rdkit.Chem.TorsionFingerprints module¶
Torsion Fingerprints (Deviation) (TFD) According to a paper from Schulz-Gasch et al., JCIM, 52, 1499-1512 (2012).
- rdkit.Chem.TorsionFingerprints.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)
- rdkit.Chem.TorsionFingerprints.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
- rdkit.Chem.TorsionFingerprints.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
- rdkit.Chem.TorsionFingerprints.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)
- rdkit.Chem.TorsionFingerprints.GetBestTFDBetweenMolecules(mol1, mol2, confId1=-1, useWeights=True, maxDev='equal', symmRadius=2, ignoreColinearBonds=True)¶
Wrapper to calculate the best TFD between a single conformer of mol1 and all the conformers of mol2 Important: The two molecules must be isomorphic
Arguments: - mol1: first instance of the molecule of interest - mol2: second instance the molecule of interest - confId1: conformer index for mol1 (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
- rdkit.Chem.TorsionFingerprints.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
- rdkit.Chem.TorsionFingerprints.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 isomorphic
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
- rdkit.Chem.TorsionFingerprints.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]
