schrodinger.application.jaguar.jagconvert module

This script is for converting jaguar input and output files to other formats.

exception schrodinger.application.jaguar.jagconvert.UsageException

Bases: Exception

An exception to indicate a bad command line.

__init__(*args, **kwargs)
args
with_traceback()

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception schrodinger.application.jaguar.jagconvert.UnsupportedConversionException

Bases: Exception

An exception to indicate an unsupported or unknown conversion request.

__init__(*args, **kwargs)
args
with_traceback()

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

class schrodinger.application.jaguar.jagconvert.Options

Bases: object

__init__()
schrodinger.application.jaguar.jagconvert.jout_to_mae(jout: str, mae: str)

Convert a Jaguar output file to a maestro format .mae file.

Adds properties to the .mae file.

Parameters

  • jout – The name of the Jaguar output file to read.

  • mae – The name of the (single-structure) Maestro file to write.

schrodinger.application.jaguar.jagconvert.jout_to_jin(jout: str, jin: str) → List[schrodinger.application.jaguar.input.JaguarInput]

Convert a Jaguar output file to Jaguar input file(s).

Chains together jout_to_multimae and multimae_to_jin. First, creates a temporary directory and uses jout_to_multimae to create temp.mae there. Then, passes temp.mae to jout_to_multimae generate a/several input file(s). The temporary directory and temp.mae are deleted on return.

Parameters

  • jout – The name of the Jaguar output file to read.

  • jin – The base name of the Jaguar input files to write. For x.in, the function will create x_1.in, x_2.in, etc. if there is >1 structure.

Returns

JaguarInput representation of generated file(s)

schrodinger.application.jaguar.jagconvert.jout_to_multimae(jout: str, mae: str)

Convert a Jaguar output file to a multistructure .mae file.

Useful for getting all the structures from a geometry optimization. Default behavior for ‘jout’ to ‘mae’ conversion is to mimic the backend behavior, which is to output only the last structure unless ip472=2.

Adds properties to the .mae file.

Note to Jaguar Developers: If WAM detection becomes arduous in the future

then it might be easier to make a &gen section attribute in the JaguarOutput object such that the detection could utilize Jaguar input keywords and values for detection as is done in jexec.py

Checks are performed to determine if the .mae file should contain a WAM heading

Parameters

  • jout – The name of the Jaguar output file to read.

  • mae – The name of the (multi-structure) Maestro file to write.

schrodinger.application.jaguar.jagconvert.jin_to_mae(jin: str, mae: str)

Convert a Jaguar input file to a maestro format .mae file.

Parameters

  • jin – The name of the Jaguar input file to read.

  • mae – The name of the (single-structure) Maestro file to write.

schrodinger.application.jaguar.jagconvert.mae_to_jin(mae: str, jin: str) → schrodinger.application.jaguar.input.JaguarInput

Convert a maestro file to a Jaguar input file.

If multiple mae structures are present in the mae file, only the first will be used.

Parameters

  • mae – The name of the Maestro file to read.

  • jin – The name of the Jaguar input file to write.

Returns

JaguarInput representation of generated file

schrodinger.application.jaguar.jagconvert.multimae_to_jin(multimae: str, jin: str) → List[schrodinger.application.jaguar.input.JaguarInput]

Convert a maestro file with multiple structures to multiple Jaguar input files.

Parameters:

Parameters

  • multimae – The name of the Maestro file to read.

  • jin – The base name of the Jaguar input files to write. For x.in, the function will create x_1.in, x_2.in, etc. if there is >1 structure.

Returns

JaguarInput representation of generated file(s)

schrodinger.application.jaguar.jagconvert.lookup_function(in_format: str, out_format: str) → Callable[[str, str], Any]

Find the function to call for the provided input and output format.

schrodinger.application.jaguar.jagconvert.option_parser(orig_args: list) → Tuple[Callable, list, schrodinger.application.jaguar.jagconvert.Options]

Parse the command line arguments.

:return (function, args, options)

Return a function and the arguments/options it should be called with to complete the conversion.

schrodinger.application.jaguar.jagconvert.usage()

Print a usage statement and exit.