schrodinger.application.matsci.nano.check module

Classes and functions for checking nanostructure input.

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.application.matsci.nano.check.CheckInput

Bases: object

Check user input.

DEFAULTMSG = '\n You have specified a value for flag %s that is not supported. Values\n must be %s. Proceeding with the default value of %s.'
MIDFIX = '-'
checkElements(element1, element2, logger=None)
checkBondlength(bondlength, logger=None)
checkEdgetypes(edgetype1, edgetype2, logger=None)
checkCellDims(ncell1, ncell2, logger=None)
checkTermFrag(termfrag, logger=None)
checkBilayerSep(bilayersep, logger=None)
checkNumBilayers(nbilayers, logger=None)
checkBilayerStackType(stacktype, logger=None)
checkBilayerShift(bilayershift, logger=None)
checkIndicies(nindex, mindex, logger=None)

Check n-index and m-index.

Parameters:
  • nindex (int) – the first chiral index
  • mindex (int) – the second chiral index
  • logger (logging.getLogger) – output logger
checkNumCells(ncells, logger=None)

Check the number of unit cells.

Parameters:
  • ncells (int) – the number of unit cells
  • logger (logging.getLogger) – output logger
checkUpToIndex(up_to_nindex, up_to_mindex, logger=None)

Check the enumeration options.

Parameters:
  • up_to_nindex (bool) – enumerate on the n-index
  • up_to_mindex (bool) – enumerate on the m-index
  • logger (logging.getLogger) – output logger
checkNumWalls(nwalls, logger=None)

Check the number of walls.

Parameters:
  • nwalls (int) – the number of walls
  • logger (logging.getLogger) – output logger
checkWallSep(wallsep, logger=None)

Check the desired wall separation.

Parameters:
  • wallsep (float) – wall separation in Angstrom
  • logger (logging.getLogger) – output logger
checkMaeExt(infile)

Check that the infile has a supported Maestro extension.

Parameters:infile (str) – file name to check
Return type:str
Returns:outfile, if infile is bad return its basename plus constants.DEFAULT_MAE_EXT
checkExistingFile(infile)

Check if the infile already exists and find a new name if it does.

Parameters:infile (str) – file name to check
Return type:str
Returns:outfile, if infile is bad return new file name
__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.matsci.nano.check', '__doc__': '\n Check user input.\n ', 'DEFAULTMSG': '\n You have specified a value for flag %s that is not supported. Values\n must be %s. Proceeding with the default value of %s.', 'MIDFIX': '-', 'checkElements': <function CheckInput.checkElements>, 'checkBondlength': <function CheckInput.checkBondlength>, 'checkEdgetypes': <function CheckInput.checkEdgetypes>, 'checkCellDims': <function CheckInput.checkCellDims>, 'checkTermFrag': <function CheckInput.checkTermFrag>, 'checkBilayerSep': <function CheckInput.checkBilayerSep>, 'checkNumBilayers': <function CheckInput.checkNumBilayers>, 'checkBilayerStackType': <function CheckInput.checkBilayerStackType>, 'checkBilayerShift': <function CheckInput.checkBilayerShift>, 'checkIndicies': <function CheckInput.checkIndicies>, 'checkNumCells': <function CheckInput.checkNumCells>, 'checkUpToIndex': <function CheckInput.checkUpToIndex>, 'checkNumWalls': <function CheckInput.checkNumWalls>, 'checkWallSep': <function CheckInput.checkWallSep>, 'checkMaeExt': <function CheckInput.checkMaeExt>, 'checkExistingFile': <function CheckInput.checkExistingFile>, '__dict__': <attribute '__dict__' of 'CheckInput' objects>, '__weakref__': <attribute '__weakref__' of 'CheckInput' 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).

__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.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.matsci.nano.check'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__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).

__weakref__

list of weak references to the object (if defined)