Index A | B | C | D | E | F | G | I | J | K | L | M | N | O | P | Q | R | S | T | V | W | X | Y A add_data() (proteindf_tools.pdfgraph.DfLineChart method) add_draw_series() (proteindf_tools.pdfgraph.DfDosGraph method) aspect (proteindf_tools.pdfgraph.DfGraph property) B BarGraph (class in proteindf_tools.pdfgraph) Basis2 (class in proteindf_tools) (class in proteindf_tools.basis2) BasisSet (class in proteindf_tools) (class in proteindf_tools.basisset) basisset (proteindf_tools.gauparam.GaussianParam property) (proteindf_tools.GaussianParam property) BasisSetParser (class in proteindf_tools.basisset_parser) C CD_epsilon (proteindf_tools.pdfparam_object.PdfParamObject property) CDAM_tau (proteindf_tools.pdfparam_object.PdfParamObject property) charge (proteindf_tools.gauparam.GaussianParam property) (proteindf_tools.GaussianParam property) cmap (proteindf_tools.pdfgraph.DfMatrixGraph property) cmd() (proteindf_tools.process.Process method) coef (proteindf_tools.basisset.PrimitiveGTO property) (proteindf_tools.PrimitiveGTO property) colors (proteindf_tools.pdfgraph.Graph attribute) comment (proteindf_tools.pdfparam_object.PdfParamObject property) commit() (proteindf_tools.process.Process method) compare_energy() (proteindf_tools.pdfarchive_sqlite3.PdfArchive_Sqlite3 method) (proteindf_tools.pdfparam_object.PdfParamObject method) compare_grad() (proteindf_tools.pdfarchive_sqlite3.PdfArchive_Sqlite3 method) (proteindf_tools.pdfparam_object.PdfParamObject method) compare_info() (proteindf_tools.pdfarchive_sqlite3.PdfArchive_Sqlite3 method) (proteindf_tools.pdfparam_object.PdfParamObject method) compare_pop() (proteindf_tools.pdfarchive_sqlite3.PdfArchive_Sqlite3 method) (proteindf_tools.pdfparam_object.PdfParamObject method) connection_color (proteindf_tools.pdfgraph.DfEnergyLevelTraceGraph property) ContractedGTO (class in proteindf_tools) (class in proteindf_tools.basisset) convergence_threshold (proteindf_tools.pdfparam_object.PdfParamObject property) convergence_threshold_energy (proteindf_tools.pdfparam_object.PdfParamObject property) convergence_type (proteindf_tools.pdfparam_object.PdfParamObject property) counterpoise (proteindf_tools.pdfparam_object.PdfParamObject property) cut_value (proteindf_tools.pdfparam_object.PdfParamObject property) D dbfact() (proteindf_tools.pdfmath.Math static method) deprecated() (in module proteindf_tools.functions) DfDistanceVsElementGraph (class in proteindf_tools.pdfgraph) DfDosGraph (class in proteindf_tools.pdfgraph) DfEnergyLevelHistoryGraphH (class in proteindf_tools.pdfgraph) DfEnergyLevelHistoryGraphV (class in proteindf_tools.pdfgraph) DfEnergyLevelTraceGraph (class in proteindf_tools.pdfgraph) DfGraph (class in proteindf_tools.pdfgraph) DfGvalsGraph (class in proteindf_tools.pdfgraph) DfLineChart (class in proteindf_tools.pdfgraph) DfMatrixGraph (class in proteindf_tools.pdfgraph) DfPopulationGraph (class in proteindf_tools.pdfgraph) DfTotalEnergyHistGraph (class in proteindf_tools.pdfgraph) DfVectorGraph (class in proteindf_tools.pdfgraph) digest() (proteindf_tools.pdfparam_object.PdfParamObject method) draw_grid() (proteindf_tools.pdfgraph.Graph method) draw_legend() (proteindf_tools.pdfgraph.Graph method) E EnergyLevelChart (class in proteindf_tools.pdfgraph) exp (proteindf_tools.basisset.PrimitiveGTO property) (proteindf_tools.PrimitiveGTO property) expand() (proteindf_tools.BasisSet method) (proteindf_tools.basisset.BasisSet method) (proteindf_tools.basisset.ContractedGTO method) (proteindf_tools.ContractedGTO method) ext_basisset (proteindf_tools.gauparam.GaussianParam property) (proteindf_tools.GaussianParam property) extra_keywords (proteindf_tools.pdfparam_object.PdfParamObject property) F file_out() (proteindf_tools.pdfgraph.Graph method) filepath (proteindf_tools.pdfparam_hdf5.PdfParam_H5 property) find_atom_index() (proteindf_tools.pdfparam_object.PdfParamObject method) find_header_struct() (proteindf_tools.Matrix class method) (proteindf_tools.matrix.Matrix class method) (proteindf_tools.matrix.SymmetricMatrix class method) (proteindf_tools.SymmetricMatrix class method) (proteindf_tools.Vector class method) (proteindf_tools.vector.Vector class method) G GaussianParam (class in proteindf_tools) (class in proteindf_tools.gauparam) get_atom() (proteindf_tools.OrbInfo method) (proteindf_tools.orbinfo.OrbInfo method) get_atom_id() (proteindf_tools.OrbInfo method) (proteindf_tools.orbinfo.OrbInfo method) get_atomlist_by_param() (proteindf_tools.PopUtils static method) (proteindf_tools.poputils.PopUtils static method) get_basis2() (proteindf_tools.Basis2 method) (proteindf_tools.basis2.Basis2 method) (proteindf_tools.BasisSet method) (proteindf_tools.basisset.BasisSet method) get_basis_type() (proteindf_tools.basisset.ContractedGTO class method) (proteindf_tools.ContractedGTO class method) (proteindf_tools.OrbInfo method) (proteindf_tools.orbinfo.OrbInfo method) get_basisset() (proteindf_tools.Basis2 method) (proteindf_tools.basis2.Basis2 method) (proteindf_tools.pdfarchive_sqlite3.PdfArchive_Sqlite3 method) (proteindf_tools.pdfparam_object.PdfParamObject method) get_basisset_atomlabels() (proteindf_tools.pdfparam_object.PdfParamObject method) get_basisset_gridfree() (proteindf_tools.pdfparam_object.PdfParamObject method) get_basisset_gridfree_atomlabels() (proteindf_tools.pdfparam_object.PdfParamObject method) get_basisset_gridfree_name() (proteindf_tools.pdfparam_object.PdfParamObject method) get_basisset_j() (proteindf_tools.Basis2 method) (proteindf_tools.basis2.Basis2 method) (proteindf_tools.pdfparam_object.PdfParamObject method) get_basisset_j_atomlabels() (proteindf_tools.pdfparam_object.PdfParamObject method) get_basisset_j_name() (proteindf_tools.pdfparam_object.PdfParamObject method) get_basisset_name() (proteindf_tools.pdfarchive_sqlite3.PdfArchive_Sqlite3 method) (proteindf_tools.pdfparam_object.PdfParamObject method) get_basisset_xc() (proteindf_tools.Basis2 method) (proteindf_tools.basis2.Basis2 method) (proteindf_tools.pdfparam_object.PdfParamObject method) get_basisset_xc_atomlabels() (proteindf_tools.pdfparam_object.PdfParamObject method) get_basisset_xc_name() (proteindf_tools.pdfparam_object.PdfParamObject method) get_c_mat_path() (proteindf_tools.pdfparam_object.PdfParamObject method) get_c_matrix() (proteindf_tools.pdfparam_hdf5.PdfParam_H5 method) get_clo_mat_path() (proteindf_tools.pdfparam_object.PdfParamObject method) get_default_pdfparam() (in module proteindf_tools.pdfcommon) get_density_matrix() (proteindf_tools.pdfparam_hdf5.PdfParam_H5 method) get_density_matrix_path() (proteindf_tools.pdfparam_object.PdfParamObject method) get_energy_level() (proteindf_tools.pdfparam_hdf5.PdfParam_H5 method) get_energy_level_path() (proteindf_tools.pdfparam_object.PdfParamObject method) get_energylevel() (proteindf_tools.pdfarchive_sqlite3.PdfArchive_Sqlite3 method) get_f_mat_path() (proteindf_tools.pdfparam_object.PdfParamObject method) get_f_matrix() (proteindf_tools.pdfparam_hdf5.PdfParam_H5 method) get_gradient() (proteindf_tools.pdfarchive_sqlite3.PdfArchive_Sqlite3 method) (proteindf_tools.pdfparam_object.PdfParamObject method) get_gradient_matrix_path() (proteindf_tools.pdfparam_object.PdfParamObject method) get_gradient_rms() (proteindf_tools.pdfarchive_sqlite3.PdfArchive_Sqlite3 method) (proteindf_tools.pdfparam_object.PdfParamObject method) get_h2_mat_path() (proteindf_tools.pdfparam_object.PdfParamObject method) get_h2_matrix() (proteindf_tools.pdfparam_hdf5.PdfParam_H5 method) get_h_mat_path() (proteindf_tools.pdfparam_object.PdfParamObject method) get_h_matrix() (proteindf_tools.pdfparam_hdf5.PdfParam_H5 method) get_HOMO_level() (proteindf_tools.pdfarchive_sqlite3.PdfArchive_Sqlite3 method) (proteindf_tools.pdfparam_hdf5.PdfParam_H5 method) get_inputfile_contents() (proteindf_tools.gauparam.GaussianParam method) (proteindf_tools.GaussianParam method) (proteindf_tools.pdfparam_object.PdfParamObject method) get_molecule() (proteindf_tools.pdfarchive_sqlite3.PdfArchive_Sqlite3 method) get_mulliken_atom_population() (proteindf_tools.pdfparam_object.PdfParamObject method) get_num_of_CGTOs() (proteindf_tools.BasisSet method) (proteindf_tools.basisset.BasisSet method) get_num_of_orbitals() (proteindf_tools.OrbInfo method) (proteindf_tools.orbinfo.OrbInfo method) get_number_of_AOs() (proteindf_tools.BasisSet method) (proteindf_tools.basisset.BasisSet method) get_occ_path() (proteindf_tools.pdfparam_object.PdfParamObject method) get_occ_vector() (proteindf_tools.pdfparam_hdf5.PdfParam_H5 method) get_occupations() (proteindf_tools.pdfarchive_sqlite3.PdfArchive_Sqlite3 method) get_pop_mulliken_atom() (proteindf_tools.pdfparam_hdf5.PdfParam_H5 method) get_pop_mulliken_path() (proteindf_tools.pdfparam_object.PdfParamObject method) get_population() (proteindf_tools.pdfarchive_sqlite3.PdfArchive_Sqlite3 method) get_raw_data() (proteindf_tools.BasisSet method) (proteindf_tools.basisset.BasisSet method) (proteindf_tools.basisset.ContractedGTO method) (proteindf_tools.basisset.PrimitiveGTO method) (proteindf_tools.ContractedGTO method) (proteindf_tools.pdfparam_object.PdfParamObject method) (proteindf_tools.PrimitiveGTO method) get_RRMS() (proteindf_tools.PopEspUtils method) (proteindf_tools.poputils.PopEspUtils method) get_s_mat_path() (proteindf_tools.pdfparam_object.PdfParamObject method) get_s_matrix() (proteindf_tools.pdfparam_hdf5.PdfParam_H5 method) get_shell_type() (proteindf_tools.basisset.ContractedGTO class method) (proteindf_tools.ContractedGTO class method) (proteindf_tools.OrbInfo method) (proteindf_tools.orbinfo.OrbInfo method) get_shell_type_id() (proteindf_tools.basisset.ContractedGTO class method) (proteindf_tools.ContractedGTO class method) get_size() (proteindf_tools.Matrix class method) (proteindf_tools.matrix.Matrix class method) (proteindf_tools.matrix.SymmetricMatrix class method) (proteindf_tools.SymmetricMatrix class method) get_supported_shell_types() (proteindf_tools.basisset.ContractedGTO class method) (proteindf_tools.ContractedGTO class method) get_TEs() (proteindf_tools.pdfparam_hdf5.PdfParam_H5 method) get_total_energy() (proteindf_tools.pdfarchive_sqlite3.PdfArchive_Sqlite3 method) (proteindf_tools.pdfparam_object.PdfParamObject method) get_x_mat_path() (proteindf_tools.pdfparam_object.PdfParamObject method) get_xinv_mat_path() (proteindf_tools.pdfparam_object.PdfParamObject method) Graph (class in proteindf_tools.pdfgraph) GraphConvergenceCheck (class in proteindf_tools.pdfgraph) GraphEnergyLevelHistory (class in proteindf_tools.pdfgraph) GraphEnergyLevelSingle (class in proteindf_tools.pdfgraph) GraphTotalEnergyHistory (class in proteindf_tools.pdfgraph) gridfree_CD_epsilon (proteindf_tools.pdfparam_object.PdfParamObject property) gridfree_CDAM_tau (proteindf_tools.pdfparam_object.PdfParamObject property) gridfree_dedicated_basis (proteindf_tools.pdfparam_object.PdfParamObject property) gridfree_orthogonalize_method (proteindf_tools.pdfparam_object.PdfParamObject property) guess (proteindf_tools.pdfparam_object.PdfParamObject property) I is_diverging (proteindf_tools.pdfgraph.DfMatrixGraph property) is_draw_grid (proteindf_tools.pdfgraph.DfGraph property) is_loadable() (proteindf_tools.Matrix class method) (proteindf_tools.matrix.Matrix class method) (proteindf_tools.matrix.SymmetricMatrix class method) (proteindf_tools.SymmetricMatrix class method) (proteindf_tools.Vector class method) (proteindf_tools.vector.Vector class method) iterations (proteindf_tools.pdfarchive_sqlite3.PdfArchive_Sqlite3 property) (proteindf_tools.pdfparam_object.PdfParamObject property) J j_engine (proteindf_tools.pdfparam_object.PdfParamObject property) jobtype (proteindf_tools.gauparam.GaussianParam property) (proteindf_tools.GaussianParam property) K k_engine (proteindf_tools.pdfparam_object.PdfParamObject property) L legend (proteindf_tools.pdfgraph.DfGraph property) level_shift (proteindf_tools.pdfparam_object.PdfParamObject property) level_shift_start_iteration (proteindf_tools.pdfparam_object.PdfParamObject property) level_shift_virtual_mo (proteindf_tools.pdfparam_object.PdfParamObject property) LineChart (class in proteindf_tools.pdfgraph) lo_num_of_iterations (proteindf_tools.pdfparam_object.PdfParamObject property) lo_satisfied (proteindf_tools.pdfparam_object.PdfParamObject property) load() (proteindf_tools.basisset_parser.BasisSetParser method) (proteindf_tools.Matrix method) (proteindf_tools.matrix.Matrix method) (proteindf_tools.matrix.SymmetricMatrix method) (proteindf_tools.pdfgraph.DfDistanceVsElementGraph method) (proteindf_tools.SymmetricMatrix method) (proteindf_tools.Vector method) (proteindf_tools.vector.Vector method) load_data() (proteindf_tools.pdfgraph.DfDosGraph method) (proteindf_tools.pdfgraph.DfEnergyLevelHistoryGraphH method) (proteindf_tools.pdfgraph.DfPopulationGraph method) (proteindf_tools.pdfgraph.DfTotalEnergyHistGraph method) load_model() (proteindf_tools.pdfparam_hdf5.PdfParam_H5 method) load_pdfparam() (in module proteindf_tools.pdfcommon) M main() (in module proteindf_tools.basisset_parser) Math (class in proteindf_tools.pdfmath) Matrix (class in proteindf_tools) (class in proteindf_tools.matrix) max_iterations (proteindf_tools.pdfparam_object.PdfParamObject property) max_shell_type (proteindf_tools.BasisSet property) (proteindf_tools.basisset.BasisSet property) max_shell_type_id (proteindf_tools.BasisSet property) (proteindf_tools.basisset.BasisSet property) method (proteindf_tools.pdfarchive_sqlite3.PdfArchive_Sqlite3 property) (proteindf_tools.pdfparam_object.PdfParamObject property) (proteindf_tools.QmSim property) (proteindf_tools.qmsim.QmSim property) MidpointLogNorm (class in proteindf_tools.pdfgraph) MidpointNormalize (class in proteindf_tools.pdfgraph) module proteindf_tools proteindf_tools.basis2 proteindf_tools.basisset proteindf_tools.basisset_parser proteindf_tools.constants proteindf_tools.functions proteindf_tools.gauparam proteindf_tools.matrix proteindf_tools.orbinfo proteindf_tools.pdfarchive_object proteindf_tools.pdfarchive_sqlite3 proteindf_tools.pdfcommon proteindf_tools.pdfgraph proteindf_tools.pdfmath proteindf_tools.pdfparam proteindf_tools.pdfparam_hdf5 proteindf_tools.pdfparam_object proteindf_tools.pdfsim proteindf_tools.poputils proteindf_tools.process proteindf_tools.qmsim proteindf_tools.report proteindf_tools.vector molecule (proteindf_tools.pdfparam_object.PdfParamObject property) mpac2py() (in module proteindf_tools.pdfcommon) N name (proteindf_tools.BasisSet property) (proteindf_tools.basisset.BasisSet property) normalize() (proteindf_tools.basisset.ContractedGTO method) (proteindf_tools.basisset.PrimitiveGTO method) (proteindf_tools.ContractedGTO method) (proteindf_tools.PrimitiveGTO method) num_of_AOs (proteindf_tools.pdfarchive_sqlite3.PdfArchive_Sqlite3 property) (proteindf_tools.pdfparam_object.PdfParamObject property) num_of_atoms (proteindf_tools.pdfarchive_sqlite3.PdfArchive_Sqlite3 property) (proteindf_tools.pdfparam_object.PdfParamObject property) num_of_electrons (proteindf_tools.pdfparam_object.PdfParamObject property) num_of_MOs (proteindf_tools.pdfarchive_sqlite3.PdfArchive_Sqlite3 property) (proteindf_tools.pdfparam_object.PdfParamObject property) num_of_series (proteindf_tools.pdfgraph.DfDosGraph property) numerical_grad() (proteindf_tools.PdfSim method) (proteindf_tools.pdfsim.PdfSim method) O occupation_level (proteindf_tools.pdfparam_object.PdfParamObject property) open() (proteindf_tools.pdfparam_hdf5.PdfParam_H5 method) opt() (proteindf_tools.PdfSim method) (proteindf_tools.pdfsim.PdfSim method) OrbInfo (class in proteindf_tools) (class in proteindf_tools.orbinfo) orbital_independence_threshold (proteindf_tools.pdfparam_object.PdfParamObject property) orbital_independence_threshold_canonical (proteindf_tools.pdfparam_object.PdfParamObject property) orbital_independence_threshold_lowdin (proteindf_tools.pdfparam_object.PdfParamObject property) P parse() (proteindf_tools.basisset_parser.BasisSetParser method) pdf_home() (in module proteindf_tools.pdfcommon) pdf_id (proteindf_tools.pdfarchive_sqlite3.PdfArchive_Sqlite3 property) PdfArchive_Sqlite3 (class in proteindf_tools.pdfarchive_sqlite3) PdfArchiveObject (class in proteindf_tools.pdfarchive_object) PdfParam (class in proteindf_tools) (class in proteindf_tools.pdfparam) PdfParam_H5 (class in proteindf_tools.pdfparam_hdf5) PdfParamObject (class in proteindf_tools.pdfparam_object) PdfReport (class in proteindf_tools.report) PdfSim (class in proteindf_tools) (class in proteindf_tools.pdfsim) pipe() (proteindf_tools.process.Process method) plot() (proteindf_tools.pdfgraph.BarGraph method) (proteindf_tools.pdfgraph.GraphConvergenceCheck method) (proteindf_tools.pdfgraph.GraphTotalEnergyHistory method) plot_basis() (proteindf_tools.pdfgraph.Graph method) plot_energy_levels() (proteindf_tools.pdfgraph.GraphEnergyLevelHistory method) (proteindf_tools.pdfgraph.GraphEnergyLevelSingle method) plotLog() (proteindf_tools.pdfgraph.GraphConvergenceCheck method) pop() (proteindf_tools.PdfSim method) (proteindf_tools.pdfsim.PdfSim method) PopEspUtils (class in proteindf_tools) (class in proteindf_tools.poputils) PopUtils (class in proteindf_tools) (class in proteindf_tools.poputils) PrimitiveGTO (class in proteindf_tools) (class in proteindf_tools.basisset) Process (class in proteindf_tools.process) proteindf_tools module proteindf_tools.basis2 module proteindf_tools.basisset module proteindf_tools.basisset_parser module proteindf_tools.constants module proteindf_tools.functions module proteindf_tools.gauparam module proteindf_tools.matrix module proteindf_tools.orbinfo module proteindf_tools.pdfarchive_object module proteindf_tools.pdfarchive_sqlite3 module proteindf_tools.pdfcommon module proteindf_tools.pdfgraph module proteindf_tools.pdfmath module proteindf_tools.pdfparam module proteindf_tools.pdfparam_hdf5 module proteindf_tools.pdfparam_object module proteindf_tools.pdfsim module proteindf_tools.poputils module proteindf_tools.process module proteindf_tools.qmsim module proteindf_tools.report module proteindf_tools.vector module Q QmSim (class in proteindf_tools) (class in proteindf_tools.qmsim) R reference_line_color (proteindf_tools.pdfgraph.DfEnergyLevelTraceGraph property) report() (proteindf_tools.report.PdfReport method) run_pdf() (in module proteindf_tools.pdfcommon) run_types() (proteindf_tools.pdfparam_object.PdfParamObject method) S save() (proteindf_tools.Matrix method) (proteindf_tools.matrix.Matrix method) (proteindf_tools.matrix.SymmetricMatrix method) (proteindf_tools.pdfgraph.DfGraph method) (proteindf_tools.SymmetricMatrix method) (proteindf_tools.Vector method) (proteindf_tools.vector.Vector method) save_basic() (proteindf_tools.pdfparam_hdf5.PdfParam_H5 method) save_c_matrix() (proteindf_tools.pdfparam_hdf5.PdfParam_H5 method) save_debug() (proteindf_tools.pdfparam_hdf5.PdfParam_H5 method) save_density_matrix() (proteindf_tools.pdfparam_hdf5.PdfParam_H5 method) save_energy_level() (proteindf_tools.pdfparam_hdf5.PdfParam_H5 method) save_f_matrix() (proteindf_tools.pdfparam_hdf5.PdfParam_H5 method) save_full() (proteindf_tools.pdfparam_hdf5.PdfParam_H5 method) save_h2_matrix() (proteindf_tools.pdfparam_hdf5.PdfParam_H5 method) save_h_matrix() (proteindf_tools.pdfparam_hdf5.PdfParam_H5 method) save_model() (proteindf_tools.pdfparam_hdf5.PdfParam_H5 method) save_occ() (proteindf_tools.pdfparam_hdf5.PdfParam_H5 method) save_pdfparam() (in module proteindf_tools.pdfcommon) save_s_matrix() (proteindf_tools.pdfparam_hdf5.PdfParam_H5 method) save_standard() (proteindf_tools.pdfparam_hdf5.PdfParam_H5 method) save_TEs() (proteindf_tools.pdfparam_hdf5.PdfParam_H5 method) savefig() (proteindf_tools.pdfgraph.EnergyLevelChart method) (proteindf_tools.pdfgraph.LineChart method) scale_factor (proteindf_tools.basisset.ContractedGTO property) (proteindf_tools.ContractedGTO property) scf_acceleration (proteindf_tools.pdfparam_object.PdfParamObject property) scf_acceleration_anderson_damping_factor (proteindf_tools.pdfparam_object.PdfParamObject property) scf_acceleration_anderson_start (proteindf_tools.pdfparam_object.PdfParamObject property) scf_acceleration_damping_damping_factor (proteindf_tools.pdfparam_object.PdfParamObject property) scf_acceleration_damping_damping_type (proteindf_tools.pdfparam_object.PdfParamObject property) scf_converged (proteindf_tools.pdfarchive_sqlite3.PdfArchive_Sqlite3 property) (proteindf_tools.pdfparam_object.PdfParamObject property) select_iterations() (proteindf_tools.pdfgraph.DfEnergyLevelHistoryGraphH method) set_atomlist() (proteindf_tools.PopUtils static method) (proteindf_tools.poputils.PopUtils static method) set_basisset() (in module proteindf_tools.pdfcommon) (proteindf_tools.pdfparam_object.PdfParamObject method) set_basisset_gridfree() (proteindf_tools.pdfparam_object.PdfParamObject method) set_basisset_gridfree_name() (proteindf_tools.pdfparam_object.PdfParamObject method) set_basisset_j() (proteindf_tools.pdfparam_object.PdfParamObject method) set_basisset_j_name() (proteindf_tools.pdfparam_object.PdfParamObject method) set_basisset_name() (proteindf_tools.pdfparam_object.PdfParamObject method) set_basisset_xc() (proteindf_tools.pdfparam_object.PdfParamObject method) set_basisset_xc_name() (proteindf_tools.pdfparam_object.PdfParamObject method) set_by_raw_data() (proteindf_tools.BasisSet method) (proteindf_tools.basisset.BasisSet method) (proteindf_tools.basisset.ContractedGTO method) (proteindf_tools.basisset.PrimitiveGTO method) (proteindf_tools.ContractedGTO method) (proteindf_tools.pdfparam_object.PdfParamObject method) (proteindf_tools.PrimitiveGTO method) set_data() (proteindf_tools.pdfgraph.DfEnergyLevelTraceGraph method) (proteindf_tools.pdfgraph.DfGvalsGraph method) (proteindf_tools.pdfgraph.EnergyLevelChart method) (proteindf_tools.pdfgraph.LineChart method) set_energylevel() (proteindf_tools.pdfarchive_sqlite3.PdfArchive_Sqlite3 method) set_gradient() (proteindf_tools.pdfparam_object.PdfParamObject method) set_HOMO_level() (proteindf_tools.pdfgraph.DfEnergyLevelHistoryGraphH method) set_lcao() (proteindf_tools.pdfarchive_sqlite3.PdfArchive_Sqlite3 method) set_LUMO_level() (proteindf_tools.pdfgraph.DfEnergyLevelHistoryGraphH method) set_mulliken_atom_population() (proteindf_tools.pdfparam_object.PdfParamObject method) set_occupations() (proteindf_tools.pdfarchive_sqlite3.PdfArchive_Sqlite3 method) set_population() (proteindf_tools.pdfarchive_sqlite3.PdfArchive_Sqlite3 method) set_total_energy() (proteindf_tools.pdfparam_object.PdfParamObject method) set_xlabel() (proteindf_tools.pdfgraph.Graph method) set_xrange() (proteindf_tools.pdfgraph.Graph method) set_xscale() (proteindf_tools.pdfgraph.Graph method) set_ylabel() (proteindf_tools.pdfgraph.Graph method) set_yrange() (proteindf_tools.pdfgraph.Graph method) set_yscale() (proteindf_tools.pdfgraph.Graph method) setup() (proteindf_tools.PdfSim method) (proteindf_tools.pdfsim.PdfSim method) shell_type (proteindf_tools.basisset.ContractedGTO property) (proteindf_tools.ContractedGTO property) shell_type_id (proteindf_tools.basisset.ContractedGTO property) (proteindf_tools.ContractedGTO property) should_write_values (proteindf_tools.pdfgraph.DfMatrixGraph property) size (proteindf_tools.pdfgraph.DfGraph property) sort() (proteindf_tools.BasisSet method) (proteindf_tools.basisset.BasisSet method) sp() (proteindf_tools.PdfSim method) (proteindf_tools.pdfsim.PdfSim method) step_control (proteindf_tools.pdfparam_object.PdfParamObject property) SymmetricMatrix (class in proteindf_tools) (class in proteindf_tools.matrix) T target_line_color (proteindf_tools.pdfgraph.DfEnergyLevelTraceGraph property) TEs (proteindf_tools.pdfparam_object.PdfParamObject property) title (proteindf_tools.gauparam.GaussianParam property) (proteindf_tools.GaussianParam property) (proteindf_tools.pdfgraph.DfGraph property) total_energy() (proteindf_tools.PdfSim method) (proteindf_tools.pdfsim.PdfSim method) V Vector (class in proteindf_tools) (class in proteindf_tools.vector) vmax (proteindf_tools.pdfgraph.DfMatrixGraph property) vmin (proteindf_tools.pdfgraph.DfMatrixGraph property) W work_path (proteindf_tools.pdfparam_object.PdfParamObject property) X xc_engine (proteindf_tools.pdfparam_object.PdfParamObject property) xc_functional (proteindf_tools.pdfparam_object.PdfParamObject property) xlabel (proteindf_tools.pdfgraph.DfGraph property) xmax (proteindf_tools.pdfgraph.DfGraph property) xmin (proteindf_tools.pdfgraph.DfGraph property) xscale (proteindf_tools.pdfgraph.DfGraph property) xticklabels (proteindf_tools.pdfgraph.DfGraph property) xticks (proteindf_tools.pdfgraph.DfGraph property) Y ylabel (proteindf_tools.pdfgraph.DfGraph property) ymax (proteindf_tools.pdfgraph.DfGraph property) ymin (proteindf_tools.pdfgraph.DfGraph property) yscale (proteindf_tools.pdfgraph.DfGraph property) yticklabels (proteindf_tools.pdfgraph.DfGraph property) yticks (proteindf_tools.pdfgraph.DfGraph property)