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2016-3 Schrodinger Python API
Package schrodinger :: Package application :: Package jaguar :: Module reactiq_input
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Module reactiq_input

Functions and classes for defining the input to a Reactiq workflow.

Classes [hide private]
  ReactiqInput
A class to completely specify a Reactiq calculation.
Functions [hide private]
 
_read_mae_files(fhlist, fileonly)
Process a list of mae files and return extant file paths or associated Structure instances if requested.
 
_validate_reaction(r, p, charge, mult)
Validate a reaction specification.
 
get_argstr(kwd, val)
Get a string representing a reactiq.py cmdline flag i.e.
 
get_cmdline_args(infile)
Get a string representing the reactiq.py cmdline flag.
Variables [hide private]
  __package__ = 'schrodinger.application.jaguar'
Function Details [hide private]

_read_mae_files(fhlist, fileonly)

 

Process a list of mae files and return extant file paths or associated Structure instances if requested.

Parameters:
  • fhlist (list of strings) - list of filehandles
  • fileonly (bool) - if True, return only file paths, else Structures.
Returns:
Structures or file paths.

_validate_reaction(r, p, charge, mult)

 

Validate a reaction specification. will raise a ReactiqConservationError if the specification is invalid.

get_argstr(kwd, val)

 

Get a string representing a reactiq.py cmdline flag i.e. '-<keyword-name>=<value>'

Parameters:
  • kwd (ReactiqKeyword) - ReactiqKeyword instance
  • val (kwd.valid_type) - value of kwd
Returns:
cmdline flag

get_cmdline_args(infile)

 

Get a string representing the reactiq.py cmdline flag. Note that boolean flags are NOT written if False.

Parameters:
  • infile (str) - name of Reactiq input file
Returns:
list of cmdline arguments

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2016-3 Schrodinger Python API
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