Index A | B | C | D | E | F | G | H | I | L | M | N | O | P | Q | R | S | T | V | W | X A add() (compechem.systems.Ensemble method) append() (compechem.core.geometry.MolecularGeometry method) atomcount (compechem.core.geometry.MolecularGeometry property) (compechem.systems.Ensemble property) atomic_numbers (compechem.core.geometry.MolecularGeometry property) atoms (compechem.core.geometry.MolecularGeometry property) auto_calculate_pka() (in module compechem.functions) B boltzmann_average() (compechem.systems.Ensemble method) buried_volume_fraction() (compechem.core.geometry.MolecularGeometry method) C calc_hess (compechem.engines.orca.OrcaJobInfo attribute) calculate_fukui() (in module compechem.functions) calculate_pka() (in module compechem.functions) calculate_reduction_potential() (in module compechem.functions) compechem.core.dependency_finder module compechem.core.geometry module compechem.tools.vmdtools module compress_dftb_trajectory() (in module compechem.tools) condensed_fukui_hirshfeld (compechem.core.properties.Properties property) condensed_fukui_mulliken (compechem.core.properties.Properties property) conformer_search() (in module compechem.wrappers.crest) constraints (compechem.engines.orca.OrcaJobInfo attribute) coordinates (compechem.core.geometry.MolecularGeometry property) cpcm_block (compechem.engines.orca.OrcaJobInfo property) cube_dim (compechem.engines.orca.OrcaJobInfo attribute) cyclization_check() (in module compechem.tools) D deprotonate() (in module compechem.wrappers.crest) DFTBInput (class in compechem.engines.dftbplus) dispersion (compechem.engines.dftbplus.DFTBInput attribute) dissociation_check() (in module compechem.tools) E electronic_energy (compechem.core.properties.Properties property) elprop_block (compechem.engines.orca.OrcaJobInfo property) Engine (class in compechem.core.base) Ensemble (class in compechem.systems) F freq (compechem.engines.orca.OrcaJobInfo attribute) freq() (compechem.engines.orca.OrcaInput method) (compechem.engines.xtb.XtbInput method) from_dict() (compechem.core.geometry.MolecularGeometry class method) (compechem.core.properties.Properties class method) from_xyz() (compechem.core.geometry.MolecularGeometry class method) fullscan (compechem.engines.orca.OrcaJobInfo attribute) G geom_block (compechem.engines.orca.OrcaJobInfo property) gibbs_free_energy (compechem.core.properties.Properties property) H helmholtz_free_energy (compechem.core.properties.Properties property) hirshfeld (compechem.engines.orca.OrcaJobInfo attribute) hirshfeld_charges (compechem.core.properties.Properties property) hirshfeld_spin_populations (compechem.core.properties.Properties property) I invert_constraints (compechem.engines.orca.OrcaJobInfo attribute) is_periodic (compechem.systems.System property) is_singlet (compechem.engines.orca.OrcaJobInfo attribute) L level_of_theory_electronic (compechem.core.properties.Properties property) level_of_theory_geometry (compechem.core.geometry.MolecularGeometry attribute) level_of_theory_vibronic (compechem.core.properties.Properties property) load_xyz() (compechem.core.geometry.MolecularGeometry method) locate_crest() (in module compechem.core.dependency_finder) locate_dftbparamdir() (in module compechem.core.dependency_finder) locate_dftbplus() (in module compechem.core.dependency_finder) locate_executable() (in module compechem.core.dependency_finder) locate_orca() (in module compechem.core.dependency_finder) locate_vmd() (in module compechem.core.dependency_finder) locate_xtb() (in module compechem.core.dependency_finder) M mass (compechem.core.geometry.MolecularGeometry property) maxcore (compechem.engines.orca.OrcaJobInfo property) maxdist() (in module compechem.tools) md_nvt() (compechem.engines.dftbplus.DFTBInput method) method (compechem.engines.dftbplus.DFTBInput attribute) module compechem.core.dependency_finder compechem.core.geometry compechem.tools.vmdtools MolecularGeometry (class in compechem.core.geometry) mulliken_charges (compechem.core.properties.Properties property) mulliken_spin_populations (compechem.core.properties.Properties property) N name (compechem.systems.Ensemble attribute) ncores (compechem.engines.orca.OrcaJobInfo property) nearir (compechem.engines.orca.OrcaJobInfo attribute) neb_block (compechem.engines.orca.OrcaJobInfo property) neb_ci (compechem.engines.orca.OrcaJobInfo attribute) neb_ci() (compechem.engines.orca.OrcaInput method) neb_images (compechem.engines.orca.OrcaJobInfo attribute) neb_preopt (compechem.engines.orca.OrcaJobInfo attribute) neb_product (compechem.engines.orca.OrcaJobInfo attribute) neb_ts() (compechem.engines.orca.OrcaInput method) neb_ts_guess (compechem.engines.orca.OrcaJobInfo attribute) nfreq (compechem.engines.orca.OrcaJobInfo attribute) nfreq() (compechem.engines.orca.OrcaInput method) O opt (compechem.engines.orca.OrcaJobInfo attribute) opt() (compechem.engines.dftbplus.DFTBInput method) (compechem.engines.orca.OrcaInput method) (compechem.engines.xtb.XtbInput method) opt_ts (compechem.engines.orca.OrcaJobInfo attribute) opt_ts() (compechem.engines.orca.OrcaInput method) optimization_level (compechem.engines.orca.OrcaJobInfo property) OrcaInput (class in compechem.engines.orca) OrcaJobInfo (class in compechem.engines.orca) output_block (compechem.engines.orca.OrcaJobInfo property) output_suffix (compechem.engines.orca.OrcaInput property) (compechem.engines.xtb.XtbInput property) P packmol_cube() (in module compechem.wrappers.packmol) parallel (compechem.engines.dftbplus.DFTBInput attribute) parameters (compechem.engines.dftbplus.DFTBInput attribute) parse_output() (compechem.engines.dftbplus.DFTBInput method) (compechem.engines.orca.OrcaInput method) (compechem.engines.xtb.XtbInput method) parsed_blocks (compechem.engines.orca.OrcaJobInfo property) pka (compechem.core.properties.Properties property) plots_block (compechem.engines.orca.OrcaJobInfo property) print_level (compechem.engines.orca.OrcaJobInfo property) process_output() (in module compechem.tools) Properties (class in compechem.core.properties) properties (compechem.systems.Ensemble attribute) protonate() (in module compechem.wrappers.crest) Q qcg_ensemble() (in module compechem.wrappers.crest) qcg_grow() (in module compechem.wrappers.crest) R raman (compechem.engines.orca.OrcaJobInfo attribute) render_condensed_fukui() (in module compechem.tools.vmdtools) render_fukui_cube() (in module compechem.tools.vmdtools) render_spin_density_cube() (in module compechem.tools.vmdtools) reorder_energies() (in module compechem.tools) S save_dftb_trajectory() (in module compechem.tools) save_json() (compechem.systems.System method) scan (compechem.engines.orca.OrcaJobInfo attribute) scan() (compechem.engines.orca.OrcaInput method) scan_ts (compechem.engines.orca.OrcaJobInfo attribute) scan_ts() (compechem.engines.orca.OrcaInput method) scf_convergence_level (compechem.engines.orca.OrcaJobInfo property) scf_convergence_strategy (compechem.engines.orca.OrcaJobInfo property) set_condensed_fukui_hirshfeld() (compechem.core.properties.Properties method) set_condensed_fukui_mulliken() (compechem.core.properties.Properties method) set_electronic_energy() (compechem.core.properties.Properties method) set_gibbs_free_energy() (compechem.core.properties.Properties method) set_helmholtz_free_energy() (compechem.core.properties.Properties method) set_hirshfeld_charges() (compechem.core.properties.Properties method) set_hirshfeld_spin_populations() (compechem.core.properties.Properties method) set_mulliken_charges() (compechem.core.properties.Properties method) set_mulliken_spin_populations() (compechem.core.properties.Properties method) set_pka() (compechem.core.properties.Properties method) set_vibrational_data() (compechem.core.properties.Properties method) set_vibronic_energy() (compechem.core.properties.Properties method) simulated_annealing() (compechem.engines.dftbplus.DFTBInput method) solvent (compechem.engines.orca.OrcaJobInfo attribute) solver (compechem.engines.dftbplus.DFTBInput attribute) spe() (compechem.engines.dftbplus.DFTBInput method) (compechem.engines.orca.OrcaInput method) (compechem.engines.xtb.XtbInput method) split_multixyz() (in module compechem.tools) System (class in compechem.systems) systems (compechem.systems.Ensemble attribute) T tautomer_search() (in module compechem.wrappers.crest) to_dict() (compechem.core.geometry.MolecularGeometry method) (compechem.core.properties.Properties method) V verbose (compechem.engines.dftbplus.DFTBInput attribute) vibrational_data (compechem.core.properties.Properties property) vibronic_energy (compechem.core.properties.Properties property) W write_gen() (compechem.systems.System method) write_input() (compechem.engines.orca.OrcaInput method) write_xyz() (compechem.core.geometry.MolecularGeometry method) X XtbInput (class in compechem.engines.xtb)