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 – Sets bond_table

• angle_table – Sets angle_table

• nonbonded_table – Sets nonbonded_table

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