schrodinger.application.matsci.reaction_workflow_utils module¶
Utilities for reaction workflows.
Copyright Schrodinger, LLC. All rights reserved.
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class
schrodinger.application.matsci.reaction_workflow_utils.
TempData
(temp_start, temp_step, temp_n)¶ Bases:
tuple
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__contains__
(key, /)¶ Return key in self.
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__len__
()¶ Return len(self).
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count
(value, /)¶ Return number of occurrences of value.
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index
(value, start=0, stop=9223372036854775807, /)¶ Return first index of value.
Raises ValueError if the value is not present.
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temp_n
¶ Alias for field number 2
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temp_start
¶ Alias for field number 0
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temp_step
¶ Alias for field number 1
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class
schrodinger.application.matsci.reaction_workflow_utils.
PressData
(press_start, press_step, press_n)¶ Bases:
tuple
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__contains__
(key, /)¶ Return key in self.
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__len__
()¶ Return len(self).
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count
(value, /)¶ Return number of occurrences of value.
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index
(value, start=0, stop=9223372036854775807, /)¶ Return first index of value.
Raises ValueError if the value is not present.
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press_n
¶ Alias for field number 2
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press_start
¶ Alias for field number 0
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press_step
¶ Alias for field number 1
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schrodinger.application.matsci.reaction_workflow_utils.
get_idxs_marked_atoms
(st, prop)¶ Return a list of indices of atoms in the given structure that have the given property defined.
- Parameters
st (schrodinger.structure.Structure) – the structure
prop (str) – the property that marks the atoms
- Return type
list
- Returns
contains indices of atoms
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schrodinger.application.matsci.reaction_workflow_utils.
get_restrain_atom_idxs
(st)¶ Return a list of indices of restrain atoms in the given structure.
- Parameters
st (schrodinger.structure.Structure) – the structure
- Return type
list
- Returns
contains indices of restrain atoms
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exception
schrodinger.application.matsci.reaction_workflow_utils.
InvalidInput
¶ Bases:
Exception
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__init__
(*args, **kwargs)¶ Initialize self. See help(type(self)) for accurate signature.
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args
¶
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with_traceback
()¶ Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.
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schrodinger.application.matsci.reaction_workflow_utils.
get_idx_groups
(text)¶ Get index groups from the given string.
- Parameters
text (str) – the string
- Raise
InvalidInput if there is a formatting issue
- Return type
list
- Returns
contains list of indices
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schrodinger.application.matsci.reaction_workflow_utils.
get_restrain_distance_idxs
(st)¶ Return a list of lists of indices of restrain distances in the given structure.
- Parameters
st (schrodinger.structure.Structure) – the structure
- Return type
list
- Returns
contains lists of restrain distances
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schrodinger.application.matsci.reaction_workflow_utils.
get_restrain_angle_idxs
(st)¶ Return a list of lists of indices of restrain angles in the given structure.
- Parameters
st (schrodinger.structure.Structure) – the structure
- Return type
list
- Returns
contains lists of restrain angles
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schrodinger.application.matsci.reaction_workflow_utils.
get_restrain_dihedral_idxs
(st)¶ Return a list of lists of indices of restrain dihedrals in the given structure.
- Parameters
st (schrodinger.structure.Structure) – the structure
- Return type
list
- Returns
contains lists of restrain dihedrals
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schrodinger.application.matsci.reaction_workflow_utils.
get_idx_groups_str
(idx_groups)¶ Get a string representation of the given index groups.
- Parameters
idx_groups (list) – contains lists of indices
- Return type
str
- Returns
the string
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schrodinger.application.matsci.reaction_workflow_utils.
get_jaguar_keywords_list
(jaguar_keywords_dict)¶ Return the Jaguar keywords list from the given dict.
- Parameters
jaguar_keywords_dict (OrderedDict) – the Jaguar keywords dict
- Return type
list
- Returns
the Jaguar keywords list
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schrodinger.application.matsci.reaction_workflow_utils.
type_cast_seed
(seed)¶ Type cast the seed.
- Parameters
seed (str or unicode) – seed for random number generator
- Return type
int
- Returns
the seed
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schrodinger.application.matsci.reaction_workflow_utils.
type_cast_jaguar_keywords
(jaguar_keywords, reserved_keys={'ifreq', 'igeopt', 'itrvec', 'molchg', 'multip', 'nhesref', 'npress', 'ntemp', 'press', 'press_step', 'tmpini', 'tmpstp'}, exception_type=<class 'argparse.ArgumentTypeError'>)¶ Type cast the Jaguar keywords.
- Parameters
jaguar_keywords (str or unicode or list) – the Jaguar keywords, a whitespace delimited string of ‘<key>=<value>’ tokens or a list of such tokens
reserved_keys (set) – contains reserved Jaguar keys
exception_type (type) – the exception type to raise if invalid
- Return type
OrderedDict
- Returns
the Jaguar keywords OrderedDict
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schrodinger.application.matsci.reaction_workflow_utils.
check_ff_assignment
(sts, ffld_name='S-OPLS')¶ Check the assignment of the given force field to the given structures.
- Parameters
sts (list) – contains schrodinger.structure.Structure
ffld_name (str) – the force field name
- Raises
ValueError – if invalid
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schrodinger.application.matsci.reaction_workflow_utils.
get_molecular_weight
(st, idxs=None)¶ Return the molecular weight (amu) taken over the given atom indices in the given structure.
- Parameters
st (schrodinger.structure.Structure) – the structure
idxs (list) – the atom indices
- Return type
float
- Returns
the molecular weight (amu)
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schrodinger.application.matsci.reaction_workflow_utils.
check_conformers
(conformers, conformers_group_hash)¶ Check conformers. If the given structures are conformers then their atom numberings are all changed in place so that they are equivalent to that of the first of the given conformers.
- Parameters
conformers (list) – contains schrodinger.structure.Structure of conformers
conformers_group_hash (str) – a group hash
- Raises
ValueError – if invalid
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schrodinger.application.matsci.reaction_workflow_utils.
check_reaction_wf_structures
(rxn_sts, ffld_name=None, mass_conserved=False, keep_atoms_only=False)¶ Check the given reaction workflow structues.
- Parameters
rxn_sts (str or list) – the reaction workflow structures, a file name or list of schrodinger.structure.Structure
ffld_name (str) – the force field name to use when optionally checking its assignment to the given structures
mass_conserved (bool) – check that mass is conserved (see also keep_atoms_only kwarg)
keep_atoms_only (bool) – specifies that only keep atoms be considered when checking if mass is conserved (see also mass_conserved kwarg)
- Raises
ValueError – if invalid
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schrodinger.application.matsci.reaction_workflow_utils.
type_cast_reaction_wf_input
(reaction_wf_input, exception_type=<class 'argparse.ArgumentTypeError'>, mass_conserved=False)¶ Type cast the reaction workflow input.
- Parameters
reaction_wf_input (str or unicode or list) – the reaction workflow input, a file name or list of schrodinger.structure.Structure
exception_type (type) – the exception type to raise if invalid
mass_conserved (bool) – check that mass is conserved
- Return type
str or list
- Returns
the reaction workflow input, a file name or list of schrodinger.structure.Structure
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schrodinger.application.matsci.reaction_workflow_utils.
bin_structures_by_property
(sts, key='s_matsci_Reaction_Workflow_Conformers_Group', inner_key=None)¶ Return a dictionary of structures binned by a property with the given key. If inner_key is provided then return a dictionary of dictionaries of structures with the inner dictionaries keyed by inner_key and outer dictionaries keyed by key.
- Parameters
sts (list) – the structures
key (str) – the key for the property by which to bin
inner_key (str) – additionally bin by this inner_key
- Return type
dict or dict of dict
- Returns
dictionary where keys are properties and values are lists of structures or dictionary of dictionaries where the outer dictionary is keyed by key and inner dictionary is keyed by inner_key and values of the inner dictionary are lists of structures
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schrodinger.application.matsci.reaction_workflow_utils.
append_unique_conformers
(sts, unique_sts, rmsd_thresh=0.1, n_conformers=None)¶ Append any unique conformers found in the given structures to the given unique structures.
- Parameters
sts (list) – schrodinger.structure.Structure candidate conformers
unique_sts (list) – schrodinger.structure.Structure unique conformers
rmsd_thresh (float) – the maximum allowable RMSD (Ang.) between two structures before they can be considered different conformers
n_conformers (int or None) – number of sought conformers or None if there isn’t one
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schrodinger.application.matsci.reaction_workflow_utils.
get_conformers
(sts, n_conformers, pp_rel_energy_thresh=None, rmsd_thresh=0.1)¶ Return either (1) at most the given number of conformers or (2) all conformers with relative energies less than the given value. If (2) then an attempt is made to return at least the given number of conformers even if that means having relative energies larger than the given value.
- Parameters
sts (list) – schrodinger.structure.Structure conformers
n_conformers (int) – either the maximum number of conformers if pp_rel_energy_thresh is None or a target minimum number of conformers if pp_rel_energy_thresh is given
pp_rel_energy_thresh (None or float) – relative energy threshold in kJ/mol, if None then only the n_conformers lowest energy conformers are returned
rmsd_thresh (float) – the maximum allowable RMSD (Ang.) between two structures before they can be considered different conformers
- Return type
list
- Returns
schrodinger.structure.Structure conformers
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schrodinger.application.matsci.reaction_workflow_utils.
postprocess_conformational_search
(conformer, out_mae_path)¶ Postprocess a MacroModel conformational search. Rewrite the given MacroModel out *mae file so that the conformers in it have properly updated properties.
- Parameters
conformer (schrodinger.structure.Structure) – a representative conformer that seeded the search being postprocessed
out_mae_path (str) – the file path to the MacroModel out *mae file
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schrodinger.application.matsci.reaction_workflow_utils.
run_conformational_search
(conformers, n_conformers=5, restrain_idxs=None, seed=1234, launch_dir=None, base_name=None, job_dj=None, clean=True, ffld_name='S-OPLS', rel_energy_thresh=50.0, rmsd_thresh=0.1, pp_rel_energy_thresh=None)¶ Perform a restrained MacroModel conformational search seeded with the given conformers.
- Parameters
conformers (list) – schrodinger.structure.Structure conformers used to seed the search
n_conformers (int) – number of sought conformers
restrain_idxs (list) – indices to restrain
seed (int) – seed for random number generator
launch_dir (str) – a launch subdirectory to use for the job
base_name (str) – a base name to use for file and job naming
job_dj (queue.JobDJ) – if an instance is given then add the current job and return
clean (bool) – if not given a job_dj then this option controls cleaning up after the job that was run
ffld_name (str) – the force field name
rel_energy_thresh (float) – relative energy threshold in kJ/mol, structures with energies (relative to that of the global minimum structure) greater than this value are not considered conformers, used in MacroModel
rmsd_thresh (float) – the maximum allowable RMSD (Ang.) between two structures before they can be considered different conformers
pp_rel_energy_thresh (None or float) – relative energy threshold in kJ/mol, if None then only the n_conformers lowest energy conformers are returned, used in postprocessing MacroModel results
- Raises
RuntimeError – if the MacroModel job fails
- Return type
list
- Returns
schrodinger.structure.Structure conformers, could be less than n_conformers
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schrodinger.application.matsci.reaction_workflow_utils.
get_int_tuples_from_str_property
(st, key, separator=';')¶ Return a list of tuples of integers from the given string structure property.
- Parameters
st (schrodinger.structure.Structure) – the structure
key (str) – the property key
separator (str) – the tuple separator used for the given property
- Return type
list
- Returns
contains tuples of integers
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schrodinger.application.matsci.reaction_workflow_utils.
update_index_properties
(st, old_to_new)¶ Update the index properties of the given structure.
- Parameters
st (
structure.Structure
) – the structureold_to_new (dict) – a map of old-to-new atom indices
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schrodinger.application.matsci.reaction_workflow_utils.
get_core_idxs
(st)¶ Return a set of atom indices for the core of the given structure.
- Parameters
st (schrodinger.structure.Structure) – the structure
- Return type
set
- Returns
core atom indices
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schrodinger.application.matsci.reaction_workflow_utils.
representative_conformers
(sibling_conformers_dict, specific_sibling_group=None)¶ Generator over representative conformers.
- Parameters
sibling_conformers_dict (dict) – dictionary of dictionaries where the outer dictionary is keyed by sibling and inner dictionary is keyed by conformer and values of the inner dictionary are lists of structures
specific_sibling_group (str or None) – if not None then restrict conformers to be generated only over this sibling group
- Return type
tuple
- Returns
the sibling and conformer group names and the representative conformer or None if one doesn’t exist
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class
schrodinger.application.matsci.reaction_workflow_utils.
RepresentativeConformersMixin
¶ Bases:
object
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representativeConformers
(sibling_conformers_dict=None, specific_sibling_group=None)¶ Generator over representative conformers.
- Parameters
sibling_conformers_dict (dict or None) – dictionary of dictionaries where the outer dictionary is keyed by sibling and inner dictionary is keyed by conformer and values of the inner dictionary are lists of structures, if None then the class attr is used
specific_sibling_group (str or None) – if not None then restrict conformers to be generated only over this sibling group
- Return type
tuple
- Returns
the sibling and conformer group names and the representative conformer
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class
schrodinger.application.matsci.reaction_workflow_utils.
ReactionWorkflowFile
(rxnwf_file)¶ Bases:
schrodinger.application.matsci.reaction_workflow_utils.RepresentativeConformersMixin
Manage a reaction workflow file.
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__init__
(rxnwf_file)¶ Create an instance.
- Parameters
rxnwf_file (str) – the reaction workflow file
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getReactantsSiblingGroupName
()¶ Return the reactants sibling group name.
- Return type
str
- Returns
the reactants sibling group name
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getReactantsConformersDict
()¶ Return the reactants conformers dictionary.
- Return type
dict
- Returns
keys are conformer group names, values are lists of
structure.Structure
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representativeConformers
(sibling_conformers_dict=None, specific_sibling_group=None)¶ Generator over representative conformers.
- Parameters
sibling_conformers_dict (dict or None) – dictionary of dictionaries where the outer dictionary is keyed by sibling and inner dictionary is keyed by conformer and values of the inner dictionary are lists of structures, if None then the class attr is used
specific_sibling_group (str or None) – if not None then restrict conformers to be generated only over this sibling group
- Return type
tuple
- Returns
the sibling and conformer group names and the representative conformer
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class
schrodinger.application.matsci.reaction_workflow_utils.
ReactionWorkflowEnergyAnalysis
(rxnwf_file, energy_keys)¶ Bases:
schrodinger.application.matsci.reaction_workflow_utils.ReactionWorkflowFile
Manage a reaction workflow energy analysis.
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__init__
(rxnwf_file, energy_keys)¶ Create an instance.
- Parameters
rxnwf_file (str) – the reaction workflow file
energy_keys (list) – structure property energy keys to consider, if it is temperature dependent then include the temperature (K) as a number followed by ‘K’ in the key and the corresponding energy must be in supported units (au, kcal/mol, eV, kJ/mol) and must be present in the key as ‘(<units>)’
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static
getHeader
(energy_key)¶ Return a header for the given energy key.
- Parameters
energy_key (str) – structure property energy key
- Return type
str
- Returns
the header
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static
getTemperature
(energy_key)¶ Return the temperature (K) for the given energy key.
- Parameters
energy_key (str) – structure property energy key
- Return type
float, None
- Returns
the temperature (K) if there is one
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static
getUnits
(energy_key)¶ Return the units for the given energy key.
- Parameters
energy_key (str) – structure property energy key
- Return type
str, None
- Returns
the units if there is one
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static
getKcalPerMolConversion
(energy_key)¶ Return the kcal/mol conversion factor for the given energy key.
- Parameters
energy_key (str) – structure property energy key
- Return type
float, None
- Returns
the kcal/mol conversion factor if there is one
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getConfAvgRelEnergies
(include_x_terms=True, only_lowest_energy=False)¶ Return the conformationally averaged energies relative to that of the reactants.
- Parameters
include_x_terms (bool) – whether to include cross terms in the conformational averaging
only_lowest_energy (bool) – use only the lowest energy conformer rather than averaging over conformers
- Raises
ReactionWorkflowException – if there is an issue
- Return type
dict
- Returns
keys are sibling group names, values are dicts with energy keys as keys and energy values as values
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getGraph
()¶ Return a NetworkX directed graph of the reaction workflow energy level diagram.
- Return type
networkx.DiGraph
- Returns
nodes are sibling group names and have energy dictionary kwargs, edges are directed (parent, child) pairs
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static
getOrderedNodeNames
(graph)¶ Return an ordered list of node names from the given graph.
- Parameters
graph (networkx.DiGraph) – nodes are sibling group names and have energy dictionary kwargs, edges are directed (parent, child) pairs
- Return type
list
- Returns
contains ordered node names
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writeDataFiles
()¶ Write data files.
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getReactantsConformersDict
()¶ Return the reactants conformers dictionary.
- Return type
dict
- Returns
keys are conformer group names, values are lists of
structure.Structure
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getReactantsSiblingGroupName
()¶ Return the reactants sibling group name.
- Return type
str
- Returns
the reactants sibling group name
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representativeConformers
(sibling_conformers_dict=None, specific_sibling_group=None)¶ Generator over representative conformers.
- Parameters
sibling_conformers_dict (dict or None) – dictionary of dictionaries where the outer dictionary is keyed by sibling and inner dictionary is keyed by conformer and values of the inner dictionary are lists of structures, if None then the class attr is used
specific_sibling_group (str or None) – if not None then restrict conformers to be generated only over this sibling group
- Return type
tuple
- Returns
the sibling and conformer group names and the representative conformer
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schrodinger.application.matsci.reaction_workflow_utils.
get_stage_idx
(astr)¶ Return the stage index from the given string.
- Parameters
astr (str) – the string
- Return type
int
- Returns
the stage index
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schrodinger.application.matsci.reaction_workflow_utils.
check_TS_vetting
(out_file)¶ Return False if TS vetting failed in the given Jaguar out file.
- Parameters
out_file (str) – Jaguar out file
- Return type
bool
- Returns
False if TS vetting failed
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schrodinger.application.matsci.reaction_workflow_utils.
get_sub_host_str
(obj, sub_host_attr, n_procs_attr)¶ Return the command line -HOST argument for using a subhost.
- Parameters
obj (object) – the object, possibly having the given attributes defined
sub_host_attr (str) – the attribute for the subhost
n_procs_attr (str) – the attribute for the number of processors
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exception
schrodinger.application.matsci.reaction_workflow_utils.
ConformationalSearchException
¶ Bases:
Exception
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__init__
(*args, **kwargs)¶ Initialize self. See help(type(self)) for accurate signature.
-
args
¶
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with_traceback
()¶ Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.
-
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class
schrodinger.application.matsci.reaction_workflow_utils.
ConformationalSearchMixin
¶ Bases:
object
Manage a MacroModel conformational search.
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static
genEtaRotamers
(sibling_conformers_dict, only_rings=True)¶ Generate eta-rotamers.
- Parameters
sibling_conformers_dict (dict) – dictionary of dictionaries where the outer dictionary is keyed by sibling and inner dictionary is keyed by conformer and values of the inner dictionary are lists of structures
only_rings (bool) – if True then only allow rotation of eta-bound rings, if False then also allow rotation of ligands where the eta-bound motif is acyclic, for example ethene, etc.
- Return type
dict
- Returns
dictionary of dictionaries where the outer dictionary is keyed by sibling and inner dictionary is keyed by conformer and values of the inner dictionary are lists of structures, for eta-complexes incoming conformers have been replaced with all possible rotamers
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createConformers
(sts)¶ Create the conformers.
- Parameters
sts (list) – contains schrodinger.structure.Structure, the structures for which to create conformers, each unique type of structure should have a unique conformer group structure property keyed by CONFORMERS_GROUP_KEY, structures sharing the same CONFORMERS_GROUP_KEY should be conformers of the same structure and are used to seed the conformational search, an additional optional SIBLING_GROUP_KEY can be used to distinguish related groups of conformers, atoms marked with the property RESTRAINED_ATOM_KEY will be restrained
- Raises
ConformationalSearchException – if there is an issue
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static
-
exception
schrodinger.application.matsci.reaction_workflow_utils.
JMSWFException
¶ Bases:
Exception
-
__init__
(*args, **kwargs)¶ Initialize self. See help(type(self)) for accurate signature.
-
args
¶
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with_traceback
()¶ Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.
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class
schrodinger.application.matsci.reaction_workflow_utils.
JMSWFMixin
¶ Bases:
schrodinger.application.matsci.reaction_workflow_utils.RepresentativeConformersMixin
Manage a Jaguar multistage workflow.
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runJMSWF
()¶ Run the Jaguar multistage workflow.
- Raises
JMSWFException – if there is an issue
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prepareJMSWFOutput
()¶ Prepare Jaguar multistage workflow output.
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checkJMSWFOutputs
(out_files)¶ Return False if any of the given Jaguar out files should be treated as a failure.
- Parameters
out_files (list) – contains Jaguar output files
- Return type
bool
- Returns
False if any of the given Jaguar out files should be treated as a failure
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setRepresentatives
()¶ Associated with each structure is output data from potentially multiple Jaguar multistage workflow stages. Pick representative structures to carry the data for all stages.
- Raises
JMSWFException – if there is an issue
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finalizeJMSWFOutput
()¶ Finalize the Jaguar multistage workflow output.
- Return type
str
- Returns
the Jaguar multistage workflow output file
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representativeConformers
(sibling_conformers_dict=None, specific_sibling_group=None)¶ Generator over representative conformers.
- Parameters
sibling_conformers_dict (dict or None) – dictionary of dictionaries where the outer dictionary is keyed by sibling and inner dictionary is keyed by conformer and values of the inner dictionary are lists of structures, if None then the class attr is used
specific_sibling_group (str or None) – if not None then restrict conformers to be generated only over this sibling group
- Return type
tuple
- Returns
the sibling and conformer group names and the representative conformer
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class
schrodinger.application.matsci.reaction_workflow_utils.
DescriptorsMixin
¶ Bases:
object
Manage running descriptors.
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DEFAULT_JOB_NAME
= 'automatic_reaction_workflow'¶
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runDescriptors
(files)¶ Run descriptors.
- Parameters
files (list) – the files on which to run descriptors
-
-
exception
schrodinger.application.matsci.reaction_workflow_utils.
ReactionWorkflowException
¶ Bases:
Exception
-
__init__
(*args, **kwargs)¶ Initialize self. See help(type(self)) for accurate signature.
-
args
¶
-
with_traceback
()¶ Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.
-
-
class
schrodinger.application.matsci.reaction_workflow_utils.
ReactionWorkflow
(reaction_wf_input_sts, n_conformers=5, pp_rel_energy_thresh=None, seed=1234, only_rings=True, return_csearch_files=False, jaguar_keywords={'basis': 'LACVP**', 'dftname': 'B3LYP', 'iuhf': '1'}, temp_data=None, press_data=None, return_jaguar_files=False, anharm=False, return_anharm_files=False, anharm_max_freq=300, anharm_factor_data=None, rate_constants=False, return_rate_constant_files=False, wigner_tunnel_corr=False, extra_stages_file=None, max_i_freq=0, n_jmswf_subjobs=1, subhost=None, tpp=1, logger=None)¶ Bases:
schrodinger.application.matsci.reaction_workflow_utils.ConformationalSearchMixin
,schrodinger.application.matsci.reaction_workflow_utils.JMSWFMixin
Manage a reaction workflow.
-
__init__
(reaction_wf_input_sts, n_conformers=5, pp_rel_energy_thresh=None, seed=1234, only_rings=True, return_csearch_files=False, jaguar_keywords={'basis': 'LACVP**', 'dftname': 'B3LYP', 'iuhf': '1'}, temp_data=None, press_data=None, return_jaguar_files=False, anharm=False, return_anharm_files=False, anharm_max_freq=300, anharm_factor_data=None, rate_constants=False, return_rate_constant_files=False, wigner_tunnel_corr=False, extra_stages_file=None, max_i_freq=0, n_jmswf_subjobs=1, subhost=None, tpp=1, logger=None)¶ Create an instance.
- Parameters
reaction_wf_input_sts (list) – reaction workflow input structures
n_conformers (int) – number of conformers to search for
pp_rel_energy_thresh (None or float) – relative energy threshold in kJ/mol, if None then only the n_conformers lowest energy conformers are returned
seed (int) – seed for random number generator
only_rings (bool) – if True then only allow rotation of eta-bound rings, if False then also allow rotation of ligands where the eta-bound motif is acyclic, for example ethene, etc.
return_csearch_files (bool) – whether to return all output files from the conformational search subjobs
jaguar_keywords (OrderedDict) – Jaguar keywords
temp_data (TempData) – the temperature data for thermochemical properties
press_data (PressData) – the pressure data for thermochemical properties
return_jaguar_files (bool) – whether to return all output files from the Jaguar subjobs
anharm (bool) – whether to run the anharmonic workflow
return_anharm_files (bool) – whether to return all output files from the anharmonic workflow
anharm_max_freq (float) – anharmonic potentials are created for normal modes with harmonic frequencies less than this value in wavenumbers (cm^-1)
anharm_factor_data (anharmonic.SeqData or None) – unitless factor data for factors that multiply a normal mode displacement, if None then the defaults are used, the number of points is in the positive direction only, excluding zero and the negative direction, for example using a value of 4 in turn means 2 * 4 + 1 = 9 points total
rate_constants (bool) – whether to report rate constant(s) for the rate determining step of the reaction using canonical transition state theory
return_rate_constant_files (bool) – whether to return all output files from the rate constant subjobs
wigner_tunnel_corr (bool) – whether to include the Wigner tunneling correction when computinig rate constant(s)
extra_stages_file (str) – the name of a file containing extra stages for a Jaguar Multistage Workflow subjob that will be performed on all output structures from the reaction workflow, the first of these extra stages is always skipped so as to allow analysis to potentially be the first extra stage
max_i_freq (float) – tolerate small imaginary frequencies less than this value in wavenumbers (cm^-1)
n_jmswf_subjobs (int) – the maximum number of simultaneous Jaguar multistage workflow subjobs
subhost (str) – the host to use for subjobs
tpp (int) – the number of threads to use for Jaguar subjobs, i.e. -TPP (threads-per-process)
logger (logging.Logger or None) – output logger or None if there isn’t one
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validateRateConstants
()¶ Validate rate constants.
- Raises
ReactionWorkflowException – if there is an issue
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validateAnharmonic
()¶ Validate anharmonic.
- Raises
ReactionWorkflowException – if there is an issue
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validateSubhost
()¶ Validate subhost.
- Raises
ReactionWorkflowException – if there is an issue
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validate
()¶ Validate.
- Raises
ReactionWorkflowException – if there is an issue
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runAnharmonic
()¶ Run the anharmonic workflow.
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processAnharmonic
()¶ Process the anharmonic workflow.
- Raises
ReactionWorkflowException – if there is an issue
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runCTST
()¶ Run canonical transition state theory calculations to determine rate constant(s) for the rate determining step of the reaction.
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prepareCTSTOutput
()¶ Prepare CTST output.
- Raises
ReactionWorkflowException – if there is an issue
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run
()¶ Run the reaction workflow.
- Raises
ReactionWorkflowException – if there is an issue
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checkJMSWFOutputs
(out_files)¶ Return False if any of the given Jaguar out files should be treated as a failure.
- Parameters
out_files (list) – contains Jaguar output files
- Return type
bool
- Returns
False if any of the given Jaguar out files should be treated as a failure
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createConformers
(sts)¶ Create the conformers.
- Parameters
sts (list) – contains schrodinger.structure.Structure, the structures for which to create conformers, each unique type of structure should have a unique conformer group structure property keyed by CONFORMERS_GROUP_KEY, structures sharing the same CONFORMERS_GROUP_KEY should be conformers of the same structure and are used to seed the conformational search, an additional optional SIBLING_GROUP_KEY can be used to distinguish related groups of conformers, atoms marked with the property RESTRAINED_ATOM_KEY will be restrained
- Raises
ConformationalSearchException – if there is an issue
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finalizeJMSWFOutput
()¶ Finalize the Jaguar multistage workflow output.
- Return type
str
- Returns
the Jaguar multistage workflow output file
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static
genEtaRotamers
(sibling_conformers_dict, only_rings=True)¶ Generate eta-rotamers.
- Parameters
sibling_conformers_dict (dict) – dictionary of dictionaries where the outer dictionary is keyed by sibling and inner dictionary is keyed by conformer and values of the inner dictionary are lists of structures
only_rings (bool) – if True then only allow rotation of eta-bound rings, if False then also allow rotation of ligands where the eta-bound motif is acyclic, for example ethene, etc.
- Return type
dict
- Returns
dictionary of dictionaries where the outer dictionary is keyed by sibling and inner dictionary is keyed by conformer and values of the inner dictionary are lists of structures, for eta-complexes incoming conformers have been replaced with all possible rotamers
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prepareJMSWFOutput
()¶ Prepare Jaguar multistage workflow output.
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representativeConformers
(sibling_conformers_dict=None, specific_sibling_group=None)¶ Generator over representative conformers.
- Parameters
sibling_conformers_dict (dict or None) – dictionary of dictionaries where the outer dictionary is keyed by sibling and inner dictionary is keyed by conformer and values of the inner dictionary are lists of structures, if None then the class attr is used
specific_sibling_group (str or None) – if not None then restrict conformers to be generated only over this sibling group
- Return type
tuple
- Returns
the sibling and conformer group names and the representative conformer
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runJMSWF
()¶ Run the Jaguar multistage workflow.
- Raises
JMSWFException – if there is an issue
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setRepresentatives
()¶ Associated with each structure is output data from potentially multiple Jaguar multistage workflow stages. Pick representative structures to carry the data for all stages.
- Raises
JMSWFException – if there is an issue
-