schrodinger.application.medchem.property module

Functions for computing medchem properties.

To add a new property to be calculated simply add another tuple to the properties list. To remove a property, remove its tuple from the properties list.

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schrodinger.application.medchem.property.compute_title(structure, program, name, *args)[source]

Returns the title of the structure.

Parameters

  • structure (schrodinger.structure.Structure object) – structure object to run the calculation on

  • program (string) – abbreviation of the program running this calculation, for purposes of creating the key to store the calculation in structure.property[‘r_”program”_”name”’]

  • name (string) – name of the property when storing the calculation in structure.property[‘r_”program”_”name”]

Return type

string, string

Returns

Title of the structure, structure.property key

schrodinger.application.medchem.property.compute_mw(structure, program, name, *args)[source]

Returns the molecular weight of the structure.

Parameters

  • structure (schrodinger.structure.Structure object) – structure object to run the calculation on

  • program (string) – abbreviation of the program running this calculation, for purposes of creating the key to store the calculation in structure.property[‘r_”program”_”name”’]

  • name (string) – name of the property when storing the calculation in structure.property[‘r_”program”_”name”]

Return type

float, string

Returns

Molecular weight of the structure, structure.property key

schrodinger.application.medchem.property.compute_alogp(structure, program, name, mol, *args)[source]

Returns the ALogP of the structure and stores it in structure.property

Parameters

  • structure (schrodinger.structure.Structure object) – structure object to run the calculation on

  • program (string) – abbreviation of the program running this calculation, for purposes of creating the key to store the calculation in structure.property[‘r_”program”_”name”’]

  • name (string) – name of the property when storing the calculation in structure.property[‘r_”program”_”name”]

  • structure – ChmMol object to run the calculation on

Return type

float, string

Returns

ALogP of the structure, structure.property key

schrodinger.application.medchem.property.compute_polar_surf_area(structure, program, name, mol, *args)[source]

Returns the polar surface area of the structure and stores it in structure.property

Parameters

  • structure (schrodinger.structure.Structure object) – structure object to store the calculation on

  • structure – ChmMol object to run the calculation on

  • program (string) – abbreviation of the program running this calculation, for purposes of creating the key to store the calculation in structure.property[‘r_”program”_”name”’]

  • name (string) – name of the property when storing the calculation in structure.property[‘r_”program”_”name”’]

Return type

int, string

Returns

Polar Surface Area of the structure, structure.property key

schrodinger.application.medchem.property.compute_num_rot_bonds(structure, program, name, *args)[source]

Returns the number of rotatable bonds in the structure and stores it in structure.property

Parameters

  • structure (schrodinger.structure.Structure object) – structure object to run the calculation on

  • program (string) – abbreviation of the program running this calculation, for purposes of creating the key to store the calculation in structure.property[‘i_”program”_”name”’]

  • name (string) – name of the property when storing the calculation in structure.property[‘i_”program”_”name”’]

Return type

float, string

Returns

Number of Rotatable Bonds in the structure, structure.property key

schrodinger.application.medchem.property.compute_num_hbond_donors(structure, program, name, mol, *args)[source]

Returns the number of HBond donors in the structure and stores it in structure.property

Parameters

  • structure (schrodinger.structure.Structure object) – structure object to store the calculation on

  • structure – ChmMol object to run the calculation on

  • program (string) – abbreviation of the program running this calculation, for purposes of creating the key to store the calculation in structure.property[‘i_”program”_”name”’]

  • name (string) – name of the property when storing the calculation in structure.property[‘i_”program”_”name”’]

Return type

int, string

Returns

number of Hbond donors in the structure, structure.property key

schrodinger.application.medchem.property.compute_num_hbond_acceptors(structure, program, name, mol, *args)[source]

Returns the number of HBond acceptors in the structure and stores it in structure.property

Parameters

  • structure (schrodinger.structure.Structure object) – structure object to store the calculation on

  • structure – ChmMol object to run the calculation on

  • program (string) – abbreviation of the program running this calculation, for purposes of creating the key to store the calculation in structure.property[‘i_”program”_”name”’]

  • name (string) – name of the property when storing the calculation in structure.property[‘i_”program”_”name”’]

Return type

int, string

Returns

number of Hbond acceptors in the structure, structure.property key

schrodinger.application.medchem.property.compute_smiles(structure, program, name, *args)[source]

Returns the SMILES string for the structure and stores it in structure.property

Parameters

  • structure (schrodinger.structure.Structure object) – structure object to run the calculation on

  • program (string) – abbreviation of the program running this calculation, for purposes of creating the key to store the calculation in structure.property[‘s_”program”_”name”’]

  • name (string) – name of the property when storing the calculation in structure.property[‘s_”program”_”name”]

Return type

string, string

Returns

SMILES string for the structure, structure.property key

schrodinger.application.medchem.property.compute_medchem_properties(structure, program='mpc')[source]

Calculates the medchem molecular properties for the structure

Parameters

  • structure (schrodinger.structure.Structure class object) – structure to compute properties of

  • program (string) – Abbreviation of the program running this calculation, so that the result of the calculation is stored properly in the structure.property dictionary, which uses keys of the form “type_program_property”.

Return type

list

Returns

A list of results, each member of the list is a tuple of the form (diplay property name, property value, key), where key is the key used to store the property value in the structure.property dictionary