Index

Symbols

--alignment ALIGNMENT propka3 command line option --chain CHAINS propka3 command line option --display-coupled-residues propka3 command line option --file FILENAMES propka3 command line option --generate-propka-input propka3 command line option --grid GRID GRID GRID propka3 command line option --help propka3 command line option --keep-protons propka3 command line option --log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL} propka3 command line option --mutation MUTATIONS propka3 command line option --mutator MUTATOR propka3 command line option --mutator-option MUTATOR_OPTIONS propka3 command line option --parameters PARAMETERS propka3 command line option --pH PH propka3 command line option --protonate-all propka3 command line option --quiet propka3 command line option --reference REFERENCE propka3 command line option --reuse-ligand-mol2-files propka3 command line option --thermophile THERMOPHILES propka3 command line option --titrate_only TITRATE_ONLY propka3 command line option

--version VERSION_LABEL propka3 command line option --window WINDOW WINDOW WINDOW propka3 command line option -a ALIGNMENT propka3 command line option -c CHAINS propka3 command line option -d propka3 command line option -f FILENAMES propka3 command line option -g GRID GRID GRID propka3 command line option -h propka3 command line option -i TITRATE_ONLY propka3 command line option -k propka3 command line option -l propka3 command line option -m MUTATIONS propka3 command line option -o PH propka3 command line option -p PARAMETERS propka3 command line option -q propka3 command line option -r REFERENCE propka3 command line option -t THERMOPHILES propka3 command line option -v VERSION_LABEL propka3 command line option -w WINDOW WINDOW WINDOW propka3 command line option

A

add() (propka.determinant.Determinant method) (propka.parameters.InteractionMatrix method) (propka.parameters.PairwiseMatrix method) add_amd_hydrogen() (in module propka.hydrogens) add_arg_hydrogen() (in module propka.hydrogens) add_atom() (propka.conformation_container.ConformationContainer method) add_backbone_hydrogen() (in module propka.hydrogens) add_coulomb_acid_pair() (in module propka.determinants) add_coulomb_base_pair() (in module propka.determinants) add_coulomb_determinants() (in module propka.determinants) add_coulomb_ion_pair() (in module propka.determinants) add_determinant() (propka.group.Group method) add_determinants() (in module propka.determinants) (in module propka.iterative) add_his_hydrogen() (in module propka.hydrogens) add_iterative_acid_pair() (in module propka.iterative) add_iterative_base_pair() (in module propka.iterative) add_iterative_ion_pair() (in module propka.iterative)

add_pi_electron_information() (propka.bonds.BondMaker method) add_pi_electron_table_info() (propka.bonds.BondMaker method) add_proton() (propka.protonate.Protonate static method) add_protons() (propka.protonate.Protonate method) add_sidechain_determinants() (in module propka.determinants) add_to_determinant_list() (in module propka.iterative) add_trp_hydrogen() (in module propka.hydrogens) additional_setup_when_reading_input_file() (propka.conformation_container.ConformationContainer method) (propka.molecular_container.MolecularContainer method) ALL_SYBYL_TYPES (in module propka.ligand) AMDGroup (class in propka.group) angle() (in module propka.vector_algebra) angle_degrees() (in module propka.vector_algebra) angle_distance_factors() (in module propka.energy) are_atoms_planar() (in module propka.ligand) ARGGroup (class in propka.group) assign_sybyl_type() (in module propka.ligand) Atom (class in propka.atom) average_of_conformations() (propka.molecular_container.MolecularContainer method)

B

backbone_reorganization() (in module propka.energy) BBCGroup (class in propka.group)

BBNGroup (class in propka.group) BondMaker (class in propka.bonds) build_parser() (in module propka.lib)

C

C2NGroup (class in propka.group) calculate_backbone_reorganization() (propka.version.Version method) calculate_charge() (propka.conformation_container.ConformationContainer method) (propka.group.Group method) calculate_coulomb_energy() (propka.version.Version method) calculate_desolvation() (propka.version.Version method) calculate_folding_energy() (propka.conformation_container.ConformationContainer method) (propka.group.Group method) calculate_intrinsic_pka() (propka.group.Group method) calculate_pair_weight() (in module propka.energy) (propka.version.Version method) calculate_pka() (propka.conformation_container.ConformationContainer method) (propka.molecular_container.MolecularContainer method) calculate_scale_factor() (in module propka.energy) calculate_side_chain_energy() (propka.version.Version method) calculate_total_pka() (propka.group.Group method) calculate_weight() (in module propka.energy) CGGroup (class in propka.group) check_buried() (in module propka.energy) check_coo_arg_exception() (in module propka.energy) check_coo_coo_exception() (in module propka.energy) check_coo_his_exception() (in module propka.energy) check_coulomb_pair() (in module propka.energy) (propka.version.Version method)

check_cys_cys_exception() (in module propka.energy) check_cys_his_exception() (in module propka.energy) check_distance() (propka.bonds.BondMaker method) check_exceptions() (in module propka.energy) (propka.version.Version method) check_for_cysteine_bonds() (propka.bonds.BondMaker method) check_oco_his_exception() (in module propka.energy) ClGroup (class in propka.group) clone() (propka.group.Group method) configuration_compare() (in module propka.lib) conformation_sorter() (in module propka.input) ConformationContainer (class in propka.conformation_container) connect_backbone() (propka.bonds.BondMaker method) COOGroup (class in propka.group) copy_atom() (propka.conformation_container.ConformationContainer method) coulomb_energy() (in module propka.energy) count_bonded_elements() (propka.atom.Atom method) couple_covalently() (propka.group.Group method) couple_non_covalently() (propka.group.Group method) coupling_effects() (propka.conformation_container.ConformationContainer method) CtermGroup (class in propka.group) CYSGroup (class in propka.group)

D

debug() (in module propka.lib) decode() (in module propka.hybrid36) Determinant (class in propka.determinant)

distance() (in module propka.calculations) DISTANCES (in module propka.parameters) do_job() (propka.vector_algebra.MultiVector method)

E

electrostatic_interaction() (in module propka.energy) (propka.version.Version method) ElementBasedLigandInteractions (class in propka.version) empty_function() (propka.version.Version static method)

EXPECTED_ATOMS_ACID_INTERACTIONS (in module propka.group) EXPECTED_ATOMS_BASE_INTERACTIONS (in module propka.group) extract_groups() (propka.conformation_container.ConformationContainer method) (propka.molecular_container.MolecularContainer method) extract_pkas() (propka.ligand_pka_values.LigandPkaValues static method)

F

FGroup (class in propka.group) find_bonded_titratable_groups() (propka.conformation_container.ConformationContainer method) find_bonds_for_atoms() (propka.bonds.BondMaker method) find_bonds_for_atoms_using_boxes() (propka.bonds.BondMaker method) find_bonds_for_ligand() (propka.bonds.BondMaker method) find_bonds_for_molecules_using_boxes() (propka.bonds.BondMaker method) find_bonds_for_protein() (propka.bonds.BondMaker method) find_bonds_for_protein_by_distance() (propka.bonds.BondMaker method) find_bonds_for_residue_backbone() (propka.bonds.BondMaker method)

find_bonds_for_side_chain() (propka.bonds.BondMaker method) find_bonds_for_terminal_oxygen() (propka.bonds.BondMaker method) find_covalently_coupled_groups() (propka.conformation_container.ConformationContainer method) (propka.molecular_container.MolecularContainer method) find_group() (propka.conformation_container.ConformationContainer method) find_in_path() (propka.ligand_pka_values.LigandPkaValues static method) find_iterative() (in module propka.iterative) find_non_covalently_coupled_groups() (propka.conformation_container.ConformationContainer method) (propka.molecular_container.MolecularContainer method)

G

generate_combinations() (in module propka.lib) generate_protein_bond_dictionary() (propka.bonds.BondMaker method) generic_operation() (propka.vector_algebra.MultiVector method) generic_self_operation() (propka.vector_algebra.MultiVector static method) get_a_coupled_system_of_groups() (propka.conformation_container.ConformationContainer method) get_acids() (propka.conformation_container.ConformationContainer method) get_atom_lines_from_input() (in module propka.input) get_atom_lines_from_pdb() (in module propka.input) get_backbone_co_groups() (propka.conformation_container.ConformationContainer method) get_backbone_groups() (propka.conformation_container.ConformationContainer method) get_backbone_hydrogen_bond_parameters() (propka.version.ElementBasedLigandInteractions method) (propka.version.SimpleHB method) (propka.version.VersionA method) get_backbone_nh_groups() (propka.conformation_container.ConformationContainer method) get_backbone_reorganisation_groups() (propka.conformation_container.ConformationContainer method) get_bond_order() (in module propka.output) get_bonded_elements() (propka.atom.Atom method) get_bonded_heavy_atoms() (propka.atom.Atom method) get_chain() (propka.conformation_container.ConformationContainer method) get_charge_profile() (propka.molecular_container.MolecularContainer method) get_charge_profile_section() (in module propka.output) get_coupled_systems() (propka.conformation_container.ConformationContainer method) get_covalently_coupled_groups() (propka.conformation_container.ConformationContainer method) (propka.group.Group method) get_determinant_for_string() (propka.group.Group method) get_determinant_section() (in module propka.output) get_determinant_string() (propka.group.Group method) get_determinants_header() (in module propka.output) get_folding_profile() (propka.molecular_container.MolecularContainer method) get_folding_profile_section() (in module propka.output) get_free_energy_diff_factor() (propka.coupled_groups.NonCovalentlyCoupledGroups method) get_group_names() (propka.conformation_container.ConformationContainer method) get_groups_for_calculations() (propka.conformation_container.ConformationContainer method) get_groups_in_residue() (propka.conformation_container.ConformationContainer method) get_heavy_ligand_atoms() (propka.conformation_container.ConformationContainer method)

get_hydrogen_bond_parameters() (propka.version.ElementBasedLigandInteractions method) (propka.version.Propka30 method) (propka.version.SimpleHB method) (propka.version.VersionA method) get_input_parameters() (propka.atom.Atom method) get_interaction() (propka.coupled_groups.NonCovalentlyCoupledGroups static method) get_interaction_atoms() (propka.group.Group method) get_interaction_factor() (propka.coupled_groups.NonCovalentlyCoupledGroups method) get_ions() (propka.conformation_container.ConformationContainer method) get_ligand_atoms() (propka.conformation_container.ConformationContainer method) get_marvin_pkas_for_atoms() (propka.ligand_pka_values.LigandPkaValues method) get_marvin_pkas_for_conformation_container() (propka.ligand_pka_values.LigandPkaValues method) get_marvin_pkas_for_molecular_container() (propka.ligand_pka_values.LigandPkaValues method) get_marvin_pkas_for_molecule() (propka.ligand_pka_values.LigandPkaValues method) get_marvin_pkas_for_pdb_file() (propka.ligand_pka_values.LigandPkaValues method) get_non_covalently_coupled_groups() (propka.conformation_container.ConformationContainer method) (propka.group.Group method) get_non_hydrogen_atoms() (propka.conformation_container.ConformationContainer method) get_pi() (propka.molecular_container.MolecularContainer method) get_pka_diff_factor() (propka.coupled_groups.NonCovalentlyCoupledGroups method) get_propka_header() (in module propka.output) get_references_header() (in module propka.output) get_result() (propka.vector_algebra.MultiVector property) get_sidechain_groups() (propka.conformation_container.ConformationContainer method) get_smallest_distance() (in module propka.calculations) get_sorted_configurations() (in module propka.lib) get_summary_header() (in module propka.output) get_summary_section() (in module propka.output) get_summary_string() (propka.group.Group method) get_the_line() (in module propka.output) get_tidy_label() (propka.atom.Atom method) get_titratable_groups() (propka.conformation_container.ConformationContainer method) get_value() (propka.parameters.InteractionMatrix method) (propka.parameters.PairwiseMatrix method) get_warning_header() (in module propka.output) Group (class in propka.group)

H

has_bond() (propka.bonds.BondMaker static method) HISGroup (class in propka.group)

hydrogen_bond_energy() (in module propka.energy) hydrogen_bond_interaction() (in module propka.energy) (propka.version.Version method)

I

identify_non_covalently_coupled_groups() (propka.coupled_groups.NonCovalentlyCoupledGroups method) identify_ring() (in module propka.ligand) info() (in module propka.lib) init_group() (propka.conformation_container.ConformationContainer method) initialize_atom_group() (in module propka.group) input_pdb propka3 command line option insert() (propka.parameters.PairwiseMatrix method) InteractionMatrix (class in propka.parameters) IonGroup (class in propka.group)

is_aromatic_ring() (in module propka.ligand) is_atom_within_bond_distance() (propka.atom.Atom method) is_coupled_protonation_state_probability() (propka.coupled_groups.NonCovalentlyCoupledGroups method) is_group() (in module propka.group) is_ion_group() (in module propka.group) is_ligand_group_by_groups() (in module propka.group) is_ligand_group_by_marvin_pkas() (in module propka.group) is_planar() (in module propka.ligand) is_protein_group() (in module propka.group) is_ring_member() (in module propka.ligand) Iterative (class in propka.iterative)

K

keys() (propka.parameters.InteractionMatrix method) (propka.parameters.PairwiseMatrix method)

L

length() (propka.vector_algebra.Vector method) LigandPkaValues (class in propka.ligand_pka_values)

LIST_DICTIONARIES (in module propka.parameters) loadOptions() (in module propka.lib) LYSGroup (class in propka.group)

M

main() (in module propka.run) make_bond() (propka.bonds.BondMaker static method) make_combination() (in module propka.lib) make_conect_line() (propka.atom.Atom method) make_copy() (propka.atom.Atom method) make_covalently_coupled_line() (propka.group.Group method) make_data_to_string() (propka.coupled_groups.NonCovalentlyCoupledGroups static method) make_grid() (in module propka.lib) make_input_line() (propka.atom.Atom method) make_interaction_map() (in module propka.output) make_mol2_line() (propka.atom.Atom method) make_molecule() (in module propka.lib) make_new_h() (in module propka.hydrogens) make_non_covalently_coupled_line() (propka.group.Group method) make_pdb_line() (propka.atom.Atom method) make_pdb_line2() (propka.atom.Atom method) make_tidy_atom_label() (in module propka.lib) MATRICES (in module propka.parameters) Matrix4x4 (class in propka.vector_algebra) MAX_DISTANCE (in module propka.calculations) module propka propka.atom propka.bonds propka.calculations propka.conformation_container propka.coupled_groups propka.determinant propka.determinants propka.energy propka.group propka.hybrid36 propka.hydrogens propka.input propka.iterative propka.lib propka.ligand propka.ligand_pka_values propka.molecular_container propka.output propka.parameters propka.protonate propka.run propka.vector_algebra propka.version

MolecularContainer (class in propka.molecular_container) MultiVector (class in propka.vector_algebra)

N

N1Group (class in propka.group) N30Group (class in propka.group) N31Group (class in propka.group) N32Group (class in propka.group) N33Group (class in propka.group) NAMGroup (class in propka.group)

NARGroup (class in propka.group) NonCovalentlyCoupledGroups (class in propka.coupled_groups) NonTitratableLigandGroup (class in propka.group) NP1Group (class in propka.group) NtermGroup (class in propka.group) NUMBER_DICTIONARIES (in module propka.parameters)

O

O2Group (class in propka.group) O3Group (class in propka.group) OCOGroup (class in propka.group) OHGroup (class in propka.group)

open_file_for_reading() (in module propka.input) open_file_for_writing() (in module propka.output) OPGroup (class in propka.group) orthogonal() (propka.vector_algebra.Vector method)

P

PAIR_WISE_MATRICES (in module propka.parameters) PairwiseMatrix (class in propka.parameters) Parameters (class in propka.parameters) PARAMETERS (in module propka.parameters) parse_distance() (propka.parameters.Parameters method) parse_line() (propka.parameters.Parameters method) parse_parameter() (propka.parameters.Parameters method) parse_res_string() (in module propka.lib) parse_string() (propka.parameters.Parameters method) parse_to_list_dictionary() (propka.parameters.Parameters method) parse_to_matrix() (propka.parameters.Parameters method) parse_to_number_dictionary() (propka.parameters.Parameters method) parse_to_string_dictionary() (propka.parameters.Parameters method) parse_to_string_list() (propka.parameters.Parameters method) print_determinants_section() (propka.coupled_groups.NonCovalentlyCoupledGroups method) print_header() (in module propka.output) print_interaction_parameters() (propka.parameters.Parameters method) print_interaction_parameters_latex() (propka.parameters.Parameters method) print_interactions_latex() (propka.parameters.Parameters method) print_out_swaps() (propka.coupled_groups.NonCovalentlyCoupledGroups method) print_pka_section() (in module propka.output) print_result() (in module propka.output) print_system() (propka.coupled_groups.NonCovalentlyCoupledGroups method) print_tm_profile() (in module propka.output) propka module propka.atom module propka.bonds module propka.calculations module propka.conformation_container module propka.coupled_groups module propka.determinant module propka.determinants module propka.energy module propka.group module propka.hybrid36 module propka.hydrogens module propka.input module propka.iterative module propka.lib module propka.ligand module propka.ligand_pka_values module propka.molecular_container module propka.output module

propka.parameters module propka.protonate module propka.run module propka.vector_algebra module propka.version module propka3 command line option --alignment ALIGNMENT --chain CHAINS --display-coupled-residues --file FILENAMES --generate-propka-input --grid GRID GRID GRID --help --keep-protons --log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL} --mutation MUTATIONS --mutator MUTATOR --mutator-option MUTATOR_OPTIONS --parameters PARAMETERS --pH PH --protonate-all --quiet --reference REFERENCE --reuse-ligand-mol2-files --thermophile THERMOPHILES --titrate_only TITRATE_ONLY --version VERSION_LABEL --window WINDOW WINDOW WINDOW -a ALIGNMENT -c CHAINS -d -f FILENAMES -g GRID GRID GRID -h -i TITRATE_ONLY -k -l -m MUTATIONS -o PH -p PARAMETERS -q -r REFERENCE -t THERMOPHILES -v VERSION_LABEL -w WINDOW WINDOW WINDOW input_pdb Propka30 (class in propka.version) PROPKA_INPUT_TYPES (in module propka.ligand) protein_precheck() (in module propka.lib) Protonate (class in propka.protonate) protonate() (propka.protonate.Protonate method) protonate_30_style() (in module propka.hydrogens) protonate_atom() (propka.protonate.Protonate method) protonate_average_direction() (in module propka.hydrogens) protonate_direction() (in module propka.hydrogens) protonate_sp2() (in module propka.hydrogens) put_atom_in_box() (propka.bonds.BondMaker method)

R

radial_volume_desolvation() (in module propka.energy) read_molecule_file() (in module propka.input) read_parameter_file() (in module propka.input) read_pdb() (in module propka.input) read_propka() (in module propka.input) remove_all_hydrogen_atoms() (propka.protonate.Protonate static method) remove_determinants() (propka.group.Group method) rescale() (propka.vector_algebra.MultiVector method) (propka.vector_algebra.Vector method)

resid_from_atom() (in module propka.lib) RESIDUE_MULTIPLIER (in module propka.conformation_container) ROHGroup (class in propka.group) rotate_atoms_around_y_axis() (in module propka.vector_algebra) rotate_atoms_around_z_axis() (in module propka.vector_algebra) rotate_multi_vector_around_an_axis() (in module propka.vector_algebra) rotate_vector_around_an_axis() (in module propka.vector_algebra)

S

SERGroup (class in propka.group) set_backbone_determinants() (in module propka.determinants) set_bond_distance() (propka.protonate.Protonate method) set_center() (propka.group.Group method) set_charge() (propka.protonate.Protonate method) set_common_charge_centres() (propka.conformation_container.ConformationContainer method) set_determinant() (propka.group.Group method) set_determinants() (in module propka.determinants) set_group_type() (propka.atom.Atom method) set_interaction_atoms() (propka.group.Group method) set_ion_determinants() (in module propka.determinants) set_ligand_atom_names() (in module propka.hydrogens) (propka.conformation_container.ConformationContainer method) set_number_of_protons_to_add() (propka.protonate.Protonate method) set_properties() (propka.atom.Atom method) set_property() (propka.atom.Atom method) set_proton_names() (propka.protonate.Protonate static method) set_residue() (propka.atom.Atom method) set_steric_number_and_lone_pairs() (propka.protonate.Protonate method) set_type() (in module propka.ligand) set_up_data_structures() (propka.parameters.Parameters method) setup() (propka.group.Group method) setup_and_add_group() (propka.conformation_container.ConformationContainer method) setup_atoms() (propka.group.AMDGroup method) (propka.group.ARGGroup method) (propka.group.BBCGroup method) (propka.group.BBNGroup method) (propka.group.C2NGroup method) (propka.group.CGGroup method) (propka.group.COOGroup method) (propka.group.CtermGroup method) (propka.group.Group method) (propka.group.HISGroup method) (propka.group.N30Group method) (propka.group.N31Group method) (propka.group.N32Group method) (propka.group.N33Group method) (propka.group.NAMGroup method) (propka.group.NARGroup method) (propka.group.NP1Group method) (propka.group.OCOGroup method) (propka.group.OHGroup method) (propka.group.OPGroup method) (propka.group.TRPGroup method)

setup_bonding() (in module propka.hydrogens) (propka.version.Version method) setup_bonding_and_protonation() (in module propka.hydrogens) (propka.version.Version method) setup_bonding_and_protonation_30_style() (in module propka.hydrogens) share_determinant() (propka.group.Group method) share_determinants() (propka.conformation_container.ConformationContainer static method) (propka.group.Group method) SHGroup (class in propka.group) signed_angle_around_axis() (in module propka.vector_algebra) SimpleHB (class in propka.version) single() (in module propka.run) sort_atoms() (propka.conformation_container.ConformationContainer method) sort_atoms_key() (propka.conformation_container.ConformationContainer static method) split_atoms_into_molecules() (in module propka.lib) sq_length() (propka.vector_algebra.Vector method) squared_distance() (in module propka.calculations) STRING_DICTIONARIES (in module propka.parameters) STRING_LISTS (in module propka.parameters) swap_interactions() (propka.coupled_groups.NonCovalentlyCoupledGroups method)

T

tagged_format() (propka.coupled_groups.NonCovalentlyCoupledGroups static method) tetrahedral() (propka.protonate.Protonate method) TitratableLigandGroup (class in propka.group) top_up() (propka.conformation_container.ConformationContainer method)

top_up_conformations() (propka.molecular_container.MolecularContainer method) transfer_determinant() (propka.coupled_groups.NonCovalentlyCoupledGroups static method) trigonal() (propka.protonate.Protonate method) TRPGroup (class in propka.group) TYRGroup (class in propka.group)

U

UNICODE_MULTIPLIER (in module propka.conformation_container)

use_in_calculations() (propka.group.Group method)

V

Vector (class in propka.vector_algebra)

Version (class in propka.version) VersionA (class in propka.version)

W

warning() (in module propka.lib) write_file() (in module propka.output) write_jackal_scap_file() (in module propka.output) write_mol2_for_atoms() (in module propka.output) write_pdb_for_atoms() (in module propka.output) write_pdb_for_conformation() (in module propka.output)

write_pdb_for_protein() (in module propka.output) write_pka() (in module propka.output) (propka.molecular_container.MolecularContainer method) write_propka() (in module propka.output) (propka.molecular_container.MolecularContainer method) write_scwrl_sequence_file() (in module propka.output)