schrodinger.application.desmond.mxmd.mxmd_system_builder module

Script to setup cosolvent system

class schrodinger.application.desmond.mxmd.mxmd_system_builder.Cosolvent(pdbtype, density, mass, nheavy, filename)

Bases: tuple

__contains__

Return key in self.

__init__

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

__len__

Return len(self).

count(value) → integer -- return number of occurrences of value

density

Alias for field number 1

filename

Alias for field number 4

index(value[, start[, stop]]) → integer -- return first index of value.

Raises ValueError if the value is not present.

mass

Alias for field number 2

nheavy

Alias for field number 3

pdbtype

Alias for field number 0

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 = 12.0, 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 = 12.0, 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) → None