Classes
class	difference_map_peaks_info_t
	difference maps peaks class More...

class	histogram_info_t
	map histogram class More...

class	interesting_place_t

class	rotamer_change_info_t
	a container class for information about changing rotamers More...

Public Member Functions
	molecule_t (const std::string &name_in, int mol_no_in)
	constructor

	molecule_t (const std::string &name_in, int mol_no_in, short int is_em_map)
	constructor, when we know we are giving it an em map

	molecule_t (const std::string &name_in, int mol_no_in, const clipper::Xmap< float > &xmap_in, bool is_em_map_flag)
	constructor

	molecule_t (atom_selection_container_t asc, int imol_no_in, const std::string &name_in)
	constructor

float	get_median_temperature_factor () const

float	get_temperature_factor_of_atom (const std::string &atom_cid) const

int	close_yourself ()

bool	is_closed () const

void	set_really_do_backups (bool state)

void	add_neighbor_residues_for_refinement_help (mmdb::Manager *mol)

void	fill_fobs_sigfobs ()

clipper::HKL_data< clipper::data32::F_sigF > *	get_original_fobs_sigfobs () const

clipper::HKL_data< clipper::data32::Flag > *	get_original_rfree_flags () const

int	sfcalc_genmap (const clipper::HKL_data< clipper::data32::F_sigF > &fobs, const clipper::HKL_data< clipper::data32::Flag > &free, clipper::Xmap< float > *xmap_p)

util::sfcalc_genmap_stats_t	sfcalc_genmaps_using_bulk_solvent (const clipper::HKL_data< clipper::data32::F_sigF > &fobs, const clipper::HKL_data< clipper::data32::Flag > &free, clipper::Xmap< float > xmap_2fofc_p, clipper::Xmap< float > xmap_fofc_p)

std::pair< std::string, std::string >	make_import_datanames (const std::string &fcol, const std::string &phi_col, const std::string &weight_col, int use_weights) const

std::string	Refmac_fobs_col () const

std::string	Refmac_sigfobs_col () const

std::string	Refmac_mtz_filename () const

void	associate_data_mtz_file_with_map (const std::string &data_mtz_file_name, const std::string &f_col, const std::string &sigf_col, const std::string &r_free_col)

util::map_molecule_centre_info_t	get_map_molecule_centre () const

void	replace_molecule_by_model_from_file (const std::string &pdb_file_name)

std::string	get_name () const

void	set_molecule_name (const std::string &n)

int	get_molecule_index () const

bool	is_valid_model_molecule () const

bool	is_valid_map_molecule () const

unsigned int	get_number_of_atoms () const

int	get_number_of_hydrogen_atoms () const

float	get_molecule_diameter () const

double	get_radius_of_gyration () const

std::vector< std::string >	get_types_in_molecule () const
	get types

mmdb::Residue *	cid_to_residue (const std::string &cid) const

std::vector< mmdb::Residue * >	cid_to_residues (const std::string &cid) const

mmdb::Atom *	cid_to_atom (const std::string &cid) const

std::pair< bool, residue_spec_t >	cid_to_residue_spec (const std::string &cid) const

std::pair< bool, atom_spec_t >	cid_to_atom_spec (const std::string &cid) const

std::vector< std::string >	get_residue_names_with_no_dictionary (const protein_geometry &geom) const

int	insert_waters_into_molecule (const minimol::molecule &water_mol, const std::string &res_name)

std::string	get_molecule_selection_as_json (const std::string &cid) const

std::vector< residue_range_t >	get_missing_residue_ranges () const

void	make_bonds (protein_geometry geom, rotamer_probability_tables rot_prob_tables_p, bool draw_hydrogen_atoms_flag, bool draw_missing_loops_flag)

std::vector< glm::vec4 >	make_colour_table (bool against_a_dark_background) const
	useful for debugging, perhaps

std::vector< glm::vec4 >	make_colour_table_for_goodsell_style (float colour_wheel_rotation_step, float saturation, float goodselliness) const

void	print_colour_table (const std::string &debugging_label) const

void	print_secondary_structure_info () const

mmdb::Atom *	get_atom (const atom_spec_t &atom_spec) const

mmdb::Residue *	get_residue (const residue_spec_t &residue_spec) const

mmdb::Residue *	get_residue (const std::string &residue_cid) const

std::string	get_residue_name (const residue_spec_t &residue_spec) const

bool	have_unsaved_changes () const

int	undo ()

int	redo ()

int	write_coordinates (const std::string &file_name) const

std::string	molecule_to_PDB_string () const

std::string	molecule_to_mmCIF_string () const

std::vector< atom_spec_t >	get_fixed_atoms () const

std::vector< std::string >	chains_in_model () const

std::vector< std::pair< residue_spec_t, std::string > >	get_single_letter_codes_for_chain (const std::string &chain_id) const

residue_spec_t	get_residue_closest_to (mmdb::Manager *mol, const clipper::Coord_orth &co) const

std::vector< std::string >	get_chain_ids () const

std::vector< std::vector< std::string > >	get_ncs_related_chains () const
	Get the chains that are related by NCS:

bool	copy_ncs_chain (const std::string &from_chain_id, const std::string &to_chain_id)
	copy chain using NCS matrix

std::vector< double >	get_residue_CA_position (const std::string &cid) const

std::vector< double >	get_residue_average_position (const std::string &cid) const

std::vector< double >	get_residue_sidechain_average_position (const std::string &cid) const

void	set_occupancy (const std::string &cid, float occ_new)

simple_mesh_t	get_bonds_mesh (const std::string &mode, protein_geometry *geom, bool against_a_dark_background, float bonds_width, float atom_radius_to_bond_width_ratio, int smoothness_factor, bool draw_hydrogen_atoms_flag, bool draw_missing_residue_loops)

simple_mesh_t	get_goodsell_style_mesh (protein_geometry *geom_p, float colour_wheel_rotation_step, float saturation, float goodselliness)

instanced_mesh_t	get_bonds_mesh_instanced (const std::string &mode, protein_geometry *geom, bool against_a_dark_background, float bonds_width, float atom_radius_to_bond_width_ratio, bool render_atoms_as_aniso, float aniso_probability, bool render_aniso_atoms_as_ortep, int smoothness_factor, bool draw_hydrogen_atoms_flag, bool draw_missing_residue_loops)

instanced_mesh_t	get_bonds_mesh_for_selection_instanced (const std::string &mode, const std::string &selection_cid, protein_geometry *geom, bool against_a_dark_background, float bonds_width, float atom_radius_to_bond_width_ratio, bool render_atoms_as_aniso, bool render_aniso_atoms_as_ortep, int smoothness_factor, bool draw_hydrogen_atoms_flag, bool draw_missing_residue_loops)

instanced_mesh_t	get_goodsell_style_mesh_instanced (protein_geometry *geom_p, float colour_wheel_rotation_step, float saturation, float goodselliness)

void	set_user_defined_bond_colours (const std::map< unsigned int, std::array< float, 4 > > &colour_map)

void	set_user_defined_atom_colour_by_selections (const std::vector< std::pair< std::string, unsigned int > > &indexed_residues_cids, bool colour_applies_to_non_carbon_atoms_also, mmdb::Manager *mol)
	user-defined atom selection to colour index.

void	store_user_defined_atom_colour_selections (const std::vector< std::pair< std::string, unsigned int > > &indexed_residues_cids, bool colour_applies_to_non_carbon_atoms_also)

void	apply_user_defined_atom_colour_selections (const std::vector< std::pair< std::string, unsigned int > > &indexed_residues_cids, bool colour_applies_to_non_carbon_atoms_also, mmdb::Manager *mol)

void	set_colour_wheel_rotation_base (float r)
	set the colour wheel rotation base for the specified molecule

void	set_base_colour_for_bonds (float r, float g, float b)
	set the base colour - to be used as a base for colour wheel rotation

void	add_to_non_drawn_bonds (const std::string &atom_selection_cid)

void	clear_non_drawn_bonds ()

void	print_non_drawn_bonds () const

void	fill_default_colour_rules ()

void	add_colour_rule (const std::string &selection, const std::string &colour_name)
	Add a colour rule: eg. ("//A", "red")

void	delete_colour_rules ()
	delete all the colour rules

void	print_colour_rules () const

std::vector< std::pair< std::string, std::string > >	get_colour_rules () const

void	M2T_updateFloatParameter (const std::string &param_name, float value)
	Update float parameter for MoleculesToTriangles molecular mesh.

void	M2T_updateFloatParameter (const std::string &param_name, int value)
	Update int parameter for MoleculesToTriangles molecular mesh.

void	print_M2T_FloatParameters () const

void	print_M2T_IntParameters () const

void	M2T_updateIntParameter (const std::string &param_name, int value)
	Update int parameter for MoleculesToTriangles molecular mesh.

simple_mesh_t	get_molecular_representation_mesh (const std::string &cid, const std::string &colour_scheme, const std::string &style, int secondaryStructureUsageFlag) const

simple_mesh_t	get_gaussian_surface (float sigma, float contour_level, float box_radius, float grid_scale, float fft_b_factor) const

simple_mesh_t	get_chemical_features_mesh (const std::string &cid, const protein_geometry &geom) const

bool	hydrogen_atom_should_be_drawn () const

void	set_use_bespoke_carbon_atom_colour (bool state)

void	set_bespoke_carbon_atom_colour (const colour_t &col)

void	export_map_molecule_as_gltf (clipper::Coord_orth &position, float radius, float contour_level, const std::string &file_name)
	export map molecule as glTF

void	export_model_molecule_as_gltf (const std::string &mode, const std::string &selection_cid, protein_geometry *geom, bool against_a_dark_background, float bonds_width, float atom_radius_to_bond_width_ratio, int smoothness_factor, bool draw_hydrogen_atoms_flag, bool draw_missing_residue_loops, const std::string &file_name)
	export model molecule as glTF - this is the bonds and atoms API

void	export_molecular_representation_as_gltf (const std::string &atom_selection_cid, const std::string &colour_scheme, const std::string &style, int secondary_structure_usage_flag, const std::string &file_name)

void	export_chemical_features_as_gltf (const std::string &cid, const protein_geometry &geom, const std::string &file_name) const

void	set_show_symmetry (bool f)

bool	get_show_symmetry ()

void	transform_by (mmdb::mat44 SSMAlign_TMatrix)

void	transform_by (const clipper::RTop_orth &rtop, mmdb::Residue *res)

void	transform_by (const clipper::RTop_orth &rtop)

symmetry_info_t	get_symmetry (float symmetry_search_radius, const Cartesian &symm_centre) const

std::vector< std::string >	non_standard_residue_types_in_model () const

std::vector< phi_psi_prob_t >	ramachandran_validation (const ramachandrans_container_t &rc) const

simple_mesh_t	get_rotamer_dodecs (protein_geometry geom_p, rotamer_probability_tables rpt)

instanced_mesh_t	get_rotamer_dodecs_instanced (protein_geometry geom_p, rotamer_probability_tables rpt)

omega_distortion_info_container_t	peptide_omega_analysis (const protein_geometry &geom, const std::string &chain_id, bool mark_cis_peptides_as_bad_flag) const

std::vector< residue_spec_t >	get_non_standard_residues_in_molecule () const

std::vector< std::string >	get_residue_types_without_dictionaries (const protein_geometry &geom) const

instanced_mesh_t	contact_dots_for_ligand (const std::string &cid, const protein_geometry &geom, unsigned int num_subdivisions) const

instanced_mesh_t	all_molecule_contact_dots (const coot::protein_geometry &geom, unsigned int num_subdivisions) const

generic_3d_lines_bonds_box_t	make_exportable_environment_bond_box (coot::residue_spec_t &spec, float max_dist, coot::protein_geometry &geom) const

simple::molecule_t	get_simple_molecule (int imol, const std::string &residue_cid, const bool draw_hydrogen_atoms_flag, coot::protein_geometry *geom_p)

simple::molecule_t	get_simple_molecule (int imol, mmdb::Residue residue_p, bool draw_hydrogen_atoms_flag, coot::protein_geometry geom_p)

coot::simple_mesh_t	get_mesh_for_ligand_validation_vs_dictionary (const std::string &ligand_cid, coot::protein_geometry &geom, ctpl::thread_pool &static_thread_pool)

std::vector< coot::geometry_distortion_info_container_t >	geometric_distortions_for_one_residue_from_mol (const std::string &ligand_cid, bool with_nbcs, coot::protein_geometry &geom, ctpl::thread_pool &static_thread_pool)

std::vector< coot::geometry_distortion_info_container_t >	geometric_distortions_for_selection_from_mol (const std::string &selection_cid, bool with_nbcs, coot::protein_geometry &geom, ctpl::thread_pool &static_thread_pool)

std::pair< int, double >	simple_geometric_distortions_from_mol (const std::string &ligand_cid, bool with_nbcs, coot::protein_geometry &geom, ctpl::thread_pool &static_thread_pool)

coot::instanced_mesh_t	get_extra_restraints_mesh (int mode) const

std::vector< coot::residue_spec_t >	residues_near_residue (const std::string &residue_cid, float dist) const

std::vector< coot::atom_distance_t >	get_distances_between_atoms_of_residues (const std::string &cid_res_1, const std::string &cid_res_2, float dist_max) const

std::vector< plain_atom_overlap_t >	get_atom_overlaps (protein_geometry *geom_p)
	not const because it can dynamically add dictionaries

float	get_atom_overlap_score (protein_geometry *geom_p) const
	get the atom overlap

std::vector< plain_atom_overlap_t >	get_overlaps_for_ligand (const std::string &cid_ligand, protein_geometry *geom_p)
	not const because it can dynamically add dictionaries

coot::atom_overlaps_dots_container_t	get_overlap_dots (protein_geometry *geom_p)
	not const because it can dynamically add dictionaries

coot::atom_overlaps_dots_container_t	get_overlap_dots_for_ligand (const std::string &cid_ligand, protein_geometry *geom_p)
	not const because it can dynamically add dictionaries

instanced_mesh_t	get_HOLE (const clipper::Coord_orth &start_pos, const clipper::Coord_orth &end_pos, const protein_geometry &geom) const

std::string	get_pucker_analysis_info () const

std::string	get_svg_for_2d_ligand_environment_view (const std::string &residue_cid, protein_geometry *geom, bool add_key) const

RDKit::ROMol *	rdkit_mol (const std::string &ligand_cid)

int	move_molecule_to_new_centre (const coot::Cartesian &new_centre)

coot::Cartesian	get_molecule_centre () const

int	flip_peptide (const atom_spec_t &rs, const std::string &alt_conf)

int	auto_fit_rotamer (const std::string &chain_id, int res_no, const std::string &ins_code, const std::string &alt_conf, const clipper::Xmap< float > &xmap, const coot::protein_geometry &pg)

std::pair< bool, float >	backrub_rotamer (mmdb::Residue *residue_p, const clipper::Xmap< float > &xmap, const coot::protein_geometry &pg)

std::pair< bool, float >	backrub_rotamer (const std::string &chain_id, int res_no, const std::string &ins_code, const std::string &alt_conf, const clipper::Xmap< float > &xmap, const coot::protein_geometry &pg)

int	delete_atoms (const std::vector< atom_spec_t > &atoms)

int	delete_atom (atom_spec_t &atom_spec)

int	delete_residue (residue_spec_t &residue_spec)

int	delete_residue_atoms_with_alt_conf (coot::residue_spec_t &residue_spec, const std::string &alt_conf)

int	delete_chain_using_atom_cid (const std::string &cid)

int	delete_literal_using_cid (const std::string &cid)

int	change_alt_locs (const std::string &cid, const std::string &change_mode)

std::pair< int, std::string >	add_terminal_residue_directly (const residue_spec_t &spec, const std::string &new_res_type, const protein_geometry &geom, const clipper::Xmap< float > &xmap, mmdb::Manager *standard_residues_asc_mol, ctpl::thread_pool &static_thread_pool)

void	execute_simple_nucleotide_addition (const std::string &term_type, mmdb::Residue res_p, const std::string &chain_id, mmdb::Manager standard_residues_asc_mol)

void	execute_simple_nucleotide_addition (mmdb::Residue residue_p, mmdb::Manager standard_residues_asc_mol)

void	execute_simple_nucleotide_addition (const std::string &cid, mmdb::Manager *standard_residues_asc_mol)

int	add_compound (const dictionary_residue_restraints_t &monomer_restraints, const Cartesian &position, const clipper::Xmap< float > &xmap, float map_rmsd)

int	add_alternative_conformation (const std::string &cid)
	add an alternative conformation for the specified residue

int	fill_partial_residue (const residue_spec_t &res_spec, const std::string &alt_conf, const clipper::Xmap< float > &xmap, const protein_geometry &geom)
	add atoms to a partially-filled side chaain

int	fill_partial_residues (const clipper::Xmap< float > &xmap, protein_geometry *geom)
	add atoms to a partially-filled side chaain

int	mutate (const residue_spec_t &spec, const std::string &new_res_type)

void	add_named_glyco_tree (const std::string &glycosylation_name, const std::string &chain_id, int res_no, const clipper::Xmap< float > &xmap, protein_geometry *geom)

int	side_chain_180 (const residue_spec_t &residue_spec, const std::string &alt_conf, coot::protein_geometry *geom_p)

int	delete_side_chain (const residue_spec_t &residue_spec)

std::string	jed_flip (coot::residue_spec_t &spec, const std::string &atom_name, const std::string &alt_conf, bool invert_selection, protein_geometry *geom)

std::string	jed_flip_internal (coot::atom_tree_t &tree, const std::vector< coot::dict_torsion_restraint_t > &interesting_torsions, const std::string &atom_name, bool invert_selection)

std::string	jed_flip_internal (coot::atom_tree_t &tree, const dict_torsion_restraint_t &torsion, const std::string &atom_name, bool invert_selection)

int	match_torsions (mmdb::Residue *res_ref, const std::vector< coot::dict_torsion_restraint_t > &tr_ligand, const coot::protein_geometry &geom)

coot::minimol::molecule	eigen_flip_residue (const residue_spec_t &residue_spec)

int	apply_transformation_to_atom_selection (const std::string &atom_selection_cid, int n_atoms_in_selection, clipper::Coord_orth &rotation_centre, clipper::RTop_orth &rtop)

void	multiply_residue_temperature_factors (const std::string &cid, float factor)

int	add_hydrogen_atoms (protein_geometry *geom)

int	delete_hydrogen_atoms ()

bool	delete_all_carbohydrate ()

bool	residue_is_nucleic_acid (const std::string &cid) const

std::pair< int, std::string >	change_chain_id (const std::string &from_chain_id, const std::string &to_chain_id, bool use_resno_range, int start_resno, int end_resno)

std::pair< int, std::string >	change_chain_id_with_residue_range (const std::string &from_chain_id, const std::string &to_chain_id, int start_resno, int end_resno)

void	change_chain_id_with_residue_range_helper_insert_or_add (mmdb::Chain to_chain_p, mmdb::Residue new_residue)

int	new_positions_for_residue_atoms (const std::string &residue_cid, const std::vector< api::moved_atom_t > &moved_atoms)
	set new positions for the atoms in the specified residue

int	new_positions_for_atoms_in_residues (const std::vector< api::moved_residue_t > &moved_residues)
	set new positions for the atoms of the specified residues

int	new_positions_for_residue_atoms (mmdb::Residue *residue_p, const std::vector< api::moved_atom_t > &moved_atoms, bool do_backup)

int	merge_molecules (const std::vector< mmdb::Manager * > &mols)

float	fit_to_map_by_random_jiggle (const residue_spec_t &res_spec, const clipper::Xmap< float > &xmap, float map_rmsd, int n_trials, float translation_scale_factor)

float	fit_to_map_by_random_jiggle_using_atom_selection (const std::string &cid, const clipper::Xmap< float > &xmap, float map_rmsd, int n_trials, float translation_scale_factor)

int	cis_trans_conversion (const std::string &atom_cid, mmdb::Manager *standard_residues_mol)

int	replace_residue (const std::string &residue_cid, const std::string &new_residue_type, int imol_enc, const protein_geometry &geom)

int	mutate_by_overlap (mmdb::Residue *residue_p, const dictionary_residue_restraints_t &restraints)

int	replace_fragment (atom_selection_container_t asc)

int	replace_fragment (mmdb::Manager *mol_ref, int old_atom_index_handle, int SelHnd)

rotamer_change_info_t	change_to_next_rotamer (const coot::residue_spec_t &res_spec, const std::string &alt_conf, const coot::protein_geometry &pg)
	change rotamers

rotamer_change_info_t	change_to_previous_rotamer (const coot::residue_spec_t &res_spec, const std::string &alt_conf, const coot::protein_geometry &pg)

rotamer_change_info_t	change_to_first_rotamer (const coot::residue_spec_t &res_spec, const std::string &alt_conf, const coot::protein_geometry &pg)

rotamer_change_info_t	change_rotamer_number (const coot::residue_spec_t &res_spec, const std::string &alt_conf, int rotamer_change_direction, const coot::protein_geometry &pg)

int	set_residue_to_rotamer_number (coot::residue_spec_t res_spec, const std::string &alt_conf_in, int rotamer_number, const coot::protein_geometry &pg)

void	associate_sequence_with_molecule (const std::string &chain_id, const std::string &sequence)

void	assign_sequence (const clipper::Xmap< float > &xmap, const coot::protein_geometry &geom)
	try to fit all of the sequences to all of the chains

std::vector< std::pair< std::string, std::string > >	get_sequence_info () const
	simple return the associated sequences

chain_mutation_info_container_t	get_mutation_info () const
	return the mismatches/mutations:

bool	is_het_residue (mmdb::Residue *residue_p) const

std::pair< short int, int >	next_residue_number_in_chain (mmdb::Chain *w, bool new_res_no_by_hundreds=false) const

mmdb::Residue *	copy_and_add_residue_to_chain (mmdb::Chain this_model_chain, mmdb::Residue add_model_residue, bool new_resno_by_hundreds_flag=true)

void	copy_and_add_chain_residues_to_chain (mmdb::Chain new_chain, mmdb::Chain this_molecule_chain)

std::vector< std::string >	map_chains_to_new_chains (const std::vector< std::string > &adding_model_chains, const std::vector< std::string > &this_model_chains) const

std::string	suggest_new_chain_id (const std::string &current_chain_id) const

std::pair< bool, std::vector< std::string > >	try_add_by_consolidation (mmdb::Manager *adding_mol)

bool	merge_molecules_just_one_residue_homogeneous (atom_selection_container_t molecule_to_add)

bool	merge_molecules_just_one_residue_at_given_spec (atom_selection_container_t molecule_to_add, residue_spec_t target_spec)

std::pair< bool, coot::residue_spec_t >	merge_ligand_to_near_chain (mmdb::Manager *mol)

std::pair< int, std::vector< merge_molecule_results_info_t > >	merge_molecules (const std::vector< atom_selection_container_t > &add_molecules)

std::pair< int, double >	get_torsion (const std::string &cid, const std::vector< std::string > &atom_names) const

void	set_temperature_factors_using_cid (const std::string &cid, float temp_fact)

int	read_extra_restraints (const std::string &file_name)
	read extra restraints (e.g. from ProSMART)

std::vector< mmdb::Residue * >	select_residues (const residue_spec_t &spec, const std::string &mode) const
	refinement tool

std::vector< mmdb::Residue * >	select_residues (const std::string &chain_id, int resno_start, int resno_end) const
	resno_start and resno_end are inclusive

std::vector< mmdb::Residue * >	select_residues (const std::string &multi_cid, const std::string &mode) const
	select residues given a multi-cid

int	refine_direct (std::vector< mmdb::Residue * > rv, const std::string &alt_loc, const clipper::Xmap< float > &xmap, unsigned int max_number_of_threads, float map_weight, int n_cycles, const coot::protein_geometry &geom, bool do_rama_plot_restraints, float rama_plot_weight, bool do_torsion_restraints, float torsion_weight, bool refinement_is_quiet)
	real space refinement

int	minimize (const std::string &atom_selection_cid, int n_cycles, bool do_rama_plot_restraints, float rama_plot_weight, bool do_torsion_restraints, float torsion_weight, bool refinement_is_quiet, coot::protein_geometry *geom_p)

bool	shiftfield_b_factor_refinement (const clipper::HKL_data< clipper::data32::F_sigF > &F_sigF, const clipper::HKL_data< clipper::data32::Flag > &free_flag)

void	fix_atom_selection_during_refinement (const std::string &atom_selection_cid)

void	init_all_molecule_refinement (int imol_ref_mol, coot::protein_geometry &geom, const clipper::Xmap< float > &xmap, float map_weight, ctpl::thread_pool *thread_pool)

void	add_target_position_restraint (const std::string &atom_cid, float pos_x, float pos_y, float pos_z)

void	turn_off_when_close_target_position_restraint ()

instanced_mesh_t	add_target_position_restraint_and_refine (const std::string &atom_cid, float pos_x, float pos_y, float pos_z, int n_cyles, coot::protein_geometry *geom_p)

void	clear_target_position_restraint (const std::string &atom_cid)
	clear

int	refine_using_last_restraints (int n_steps)

restraints_container_t *	get_last_restraints ()

void	clear_target_position_restraints ()
	clear any and all drag-atom target position restraints

void	clear_refinement ()

void	generate_self_restraints (float local_dist_max, const coot::protein_geometry &geom)

void	generate_chain_self_restraints (float local_dist_max, const std::string &chain_id, const coot::protein_geometry &geom)

void	generate_local_self_restraints (float local_dist_max, const std::vector< coot::residue_spec_t > &residue_specs, const coot::protein_geometry &geom)

void	generate_local_self_restraints (float local_dist_max, const std::string &multi_selection_cid, const coot::protein_geometry &geom)

void	generate_local_self_restraints (int selHnd, float local_dist_max, const coot::protein_geometry &geom)

void	add_parallel_plane_restraint (coot::residue_spec_t spec_1, coot::residue_spec_t spec_2)

std::vector< std::string >	nucelotide_residue_name_to_base_atom_names (const std::string &rn) const

std::vector< std::string >	residue_name_to_plane_atom_names (const std::string &rn) const

void	clear_extra_restraints ()

int	rigid_body_fit (const std::string &mult_cids, const clipper::Xmap< float > &xmap)

int	rotate_around_bond (const std::string &residue_cid, const std::string &alt_conf, coot::atom_name_quad quad, double torsion_angle, protein_geometry &geom)

void	scale_map (float scale_factor)

bool	is_EM_map () const

float	get_density_at_position (const clipper::Coord_orth &pos) const

float	get_map_mean () const

float	get_map_rmsd_approx () const

int	write_map (const std::string &file_name) const

void	set_map_is_difference_map (bool flag)

bool	is_difference_map_p () const

void	set_updating_maps_diff_diff_map_peaks (const std::vector< std::pair< clipper::Coord_orth, float > > &v)

std::vector< std::pair< clipper::Coord_orth, float > >	get_updating_maps_diff_diff_map_peaks (const clipper::Coord_orth &screen_centre) const
	does the peaks-move operation.

float	get_suggested_initial_contour_level () const

simple_mesh_t	get_map_contours_mesh (clipper::Coord_orth position, float radius, float contour_level, bool use_thread_pool, ctpl::thread_pool *thread_pool_p)

simple_mesh_t	get_map_contours_mesh_using_other_map_for_colours (const clipper::Coord_orth &position, float radius, float contour_level, const clipper::Xmap< float > &xmap)

simple_mesh_t	get_map_contours_mesh_using_other_map_for_colours (const clipper::Coord_orth &position, float radius, float contour_level, const user_defined_colour_table_t &udct, const clipper::Xmap< float > &xmap)

histogram_info_t	get_map_histogram (unsigned int n_bins, float zoom_factor) const

histogram_info_t	get_map_vertices_histogram (const clipper::Xmap< float > &other_xmap, const clipper::Coord_orth &pt, float radius, float contour_level, bool use_thread_pool, ctpl::thread_pool *thread_pool_p, unsigned int n_bins)

void	set_map_colour (colour_holder holder)

void	set_map_colour_saturation (float s)

void	set_other_map_for_colouring_min_max (float min_v, float max_v)

void	set_other_map_for_colouring_invert_colour_ramp (bool state)

double	sum_density_for_atoms_in_residue (const std::string &cid, const std::vector< std::string > &atom_names, const clipper::Xmap< float > &xmap) const

std::vector< interesting_place_t >	difference_map_peaks (mmdb::Manager *mol, float n_rmsd) const

texture_as_floats_t	get_map_section_texture (int section_index, int axis, float data_value_for_bottom, float data_value_for_top) const

int	get_number_of_map_sections (int axis_id) const

std::vector< float >	get_vertices_for_blender () const

std::vector< int >	get_triangles_for_blender () const

std::vector< float >	get_colour_table_for_blender () const

void	make_mesh_for_bonds_for_blender (const std::string &mode, protein_geometry *geom, bool against_a_dark_background, float bond_width, float atom_radius_to_bond_width_ratio, int smoothness_factor)

void	make_mesh_for_molecular_representation_for_blender (const std::string &cid, const std::string &colour_scheme, const std::string &style, int secondary_structure_usage_flag)

void	make_mesh_for_goodsell_style_for_blender (protein_geometry *geom_p, float colour_wheel_rotation_step, float saturation, float goodselliness)

void	make_mesh_for_map_contours_for_blender (Cartesian position, float contour_level, float radius)

void	make_mesh_for_gaussian_surface_for_blender (float sigma, float contour_level, float box_radius, float grid_scale, float b_factor)

Public Attributes
atom_selection_container_t	atom_sel

float	default_temperature_factor_for_new_atoms

std::vector< std::pair< bool, mmdb::Residue * > >	neighbouring_residues

std::string	refmac_fobs_col

std::string	refmac_sigfobs_col

std::string	refmac_mtz_filename

std::string	refmac_r_free_col

bool	refmac_r_free_flag_sensible

clipper::Xmap< float >	xmap

std::map< unsigned int, colour_holder >	user_defined_bond_colours

std::vector< std::pair< std::string, unsigned int > >	indexed_user_defined_colour_selection_cids

bool	indexed_user_defined_colour_selection_cids_apply_to_non_carbon_atoms_also

colour_holder	base_colour_for_bonds

std::set< int >	no_bonds_to_these_atom_indices

std::vector< std::pair< std::string, std::string > >	colour_rules

std::vector< std::pair< std::string, float > >	M2T_float_params

std::vector< std::pair< std::string, int > >	M2T_int_params

float	gltf_pbr_roughness

float	gltf_pbr_metalicity

coot::extra_restraints_t	extra_restraints

std::vector< std::pair< mmdb::Atom *, clipper::Coord_orth > >	atoms_with_position_restraints

clipper::Xmap< float >	updating_maps_previous_difference_map

std::vector< std::pair< clipper::Coord_orth, float > >	updating_maps_diff_diff_map_peaks

blender_mesh_t	blender_mesh

Static Public Attributes
static std::atomic< bool >	draw_vector_sets_lock

Member Function Documentation

◆ add_hydrogen_atoms()

int coot::molecule_t::add_hydrogen_atoms ( protein_geometry * geom )

Returns: 1 on a successful additions, 0 on failure.

◆ all_molecule_contact_dots()

instanced_mesh_t coot::molecule_t::all_molecule_contact_dots	(	const coot::protein_geometry &	geom,
		unsigned int	num_subdivisions ) const

Returns: the instanced mesh for the specified molecule

◆ clear_refinement()

void coot::molecule_t::clear_refinement ( )

call this after molecule refinement has finished (say when the molecule molecule is accepted into the original molecule)

◆ contact_dots_for_ligand()

instanced_mesh_t coot::molecule_t::contact_dots_for_ligand	(	const std::string &	cid,
		const protein_geometry &	geom,
		unsigned int	num_subdivisions ) const

Returns: the instanced mesh for the specified ligand

◆ delete_all_carbohydrate()

bool coot::molecule_t::delete_all_carbohydrate ( )

delete all carbohydrate

Returns: true on successful deletion, return false on no deletion.

◆ delete_hydrogen_atoms()

int coot::molecule_t::delete_hydrogen_atoms ( )

Returns: 1 on a successful additions, 0 on failure.

◆ fit_to_map_by_random_jiggle_using_atom_selection()

float coot::molecule_t::fit_to_map_by_random_jiggle_using_atom_selection	(	const std::string &	cid,
		const clipper::Xmap< float > &	xmap,
		float	map_rmsd,
		int	n_trials,
		float	translation_scale_factor )

My ligands don't jiggle-jiggle...

Hey, what do you know, they actually do.

◆ geometric_distortions_for_one_residue_from_mol()

std::vector< coot::geometry_distortion_info_container_t > coot::molecule_t::geometric_distortions_for_one_residue_from_mol	(	const std::string &	ligand_cid,
		bool	with_nbcs,
		coot::protein_geometry &	geom,
		ctpl::thread_pool &	static_thread_pool )

this function is another version of the above function, but returns distortion values

this function returns a vector of the wrong type (it has pointers to expired molecules).

◆ geometric_distortions_for_selection_from_mol()

std::vector< coot::geometry_distortion_info_container_t > coot::molecule_t::geometric_distortions_for_selection_from_mol	(	const std::string &	selection_cid,
		bool	with_nbcs,
		coot::protein_geometry &	geom,
		ctpl::thread_pool &	static_thread_pool )

this function is another version of the above function, but returns distortion values

this function returns a vector of the wrong type (it has pointers to expired molecules).

◆ get_colour_rules()

std::vector< std::pair< std::string, std::string > > coot::molecule_t::get_colour_rules ( ) const

get the colour rules. Preferentially return the user-defined colour rules.

Returns: If there are no user-defined colour rules, then return the stand-in rules

◆ get_distances_between_atoms_of_residues()

std::vector< coot::atom_distance_t > coot::molecule_t::get_distances_between_atoms_of_residues	(	const std::string &	cid_res_1,
		const std::string &	cid_res_2,
		float	dist_max ) const

get atom distances other stuff here

◆ get_map_histogram()

histogram_info_t coot::molecule_t::get_map_histogram	(	unsigned int	n_bins,
		float	zoom_factor ) const

Returns: the map histogram The caller should select the number of bins - 200 is a reasonable default. The caller should also set the zoom factor (which reduces the range by the given factor) centred around the median (typically 1.0 but usefully can vary until ~20.0).

◆ get_mesh_for_ligand_validation_vs_dictionary()

coot::simple_mesh_t coot::molecule_t::get_mesh_for_ligand_validation_vs_dictionary	(	const std::string &	ligand_cid,
		coot::protein_geometry &	geom,
		ctpl::thread_pool &	static_thread_pool )

get the mesh for ligand validation vs dictionary, coloured by badness. greater then 3 standard deviations is fully red. Less than 0.5 standard deviations is fully green.

◆ get_missing_residue_ranges()

std::vector< residue_range_t > coot::molecule_t::get_missing_residue_ranges ( ) const

get missing residue ranges

Parameters

imol	is the model molecule index

Returns: missing residue ranges

◆ get_number_of_map_sections()

int coot::molecule_t::get_number_of_map_sections ( int axis_id ) const

Returns: the number of section in the map along the give axis. (0 for X-axis, 1 for y-axis, 2 for Z-axis). return -1 on failure.

◆ get_pucker_analysis_info()

std::string coot::molecule_t::get_pucker_analysis_info ( ) const

get pucker info

Parameters

imol2 is the model molecule index

Returns: a json string or an empty string on failure

◆ get_radius_of_gyration()

double coot::molecule_t::get_radius_of_gyration ( ) const

Get Radius of Gyration

Parameters

imol	is the model molecule index

Returns: the molecule centre. If the number is less than zero, there was a problem finding the molecule or atoms.

◆ get_residue_average_position()

std::vector< double > coot::molecule_t::get_residue_average_position ( const std::string & cid ) const

get the avarge residue position

Returns: a vector. The length of the vector is 0 on failure, otherwise it is the x,y,z values

◆ get_residue_CA_position()

std::vector< double > coot::molecule_t::get_residue_CA_position ( const std::string & cid ) const

get the residue CA position

Returns: a vector. The length of the vector is 0 on failure, otherwise it is the x,y,z values

◆ get_residue_sidechain_average_position()

std::vector< double > coot::molecule_t::get_residue_sidechain_average_position ( const std::string & cid ) const

get the avarge residue side-chain position

Returns: a vector. The length of the vector is 0 on failure, otherwise it is the x,y,z values

◆ get_simple_molecule()

simple::molecule_t coot::molecule_t::get_simple_molecule	(	int	imol,
		const std::string &	residue_cid,
		const bool	draw_hydrogen_atoms_flag,
		coot::protein_geometry *	geom_p )

we pass the imol because we use that to look up the residue type in the dictionary annoyingly, we pass a non-const pointer to the protein-geometry because that is what is passed in the Bond_lines_container. Think about changin that one day.

◆ get_suggested_initial_contour_level()

float coot::molecule_t::get_suggested_initial_contour_level ( ) const

Returns: the suggested initial contour level. Return -1 on not-a-map

◆ get_svg_for_2d_ligand_environment_view()

std::string coot::molecule_t::get_svg_for_2d_ligand_environment_view	(	const std::string &	residue_cid,
		protein_geometry *	geom,
		bool	add_key ) const

Get SVG for 2d ligand environment view (FLEV)

The caller should make sure that the dictionary for the ligand has been loaded - this function won't do that. It will add hydrogen atoms if needed. The can modify the protein_geometry

Parameters

residue_cid is the cid for the residue

◆ make_mesh_for_molecular_representation_for_blender()

void coot::molecule_t::make_mesh_for_molecular_representation_for_blender	(	const std::string &	cid,
		const std::string &	colour_scheme,
		const std::string &	style,
		int	secondary_structure_usage_flag )

Make an (internal) mesh

this function doesn't return a value, instead it stores a blender_mesh_t blender_mesh in this model

@modifies internal state to fill the internal blender_mesh object

◆ merge_molecules()

int coot::molecule_t::merge_molecules ( const std::vector< mmdb::Manager * > & mols )

merge molecules - copy the atom of mols into this molecule

Returns: the number of atoms added.

◆ molecule_to_mmCIF_string()

std::string coot::molecule_t::molecule_to_mmCIF_string ( ) const

Returns: a model molecule imol as a string. Return emtpy string on error

◆ molecule_to_PDB_string()

std::string coot::molecule_t::molecule_to_PDB_string ( ) const

Returns: a model molecule imol as a string. Return emtpy string on error

◆ multiply_residue_temperature_factors()

void coot::molecule_t::multiply_residue_temperature_factors	(	const std::string &	cid,
		float	factor )

Interactive B-factor refinement (fun). "factor" might typically be say 0.9 or 1.1

◆ new_positions_for_residue_atoms()

int coot::molecule_t::new_positions_for_residue_atoms	(	mmdb::Residue *	residue_p,
		const std::vector< api::moved_atom_t > &	moved_atoms,
		bool	do_backup )

not for wrapping (should be private). We don't want this function to backup if the backup happens in the calling function (i.e. new_positions_for_atoms_in_residues).

◆ rdkit_mol()

RDKit::ROMol * coot::molecule_t::rdkit_mol ( const std::string & ligand_cid )

if the ligand cid specifies more than one residue, only the first is returned.

Returns: nullptr on error or failure to specify a ligand.

◆ refine_using_last_restraints()

int coot::molecule_t::refine_using_last_restraints ( int n_steps )

refine (again).

Returns: the status of the refinement: GSL_CONTINUE, GSL_SUCCESS, GSL_ENOPROG (no progress). i.e. don't call thus function again unless the status is GSL_CONTINUE (-2);

◆ replace_fragment()

int coot::molecule_t::replace_fragment ( atom_selection_container_t asc )

Returns: the success status

◆ residue_is_nucleic_acid()

bool coot::molecule_t::residue_is_nucleic_acid ( const std::string & cid ) const

Residue is nucleic acid?

Every residue in the selection is checked

Parameters

imol	is the model molecule index
cid	is the selection CID e.g "//A/15" (residue 15 of chain A)

Returns: a bool

◆ residues_near_residue()

std::vector< coot::residue_spec_t > coot::molecule_t::residues_near_residue	(	const std::string &	residue_cid,
		float	dist ) const

Returns: a list of residues specs that have atoms within dist of the atoms of the specified residue

◆ set_occupancy()

void coot::molecule_t::set_occupancy	(	const std::string &	cid,
		float	occ_new )

set occupancy

set the occupancy for the given atom selection

Parameters

imol	is the model molecule index
cod	is the atom selection CID

◆ set_other_map_for_colouring_min_max()

void coot::molecule_t::set_other_map_for_colouring_min_max	(	float	min_v,
		float	max_v )

Set the limit for the colour range for the values from the other map. If the other map were, for example, a map of correlation values, then you'd pass -1.0 and 1.0.

◆ set_user_defined_bond_colours()

void coot::molecule_t::set_user_defined_bond_colours ( const std::map< unsigned int, std::array< float, 4 > > & colour_map )

user-defined colour-index to colour (internallly, this converts the colour_map to the above vector of colour holders, so it's probably a good idea if the colour (index) keys are less than 200 or so.

Member Data Documentation

◆ colour_rules

std::vector<std::pair<std::string, std::string> > coot::molecule_t::colour_rules

If any colour rule has been set for this molecule, then we will use these (and that his its internal colour-by-chain colouring scheme).

the colour_rules is a vector of things like: ("//A", "red")

The documentation for this class was generated from the following file:

/opt/mambaforge/envs/bioconda/conda-bld/coot-headless_1766554005715/work/api/coot-molecule.hh

Classes

Public Member Functions

Public Attributes

Static Public Attributes

Member Function Documentation

◆ add_hydrogen_atoms()

◆ all_molecule_contact_dots()

◆ clear_refinement()

◆ contact_dots_for_ligand()

◆ delete_all_carbohydrate()

◆ delete_hydrogen_atoms()

◆ fit_to_map_by_random_jiggle_using_atom_selection()

◆ geometric_distortions_for_one_residue_from_mol()

◆ geometric_distortions_for_selection_from_mol()

◆ get_colour_rules()

◆ get_distances_between_atoms_of_residues()

◆ get_map_histogram()

◆ get_mesh_for_ligand_validation_vs_dictionary()

◆ get_missing_residue_ranges()

◆ get_number_of_map_sections()

◆ get_pucker_analysis_info()

◆ get_radius_of_gyration()

◆ get_residue_average_position()

◆ get_residue_CA_position()

◆ get_residue_sidechain_average_position()

◆ get_simple_molecule()

◆ get_suggested_initial_contour_level()

◆ get_svg_for_2d_ligand_environment_view()

◆ make_mesh_for_molecular_representation_for_blender()

◆ merge_molecules()

◆ molecule_to_mmCIF_string()

◆ molecule_to_PDB_string()

◆ multiply_residue_temperature_factors()

◆ new_positions_for_residue_atoms()

◆ rdkit_mol()

◆ refine_using_last_restraints()

◆ replace_fragment()

◆ residue_is_nucleic_acid()

◆ residues_near_residue()

◆ set_occupancy()

◆ set_other_map_for_colouring_min_max()

◆ set_user_defined_bond_colours()

Member Data Documentation

◆ colour_rules