schrodinger.application.desmond.mxmd.mxmd_system_builder module

Script to setup cosolvent system

class schrodinger.application.desmond.mxmd.mxmd_system_builder.Cosolvent(filename: str)

Bases: object

__init__(filename: str)

filename should follow the pattern <probe_name>.box.mae and it should be in BOX_DATA folder.

box_strucs

Decorator that converts a method with a single self argument into a property cached on the instance.

Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.

This class is based on code that is Copyright (c) Django Software Foundation

probe_pdbres

Decorator that converts a method with a single self argument into a property cached on the instance.

Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.

This class is based on code that is Copyright (c) Django Software Foundation

density

Decorator that converts a method with a single self argument into a property cached on the instance.

Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.

This class is based on code that is Copyright (c) Django Software Foundation

probe_nheavy

Decorator that converts a method with a single self argument into a property cached on the instance.

Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.

This class is based on code that is Copyright (c) Django Software Foundation

probe_mass

Decorator that converts a method with a single self argument into a property cached on the instance.

Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.

This class is based on code that is Copyright (c) Django Software Foundation

filename

schrodinger.application.desmond.mxmd.mxmd_system_builder.convert_vv2mol(probe_name: str, target_vv_ratio: float = 5.0) → int

This function reports the number of water molecules required to maintain the required volume/volume ratio for each molecules of the probe Assumes that density is provided in gm/cm3 molecular mass also should be specified in gm/mol :param probe_name: Name of the cosolvent used to build mixed-solvent box :param target_vv_ratio: Volume over volume ratio in percent

class schrodinger.application.desmond.mxmd.mxmd_system_builder.CosolventBoxGenerator(solute_fname: str, probe_name: str, box_number: int, init_water_buffer: float = 15.0, cosolvent_layer_size: float = 7.0, cosolvent_volume_ratio: float = 5.0, cosolvent_vdw_scaling: Optional[float] = None, water='SPC')

Bases: object

Example:

gen = CosolventBoxGenerator(

inp_fname, ‘acetonitrile’, 1, cosolvent_layer_size=5.0, cosolvent_volume_ratio=2.0)

gen.generate(out_fname)

__init__(solute_fname: str, probe_name: str, box_number: int, init_water_buffer: float = 15.0, cosolvent_layer_size: float = 7.0, cosolvent_volume_ratio: float = 5.0, cosolvent_vdw_scaling: Optional[float] = None, water='SPC')

Initialize self. See help(type(self)) for accurate signature.

generate(fname: str)