Templates#
- class autode.transition_states.templates.TStemplate(graph=None, charge=None, mult=None, solvent=None, species=None, filename=None)#
- __init__(graph=None, charge=None, mult=None, solvent=None, species=None, filename=None)#
TS template
neighbours
- Keyword Arguments:
solvent (autode.solvent.solvents.Solvent)
charge (int)
mult (int)
species (autode.species.Species)
filename (str) – Saved template to load
- property filename: str#
- graph_has_correct_structure()#
Check that the graph has some active edges and distances
- load(filename)#
Load a template from a saved file
- Raises:
- save(basename='template', folder_path=None)#
Save the TS template object in a plain text .txt file. With folder_path =None then the template will be saved to the default directory (see get_ts_template_folder_path). The name of the file will be basename.txt where i is an integer iterated until the file doesn’t already exist.
- Keyword Arguments:
folder_path (str or None)
- autode.transition_states.templates.get_ts_template_folder_path(folder_path)#
Get the full path to the directory containing the transition state templates, if it’s unset then use the default folder in Config if it is set, or the autode/transition_states/lib folder where autodE is installed
- Returns:
Path to the folder containing TS templates
- Return type:
(str)
- autode.transition_states.templates.get_ts_templates(folder_path=None)#
Get all the transition state templates from a folder, or the default if folder path is None. Transition state templates should be .txt files with at least a charge, multiplicity, solvent, and a graph with some active edge including distances.
- Returns:
List of templates
- Return type:
- autode.transition_states.templates.get_value_from_file(key, file_lines)#
Get the value given a key from a list of file lines i.e. a saved template
Example:
Input: file_lines= _________________________ . multiplicity: 1 . ------------------------ key='multiplicity' Output: 1
- Parameters:
file_lines (list(str))
- Returns:
Value
- Return type:
(str)
- Raises:
(autode.exceptions.TemplateLoadingFailed) – If values not found
- autode.transition_states.templates.get_values_dict_from_file(key, file_lines)#
Get the value given a key from a list of file lines i.e. a saved template. Example:
Input: file_lines= _________________________ . . multiplicity: 1 nodes: 0: atom_label=F 2: atom_label=C . . ------------------------ key='nodes' Output: {0: {'atom_label': 'F'}, 2: {'atom_label': 'C'}, ..}
- Parameters:
file_lines (list(str))
- Returns:
Value
- Return type:
(dict)
- Raises:
(autode.exceptions.TemplateLoadingFailed) – If values not found
- autode.transition_states.templates.template_matches(reactant, truncated_graph, ts_template)#
Determine if a transition state template matches a truncated graph. The truncated graph includes all the active bonds in the reaction and the nearest neighbours to those atoms e.g. for a Diels-Alder reaction:
H H \ / H-C----C-H where the dotted lines represent active bonds . . H . . H \. . / H - C C - H \ / C C
where the full reaction is between ethene and butadiene.#
- param reactant:
- type reactant:
autode.complex.ReactantComplex
- param truncated_graph:
- type truncated_graph:
nx.Graph
- param ts_template:
- type ts_template:
autode.transition_states.templates.TStemplate
- returns:
Template matches
- rtype:
(bool)