Components (Settings, Job, …)¶
This section contains description of all components (classes, functions, decorators) that can be used within PLAMS 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 usage.
- Settings
- Tree-like structure
- Dot notation
- Case sensitivity
- API
SettingsSettings.__init__()Settings.copy()Settings.soft_update()Settings.update()Settings.merge()Settings.remove()Settings.difference()Settings.find_case()Settings.get()Settings.pop()Settings.popitem()Settings.setdefault()Settings.as_dict()Settings.suppress_missing()Settings.contains_nested()Settings.get_nested()Settings.set_nested()Settings.pop_nested()Settings.nested_keys()Settings.block_keys()Settings.compare()Settings.flatten()Settings.unflatten()Settings.__iter__()Settings.__missing__()Settings.__contains__()Settings.__getitem__()Settings.__setitem__()Settings.__delitem__()Settings.__getattr__()Settings.__setattr__()Settings.__delattr__()Settings._str()Settings.__str__()Settings.__dir__()Settings.__repr__()Settings.__isub__()Settings.__sub__()
- Global settings
ConfigSettingsConfigSettings.__init__()ConfigSettings.initConfigSettings._explicit_initConfigSettings.previewConfigSettings.sleepstepConfigSettings.ignore_failureConfigSettings.daemon_threadsConfigSettings.erase_workdirConfigSettings.jobmanagerConfigSettings.jobConfigSettings.logConfigSettings.saferunConfigSettings.default_jobrunnerConfigSettings.default_jobmanager
JobSettingsJobManagerSettingsLogSettingsRunScriptSettingsSafeRunSettings
- Jobs
- Results
- Files in the job folder
- Synchronization of parallel job executions
- Cleaning job folder
- API
ResultsResults.__init__()Results.refresh()Results.collect()Results.wait()Results.grep_file()Results.grep_output()Results.read_file()Results.regex_file()Results.awk_file()Results.awk_output()Results.rename()Results.get_file_chunk()Results.get_output_chunk()Results.recreate_molecule()Results.recreate_settings()Results._clean()Results._copy_to()Results._export_attribute()Results._replace_job_name()Results.__getitem__()Results.__contains__()Results._process_file()
ApplyRestrict_caller_name_and_arg()_privileged_access()
- Job runners
- Job manager
- Public functions
- Molecule
- Molecule
MoleculeMolecule.__init__()Molecule.copy()Molecule.add_molecule()Molecule._validate_atom()Molecule._validate_bond()Molecule.add_atom()Molecule.delete_atom()Molecule.delete_atoms()Molecule.add_bond()Molecule.delete_bond()Molecule.delete_all_bonds()Molecule.find_bond()Molecule.set_atoms_id()Molecule.unset_atoms_id()Molecule.neighbors()Molecule.bond_matrix()Molecule.separate()Molecule.guess_bonds()Molecule.guess_system_charge()Molecule.guess_atomic_charges()Molecule.in_ring()Molecule.supercell()Molecule.unit_cell_volume()Molecule.cell_lengths()Molecule.cell_angles()Molecule.set_integer_bonds()Molecule.index()Molecule.round_coords()Molecule.get_connection_table()Molecule.get_molecule_indices()Molecule.get_fragment()Molecule.get_complete_molecules_within_threshold()Molecule.locate_rings()Molecule.locate_rings_acm()Molecule.order_ring()Molecule.locate_rings_networkx()Molecule.shortest_path_dijkstra()Molecule.translate()Molecule.rotate_lattice()Molecule.rotate()Molecule.align_lattice()Molecule.rotate_bond()Molecule.resize_bond()Molecule.closest_atom()Molecule.distance_to_point()Molecule.distance_to_mol()Molecule.wrap()Molecule.get_center_of_mass()Molecule.get_masses()Molecule.get_mass()Molecule.get_density()Molecule.set_density()Molecule.get_formula()Molecule.get_inertia_matrix()Molecule.get_moments_of_inertia()Molecule.get_gyration_radius()Molecule.apply_strain()Molecule.map_to_central_cell()Molecule.perturb_atoms()Molecule.perturb_lattice()Molecule.substitute()Molecule.map_atoms_to_bonds()Molecule.__repr__()Molecule.__len__()Molecule.__str__()Molecule.str()Molecule.__iter__()Molecule.__getitem__()Molecule.__add__()Molecule.__iadd__()Molecule.__round__()Molecule.__getstate__()Molecule.__setstate__()Molecule.as_dict()Molecule.from_dict()Molecule.from_elements()Molecule.as_arrayMolecule.from_array()Molecule.__array__()Molecule.readxyz()Molecule.writexyz()Molecule.readpdb()Molecule.writepdb()Molecule.hydrogen_to_deuterium()Molecule._mol_from_rkf_section()Molecule.forcefield_params_from_rkf()Molecule.readin()Molecule.writein()Molecule.read()Molecule.write()Molecule.add_hatoms()Molecule.rmsd()Molecule.align2mol()Molecule.assign_chirality()Molecule.find_permutation()Molecule.get_chirality()Molecule.label()Molecule.numbersMolecule.readase()Molecule.set_local_labels()Molecule.writease()Molecule.symbolsMolecule._get_bond_id()Molecule.get_unique_bonds()Molecule.get_unique_angles()
- Atom labeling
- Atom
- Bond
- RDKit interface
add_Hs()apply_reaction_smarts()apply_template()get_backbone_atoms()modify_atom()to_rdmol()from_rdmol()from_sequence()from_smiles()from_smarts()to_smiles()partition_protein()readpdb()writepdb()get_substructure()get_conformations()yield_coords()canonicalize_mol()to_image()get_reaction_image()
- ASE interface
- Packmol interface
- Molecule
- Utilities
- Periodic Table
PeriodicTablePeriodicTable.__init__()PeriodicTable.get_atomic_number()PeriodicTable.get_symbol()PeriodicTable.get_mass()PeriodicTable.get_radius()PeriodicTable.get_connectors()PeriodicTable.get_metallic()PeriodicTable.get_electronegative()PeriodicTable.set_mass()PeriodicTable.set_radius()PeriodicTable.set_connectors()PeriodicTable._get_property()PeriodicTable.get_electron_affinity()PeriodicTable.get_ionization_energy()
- Units
- Geometry tools
- File format conversion tools
- Reaction energies
- Plotting tools
- Postprocess results
- Periodic Table
- Trajectories
- XYZ trajectory files
XYZTrajectoryFileXYZTrajectoryFile.__init__()XYZTrajectoryFile.store_historydata()XYZTrajectoryFile.set_name()XYZTrajectoryFile.read_next()XYZTrajectoryFile.write_next()XYZTrajectoryFile.__call__()XYZTrajectoryFile._move_cursor_to_append_pos()XYZTrajectoryFile.close()XYZTrajectoryFile.connection_tableXYZTrajectoryFile.get_elements()XYZTrajectoryFile.get_length()XYZTrajectoryFile.get_plamsmol()XYZTrajectoryFile.moleculeXYZTrajectoryFile.read_frame()XYZTrajectoryFile.read_last_frame()XYZTrajectoryFile.rewind()XYZTrajectoryFile.set_elements()
- XYZ history files
- RKF trajectory files
RKFTrajectoryFileRKFTrajectoryFile.__init__()RKFTrajectoryFile.store_mddata()RKFTrajectoryFile.store_historydata()RKFTrajectoryFile.close()RKFTrajectoryFile._rewrite_molecule()RKFTrajectoryFile._set_mddata_items()RKFTrajectoryFile._move_cursor_to_append_pos()RKFTrajectoryFile._update_celldata()RKFTrajectoryFile.get_plamsmol()RKFTrajectoryFile.read_frame()RKFTrajectoryFile._store_historydata_for_step()RKFTrajectoryFile.read_next()RKFTrajectoryFile.write_next()RKFTrajectoryFile._set_energy()RKFTrajectoryFile._write_dictionary_to_history()RKFTrajectoryFile._flatten_variable()RKFTrajectoryFile.rewind()RKFTrajectoryFile.get_length()RKFTrajectoryFile.read_last_frame()
- RKF history files
- DCD trajectory files
DCDTrajectoryFileDCDTrajectoryFile.__init__()DCDTrajectoryFile.set_byteorder()DCDTrajectoryFile.read_next()DCDTrajectoryFile.write_next()DCDTrajectoryFile.__call__()DCDTrajectoryFile._move_cursor_to_append_pos()DCDTrajectoryFile.close()DCDTrajectoryFile.connection_tableDCDTrajectoryFile.get_elements()DCDTrajectoryFile.get_length()DCDTrajectoryFile.get_plamsmol()DCDTrajectoryFile.moleculeDCDTrajectoryFile.read_frame()DCDTrajectoryFile.read_last_frame()DCDTrajectoryFile.rewind()DCDTrajectoryFile.set_elements()
- Trajectory class
- XYZ trajectory files
- Job Analysis
- Adding Jobs
- Adding Analysis Fields
- Modifying Analysis
- Extracting Analysis
- API
JobAnalysisJobAnalysis.__init__()JobAnalysis.copy()JobAnalysis.jobsJobAnalysis.field_keysJobAnalysis.get_analysis()JobAnalysis._expand_analysis()JobAnalysis.to_dataframe()JobAnalysis.to_table()JobAnalysis.display_table()JobAnalysis.to_csv_file()JobAnalysis.get_timeline()JobAnalysis.display_timeline()JobAnalysis.add_job()JobAnalysis.remove_job()JobAnalysis.load_job()JobAnalysis.filter_jobs()JobAnalysis.sort_jobs()JobAnalysis.add_field()JobAnalysis.set_field()JobAnalysis.format_field()JobAnalysis.rename_field()JobAnalysis.expand_field()JobAnalysis.collapse_field()JobAnalysis.reorder_fields()JobAnalysis.sort_fields()JobAnalysis.remove_field()JobAnalysis.remove_fields()JobAnalysis.filter_fields()JobAnalysis.remove_empty_fields()JobAnalysis.remove_uniform_fields()JobAnalysis.add_standard_fields()JobAnalysis.add_standard_field()JobAnalysis.add_settings_field()JobAnalysis.add_settings_fields()JobAnalysis.add_settings_input_fields()JobAnalysis.remove_settings_fields()JobAnalysis.__str__()JobAnalysis.__repr__()JobAnalysis.__getitem__()JobAnalysis.__setitem__()JobAnalysis.__delitem__()JobAnalysis.__getattr__()JobAnalysis.__setattr__()JobAnalysis.__delattr__()JobAnalysis.__contains__()