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.