rdkit.Chem.Features.FeatDirUtilsRD module — The RDKit 2016.09.1 documentation

# 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’

  2. 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
  ARGUMENTS:
    featAtoms - list of atoms that are part of the feature scale - length of the direction vector

`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

  ARGUMENTS:
    featAtoms - list of atoms that are part of the feature scale - length of the direction vector

`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 arrangment

  ARGUMENTS:
    featAtoms - list of atoms that are part of the feature scale - length of the direction vector

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

  Compute the direction vector for an aromatic feature

  ARGUMENTS:
    conf - a conformer featAtoms - list of atom IDs that make up the feature featLoc - location of the aromatic feature specified as point3d scale - the size of the direction vector

`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

  ARGUMENTS:

  > featAtoms - list of atoms that are part of the feature scale - length of the direction vector

`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

  ARGUMENTS:
    featAtoms - list of atoms that are part of the feature scale - length of the direction vector

`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 arrangment

  ARGUMENTS:
    featAtoms - list of atoms that are part of the feature scale - length of the direction vector

`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