schrodinger.application.matsci.nano.check module

Classes and functions for checking nanostructure input.

Copyright Schrodinger, LLC. All rights reserved.

schrodinger.application.matsci.nano.check.validate_options(parser)

Check the user-specified input options.

Parameters

parser (parserutils.DriverParser) – The parser to get the options from

Return type

Named tuple

Returns

The parsed command line options

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