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.
API¶
Ligand Screener¶
- class ccdc.screening.Screener(overlay, settings=None, nthreads=1)[source]¶
Performs field-based ligand screening.
- class ScreenHitList(confs, atom_types, _drs)[source]¶
List of screening results.
- class ScreenHit(molecules, atom_types, _dr)[source]¶
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[source]¶
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)[source]¶
Screen conformers against the overlay.
- Parameters
molecules – a list of lists of
ccdc.molecule.Molecule- Returns
ccdc.Screener.ScreenHitList
