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
__init__

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