Package schrodinger :: Package application :: Package matsci :: Package nano :: Module surfaces_interfaces_mod

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Module surfaces_interfaces_mod

Classes and functions to enumerate surfaces and interfaces.

Classes

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ParserWrapper
Manages the argparse module to parse user command line arguments.

Surfaces
Manage the enumeration of surfaces.

Interfaces
Manage the enumeration of interfaces.

SurfacesInterfaces
Manage the enumeration of surfaces and interfaces.

Functions

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str, str or None, str

get_base_names(ref_xtal_asu, ref_base_name_in=None, ads_xtal_asu=None, ads_base_name_in=None)
Return the reference, adsorption, and final combined base names.

list

get_word_list_from_file(afile)
Return a list of words from the given file.

dict

get_surface_kwargs(options_file)
Return a dictionary of surface options from the given options file.

dict

get_interface_kwargs(options_file)
Return a dictionary of interface options from the given options file.

float

ceil_mod(var, thresh=0.001)
Return the modified ceil of the given float.

float

floor_mod(var, thresh=0.001)
Return the modified floor of the given float.

Variables

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__doc__ = ...

MSGWIDTH = 100

LATTICE_PARAM_KEYS = ['r_pdb_PDB_CRYST1_a', 'r_pdb_PDB_CRYST1_...

CEIL_FLOOR_THRESH = 0.001

BASE_ASU_FLAG = '-ref_xtal_asu'

BASE_OPTIONS_FLAG = '-ref_surface_options'

ADSORPTION_ASU_FLAG = '-ads_xtal_asu'

ADSORPTION_OPTIONS_FLAG = '-ads_surface_options'

INTERFACE_OPTIONS_FLAG = '-interface_options'

__package__ = 'schrodinger.application.matsci.nano'

Function Details

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get_base_names(ref_xtal_asu, ref_base_name_in=None, ads_xtal_asu=None, ads_base_name_in=None)

Return the reference, adsorption, and final combined base names.

Parameters:

ref_xtal_asu (str) - reference xtal input file
ref_base_name_in (str or None) - reference base name or None if none has been given
ads_xtal_asu (str or None) - adsorption xtal input file or None if none has been given
ads_base_name_in (str or None) - adsorption base name or None if none has been given

Returns: str, str or None, str

reference, adsorption, and final combined base names, the adsorption base name will be None if no adsorption xtal asu is provided

get_word_list_from_file(afile)

Return a list of words from the given file.

Parameters:

afile (str) - file name

Returns: list

contains words from the given file

get_surface_kwargs(options_file)

Return a dictionary of surface options from the given options file.

Parameters:

options_file (str or None) - contains options for the surface build or None if there are none in which case the defaults are used

Returns: dict

contains options for the surface build

get_interface_kwargs(options_file)

Return a dictionary of interface options from the given options file.

Parameters:

options_file (str or None) - contains options for the interface build or None if there are none in which case the defaults are used

Returns: dict

contains options for the interface build

ceil_mod(var, thresh=0.001)

Return the modified ceil of the given float.

Parameters:

var (float) - the number to find the ceil for
thresh (float) - the threshold to use for when math.ceil begins

Returns: float

the ceil

floor_mod(var, thresh=0.001)

Return the modified floor of the given float.

Parameters:

var (float) - the number to find the floor for
thresh (float) - the threshold to use for when math.floor begins

Returns: float

the floor

Variables Details

[hide private]

doc

Value:

"""
Classes and functions to enumerate surfaces and interfaces.

Copyright Schrodinger, LLC.  All rights reserved."""

LATTICE_PARAM_KEYS

Value:

['r_pdb_PDB_CRYST1_a',
 'r_pdb_PDB_CRYST1_b',
 'r_pdb_PDB_CRYST1_c',
 'r_pdb_PDB_CRYST1_alpha',
 'r_pdb_PDB_CRYST1_beta',
 'r_pdb_PDB_CRYST1_gamma']