2. Components¶
This chapter contains a description of the main classes that can be used in AMSConformers scripts. In each part you can find API specification of a particular component, an explanation of its role in the whole environment and examples of its usage.
- 2.1. Conformers
- 2.1.1. UniqueConformersCrest
UniqueConformersCrestUniqueConformersCrest.__init__()UniqueConformersCrest.add_conformer()UniqueConformersCrest.get_diffs_for_candidate()UniqueConformersCrest._is_prepared()UniqueConformersCrest.add_conformers()UniqueConformersCrest.clear()UniqueConformersCrest.convert_key_to_camelcase()UniqueConformersCrest.convert_key_to_underscore_case()UniqueConformersCrest.convert_keys_to_camelcase()UniqueConformersCrest.convert_keys_to_underscore_case()UniqueConformersCrest.copy()UniqueConformersCrest.create_json_entry()UniqueConformersCrest.filter()UniqueConformersCrest.find_clusters()UniqueConformersCrest.find_nth_conformer()UniqueConformersCrest.fit()UniqueConformersCrest.from_rdkitmol()UniqueConformersCrest.fromfile()UniqueConformersCrest.generate()UniqueConformersCrest.get_all_energies()UniqueConformersCrest.get_all_geometries()UniqueConformersCrest.get_all_rmsds()UniqueConformersCrest.get_conformers()UniqueConformersCrest.get_dendrogram()UniqueConformersCrest.get_energies()UniqueConformersCrest.get_json_settings()UniqueConformersCrest.get_molecule()UniqueConformersCrest.get_plot_dendrogram()UniqueConformersCrest.get_rdkitmol()UniqueConformersCrest.get_rmsds_from_frame()UniqueConformersCrest.handle_input()UniqueConformersCrest.indices_to_names()UniqueConformersCrest.moleculeUniqueConformersCrest.optimize()UniqueConformersCrest.pass_settings()UniqueConformersCrest.prepare_state()UniqueConformersCrest.read()UniqueConformersCrest.read_settings()UniqueConformersCrest.remove_conformer()UniqueConformersCrest.remove_high_energy()UniqueConformersCrest.remove_non_minima()UniqueConformersCrest.reorder()UniqueConformersCrest.rmsdsUniqueConformersCrest.score()UniqueConformersCrest.set_blocknames()UniqueConformersCrest.set_energies()UniqueConformersCrest.set_generator()UniqueConformersCrest.subset_indicesUniqueConformersCrest.to_json()UniqueConformersCrest.write()
- 2.1.2. UniqueConformersTFD
- 2.1.3. UniqueConformersRMSD
- 2.1.4. UniqueConformersAMS
UniqueConformersAMSUniqueConformersAMS.__init__()UniqueConformersAMS.prepare_state()UniqueConformersAMS.add_conformer()UniqueConformersAMS.get_diffs_for_candidate()UniqueConformersAMS.get_group_indices()UniqueConformersAMS.get_cost()UniqueConformersAMS.get_partial_cost()UniqueConformersAMS.create_tree()UniqueConformersAMS.set_partial_permutator_checks()
- 2.1.1. UniqueConformersCrest
- 2.2. Generators
- 2.2.1. RDKitGenerator
RDKitGeneratorRDKitGenerator.__init__()RDKitGenerator.set_number_initial_conformers()RDKitGenerator.generate()RDKitGenerator._rdkit_call_from_thread()RDKitGenerator.are_geometries_local_minima()RDKitGenerator.convert_key_to_camelcase()RDKitGenerator.convert_key_to_underscore_case()RDKitGenerator.convert_keys_to_camelcase()RDKitGenerator.convert_keys_to_underscore_case()RDKitGenerator.create_json_entry()RDKitGenerator.estimate_runtime()RDKitGenerator.get_json_settings()RDKitGenerator.handle_input()RDKitGenerator.optimize_and_filter()RDKitGenerator.optimize_conformers()RDKitGenerator.pass_settings()RDKitGenerator.read_settings()RDKitGenerator.set_blocknames()RDKitGenerator.set_convergence_quality()RDKitGenerator.set_max_energy()RDKitGenerator.set_optimizer()RDKitGenerator.set_preoptimizer()RDKitGenerator.set_printing_level()RDKitGenerator.set_rngseed()RDKitGenerator.time_to_timestring()RDKitGenerator.to_json()RDKitGenerator.write_geometries()
- 2.2.2. CRESTGenerator
CRESTGeneratorCRESTGenerator.__init__()CRESTGenerator.set_optimizer()CRESTGenerator.set_printing_level()CRESTGenerator.set_shake()CRESTGenerator.set_rngseed()CRESTGenerator.set_convergence_quality()CRESTGenerator.set_max_energy()CRESTGenerator.generate()CRESTGenerator._rdkit_call_from_thread()CRESTGenerator.are_geometries_local_minima()CRESTGenerator.convert_key_to_camelcase()CRESTGenerator.convert_key_to_underscore_case()CRESTGenerator.convert_keys_to_camelcase()CRESTGenerator.convert_keys_to_underscore_case()CRESTGenerator.create_json_entry()CRESTGenerator.estimate_runtime()CRESTGenerator.get_json_settings()CRESTGenerator.handle_input()CRESTGenerator.optimize_and_filter()CRESTGenerator.optimize_conformers()CRESTGenerator.pass_settings()CRESTGenerator.read_settings()CRESTGenerator.set_blocknames()CRESTGenerator.set_preoptimizer()CRESTGenerator.time_to_timestring()CRESTGenerator.to_json()
- 2.2.3. MetadynamicsGenerator
MetadynamicsGeneratorMetadynamicsGenerator.__init__()MetadynamicsGenerator.set_shake()MetadynamicsGenerator.set_convergence_quality()MetadynamicsGenerator.generate()MetadynamicsGenerator.optimize_and_filter()MetadynamicsGenerator._rdkit_call_from_thread()MetadynamicsGenerator.are_geometries_local_minima()MetadynamicsGenerator.convert_key_to_camelcase()MetadynamicsGenerator.convert_key_to_underscore_case()MetadynamicsGenerator.convert_keys_to_camelcase()MetadynamicsGenerator.convert_keys_to_underscore_case()MetadynamicsGenerator.create_json_entry()MetadynamicsGenerator.estimate_runtime()MetadynamicsGenerator.get_json_settings()MetadynamicsGenerator.handle_input()MetadynamicsGenerator.optimize_conformers()MetadynamicsGenerator.pass_settings()MetadynamicsGenerator.read_settings()MetadynamicsGenerator.set_blocknames()MetadynamicsGenerator.set_max_energy()MetadynamicsGenerator.set_optimizer()MetadynamicsGenerator.set_preoptimizer()MetadynamicsGenerator.set_printing_level()MetadynamicsGenerator.set_rngseed()MetadynamicsGenerator.time_to_timestring()MetadynamicsGenerator.to_json()
- 2.2.4. MDExpander
MDExpanderMDExpander.__init__()MDExpander.set_shake()MDExpander.set_number_of_identical_mdruns()MDExpander.set_number_of_starting_geometries()MDExpander.generate()MDExpander._rdkit_call_from_thread()MDExpander.are_geometries_local_minima()MDExpander.convert_key_to_camelcase()MDExpander.convert_key_to_underscore_case()MDExpander.convert_keys_to_camelcase()MDExpander.convert_keys_to_underscore_case()MDExpander.create_json_entry()MDExpander.estimate_runtime()MDExpander.get_json_settings()MDExpander.handle_input()MDExpander.optimize_and_filter()MDExpander.optimize_conformers()MDExpander.pass_settings()MDExpander.read_settings()MDExpander.set_blocknames()MDExpander.set_convergence_quality()MDExpander.set_max_energy()MDExpander.set_optimizer()MDExpander.set_preoptimizer()MDExpander.set_printing_level()MDExpander.set_rngseed()MDExpander.time_to_timestring()MDExpander.to_json()
- 2.2.5. GCExpander
GCExpanderGCExpander.__init__()GCExpander.generate()GCExpander.set_maxgeoms()GCExpander.determine_maxgeoms()GCExpander.get_rmsd_time()GCExpander.estimate_gctime()GCExpander.are_geometries_local_minima()GCExpander.convert_key_to_camelcase()GCExpander.convert_key_to_underscore_case()GCExpander.convert_keys_to_camelcase()GCExpander.convert_keys_to_underscore_case()GCExpander.create_json_entry()GCExpander.estimate_runtime()GCExpander.get_json_settings()GCExpander.handle_input()GCExpander.optimize_and_filter()GCExpander.optimize_conformers()GCExpander.pass_settings()GCExpander.read_settings()GCExpander.set_blocknames()GCExpander.set_convergence_quality()GCExpander.set_max_energy()GCExpander.set_optimizer()GCExpander.set_preoptimizer()GCExpander.set_printing_level()GCExpander.set_rngseed()GCExpander.time_to_timestring()GCExpander.to_json()
- 2.2.1. RDKitGenerator
- 2.3. ConformerOptimizer
ConformerOptimizerConformerOptimizer.__init__()ConformerOptimizer.last_timingsConformerOptimizer.set_atom_types()ConformerOptimizer.set_cleaning_preference()ConformerOptimizer.keep_ams_running()ConformerOptimizer.optimize_geometries()ConformerOptimizer.optimize_molecules()ConformerOptimizer.geometry_writer()ConformerOptimizer.convert_key_to_camelcase()ConformerOptimizer.convert_key_to_underscore_case()ConformerOptimizer.convert_keys_to_camelcase()ConformerOptimizer.convert_keys_to_underscore_case()ConformerOptimizer.create_json_entry()ConformerOptimizer.get_json_settings()ConformerOptimizer.handle_input()ConformerOptimizer.pass_settings()ConformerOptimizer.read_settings()ConformerOptimizer.set_blocknames()ConformerOptimizer.to_json()