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2015-3 Schrodinger Python API
Package schrodinger :: Package application :: Package medchem :: Module property
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Module property

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

Functions [hide private]
string, string
compute_title(structure, program, name, *args)
Returns the title of the structure.
float, string
compute_mw(structure, program, name, *args)
Returns the molecular weight of the structure.
float, string
compute_alogp(structure, program, name, mol, *args)
Returns the ALogP of the structure and stores it in structure.property
int, string
compute_polar_surf_area(structure, program, name, mol, *args)
Returns the polar surface area of the structure and stores it in structure.property
float, string
compute_num_rot_bonds(structure, program, name, *args)
Returns the number of rotatable bonds in the structure and stores it in structure.property
int, string
compute_num_hbond_donors(structure, program, name, mol, *args)
Returns the number of HBond donors in the structure and stores it in structure.property
int, string
compute_num_hbond_acceptors(structure, program, name, mol, *args)
Returns the number of HBond acceptors in the structure and stores it in structure.property
string, string
compute_smiles(structure, program, name, *args)
Returns the SMILES string for the structure and stores it in structure.property
list
compute_medchem_properties(structure, program="mpc")
Calculates the medchem molecular properties for the structure
Variables [hide private]
  _version = 0.10
  canvas_license = canvasutils.get_license(canvasutils.LICENSE_S...
  properties = [('Molecular Weight', compute_mw), ('ALogP', comp...
Function Details [hide private]

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"]
Returns: string, string
Title of the structure, structure.property key

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"]
Returns: float, string
Molecular weight of the structure, structure.property key

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 (schrodinger.structure.Structure object) - ChmMol object to run the calculation on
  • mol (ChmMol object)
Returns: float, string
ALogP of the structure, structure.property key

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 (schrodinger.structure.Structure object) - 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"']
  • mol (ChmMol object)
Returns: int, string
Polar Surface Area of the structure, structure.property key

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"']
Returns: float, string
Number of Rotatable Bonds in the structure, structure.property key

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 (schrodinger.structure.Structure object) - 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"']
  • mol (ChmMol object)
Returns: int, string
number of Hbond donors in the structure, structure.property key

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 (schrodinger.structure.Structure object) - 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"']
  • mol (ChmMol object)
Returns: int, string
number of Hbond acceptors in the structure, structure.property key

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"]
Returns: string, string
SMILES string for the structure, structure.property key

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".
Returns: list
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

Variables Details [hide private]

canvas_license

Value:
canvasutils.get_license(canvasutils.LICENSE_SHARED)

properties

Value:
[('Molecular Weight', compute_mw), ('ALogP', compute_alogp), ('Polar S\
urface Area', compute_polar_surf_area), ('Rotatable Bonds', compute_nu\
m_rot_bonds), ('Hbond Donors', compute_num_hbond_donors), ('Hbond Acce\
ptors', compute_num_hbond_acceptors), ('SMILES', compute_smiles)]

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2015-3 Schrodinger Python API
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