Stereochemistry (deprecated)

CheckStructure(ent, bond_table, angle_table, nonbonded_table, bond_tolerance, angle_tolerance)

Perform structural checks and filters the structure.

Parameters:

  • ent (EntityView) – Structure to check

  • bond_table (StereoChemicalParams) – List of bond stereo chemical parameters obtained from StereoChemicalParamsReader or FillStereoChemicalParams()

  • angle_table (StereoChemicalParams) – List of angle stereo chemical parameters obtained from StereoChemicalParamsReader or FillStereoChemicalParams()

  • nonbonded_table (ClashingDistances) – Information about the clashing distances obtained from StereoChemicalParamsReader or FillClashingDistances()

  • bond_tolerance (float) – Tolerance in stddev for bonds

  • angle_tolerance (float) – Tolerance in stddev for angles

class StereoChemicalProps(bond_table, angle_table, nonbonded_table)

Object containing the stereo-chemical properties read form stereochmical_props.txt file.

Parameters:
bond_table

Object containing bond parameters

Type:

StereoChemicalParams

angle_table

Object containing angle parameters

Type:

StereoChemicalParams

nonbonded_table

Object containing clashing distances parameters

Type:

ClashingDistances