MolecularDiffusion.utils.shepherd_score.pharm_utils.pharmvec

Generate the vector features for pharmacophores from a rdkit conformer.

Adapted from rdkit:

https://github.com/rdkit/rdkit/blob/master/rdkit/Chem/Features/FeatDirUtilsRD.py https://github.com/rdkit/rdkit/blob/master/rdkit/Chem/Features/ShowFeats.py

Changed to return anchor position and relative unit vector.

Functions

GetAcceptor1FeatVects(conf, featAtoms[, scale])

Get the direction vectors for Acceptor of type 1 (multi-vector representation).

GetAcceptor1FeatVects_single(conf, featAtoms[, scale])

Get the direction vectors for Acceptor of type 1 (single vector representation).

GetAcceptor2FeatVects(conf, featAtoms[, scale])

Get the direction vectors for Acceptor of type 2.

GetAcceptor2FeatVects_single(conf, featAtoms[, scale])

Get the direction vectors for Acceptor of type 2.

GetAcceptor3FeatVects(conf, featAtoms[, scale])

Get the direction vectors for Donor of type 3.

GetAcceptor3FeatVects_single(conf, featAtoms[, scale])

Get the direction vectors for Donor of type 3.

GetAcceptorFeatVects(conf, featAtoms[, scale])

Get the anchor positions and relative unit vectors of an acceptor atom.

GetAromaticFeatVects(conf, featAtoms, featLoc[, ...])

Compute the direction vector for an aromatic feature

GetDonor1FeatVects_single(conf, featAtoms[, scale])

Get the direction vectors for Donor of type 1.

GetDonor2FeatVects_single(conf, featAtoms[, scale])

Get the direction vectors for Donor of type 2.

GetDonor3FeatVects_single(conf, featAtoms[, scale])

Get the direction vectors for Donor of type 3.

GetDonorFeatVects(conf, featAtoms[, scale, exclude])

Get vectors for hydrogen bond donors in the direction of the hydrogens.

GetHalogenFeatVects(conf, featAtoms[, scale])

Get the anchor positions and relative unit vectors of a halogen atom.

Module Contents

MolecularDiffusion.utils.shepherd_score.pharm_utils.pharmvec.GetAcceptor1FeatVects(conf, featAtoms, scale=1.0)

Get the direction vectors for Acceptor of type 1 (multi-vector representation).

This is an acceptor with one heavy atom neighbor. There are two possibilities:

  • The bond to the heavy atom is a single bond (e.g. CO): We use the inversion of this bond direction and mark it as a ‘cone’.

  • The bond to the heavy atom is a double bond (e.g. C=O): We have two possible directions except in some special cases (e.g. SO2) where we use bond direction.

Notes

Modified to change return format, with fixes for methanamine and two vectors for hydroxyls.

Parameters:

  • conf (Chem.Mol) – RDKit Mol object with a conformer.

  • featAtoms (list) – List containing RDKit Atom object of atom attributed as an acceptor.

  • scale (float, optional) – Length of direction vector. Default is 1.0.

Returns:

(list of anchor position(s) as RDKit Point3D or None, list of relative unit vector(s) as RDKit Point3D or None)

Return type:

tuple

MolecularDiffusion.utils.shepherd_score.pharm_utils.pharmvec.GetAcceptor1FeatVects_single(conf, featAtoms, scale=1.0)

Get the direction vectors for Acceptor of type 1 (single vector representation).

This is an acceptor with one heavy atom neighbor. There are two possibilities:

  • The bond to the heavy atom is a single bond (e.g. CO): We use the inversion of this bond direction and mark it as a ‘cone’.

  • The bond to the heavy atom is a double bond (e.g. C=O): We have two possible directions except in some special cases (e.g. SO2) where we use bond direction.

Notes

Modified to condition on the number of hydrogens with methanamine fix:

  • Case 1: If one hydrogen, vector points in the opposite direction of the bisection of the acute angle formed by the heavy-acceptor-hydrogen. If two hydrogens, assume sp3 and project in that lone-pair direction. If not tetrahedral, return None.

  • Case 2: Return the bisecting vector of the two lone-pairs.

Parameters:

  • conf (Chem.Mol) – RDKit Mol object with conformer.

  • featAtoms (list) – List of atoms that are part of the feature.

  • scale (float, optional) – Length of the direction vector. Default is 1.0.

Returns:

(anchor position as RDKit Point3D or None, relative unit vector(s) as RDKit Point3D or None)

Return type:

tuple

MolecularDiffusion.utils.shepherd_score.pharm_utils.pharmvec.GetAcceptor2FeatVects(conf, featAtoms, scale=1.0)

Get the direction vectors for Acceptor of type 2. Made to generate a single vector representation.

This is the acceptor with two adjacent heavy atoms. We will special case a few things here. If the acceptor atom is an oxygen we will assume a sp3 hybridization the acceptor directions (two of them) reflect that configurations. Otherwise the direction vector in plane with the neighboring heavy atoms

Changed: return format

Parameters:

  • conf (rdkit Mol object with a conformer.)

  • featAtoms (list containing rdkit Atom object of atom attributed as an acceptor.)

  • scale (float (default = 1.) length of direction vector.)

Returns:

list of anchor position(s) as rdkit Point3D or None list of relative unit vector(s) as rdkit Point3D or None

Return type:

Tuple

MolecularDiffusion.utils.shepherd_score.pharm_utils.pharmvec.GetAcceptor2FeatVects_single(conf, featAtoms, scale=1.0)

Get the direction vectors for Acceptor of type 2. Made to generate a single vector representation.

This is the acceptor with two adjacent heavy atoms. We will special case a few things here. If the acceptor atom is an oxygen we will assume a sp3 hybridization the acceptor directions (two of them) reflect that configurations. Otherwise the direction vector in plane with the neighboring heavy atoms

Changed: Only generate one vector Rather than generating 2 vectors for sp3 oxygen, just keep the average vector.

Parameters:

  • conf (rdkit Mol object with conformer)

  • featAtoms (list of atoms that are part of the feature)

  • scale (float for length of the direction vector (default = 1.0))

Returns:

anchor position as rdkit Point3D or None relative unit vector(s) as rdkit Point3D or None

Return type:

Tuple

MolecularDiffusion.utils.shepherd_score.pharm_utils.pharmvec.GetAcceptor3FeatVects(conf, featAtoms, scale=1.0)

Get the direction vectors for Donor of type 3. Made to generate a single vector representation.

This is a donor with three heavy atoms as neighbors. We will assume a tetrahedral arrangement of these neighbors. So the direction we are seeking is the last fourth arm of the sp3 arrangement

Changed: return format

Parameters:

  • conf (rdkit Mol object with a conformer.)

  • featAtoms (list containing rdkit Atom object of atom attributed as an acceptor.)

  • scale (float (default = 1.) length of direction vector.)

Returns:

list of anchor position(s) as rdkit Point3D or None list of relative unit vector(s) as rdkit Point3D or None

Return type:

Tuple

MolecularDiffusion.utils.shepherd_score.pharm_utils.pharmvec.GetAcceptor3FeatVects_single(conf, featAtoms, scale=1.0)

Get the direction vectors for Donor of type 3. Made to generate a single vector representation.

This is a donor with three heavy atoms as neighbors. We will assume a tetrahedral arrangement of these neighbors. So the direction we are seeking is the last fourth arm of the sp3 arrangement

Changed: to return anchor and relative unit vector tuple

Parameters:

  • conf (rdkit Mol object with conformer)

  • featAtoms (list of atoms that are part of the feature)

  • scale (float for length of the direction vector (default = 1.0))

Returns:

anchor position as rdkit Point3D or None relative unit vector(s) as rdkit Point3D or None

Return type:

Tuple

MolecularDiffusion.utils.shepherd_score.pharm_utils.pharmvec.GetAcceptorFeatVects(conf: rdkit.Chem.rdchem.Mol, featAtoms: rdkit.Chem.rdchem.Atom, scale: float = 1.0)

Get the anchor positions and relative unit vectors of an acceptor atom.

Assumes HBA’s are only O and N as defined by smarts_features.fdef. If HBA is not one of those, then it assumes the atom has one lone pair.

Parameters:

  • conf (Chem.Mol) – RDKit Mol object with a conformer.

  • featAtoms (list) – List containing RDKit Atom object of atom attributed as an acceptor.

  • scale (float, optional) – Length of direction vector. Default is 1.0.

Returns:

(list of anchor position(s) as RDKit Point3D or [None], list of relative unit vector(s) as RDKit Point3D or [None])

Return type:

tuple

MolecularDiffusion.utils.shepherd_score.pharm_utils.pharmvec.GetAromaticFeatVects(conf, featAtoms, featLoc, return_both: bool = False, scale=1.0)

Compute the direction vector for an aromatic feature

Changed: only return one vector, process later for visualization and scoring

Parameters:

  • conf (a conformer)

  • featAtoms (list of atom IDs that make up the feature)

  • featLoc (location of the aromatic feature specified as point3d)

  • return_both (bool for whether to return both vectors or just one.)

  • scale (the size of the direction vector)

Returns:

list of anchor position(s) as rdkit Point3D list of relative unit vector(s) as rdkit Point3D

Return type:

Tuple

MolecularDiffusion.utils.shepherd_score.pharm_utils.pharmvec.GetDonor1FeatVects_single(conf, featAtoms, scale=1.0)

Get the direction vectors for Donor of type 1. Made to generate a single vector representation.

This is a donor with one heavy atom. It is not clear where we should we should be putting the direction vector for this. It should probably be a cone. In this case we will just use the direction vector from the donor atom to the heavy atom.

Changed: conditioning based on the number of hydrogens 1. If 1 hydrogen, vector should point in the direction of the hydrogen. 2. If 2 hydrogens, vector should point in a bisecting direction of the two hydrogens. 3. If 3 hydrogens, point in the direction of the bond.

Parameters:

  • conformer (conf - rdkit Mol object with)

  • feature (featAtoms - list of atoms that are part of the)

  • 1.0) (scale - float for length of the direction vector (default =)

Returns:

anchor position as rdkit Point3D or None relative unit vector(s) as rdkit Point3D or None list of hydrogen rdkit Atom objects

Return type:

Tuple

MolecularDiffusion.utils.shepherd_score.pharm_utils.pharmvec.GetDonor2FeatVects_single(conf, featAtoms, scale=1.0)

Get the direction vectors for Donor of type 2. Made to generate a single vector representation.

This is a donor with two heavy atoms as neighbors. The atom may are may not have hydrogen on it. Here are the situations with the neighbors that will be considered here 1. two heavy atoms and two hydrogens: we will assume a sp3 arrangement here 2. two heavy atoms and one hydrogen: this can either be sp2 or sp3 3. two heavy atoms and no hydrogens

Changed: conditioning based on the number of hydrogens 1. For case 1, point in the direction bisecting the two hydrogens. 2. For case 2, point in the direction of the hydrogen. 3. For case 3, no changes.

Parameters:

  • conf (rdkit Mol object with conformer)

  • featAtoms (list of atoms that are part of the feature)

  • scale (float for length of the direction vector (default = 1.0))

Returns:

anchor position as rdkit Point3D or None relative unit vector(s) as rdkit Point3D or None list of hydrogen rdkit Atom objects

Return type:

Tuple

MolecularDiffusion.utils.shepherd_score.pharm_utils.pharmvec.GetDonor3FeatVects_single(conf, featAtoms, scale=1.0)

Get the direction vectors for Donor of type 3. Made to generate a single vector representation.

This is a donor with three heavy atoms as neighbors. We will assume a tetrahedral arrangement of these neighbors. So the direction we are seeking is the last fourth arm of the sp3 arrangement

Changed: Return anchor and relative unit vector tuple

Parameters:

  • conf (rdkit Mol object with conformer)

  • featAtoms (list of atoms that are part of the feature)

  • scale (float for length of the direction vector (default = 1.0))

Returns:

anchor position as rdkit Point3D or None relative unit vector(s) as rdkit Point3D or None list of hydrogen rdkit Atom objects

Return type:

Tuple

MolecularDiffusion.utils.shepherd_score.pharm_utils.pharmvec.GetDonorFeatVects(conf, featAtoms, scale=1.0, exclude=[])

Get vectors for hydrogen bond donors in the direction of the hydrogens.

Parameters:

  • conf (rdkit Mol object with a conformer.)

  • featAtoms (list containing rdkit Atom object of atom attributed as a donor.)

  • scale (float (default = 1.) length of direction vector.)

  • exclude (list of atom indices that should not be included as a donatable H.)

Returns:

list of anchor position(s) as rdkit Point3D or None list of relative unit vector(s) as rdkit Point3D or None list of neighboring hydrogens or None

Return type:

Tuple

MolecularDiffusion.utils.shepherd_score.pharm_utils.pharmvec.GetHalogenFeatVects(conf: rdkit.Chem.rdchem.Mol, featAtoms: rdkit.Chem.rdchem.Atom, scale: float = 1.0)

Get the anchor positions and relative unit vectors of a halogen atom. Assumes only one connection.

Parameters:

  • conf (rdkit Mol object with a conformer.)

  • featAtoms (list containing rdkit Atom object of atom attributed as an acceptor.)

  • scale (float (default = 1.) length of direction vector.)

Returns:

list of anchor position(s) as rdkit Point3D or [None] list of relative unit vector(s) as rdkit Point3D or [None]

Return type:

Tuple