CSD Landscape Generator

Introduction

csd_landscape_generator.py - an API for crystal structure prediction landscape generation.

Simplest operation is:

>>> from ccdc import io
>>> from ccdc.csp.csd_landscape_generator import CSDLandscapeGenerator
>>> csd = io.EntryReader('csd')
>>> mol = csd.molecule('HXACAN')
>>> landscape_generator = CSDLandscapeGenerator()
>>> landscape_generator.settings.nstructures=3
>>> landscape = list(landscape_generator.generate(mol))
>>> print(sorted([round(prediction.relative_score) for prediction in landscape]))
[0, 27, 32]

API

class ccdc.csp.csd_landscape_generator.CSDLandscapeGenerator(settings=None)[source]

Crystal structure prediction landscape generation using experimentally observed crystal structures as templates for predictions.

class GeneratedEntry(_prediction)[source]

A generated crystal structure prediction entry. This is a ccdc.entry.Entry with associated scores.

property relative_score

The prediction’s score relative to the lowest scoring prediction in the prediction run.

This value will be zero until after the landscape generation run is finished.

property score

The prediction’s absolute score.

class Settings(_settings=None)[source]

Settings pertaining to landscape generation.

property database_file

The database file containing the template structures. If this is not set, the current release of the CSD will be used.

property format

The output crystal file format, one of ‘cif’ or ‘mol2’.

property nstructures

The number of structures to generate, default is 100. There may be fewer structures generated if sufficient template structures cannot be found.

property nthreads

Number of threads to allocate for the template predictor.

property shape_database_location

The database file containing molecule shape information. If this is not set, the current release of the CSD will be used.

property sohncke_only

Returns true if structures should be generated only in Sohncke space groups. These are the space groups that are possible for single enantiomers of chiral molecules.

property working_directory

The working and output directory for the landscape.

generate(molecule)[source]

Generate a crystal structure prediction landscape for the input molecule.

This will yield ccdc.csp.csd_landscape_generator.GeneratedEntry as they become ready. The ccdc.csp.csd_landscape_generator.GeneratedEntry will be given valid relative_score values when landscape generation is completed.