gt4sd.properties.molecules.functions module

Summary

Functions:

activity_against_target	Calculate the activity of a molecule against a target molecule.
bertz	Calculate Bertz index of a molecule.
esol	Estimate the water solubility of a molecule.
is_scaffold	Whether a molecule is identical to its Murcko Scaffold.
lipinski	Calculate whether a molecule adheres to the Lipinski-rule-of-5.
logp	Calculates the partition coefficient of a molecule.
molecular_weight	Calculate molecular weight of a molecule.
number_of_aromatic_rings	Calculate number of aromatic rings of a molecule.
number_of_atoms	Calculate number of atoms of a molecule.
number_of_h_acceptors	Calculate number of H acceptors of a molecule.
number_of_h_donors	Calculate number of H donors of a molecule.
number_of_heterocycles	The amount of heterocycles of a molecule.
number_of_large_rings	Calculate the amount of large rings (> 6 atoms) of a molecule.
number_of_rings	Calculate number of rings of a molecule.
number_of_rotatable_bonds	Calculate number of rotatable bonds of a molecule.
number_of_stereocenters	The amount of stereo centers of a molecule.
plogp	Calculate the penalized logP of a molecule.
qed	Calculate the quantitative estimate of drug-likeness (QED) of a molecule.
sas	Calculate the synthetic accessibility score (SAS) for a molecule.
scscore	Calculate the synthetic complexity score (SCScore) of a molecule.
similarity_to_seed	Calculate the similarity of a molecule to a seed molecule.
tpsa	Calculate the total polar surface area of a molecule.

Reference

plogp(mol)

Calculate the penalized logP of a molecule. This is the logP minus the number of rings with > 6 atoms minus the SAS.

Gómez-Bombarelli, R., Wei, J. N., Duvenaud, D., Hernández-Lobato, J. M., Sánchez-Lengeling, B., Sheberla, D., … & Aspuru-Guzik, A. (2018). Automatic chemical design using a data-driven continuous representation of molecules. ACS central science, 4(2), 268-276.

NOTE: Check the initial arXiv for the plogp reference: https://arxiv.org/abs/1610.02415v1

Return type

float

lipinski(mol)

Calculate whether a molecule adheres to the Lipinski-rule-of-5. A crude approximation of druglikeness.

Lipinski, C. A., Lombardo, F., Dominy, B. W., & Feeney, P. J. (1997). Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Advanced drug delivery reviews, 23(1-3), 3-25.

Return type

int

esol(mol)

Estimate the water solubility of a molecule.

Delaney, J. S. (2004). ESOL: estimating aqueous solubility directly from molecular structure. Journal of chemical information and computer sciences, 44(3), 1000-1005.

Return type

float

scscore(mol)

Calculate the synthetic complexity score (SCScore) of a molecule.

Coley, C. W., Rogers, L., Green, W. H., & Jensen, K. F. (2018). SCScore: synthetic complexity learned from a reaction corpus. Journal of chemical information and modeling, 58(2), 252-261.

Return type

float

sas(mol)

Calculate the synthetic accessibility score (SAS) for a molecule.

Ertl, P., & Schuffenhauer, A. (2009). Estimation of synthetic accessibility score of drug-like molecules based on molecular complexity and fragment contributions. Journal of cheminformatics, 1(1), 1-11.

Return type

float

bertz(mol)

Calculate Bertz index of a molecule.

Bertz, S. H. (1981). The first general index of molecular complexity. Journal of the American Chemical Society, 103(12), 3599-3601.

Return type

float

tpsa(mol)

Calculate the total polar surface area of a molecule.

Ertl, P., Rohde, B., & Selzer, P. (2000). Fast calculation of molecular polar surface area as a sum of fragment-based contributions and its application to the prediction of drug transport properties. Journal of medicinal chemistry, 43(20), 3714-3717.

Return type

float

logp(mol)

Calculates the partition coefficient of a molecule.

Wildman, S. A., & Crippen, G. M. (1999). Prediction of physicochemical parameters by atomic contributions. Journal of chemical information and computer sciences, 39(5), 868-873.

Return type

float

qed(mol)

Calculate the quantitative estimate of drug-likeness (QED) of a molecule.

Bickerton, G. R., Paolini, G. V., Besnard, J., Muresan, S., & Hopkins, A. L. (2012). Quantifying the chemical beauty of drugs. Nature chemistry, 4(2), 90-98.

Return type

float

number_of_h_acceptors(mol)

Calculate number of H acceptors of a molecule.

Return type

int

number_of_atoms(mol)

Calculate number of atoms of a molecule.

Return type

int

number_of_h_donors(mol)

Calculate number of H donors of a molecule.

Return type

int

number_of_aromatic_rings(mol)

Calculate number of aromatic rings of a molecule.

Return type

int

number_of_rings(mol)

Calculate number of rings of a molecule.

Return type

int

number_of_rotatable_bonds(mol)

Calculate number of rotatable bonds of a molecule.

Return type

int

number_of_large_rings(mol)

Calculate the amount of large rings (> 6 atoms) of a molecule.

Return type

int

molecular_weight(mol)

Calculate molecular weight of a molecule.

Return type

float

is_scaffold(mol)

Whether a molecule is identical to its Murcko Scaffold.

Return type

int

number_of_heterocycles(mol)

The amount of heterocycles of a molecule.

Return type

int

number_of_stereocenters(mol)

The amount of stereo centers of a molecule.

Return type

int

similarity_to_seed(mol, similarity_fn)

Calculate the similarity of a molecule to a seed molecule.

Example

An example:

from gt4sd.properties.molecules import similarity_to_seed, get_similarity_fn
func = get_similarity_fn(target_mol='CCO', fp_key='FCFP4')
similarity_to_seed(mol='CCC', similarity_fn=func)

Return type

float

activity_against_target(mol, affinity_fn)

Calculate the activity of a molecule against a target molecule.

Example

An example:

from gt4sd.properties.molecules import activity_against_target, get_activity_fn
func = get_activity_fn(target_mol='DRD2')
activity_against_target(mol='CCC', affinity_fn=func)

Return type

float