Index

A

add_fragment() (ADFFragmentJob method) add_nics_point() (NMRJob method) add_postamble() (Job method) add_postscript() (Job method) add_preamble() (Job method) add_server() (Job method) ADFFragmentJob (class in tcutility.job.adf) ADFJob (class in tcutility.job.adf) align_to_plane() (MolTransform method) align_to_vector() (MolTransform method)

alpb() (QCGJob method) AMSJob (class in tcutility.job.ams) ANGLE (GeometricParameter attribute) angstrom (Emojis attribute) apply() (Transform method) apply_rotmat() (in module tcutility.geometry) as_plams_settings() (Result method) atom_index (VDDCharge attribute) atom_number() (in module tcutility.data.atom) atom_symbol (VDDCharge attribute) avg_relative_bond_length_delta() (in module tcutility.analysis.vibration.ts_vibration)

B

basis_set() (ADFJob method) (ORCAJob method) Bazis (class in tcutility.connect)

best_conformer_path (CRESTJob property) best_ensemble_path (QCGJob property) boxed() (in module tcutility.log)

C

cache() (in module tcutility.cache) cache_file() (in module tcutility.cache) calc_dir (VDDChargeManager attribute) caller_name() (in module tcutility.log) can_skip() (DensfJob method) (Job method) cancel (Emojis attribute) cd() (Connection method) center() (MolTransform method) change_unit() (VDDCharge method) (VDDChargeManager method) change_unit_decorator() (in module tcutility.analysis.vdd.manager) charge (VDDCharge attribute) charge() (AMSJob method) (CRESTJob method) (ORCAJob method) (XTBJob method)

charge_is_conserved() (VDDChargeManager method) check() (in module tcutility.spell_check) chmod() (Connection method) (Local method) cite() (in module tcutility.cite) close() (Connection method) color() (in module tcutility.data.atom) combine_transforms() (Transform method) conformer_directory (CRESTJob property) Connection (class in tcutility.connect) coord() (PyFragResult method) COORDINATE (GeometricParameter attribute) copy() (Job method) (Result method) create_vdd_charge_manager() (in module tcutility.analysis.vdd.manager) CRESTJob (class in tcutility.job.crest) critical() (in module tcutility.log)

D

debug() (in module tcutility.log) DensfJob (class in tcutility.job.adf) density() (DensfJob method) dependency() (Job method) determine_ts_reactioncoordinate() (in module tcutility.analysis.vibration.ts_vibration)

DFTBJob (class in tcutility.job.dftb) DIHEDRAL (GeometricParameter attribute) DISTANCE (GeometricParameter attribute) Docx (class in tcutility.cli_scripts.cite) download() (Connection method) (Local method)

E

electric_field() (AMSJob method) element() (in module tcutility.data.atom) Emojis (class in tcutility.log) empty (Emojis attribute) ensemble_directory (QCGJob property) ensemble_mode() (QCGJob method)

ensure_2d() (in module tcutility) ensure_list() (in module tcutility) error() (in module tcutility.log) excitations() (ADFJob method) execute() (Connection method) (Local method)

F

fail (Emojis attribute) finish (Emojis attribute) flow() (in module tcutility.log) format_paragraph() (in module tcutility.cli_scripts.cite) frag_index (VDDCharge attribute)

frag_occupations() (ADFFragmentJob method) fragments (PyFragResult property) from_string() (in module tcutility.molecule) full_path() (Connection method) functional() (ADFJob method) functional_name_from_path_safe_name() (in module tcutility.data.functionals)

G

GeometricParameter (class in tcutility.cli_scripts.geo) geometry_convergence() (AMSJob method) get() (in module tcutility.data.functionals) (in module tcutility.data.molecules) (in module tcutility.results.cache) get_ams_info() (in module tcutility.results.ams) get_ams_input() (in module tcutility.results.ams) get_ams_version() (in module tcutility.results.ams) get_available_functionals() (in module tcutility.data.functionals) get_calc_files() (in module tcutility.results.ams) (in module tcutility.results.crest) (in module tcutility.results.orca) (in module tcutility.results.xtb) get_calc_settings() (in module tcutility.results.adf) (in module tcutility.results.dftb) (in module tcutility.results.orca) get_calculation_status() (in module tcutility.results.ams) (in module tcutility.results.crest) (in module tcutility.results.orca) (in module tcutility.results.xtb) get_closest() (in module tcutility.spell_check) get_conformer_xyz() (CRESTJob method) get_current_server() (in module tcutility.connect) get_ensemble_xyz() (QCGJob method) get_geometry() (PyFragResult method) get_history() (in module tcutility.results.ams) get_info() (in module tcutility.results) (in module tcutility.results.crest) (in module tcutility.results.orca) (in module tcutility.results.xtb) get_input() (in module tcutility.results.crest) (in module tcutility.results.orca) (in module tcutility.results.xtb) (ORCAJob method) get_input_blocks() (in module tcutility.results.ams) get_level_of_theory() (in module tcutility.results.adf) (in module tcutility.results.orca) get_memory_usage() (ORCAJob method)

get_molecules() (in module tcutility.data.molecules) (in module tcutility.results.ams) (in module tcutility.results.crest) (in module tcutility.results.orca) (in module tcutility.results.xtb) get_multi_key() (Result method) get_os_name() (in module tcutility.environment) get_pages() (in module tcutility.cite) get_parent_tree() (Result method) get_pes() (in module tcutility.results.ams) get_pixel_width() (in module tcutility.report.character) get_properties() (in module tcutility.results.adf) (in module tcutility.results.dftb) (in module tcutility.results.orca) (in module tcutility.results.xtb) get_property() (PyFragResult method) get_rotamer_xyz() (CRESTJob method) get_rotmat() (in module tcutility.geometry) (Transform method) get_subdirectories() (in module tcutility.pathfunc) get_summed_vdd_charges() (VDDChargeManager method) get_summed_vdd_charges_dataframe() (VDDChargeManager method) get_summed_vdd_charges_table() (VDDChargeManager method) get_timing() (in module tcutility.results.ams) get_translation() (Transform method) get_vdd_charges() (VDDChargeManager method) get_vdd_charges_dataframe() (VDDChargeManager method) get_vdd_charges_table() (VDDChargeManager method) get_version() (in module tcutility.results.crest) (in module tcutility.results.orca) (in module tcutility.results.xtb) get_vibrations() (in module tcutility.results.orca) getsizeof() (Result method) ghost_atoms() (ORCAJob method) good (Emojis attribute) grid() (DensfJob method) gridsize() (DensfJob method) guess_fragments() (ADFFragmentJob method) (in module tcutility.molecule)

H

has_slurm() (in module tcutility.slurm)

I

in_queue() (Job method) info (Emojis attribute) info() (in module tcutility.log) inputfile_path (Job property) interaction_energy() (PyFragResult method)

IRC() (AMSJob method) irreps (VDDChargeManager attribute) is_accepted() (in module tcutility.cite) is_fragment_calculation (VDDChargeManager attribute) items() (Result method)

J

Job (class in tcutility.job.generic)

K

KabschTransform (class in tcutility.geometry)

keys() (Result method) kspace() (DFTBJob method)

L

larrow (Emojis attribute) LINUX (OSName attribute) load() (in module tcutility.molecule) loadbar() (in module tcutility.log)

Local (class in tcutility.connect) log() (in module tcutility.log) lrarrow (Emojis attribute) ls() (Connection method) (Local method)

M

MACOS (OSName attribute) main() (ORCAJob method) make_suggestion() (in module tcutility.spell_check) match() (in module tcutility.pathfunc) md_length() (CRESTJob method) md_temperature() (CRESTJob method) method() (ORCAJob method) mkdir() (Connection method) (Local method) model() (DFTBJob method) (XTBJob method) module tcutility tcutility.analysis tcutility.analysis.pyfrag tcutility.analysis.vdd tcutility.analysis.vdd.charge tcutility.analysis.vdd.manager tcutility.analysis.vibration tcutility.analysis.vibration.ts_vibration tcutility.cache tcutility.cite tcutility.cli_scripts tcutility.cli_scripts.cite tcutility.cli_scripts.geo tcutility.cli_scripts.job_script tcutility.cli_scripts.read tcutility.cli_scripts.resize_figures tcutility.connect tcutility.constants tcutility.data tcutility.data.atom tcutility.data.basis_sets tcutility.data.cosmo tcutility.data.functionals tcutility.data.molecules tcutility.environment tcutility.errors tcutility.formula tcutility.geometry tcutility.job tcutility.job.adf tcutility.job.ams tcutility.job.crest tcutility.job.dftb tcutility.job.generic tcutility.job.nmr tcutility.job.orca tcutility.job.postscripts tcutility.job.postscripts.clean_workdir tcutility.job.postscripts.split_crest_xyz tcutility.job.postscripts.write_converged_geoms tcutility.job.xtb tcutility.log tcutility.molecule tcutility.pathfunc tcutility.report, [1] tcutility.report.character tcutility.report.figure_resizer tcutility.results tcutility.results.adf tcutility.results.ams tcutility.results.cache tcutility.results.crest tcutility.results.dftb tcutility.results.orca tcutility.results.result tcutility.results.xtb tcutility.slurm tcutility.spell_check tcutility.tc_typing tcutility.tc_typing.arrays tcutility.timer

mol_charge (VDDChargeManager attribute) molecule() (in module tcutility.formula) (Job method) (ORCAJob method) MolTransform (class in tcutility.geometry) multi_keys() (Result method) multiplicity() (ADFJob method) (CRESTJob method) (ORCAJob method) (XTBJob method)

N

naive_recursive() (in module tcutility.spell_check) name (VDDChargeManager attribute) NCI() (DensfJob method) NMRJob (class in tcutility.job.nmr) nofix() (QCGJob method)

NoPrint (class in tcutility.log) nsolv() (QCGJob method) number_of_electrons() (in module tcutility.molecule) number_of_orbitals() (in module tcutility.data.basis_sets) number_of_virtuals() (in module tcutility.data.basis_sets)

O

occupations() (ADFJob method) open() (Connection method) (Docx method) open_file() (Connection method) (Local method) optimization() (AMSJob method) (ORCAJob method) (XTBJob method) orbital() (DensfJob method)

orbital_energy_gap() (PyFragResult method) orbs() (PyFragResult method) ORCAJob (class in tcutility.job.orca) OSName (class in tcutility.environment) output_cub_paths (DensfJob property) output_mol_path (AMSJob property) (Job property) (ORCAJob property) (XTBJob property) overlap() (PyFragResult method)

P

parameter() (in module tcutility.geometry) parse_element() (in module tcutility.data.atom) parse_molecule() (in module tcutility.formula) path_depth() (in module tcutility.pathfunc) path_exists() (Connection method) (Local method) PESScan() (AMSJob method) (XTBJob method) plot_vdd_charges_per_atom() (VDDChargeManager method) postamble_defaults (Bazis attribute) (Local attribute) (Server attribute)

preamble_defaults (Bazis attribute) (Local attribute) (Server attribute) print_timings() (in module tcutility.timer) program_modules (Bazis attribute) (Local attribute) (Server attribute) (Snellius attribute) prune() (Result method) pwd() (Connection method) (Local method) PyFragResult (class in tcutility.analysis.pyfrag) PYRAMIDAL (GeometricParameter attribute)

Q

QCGJob (class in tcutility.job.crest) QRO() (ORCAJob method)

quality() (ADFJob method) question (Emojis attribute) quick_status() (in module tcutility.results)

R

radius() (in module tcutility.data.atom) random_points_in_anular_sphere() (in module tcutility.geometry) random_points_on_sphere() (in module tcutility.geometry) random_points_on_spheroid() (in module tcutility.geometry) rarrow (Emojis attribute) read() (in module tcutility.analysis.pyfrag) (in module tcutility.results) (TrackKFReader method) receive (Emojis attribute) rectangle_list() (in module tcutility.log) reference() (ORCAJob method) reflect() (Transform method) relativity() (ADFJob method) remove_main() (ORCAJob method) remove_virtuals() (ADFFragmentJob method)

resize() (in module tcutility.report.figure_resizer) Result (class in tcutility.results.result) rlarrow (Emojis attribute) rm() (Connection method) (Local method) RMSD() (in module tcutility.geometry) rmtree() (Connection method) (Local method) rotamer_directory (CRESTJob property) rotate() (in module tcutility.geometry) (Transform method) rotmat_to_angles() (in module tcutility.geometry) run() (ADFFragmentJob method) (Job method) runfile_path (Job property)

S

save() (in module tcutility.molecule) sbatch() (in module tcutility.slurm) (Job method) sbatch_defaults (Bazis attribute) (Local attribute) (Server attribute) (Snellius attribute) scale() (Transform method) SCF() (ADFJob method) SCF_convergence() (ADFJob method) send (Emojis attribute) server (Bazis attribute) Server (class in tcutility.connect) server (Local attribute) (Server attribute) (Snellius attribute) ServerFile (class in tcutility.connect) set_coord() (PyFragResult method) set_mask() (PyFragResult method) set_property() (PyFragResult method) sfo_coefficient() (PyFragResult method)

single_point() (AMSJob method) (ORCAJob method) sleep (Emojis attribute) Snellius (class in tcutility.connect) solvent() (ADFJob method) (DFTBJob method) (QCGJob method) (XTBJob method) sort_by() (PyFragResult method) spin_polarization() (ADFJob method) (CRESTJob method) (ORCAJob method) (XTBJob method) split_all() (in module tcutility.pathfunc) squeeze_list() (in module tcutility) squeue() (in module tcutility.slurm) store() (in module tcutility.results.cache) strain_energy() (PyFragResult method) SUMOFANGLES (GeometricParameter attribute) symbol() (in module tcutility.data.atom) symmetry() (ADFJob method)

T

table() (in module tcutility.log) TCCompDetailsError TCError TCJobError TCMoleculeError tcutility module tcutility.analysis module tcutility.analysis.pyfrag module tcutility.analysis.vdd module tcutility.analysis.vdd.charge module tcutility.analysis.vdd.manager module tcutility.analysis.vibration module tcutility.analysis.vibration.ts_vibration module tcutility.cache module tcutility.cite module tcutility.cli_scripts module tcutility.cli_scripts.cite module tcutility.cli_scripts.geo module tcutility.cli_scripts.job_script module tcutility.cli_scripts.read module tcutility.cli_scripts.resize_figures module tcutility.connect module tcutility.constants module tcutility.data module tcutility.data.atom module tcutility.data.basis_sets module tcutility.data.cosmo module tcutility.data.functionals module tcutility.data.molecules module tcutility.environment module tcutility.errors module tcutility.formula module tcutility.geometry module tcutility.job module tcutility.job.adf module tcutility.job.ams module tcutility.job.crest module

tcutility.job.dftb module tcutility.job.generic module tcutility.job.nmr module tcutility.job.orca module tcutility.job.postscripts module tcutility.job.postscripts.clean_workdir module tcutility.job.postscripts.split_crest_xyz module tcutility.job.postscripts.write_converged_geoms module tcutility.job.xtb module tcutility.log module tcutility.molecule module tcutility.pathfunc module tcutility.report module, [1] tcutility.report.character module tcutility.report.figure_resizer module tcutility.results module tcutility.results.adf module tcutility.results.ams module tcutility.results.cache module tcutility.results.crest module tcutility.results.dftb module tcutility.results.orca module tcutility.results.result module tcutility.results.xtb module tcutility.slurm module tcutility.spell_check module tcutility.tc_typing module tcutility.tc_typing.arrays module tcutility.timer module text_width() (in module tcutility.report.character) time_stamp() (in module tcutility.log) timed_cache() (in module tcutility.cache) timer (class in tcutility.timer) to_vtkTransform() (Transform method) total_energy() (PyFragResult method) TrackKFReader (class in tcutility.results.cache) Transform (class in tcutility.geometry) transition_state() (AMSJob method) (ORCAJob method) translate() (Transform method) ts_idx (PyFragResult property)

U

unit (VDDChargeManager attribute) unload() (in module tcutility.results.cache) unrestricted() (ADFJob method)

upload() (Connection method) (Local method) use_version() (AMSJob method)

V

validate_transitionstate() (in module tcutility.analysis.vibration.ts_vibration) vdd_charges (VDDChargeManager attribute) VDDCharge (class in tcutility.analysis.vdd.charge) VDDChargeManager (class in tcutility.analysis.vdd.manager)

vector_align_rotmat() (in module tcutility.geometry) vibrations() (AMSJob method) (ORCAJob method) (XTBJob method)

W

wagner_fischer() (in module tcutility.spell_check) wait (Emojis attribute) wait_for_job() (in module tcutility.slurm) warn() (in module tcutility.log) warning (Emojis attribute) WINDOWS (OSName attribute)

workdir (Job property) workdir_info() (in module tcutility.slurm) write_mol_to_amv_file() (in module tcutility.molecule) write_mol_to_xyz_file() (in module tcutility.molecule) write_paragraph() (Docx method) write_to_excel() (VDDChargeManager method) write_to_txt() (VDDChargeManager static method)

X

XTBJob (class in tcutility.job.xtb)