rdkit.Chem.Features.FeatDirUtilsRD module

rdkit.Chem.Features.FeatDirUtilsRD.ArbAxisRotation(theta, ax, pt)
rdkit.Chem.Features.FeatDirUtilsRD.GetAcceptor1FeatVects(conf, featAtoms, scale=1.5)

Get the direction vectors for Acceptor of type 1

This is a acceptor with one heavy atom neighbor. There are two possibilities we will consider here 1. The bond to the heavy atom is a single bond e.g. CO

In this case we don’t know the exact direction and we just use the inversion of this bond direction and mark this direction as a ‘cone’

  1. The bond to the heavy atom is a double bond e.g. C=O In this case the we have two possible direction except in some special cases e.g. SO2 where again we will use bond direction

Parameters:

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

  • vector (scale - length of the direction) –

rdkit.Chem.Features.FeatDirUtilsRD.GetAcceptor2FeatVects(conf, featAtoms, scale=1.5)

Get the direction vectors for Acceptor of type 2

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

Parameters:

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

  • vector (scale - length of the direction) –

rdkit.Chem.Features.FeatDirUtilsRD.GetAcceptor3FeatVects(conf, featAtoms, scale=1.5)

Get the direction vectors for Donor of type 3

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

Parameters:

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

  • vector (scale - length of the direction) –

rdkit.Chem.Features.FeatDirUtilsRD.GetAromaticFeatVects(conf, featAtoms, featLoc, scale=1.5)

Compute the direction vector for an aromatic feature

Parameters:

  • conformer (conf - a) –

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

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

  • vector (scale - the size of the direction) –

rdkit.Chem.Features.FeatDirUtilsRD.GetDonor1FeatVects(conf, featAtoms, scale=1.5)

Get the direction vectors for Donor of type 1

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

Parameters:

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

  • vector (scale - length of the direction) –

rdkit.Chem.Features.FeatDirUtilsRD.GetDonor2FeatVects(conf, featAtoms, scale=1.5)

Get the direction vectors for Donor of type 2

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

Parameters:

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

  • vector (scale - length of the direction) –

rdkit.Chem.Features.FeatDirUtilsRD.GetDonor3FeatVects(conf, featAtoms, scale=1.5)

Get the direction vectors for Donor of type 3

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

Parameters:

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

  • vector (scale - length of the direction) –

rdkit.Chem.Features.FeatDirUtilsRD.cross(v1, v2)
rdkit.Chem.Features.FeatDirUtilsRD.findNeighbors(atomId, adjMat)

Find the IDs of the neighboring atom IDs

ARGUMENTS: atomId - atom of interest adjMat - adjacency matrix for the compound