Package schrodinger :: Package application :: Package jaguar :: Module reactiq_input

Module reactiq_input

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

Classes

ReactiqInput
A class to completely specify a Reactiq calculation.

Functions

_read_mae_files(fhlist, fileonly, clean_st)
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.

Variables

[hide private]

INPUT_FILE_KEYS = ['reactant', 'product', 'reactant_complex', ...

__package__ = 'schrodinger.application.jaguar'

Function Details

[hide private]

_read_mae_files(fhlist, fileonly, clean_st)

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.
clean_st (bool) - if True redefine bonding using mmlewis.

Returns:

Structures or file paths.

_validate_reaction(r, p, charge, mult)

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

Variables Details

[hide private]

INPUT_FILE_KEYS

Value:

['reactant',
 'product',
 'reactant_complex',
 'product_complex',
 'reference_reactant_complex',
 'reference_product_complex',
 'template_database_file',
 'full_path_file']