶

Splits a protein molecule into capped amino acid fragments and caps.

Parameters:	mol (Molecule or rdkit.Chem.Mol) – A protein molecule residue_bonds (tuple) – a tuple of pairs of residue number indicating which peptide bonds to split. If none, split all peptide bonds. split_heteroatoms (bool) – if True, all bonds between a heteroatom and a non-heteroatom across residues are removed
Returns:	list of fragments, list of caps

get_backbone_atoms(mol)[source]¶

Return a list of atom indices corresponding to the backbone atoms in a peptide molecule. This function assumes PDB information in properties.pdb_info of each atom, which is the case if the molecule is generated with the “readpdb” or “from_sequence” functions.

Parameters:	mol (Molecule or rdkit.Chem.Mol) – a peptide molecule
Returns:	a list of atom indices
Return type:	list

get_substructure(mol, func_list)[source]¶

Search for functional groups within a molecule based on a list of reference functional groups. SMILES strings, PLAMS and/or RDKit molecules can be used interchangeably in “func_list”.

Example:

>>> mol = from_smiles('OCCO')  # Ethylene glycol
>>> func_list = ['[H]O', 'C[N+]', 'O=PO']
>>> get_substructure(mol, func_list)

{'[H]O': [(<scm.plams.mol.atom.Atom at 0x125183518>,
           <scm.plams.mol.atom.Atom at 0x1251836a0>),
          (<scm.plams.mol.atom.Atom at 0x125183550>,
           <scm.plams.mol.atom.Atom at 0x125183240>)]}

Parameters:	mol (Molecule) – A PLAMS molecule. func_list (list) – A list of functional groups. Functional groups can be represented by SMILES strings, PLAMS and/or RDKit molecules.
Returns:	A dictionary with functional groups from “func_list” as keys and a list of n-tuples with matching PLAMS Atom as values.

yield_coords(rdmol, id=-1)[source]¶

Take an rdkit molecule and yield its coordinates as 3-tuples.

>>> from scm.plams import yield_coords
>>> from rdkit import Chem

>>> rdmol = Chem.Mol(...)  # e.g. Methane
>>> for xyz in yield_coords(rdmol):
...     print(xyz)
(-0.0, -0.0, -0.0)
(0.6405, 0.6405, -0.6405)
(0.6405, -0.6405, 0.6405)
(-0.6405, 0.6405, 0.6405)
(-0.6405, -0.6405, -0.6405)

The iterator produced by this function can, for example, be passed to Molecule.from_array() the update the coordinates of a PLAMS Molecule in-place.

>>> from scm.plams import Molecule

>>> mol = Molecule(...)

>>> xyz_iterator = yield_coords(rdmol)
>>> mol.from_array(xyz_iterator)

Parameters:	rdmol (rdkit.Chem.Mol) – An RDKit mol. id (int) – The ID of the desired conformer.
Returns:	An iterator yielding 3-tuples with rdmol’s Cartesian coordinates.
Return type:	iterator