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

__add__¶: Return self+value.

__class__¶: alias of builtins.type

__contains__¶: Return key in self.

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__getitem__¶: Return self[key].

__getnewargs__()¶: Return self as a plain tuple. Used by copy and pickle.

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__¶: Initialize self. See help(type(self)) for accurate signature.

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__iter__¶: Implement iter(self).

__le__¶: Return self<=value.

__len__¶: Return len(self).

__lt__¶: Return self<value.

__module__ = 'schrodinger.application.desmond.mxmd.mxmd_system_builder'¶

__mul__¶: Return self*value.n

__ne__¶: Return self!=value.

static __new__(_cls, pdbtype, density, mass, nheavy, filename)¶: Create new instance of Cosolvent(pdbtype, density, mass, nheavy, filename)

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__()¶: Return a nicely formatted representation string

__rmul__¶: Return self*value.

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__slots__ = ()¶

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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: Union[float, NoneType] = 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: Union[float, NoneType] = None, water='SPC')¶: Initialize self. See help(type(self)) for accurate signature.

generate(fname: str) → None¶

__class__¶: alias of builtins.type

__delattr__¶: Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.desmond.mxmd.mxmd_system_builder', '__doc__': "\n Example:\n\n gen = CosolventBoxGenerator(\n inp_fname,\n 'acetonitrile',\n 1,\n cosolvent_layer_size=5.0,\n cosolvent_volume_ratio=2.0)\n gen.generate(out_fname)\n ", '__init__': <function CosolventBoxGenerator.__init__>, 'generate': <function CosolventBoxGenerator.generate>, '_generate_cosolvent_box': <function CosolventBoxGenerator._generate_cosolvent_box>, '_make_layered_box': <function CosolventBoxGenerator._make_layered_box>, '_make_layered_shell': <function CosolventBoxGenerator._make_layered_shell>, '_solvate': <function CosolventBoxGenerator._solvate>, '_split_cosolvent_from_solute': <function CosolventBoxGenerator._split_cosolvent_from_solute>, '_shrink_water_box': <function CosolventBoxGenerator._shrink_water_box>, '__dict__': <attribute '__dict__' of 'CosolventBoxGenerator' objects>, '__weakref__': <attribute '__weakref__' of 'CosolventBoxGenerator' objects>})¶

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).