Screening API

Introduction

Note

The ccdc.screening module is available only to CSD-Discovery and CSD-Enterprise users.

The ccdc.screening module can be used to screen a library of compounds against a pharmacophore query obtained from one or multiple overlaid ligands. The algorithm generalises the 3D pharmacophore definition using atom property fields that are created around the query based on user-defined atom types and potentials.

See also

Descriptive field-based virtual screening documentation

API

Ligand Screener

class ccdc.screening.Screener(overlay, settings=None, nthreads=1)

Performs field-based ligand screening.

class ScreenHitList(confs, atom_types, _drs)

List of screening results.

class ScreenHit(molecules, atom_types, _dr)

An individual screening hit.

property score

The screening score. A lower score is better.

property best_hit

The hit with the lowest score.

class Settings

Screener settings.

property bias_conformer_selection

Whether or not to bias the conformer selection to low-energy conformers.

This assumes that lower-energy conformations come earlier in the list, such as for the CSD conformer generator.

property excluded_volume_envelop

Size of the excluded volume envelope.

property excluded_volume_penalty

Penalty to be applied for atoms in the excluded volume.

property fitting_points_cluster_radius

If the distance between two fitting points is less than the cluster radius, the fitting point with the higher score will be eliminated.

property fitting_points_threshold

Grid points with a score lower than this this threshold will create a fitting point.

property output_directory

Location where data files may be stored.

property parameter_directory

Location of parameter files.

property save_files

Whether or not to save files.

property store_atom_types

Whether or not to store atom types.

screen(molecules)

Screen conformers against the overlay.

Parameters:

molecules – a list of lists of ccdc.molecule.Molecule

Returns:

ccdc.Screener.ScreenHitList