Module desmondutils

Determine the size of a cubic box that encloses the entire structure

Parameters:

• struct (schrodinger.structure.Structure) - The structure to use in determining the box size.

Returns: float

The largest span in the X, Y or Z direction

Add the Chorus box properties to the structure for a cubic box

Parameters:

• struct (schrodinger.structure.Structure) - The structure to add the properties to

Add properties to the structure that define the periodic boundary condition in the way Desmond wants it defined.

Parameters:

• struct (schrodinger.structure.Structure) - The structure to add the properties to
• ax - The value of the ax box property
• ay - The value of the ay box property. Defaults to 0.
• az - The value of the az box property. Defaults to 0.
• bx - The value of the bx box property. Defaults to 0.
• by - The value of the by box property. If not given, this value is set the same as ax.
• bz - The value of the bz box property. Defaults to 0.
• cx - The value of the cx box property. Defaults to 0.
• cy - The value of the cy box property. Defaults to 0.
• cz - The value of the cz box property. If not given, this value is set the same as ax.

Check if the structure has all the Chorus box properties

Parameters:

• struct (schrodinger.structure.Structure) - The structure to check for properties

Returns: bool

Whether the structure has all the chorus box properties

Check if the structure has all the space group PBC properties

Parameters:

• struct (schrodinger.structure.Structure) - The structure to check for properties

Returns: bool

Whether the structure has all the space group pbc properties

Check if the structure has all the crystal builder PBC properties

Parameters:

• struct (schrodinger.structure.Structure) - The structure to check for properties

Returns: bool

Whether the structure has all the space group pbc properties

Write input for the Desmond System Builder

Parameters:

• struct (schrodinger.structure.Structure) - The structure to run the system builder on
• out_name (str) - The base name for the output files
• forcefield (str) - The forcefield to use
• rezero_system (bool) - Whether to move the center of mass to the origin

Returns: (str, str)

The names of the .msj and .mae files that were created

Run the Desmond multisim system builder

Parameters:

• struct (schrodinger.structure.Structure) - The structure to run the system builder on. If the chorus box properties are not set to define the periodic boundary condition, a cubic PBC will be imposed based on the largest span of the X, Y or Z coordinates.
• output_basename (str) - The base name of the output file
• forcefield (str) - The name of the force field to use. The default is OPLS 2005.
• custom_dir (str) - The path to the custom forcefield directory if one is to be used.
• rezero_system (bool) - Whether to move the center of mass to the origin
• logger (logging.Logger) - The logger to use to record any messages. If None, the messages are printed.

Returns: str or None

The name of the resulting .cms file, or None if the file was not produced successfully

__doc__

Value:

""" Utilities for working with Desmond. Copyright Schrodinger, LLC. All rights reserved. """

COMMAND_TEXT

Value:

''' task { task = "desmond:auto" } assign_forcefield { compress = "" } '''

CHORUS_CUBIC_PROPS

Value:

['r_chorus_box_ax', 'r_chorus_box_by', 'r_chorus_box_cz']

CHORUS_NON_CUBIC_PROPS

Value:

['r_chorus_box_ay', 'r_chorus_box_az', 'r_chorus_box_bx', 'r_chorus_box_bz', 'r_chorus_box_cx', 'r_chorus_box_cy']

CHORUS_BOX_ALL_PROPS

Value:

['r_chorus_box_ax', 'r_chorus_box_by', 'r_chorus_box_cz', 'r_chorus_box_ay', 'r_chorus_box_az', 'r_chorus_box_bx', 'r_chorus_box_bz', 'r_chorus_box_cx', ...

PDB_CRYSTAL_PROPS

Value:

['r_pdb_PDB_CRYST1_a', 'r_pdb_PDB_CRYST1_b', 'r_pdb_PDB_CRYST1_c', 'r_pdb_PDB_CRYST1_alpha', 'r_pdb_PDB_CRYST1_beta', 'r_pdb_PDB_CRYST1_gamma']

BC_BOX_PROPS

Value:

['r_m_BC_Box_A', 'r_m_BC_Box_B', 'r_m_BC_Box_C', 'r_m_BC_Box_Alpha', 'r_m_BC_Box_Beta', 'r_m_BC_Box_Gamma', 's_matsci_Lattice_Vector_A/(3*Ang.)', 's_matsci_Lattice_Vector_B/(3*Ang.)', ...