schrodinger.application.desmond.mxmd.mxmd_system_builder module¶
Script to setup cosolvent system
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class
schrodinger.application.desmond.mxmd.mxmd_system_builder.
Cosolvent
(filename: str)[source]¶ Bases:
object
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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
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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
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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
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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
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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
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property
filename
¶
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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]][source]¶ 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.
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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[source]¶ 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
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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')[source]¶ 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)
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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][source]¶ 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
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schrodinger.application.desmond.mxmd.mxmd_system_builder.
shrink_cosolvent_box
(cts: List[schrodinger.structure._structure.Structure], required_nwat: int)[source]¶ 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