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

property box_strucs

property probe_pdbres

property density

Return average density of the box in g/cm^3

property probe_nheavy

Return number of heavy atoms per probe molecule

property probe_mass

Return molecular weight of the probe

property 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.

Returns

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 = 17.0, 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 = 17.0, cosolvent_layer_size: float = 7.0, cosolvent_volume_ratio: float = 5.0, cosolvent_vdw_scaling: Optional[float] = None, water='SPC')

generate(fname: str)

schrodinger.application.desmond.mxmd.mxmd_system_builder.solvate_cosolvent(inp_mae: pathlib.Path, water_model: str = 'spc', init_water_buffer=17.0) → List[schrodinger.structure._structure.Structure]

Solvate the cosolvent ct with water

Parameters

• inp_mae – The path to the input mae. This is a system containing the cosolvent.

• 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