Reactions Discovery in Python (PLAMS)

An example of how to use Reactions Discovery with Python (PLAMS) can be found in the Python Examples documentation.

The scm.reactions_discovery.plams_job Python module contains the below classes.

class ReactionsDiscoveryResults(job)

Results class for ReactionsDiscoveryJob

get_errormsg()

Returns the error message of this calculation if any were raised.

Returns:

String containing the error message.

Return type:

str

get_md_jobs()

Returns the AMSJobs used during the calculation.

Returns:

List of AMSJobs used during the calculation.

Return type:

List[AMSJob]

rkfpath()

Returns path to reactions_discovery.rkf

Returns:

Path to reactions_discovery.rkf

Return type:

str

get_network_rd()

Returns the reaction network represented by Reactions Discovery CombinedMol and CombinedReaction classes.

Raises:

KFError – If the KF file associated with this result does not contain the required information.

Returns:

Graph representing the reaction network, a dictionairy of categories and lists of CombinedMol, a dictionairy of categories and CombinedReaction and a list of categories.

Return type:

Tuple[DiGraph, Dict[str, List[CombinedMol]], Dict[int, CombinedReaction], List[str]]

get_network()

Returns the reaction network represented by a DiGraph and a dictionairy of lists of PLAMS molecules.

Each key in the dictionary is a category.

Returns:

graph of the reaction network, dictionary of categories and lists of Molecules, and a list of categories.

Return type:

Tuple[DiGraph, Dict[str, List[Molecule]], List[str]]

get_num_md_simulations()

Returns the number of MD simulations used during the Molecular Dynamics stage.

Raises:

KFError – If the KF file associated with this result does not contain the right information.

Returns:

The number of MD simulations used during the Molecular Dynamics stage.

Return type:

int

class ReactionsDiscoveryJob(name='reactions_discovery_job', driver=None, settings=None, molecule=None, **kwargs)

PLAMS Job class for running Reactions Discovery.

This class inherits from the PLAMS SingleJob class. For usage, see the SingleJob documentation.

If you supply a Settings object to the constructor, it will be converted to a scm.inputs model.

Attributes:

• input: an alias for self.settings.input

• builder: an alias for self.settings.input.MolecularDynamics.BuildSystem

__init__(name='reactions_discovery_job', driver=None, settings=None, molecule=None, **kwargs)

Initialize the ReactionsDiscoveryJob.

namestr

The name of the job

driverscm.inputs.ReactionsDiscovery

scm.inputs model describing the input to the ReactionsDiscovery program

settings: scm.plams.Settings

All settings for the job. Input settings in the PLAMS settings format under settings.input are automatically converted to a scm.inputs model. You can specify settings.runscript.nproc to set the total number of cores to run on.

molecule: scm.plams.Molecule or Dict[str, scm.plams.Molecule]

Two possibilities:

• molecule is of type Molecule - it should then be the complete system as a PLAMS Molecule . Cannot be combined with the driver.input.MolecularDynamics.BuildSystem or settings.input.ams.MolecularDynamics.BuildSystem. It will be written to the main System block in the input.

• molecule is a dictionary with string keys and Molecule values - the keys should then be given in the driver.input.MolecularDynamics.BuildSystem.Molecule[i].SystemID input option. The molecules will then be used to build the system before the MD.

classmethod from_rkf(path)

Initialize a job from a reactions_discovery.rkf file.

Parameters:

path (str) – Path to a reactions_discovery.rkf file

Returns:

A new ReactionsDiscoveryJob instance based on the information found in path.

Return type:

ReactionsDiscoveryJob

classmethod from_input(text_input)

Initialize a job from text input.

Parameters:

text_input (str) – A multiline text input

Returns:

A ReactionsDiscoveryJob

Return type:

ReactionsDiscoveryJob

static _extract_mol_from_input(model)

Move any System block out of the ReactionsDiscovery input and return it as the job’s system(s).

get_errormsg()

Returns the contents of the jobname.err file if it exists. If the file does not exist an empty string is returned.

Returns:

The error message

Return type:

str

get_runscript()

Generates the runscript. Use self.settings.runscript.preamble_lines = ['line1', 'line2'] or similarly for self.settings.runscript.postamble_lines to set custom settings.

self.settings.runscript.nproc controls the total number of cores to run on.

check()

Returns True if “NORMAL TERMINATION” is given in the General section of reactions_discovery.rkf, AND all molecular dynamics jobs also have finished successfully.

ok()

Synonym for check()

get_md_jobs()

Returns: List of AMSJob

property input

scm.inputs model input

classmethod load_external(path, finalize=False)

Load a previous ReactionsDiscovery job from disk.

Parameters:

• path (Union[str, Path]) – A reactions discovery results folder.

• finalize (bool, optional) – See SingleJob, defaults to False

Raises:

FileError – When the path does not exist.

Returns:

An initialized ReactionsDiscoveryJob

Return type:

ReactionsDiscoveryJob

get_input()

Obtain the input string used to run the Reactions Discovery workflow script.

Returns:

An input string.

Return type:

str