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.
Copyright Schrodinger, LLC. All rights reserved
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schrodinger.application.medchem.property.
compute_title
(structure, program, name, *args)¶ 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
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schrodinger.application.medchem.property.
compute_mw
(structure, program, name, *args)¶ 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
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schrodinger.application.medchem.property.
compute_alogp
(structure, program, name, mol, *args)¶ 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
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schrodinger.application.medchem.property.
compute_polar_surf_area
(structure, program, name, mol, *args)¶ 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
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schrodinger.application.medchem.property.
compute_num_rot_bonds
(structure, program, name, *args)¶ 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
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schrodinger.application.medchem.property.
compute_num_hbond_donors
(structure, program, name, mol, *args)¶ 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
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schrodinger.application.medchem.property.
compute_num_hbond_acceptors
(structure, program, name, mol, *args)¶ 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
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schrodinger.application.medchem.property.
compute_smiles
(structure, program, name, *args)¶ 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
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schrodinger.application.medchem.property.
compute_medchem_properties
(structure, program='mpc')¶ 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