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

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.get_probe_paths(probe_names: List[str], custom_probe_dir: Optional[str] = None) → Tuple[List[str], List[str], List[str]]

Process the given probe names and return paths to their .box.mae file. Additionally return any missing probes. :return: A 3-tuple of two lists containing probe paths for custom probe

and builtin probes and a list containing probe names with missing files.

schrodinger.application.desmond.mxmd.mxmd_system_builder.convert_vv2mol(probe: schrodinger.application.desmond.mxmd.mxmd_system_builder.Cosolvent, 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_path: 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, ‘probe_directory/acetonitrile.box.mae’, 1, cosolvent_layer_size=5.0, cosolvent_volume_ratio=2.0)

gen.generate(out_fname)

__init__(solute_fname: str, probe_path: 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)

schrodinger.application.desmond.mxmd.mxmd_system_builder.solvate_cosolvent(inp_mae: pathlib.Path, water_model: str = 'spc', init_water_buffer=15.0) → List[schrodinger.structure._structure.Structure]

Solvate the cosolvent ct with water :param inp_mae: The path to the input mae. This is a system containing the

cosolvent.

Parameters:

• job_dir – A path to the directory to run the job in
• water_model – The water type to use as the solvent
• init_water_buffer – The initial size of water box

Returns:

Three structures from system_builder output: the fullsystem, solute, and solvent

schrodinger.application.desmond.mxmd.mxmd_system_builder.shrink_cosolvent_box(cts: List[schrodinger.structure._structure.Structure], required_nwat: int)

Shrink the system box so that it contains a given number of water molecules.

Parameters:

• cts – The input structures in the order of: [full system, non-solvent ct…, cosolvent ct, water ct]. These cts are modified in place.
• required_nwat – How many waters should remain after shrinking system