Package rdkit :: Package Chem :: Module TorsionFingerprints

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Module TorsionFingerprints

Torsion Fingerprints (Deviation) (TFD)
According to a paper from Schulz-Gasch et al., JCIM, 52, 1499-1512 (2012).

Functions

_doMatch(inv, atoms)
Helper function to check if all atoms in the list are the same

source code

_doNotMatch(inv, atoms)
Helper function to check if all atoms in the list are NOT the same

source code

_doMatchExcept1(inv, atoms)
Helper function to check if two atoms in the list are the same, and one not Note: Works only for three atoms

source code

_getAtomInvariantsWithRadius(mol, radius)
Helper function to calculate the atom invariants for each atom with a given radius

source code

_getHeavyAtomNeighbors(atom1, aid2=-1)
Helper function to calculate the number of heavy atom neighbors.

source code

_getIndexforTorsion(neighbors, inv)
Helper function to calculate the index of the reference atom for a given atom

source code

_getBondsForTorsions(mol, ignoreColinearBonds)
Determine the bonds (or pair of atoms treated like a bond) for which torsions should be calculated.

source code

CalculateTorsionLists(mol, maxDev='equal', symmRadius=2, ignoreColinearBonds=True)
Calculate a list of torsions for a given molecule.

source code

_getTorsionAtomPositions(atoms, conf)
Helper function to retrieve the coordinates of the four atoms in a torsion

source code

CalculateTorsionAngles(mol, tors_list, tors_list_rings, confId=-1)
Calculate the torsion angles for a list of non-ring and a list of ring torsions.

source code

_findCentralBond(mol, distmat)
Helper function to identify the atoms of the most central bond.

source code

_calculateBeta(mol, distmat, aid1)
Helper function to calculate the beta for torsion weights according to the formula in the paper.

source code

CalculateTorsionWeights(mol, aid1=-1, aid2=-1, ignoreColinearBonds=True)
Calculate the weights for the torsions in a molecule.

source code

CalculateTFD(torsions1, torsions2, weights=None)
Calculate the torsion deviation fingerprint (TFD) given two lists of torsion angles.

source code

_getSameAtomOrder(mol1, mol2)
Generate a new molecule with the atom order of mol1 and coordinates from mol2.

source code

GetTFDBetweenConformers(mol, confIds1, confIds2, useWeights=True, maxDev='equal', symmRadius=2, ignoreColinearBonds=True)
Wrapper to calculate the TFD between two list of conformers of a molecule

source code

GetTFDBetweenMolecules(mol1, mol2, confId1=-1, confId2=-1, useWeights=True, maxDev='equal', symmRadius=2, ignoreColinearBonds=True)
Wrapper to calculate the TFD between two molecules.

source code

GetTFDMatrix(mol, useWeights=True, maxDev='equal', symmRadius=2, ignoreColinearBonds=True)
Wrapper to calculate the matrix of TFD values for the conformers of a molecule.

source code

Imports: rdBase, RDConfig, Geometry, Chem, rdchem, rdMolDescriptors, math, os

Function Details

_doMatch(inv, atoms)

Helper function to check if all atoms in the list are the same

Arguments:
- inv:    atom invariants (used to define equivalence of atoms)
- atoms:  list of atoms to check

Return: boolean

_doNotMatch(inv, atoms)

Helper function to check if all atoms in the list are NOT the same

Arguments:
- inv:    atom invariants (used to define equivalence of atoms)
- atoms:  list of atoms to check

Return: boolean

_doMatchExcept1(inv, atoms)

Helper function to check if two atoms in the list are the same, 
and one not
Note: Works only for three atoms

Arguments:
- inv:    atom invariants (used to define equivalence of atoms)
- atoms:  list of atoms to check

Return: atom that is different

_getAtomInvariantsWithRadius(mol, radius)

Helper function to calculate the atom invariants for each atom 
with a given radius

Arguments:
- mol:    the molecule of interest
- radius: the radius for the Morgan fingerprint

Return: list of atom invariants

_getHeavyAtomNeighbors(atom1, aid2=-1)

Helper function to calculate the number of heavy atom neighbors.

Arguments:
- atom1:    the atom of interest
- aid2:     atom index that should be excluded from neighbors (default: none)

Return: a list of heavy atom neighbors of the given atom

_getIndexforTorsion(neighbors, inv)

Helper function to calculate the index of the reference atom for 
a given atom

Arguments:
- neighbors:  list of the neighbors of the atom
- inv:        atom invariants

Return: list of atom indices as reference for torsion

_getBondsForTorsions(mol, ignoreColinearBonds)

Determine the bonds (or pair of atoms treated like a bond) for which
torsions should be calculated.

Arguments:
- refmol: the molecule of interest
- ignoreColinearBonds: if True (default), single bonds adjacent to
                       triple bonds are ignored
                       if False, alternative not-covalently bound
                       atoms are used to define the torsion

CalculateTorsionLists(mol, maxDev='equal', symmRadius=2, ignoreColinearBonds=True)

Calculate a list of torsions for a given molecule. For each torsion
the four atom indices are determined and stored in a set.

Arguments:
- mol:      the molecule of interest
- maxDev:   maximal deviation used for normalization
            'equal': all torsions are normalized using 180.0 (default)
            'spec':  each torsion is normalized using its specific
                     maximal deviation as given in the paper
- symmRadius: radius used for calculating the atom invariants
              (default: 2)
- ignoreColinearBonds: if True (default), single bonds adjacent to
                       triple bonds are ignored
                       if False, alternative not-covalently bound
                       atoms are used to define the torsion

Return: two lists of torsions: non-ring and ring torsions

_getTorsionAtomPositions(atoms, conf)

Helper function to retrieve the coordinates of the four atoms
in a torsion

Arguments:
- atoms:   list with the four atoms
- conf:    conformation of the molecule

Return: Point3D objects of the four atoms

CalculateTorsionAngles(mol, tors_list, tors_list_rings, confId=-1)

Calculate the torsion angles for a list of non-ring and 
a list of ring torsions.

Arguments:
- mol:       the molecule of interest
- tors_list: list of non-ring torsions
- tors_list_rings: list of ring torsions
- confId:    index of the conformation (default: first conformer)

Return: list of torsion angles

_findCentralBond(mol, distmat)

Helper function to identify the atoms of the most central bond.

Arguments:
- mol:     the molecule of interest
- distmat: distance matrix of the molecule

Return: atom indices of the two most central atoms (in order)

_calculateBeta(mol, distmat, aid1)

Helper function to calculate the beta for torsion weights
according to the formula in the paper.
w(dmax/2) = 0.1

Arguments:
- mol:     the molecule of interest
- distmat: distance matrix of the molecule
- aid1:    atom index of the most central atom

Return: value of beta (float)

CalculateTorsionWeights(mol, aid1=-1, aid2=-1, ignoreColinearBonds=True)

Calculate the weights for the torsions in a molecule.
By default, the highest weight is given to the bond 
connecting the two most central atoms.
If desired, two alternate atoms can be specified (must 
be connected by a bond).

Arguments:
- mol:   the molecule of interest
- aid1:  index of the first atom (default: most central)
- aid2:  index of the second atom (default: second most central)
- ignoreColinearBonds: if True (default), single bonds adjacent to
                       triple bonds are ignored
                       if False, alternative not-covalently bound
                       atoms are used to define the torsion

Return: list of torsion weights (both non-ring and ring)

CalculateTFD(torsions1, torsions2, weights=None)

Calculate the torsion deviation fingerprint (TFD) given two lists of
torsion angles.

Arguments:
- torsions1:  torsion angles of conformation 1
- torsions2:  torsion angles of conformation 2
- weights:    list of torsion weights (default: None)

Return: TFD value (float)

_getSameAtomOrder(mol1, mol2)

Generate a new molecule with the atom order of mol1 and coordinates
from mol2.

Arguments:
- mol1:     first instance of the molecule of interest
- mol2:     second instance the molecule of interest

Return: RDKit molecule

GetTFDBetweenConformers(mol, confIds1, confIds2, useWeights=True, maxDev='equal', symmRadius=2, ignoreColinearBonds=True)

Wrapper to calculate the TFD between two list of conformers 
of a molecule

Arguments:
- mol:      the molecule of interest
- confIds1:  first list of conformer indices
- confIds2:  second list of conformer indices
- useWeights: flag for using torsion weights in the TFD calculation
- maxDev:   maximal deviation used for normalization
            'equal': all torsions are normalized using 180.0 (default)
            'spec':  each torsion is normalized using its specific
                     maximal deviation as given in the paper
- symmRadius: radius used for calculating the atom invariants
              (default: 2)
- ignoreColinearBonds: if True (default), single bonds adjacent to
                       triple bonds are ignored
                       if False, alternative not-covalently bound
                       atoms are used to define the torsion

Return: list of TFD values

GetTFDBetweenMolecules(mol1, mol2, confId1=-1, confId2=-1, useWeights=True, maxDev='equal', symmRadius=2, ignoreColinearBonds=True)

Wrapper to calculate the TFD between two molecules.
Important: The two molecules must be instances of the same molecule

Arguments:
- mol1:     first instance of the molecule of interest
- mol2:     second instance the molecule of interest
- confId1:  conformer index for mol1 (default: first conformer)
- confId2:  conformer index for mol2 (default: first conformer)
- useWeights: flag for using torsion weights in the TFD calculation
- maxDev:   maximal deviation used for normalization
            'equal': all torsions are normalized using 180.0 (default)
            'spec':  each torsion is normalized using its specific
                     maximal deviation as given in the paper
- symmRadius: radius used for calculating the atom invariants
              (default: 2)
- ignoreColinearBonds: if True (default), single bonds adjacent to
                       triple bonds are ignored
                       if False, alternative not-covalently bound
                       atoms are used to define the torsion

Return: TFD value

GetTFDMatrix(mol, useWeights=True, maxDev='equal', symmRadius=2, ignoreColinearBonds=True)

Wrapper to calculate the matrix of TFD values for the
conformers of a molecule.

Arguments:
- mol:      the molecule of interest
- useWeights: flag for using torsion weights in the TFD calculation
- maxDev:   maximal deviation used for normalization
            'equal': all torsions are normalized using 180.0 (default)
            'spec':  each torsion is normalized using its specific
                     maximal deviation as given in the paper
- symmRadius: radius used for calculating the atom invariants
              (default: 2)
- ignoreColinearBonds: if True (default), single bonds adjacent to
                       triple bonds are ignored
                       if False, alternative not-covalently bound
                       atoms are used to define the torsion

Return: matrix of TFD values
Note that the returned matrix is symmetrical, i.e. it is the
lower half of the matrix, e.g. for 5 conformers:
matrix = [ a,
           b, c,
           d, e, f,
           g, h, i, j]