CSP Prediction API

Introduction

The main class of the ccdc.csp.prediction module is ccdc.csp.prediction.Prediction.

A ccdc.csp.prediction.Prediction represents a predictied crystal structure, associated metadata and computed properties. It will normally be provided by a ccdc.csp.database.CspDatabase but can also be loaded from a CIF file with CSP annotations.

>>> from ccdc.csp.prediction import Prediction
>>> import os
>>> cif_file = os.path.join(os.path.dirname(os.path.abspath(__file__)),
...                         '..', '..', 'tests', 'csp', 'testdata',
...                         'Axitinib_00001.CIF')
>>> p=Prediction.from_cif(cif_file)
>>> len(p.molecule.atoms)
46
>>> p.classification_energy_relative
0.0
>>> p.optimisation_energy_model
'Force Field'
>>> p.BFDH_form
'Needle'

API

class ccdc.csp.prediction.Prediction(_prediction)

A class representing a crystal structure prediction.

property BFDH_form: str

The BFDH predicted morphology for the crystal structure in this prediction.

property calculated_density: float

The CSP calculated density of this prediction.

property classification_energy_relative: float

The (absolute or lattice) relative energy, in kJ/mol, of this prediction.

property crystal

The ccdc.crystal.Crystal contained in this prediction.

property entry

The ccdc.entry.Entry contained in this prediction.

property free_energy_id: str

The identifier of a 0 K structure that matches this structure.

property free_energy_method: str

The high-level defintion of the free energy method of this prediction.

property free_energy_relative: float

The relative free energy, in kJ/mol, of this prediction.

static from_cif(cif_filename: str, landscape_name=None, compute_properties=True)

Get a Prediction from a CIF file.

Parameters:

• cif_filename – The filename of a CIF file.

• landscape_name – An optional name of the CSP landscape for this entry. This will come from the directory name if None.

• compute_properties – When true (default), CSP relevant properties are computed otherwise only the raw CIF data is loaded.

property hydrogen_bonds

List of the intra- and inter-molecular hydrogen bond interactions of this prediction.

property identifier

The string identifier of the entry, e.g. axitinib_00001, in this prediction.

property landscape: str

The landscape name containing this prediction.

property matched_refcode: str

The refcode of the experimental form matching the predicted crystal structure of this prediction.

property molecular_shape_average: float

The average of the molecular shape descriptor, for ccdc.entry.molecule.Molecule.heaviest_component molecules in the asymmetric unit, of this prediction.

property molecular_shape_difference: float

The difference between the maximum and minimum value of the molecular shape descriptor, for ccdc.entry.molecule.Molecule.heaviest_component molecules in the asymmetric unit, of this prediction.

property molecule

The ccdc.molecule.Molecule contained in this prediction.

property optimisation_energy_model: str

The optimisation energy model of this prediction.

property optimisation_energy_model_definition: str

The high-level defintion of the optimisation energy model of this prediction.

property packing_coefficient: float

The packing coefficient of this prediction.

property refcode_match: float

The crystal packing similarity, range 0 - 1, between the predicted crystal structure and ccdc.csp.prediction.Prediction.matched_refcode in this prediction.

property refcode_match_rmsd: float

The RMSD value of the crystal packing similarity, between the predicted crystal structure and ccdc.csp.prediction.Prediction.matched_refcode if this prediction.

property simulation_temperature: float

The simulation temperature, in K, of this prediction.

property void_percent: float

The calculated void volume, as % of the unit cell volume, of the predicted crystal structure of this prediction.

property void_volume: float

The calculated absolute void volume in the unit cell, in cubic Angstroms, of this prediction.