Libcootapi’s Documentation

Libcootapi is a new (as of 2022) interface to the functionality of Coot. It is designed to be (is intended to be) a clean, consistent and easy-to-use interface primarily targeting WebAssembly/JavaScript and secondarily, Python.

The previous API for Coot still exists and is available for use with Python and Guile/Scheme (it provides the coot module). That interface is considerably more extensive than this one (consisting of several thousand API functions), but is significantly less easy to use as it embeds OpenGL and GTK libraries (and all of their dependencies, of course).

The Molecules Container

Coot’s molecules are referred to by index and should only be accessed via member functions of the molecules_container_t class.

The functions in this class for the most part return simple types. There are some functions that return a more complex type, such as coot::simple_mesh_t or coot::validation_information_t.

Note: The private types, functions, attributes and members are listed here, but they are not, for the most part, useful for exporting. Which is not to rule out that there may be something there that could usefully be declared as public.

class molecules_container_t

#include <molecules-container.hh>

the container of molecules. The class for all libcootapi functions.

Old Python functions

enum mesh_mode_t

Values:

enumerator UNKNOWN

enumerator SINGLE_COLOUR

enumerator MULTI_COLOUR

PyObject *simple_mesh_to_pythonic_mesh(const coot::simple_mesh_t &mesh, int mesh_mode): old function: do not use with nanobind

PyObject *get_pythonic_bonds_mesh(int imol, const std::string &mode, bool against_a_dark_background, float bond_width, float atom_radius_to_bond_width_ratio, int smoothness_factor): old function: do not use with nanobind

PyObject *get_pythonic_map_mesh(int imol, float x, float y, float z, float radius, float contour_level): old function: do not use with nanobind

PyObject *get_pythonic_molecular_representation_mesh(int imol, const std::string &atom_selection, const std::string &colour_sheme, const std::string &style, int secondary_structure_usage_flag): old function: do not use with nanobind

PyObject *get_pythonic_gaussian_surface_mesh(int imol, float sigma, float contour_level, float box_radius, float grid_scale, float fft_b_factor): old function: do not use with nanobind get Gaussion surface mesh

PyObject *get_pythonic_simple_molecule(int imol, const std::string &cid, bool include_hydrogen_atoms_flag)

old function: do not use with nanobind: get a pythonic mesh of the molecule (bonds)

0: atom-name

1: atom-element

2: position (a list of 3 floats)

3: formal charge (an integer)

4: aromaticity flag (boolean)

make a “proper” simple molecule python class one day.

Returns:: a pair - the first of which (index 0) is the list of atoms, the second (index 1) is the list of bonds. An atom is a list:

Basic Utilities

bool make_backups_flag: the backup-enable state (raw public if needed/prefered)

inline void set_make_backups(bool state)

Allow the user to disable/enable backups

Parameters:: state – is true to mean that it is enabled. The default is true.

inline bool get_make_backups() const

Returns:: the backup-enabled state

std::string file_name_to_string(const std::string &file_name) const

Returns:: the string of the contents of the given file-name.

inline unsigned int get_number_of_molecules() const

Returns:: the number of molecules

void create_empty_molecules(unsigned int n_empty): The adds a number of empty molecules to the internal vector of molecules Note that his is not like reserve as it will increase the molecule index of the next added molecule by n_empty.

inline void set_imol_refinement_map(int i): set the map used for refinement and fitting

inline void set_map_weight(float w): set the map weight

inline float get_map_weight() const

Returns:: the map weight

coot::atom_spec_t atom_cid_to_atom_spec(int imol, const std::string &cid) const: Convert atom cid string to a coot atom specifier. The test for these failing is spec.empty()

coot::residue_spec_t residue_cid_to_residue_spec(int imol, const std::string &cid) const

Convert residue cid string to a coot residue specifier.

Returns:: the residues spec. spec.empty() is true on failure.

inline void set_show_timings(bool s): this set the show_timings flag. Various (not all) functions in this class can calculate how long they took to run. Setting this will write the time to taken (in milliseconds) to stdout. The default is true.

inline coot::protein_geometry &get_geom()

moorhen::header_info_t get_header_info(int imol) const

get header info.

Returns:: an object with header info. Sparce at the moment.

int get_imol_enc_any() const

get imol_enc_any

Returns:: the value of imol_enc_any (meaning “the molecule number for dictionary that

Coordinates Utils

std::vector<coot::lsq_range_match_info_t> lsq_matchers

int read_coordinates(const std::string &file_name)

read a coordinates file (mmcif or PDB)

Returns:: the new molecule index on success and -1 on failure

int read_pdb(const std::string &file_name)

read a PDB file (or mmcif coordinates file, despite the name). It does the same job as read_coordinates but has (perhaps) a more familiar name.

Returns:: the new molecule index on success and -1 on failure

void print_secondary_structure_info(int imol) const: print the secondary structure information to standard out

void replace_molecule_by_model_from_file(int imol, const std::string &pdb_file_name): read a PDB file (or mmcif coordinates file, despite the name) to replace the current molecule. This will only work if the molecules is already a model molecule

std::vector<int> split_multi_model_molecule(int imol)

split an NMR model into multiple models - all in MODEL 1.

Returns:: the vector of new molecule indices.

int make_ensemble(const std::string &model_molecule_list)

make a multi-model molecule given the input molecules

Parameters:: ``model_molecules_list`` – is a colon-separated list of molecules, e.g. 2:3:4
Returns:: the new molecule index - -1 if no models were found in the model_molecules_list

std::string molecule_to_PDB_string(int imol) const

get the molecule as a PDB string

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

std::string molecule_to_mmCIF_string(int imol) const

get the molecule as an mmCIF string

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

std::pair<int, std::string> get_active_atom(float x, float y, float z, const std::string &displayed_model_molecules_list) const

get the active atom given the screen centre

displayed_model_molecules_list is a colon-separated list of molecules, e.g. “2:3:4”

Returns:: the molecule index and the atom cid. On failure (no molecules with atoms in them, say) then return -1 and a blank string.

int import_cif_dictionary(const std::string &cif_file_name, int imol_enc)

import a dictionary cif - imol_enc is used to specify to which molecule this dictionary should apply. Use IMOL_ENC_ANY to mean “it applies to all molecules.”

IMOL_ENC_ANY = -999999

Returns:: 1 on success and 0 on failure

std::string get_cif_file_name(const std::string &comp_id, int imol_enc) const

get the cif file name

Returns:: the dictionary read for the give residue type, return an empty string on failure to lookup the residue type

std::string get_cif_restraints_as_string(const std::string &comp_id, int imol_enc) const

get the cif restraints as a string

Returns:: a string that is the contents of a dictionary cif file

bool copy_dictionary(const std::string &monomer_name, int imol_current, int imol_new): copy the dictionary that is specific for imol_current so that it can be used with imol_new

int get_monomer(const std::string &monomer_name)

get a monomer

Parameters:: monomer_name – [in] the name of the monomer
Returns:: the new molecule index on success and -1 on failure

int get_monomer_from_dictionary(const std::string &comp_id, int imol, bool idealised_flag)

get a monomer for a particular molecule - use -999999 (IMOL_ENC_ANY) if no molecule-specific dictionary is needed.

Returns:: the new molecule index on success and -1 on failure

int get_monomer_and_position_at(const std::string &comp_id, int imol, float x, float y, float z)

get monomer and place it at the given position for a particular molecule - use -999999 if no molecule-specific dictionary is needed

Returns:: the new molecule index on success and -1 on failure

std::vector<std::string> get_groups_for_monomers(const std::vector<std::string> &residue_names) const

get the groups for a vector of monomers

Returns:: the group for the given list of residue names as a vector of strings

std::string get_group_for_monomer(const std::string &residue_name) const

get the group for a particlar monomer

Returns:: the group for the given residue name

std::string get_hb_type(const std::string &compound_id, int imol_enc, const std::string &atom_name) const

get the hydrogen bond type of a particular atom in a given residue type

Returns:: the hb_type for the given atom. On failure return an empty string. Valid types are: “HB_UNASSIGNED” ,”HB_NEITHER”, “HB_DONOR”, “HB_ACCEPTOR”, “HB_BOTH”, “HB_HYDROGEN”.

std::vector<std::pair<std::string, std::string>> get_gphl_chem_comp_info(const std::string &compound_id, int imol_enc)

get the GPhL extra restraint information (from the input cif file)

Returns:: a vector of string pairs that were part of a gphl_chem_comp_info. return an empty vector on failure to find any such info.

std::vector<std::pair<std::string, std::string>> get_acedrg_atom_types(const std::string &compound_id, int imol_enc) const

get a list of atom names and their associated atedrg atom types

Returns:: a list of atom names and their associated atedrg atom types, return an empty list on failure (atoms types are not in the dictionary or atom failure to look up the compound id)l

coot::acedrg_types_for_residue_t get_acedrg_atom_types_for_ligand(int imol, const std::string &residue_cid) const

get acedrg types for ligand bonds

Returns:: a vector of acedrg_types_for_residue_t

void write_png(const std::string &compound_id, int imol, const std::string &file_name) const

write a PNG for the given compound_id. imol can be IMOL_ENC_ANY

Currently this function does nothing (drawing is done with the not-allowed cairo)

int write_coordinates(int imol, const std::string &file_name) const

write the coordinate to the give file name

Returns:: 1 on success and 0 on failure

void set_draw_missing_residue_loops(bool state)

set the state for drawing missing loops

By default missing loops are drawn. This function allows missing loops to not be drawn. Sometimes that can clarify the representation. This is a lightweight function that sets a flag that is used by subsequent calls to get_bonds_mesh().

coot::simple_mesh_t get_bonds_mesh(int imol, const std::string &mode, bool against_a_dark_background, float bond_width, float atom_radius_to_bond_width_ratio, int smoothness_factor)

get the bonds mesh

mode is “COLOUR-BY-CHAIN-AND-DICTIONARY”, “CA+LIGANDS” or “VDW-BALLS”

against_a_dark_background allows the bond colours to be relevant for the background. When the background is dark, the colours should (as a rule) be bright and pastelly. When the background is light/white, the colour darker and more saturated.

smoothness_factor controls the number of triangles used to make the bond cylinders and spheres for the atoms - it rises in powers of 4. 1 is the smallest smoothness_factor, 2 looks nice (but maybe is slower to transfer) and 3 is best.

bond_width is the bond width in Angstroms. 0.12 is a reasonable default value.

atom_radius_to_bond_width_ratio allows the representation of “ball and stick”. To do so use a value between (say) 1.5 and 3.0. The ratio for “liquorice” representation is 1.0 (of course).

Returns:: a coot::simple_mesh_t

coot::instanced_mesh_t get_bonds_mesh_instanced(int imol, const std::string &mode, bool against_a_dark_background, float bond_width, float atom_radius_to_bond_width_ratio, int smoothness_factor)

get the instanced bonds mesh.

The arguments are as above:

mode is “COLOUR-BY-CHAIN-AND-DICTIONARY” - more modes to follow

against_a_dark_background allows the bond colours to be relevant for the background. When the background is dark, the colours should (as a rule) be bright and pastelly. When the background is light/white, the colour darker and more saturated.

smoothness_factor controls the number of triangles used to make the bond cylinders and spheres for the atoms - it rises in powers of 4. 1 is the smallest smoothness_factor, 2 looks nice and 3 is best. Instancing may mean that smoothness factor 3 should be used by default.

bond_width is the bond width in Angstroms. 0.12 is a reasonable default value.

atom_radius_to_bond_width_ratio allows the representation of “ball and stick”. To do so use a value between (say) 1.5 and 3.0. The ratio for “liquorice” representation is 1.0 (of course). 1.7 or 1.8 looks nice.

Returns:: a coot::instanced_mesh_t

coot::instanced_mesh_t get_bonds_mesh_for_selection_instanced(int imol, const std::string &atom_selection_cid, const std::string &mode, bool against_a_dark_background, float bond_width, float atom_radius_to_bond_width_ratio, int smoothness_factor)

As above, but only return the bonds for the atom selection. Typically one would call this with a wider bond_with than one would use for standards atoms (all molecule)

Returns:: a coot::instanced_mesh_t

coot::instanced_mesh_t get_goodsell_style_mesh_instanced(int imol, float colour_wheel_rotation_step, float saturation, float goodselliness)

get the Goodsell style mesh

Returns:: a coot::instanced_mesh_t

void export_map_molecule_as_gltf(int imol, float pos_x, float pos_y, float pos_z, float radius, float contour_level, const std::string &file_name)

export map molecule as glTF

(not const because maps might update?)

void export_model_molecule_as_gltf(int imol, const std::string &selection_cid, const std::string &mode, 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 API will change - we want to specify surfaces and ribbons too.

void export_molecular_represenation_as_gltf(int imol, 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)

std::vector<glm::vec4> get_colour_table(int imol, bool against_a_dark_background) const: return the colur table (for testing)

void set_colour_wheel_rotation_base(int imol, float r): set the colour wheel rotation base for the specified molecule (in degrees)

void set_base_colour_for_bonds(int imol, 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(int imol, const std::string &atom_selection_cid): add a atom selection cid for atoms and bonds not to be drawn

void clear_non_drawn_bonds(int imol): clear the set of non-drawn atoms (so that they can be displayed again)

void print_non_drawn_bonds(int imol) const: print non-drawn bonds

void set_user_defined_bond_colours(int imol, const std::map<unsigned int, std::array<float, 4>> &colour_map): user-defined colour-index to colour

void set_user_defined_atom_colour_by_selection(int imol, const std::vector<std::pair<std::string, unsigned int>> &indexed_residues_cids, bool colour_applies_to_non_carbon_atoms_also): set the user-defined residue selections (CIDs) to colour index

void add_colour_rule(int imol, const std::string &selection_cid, const std::string &colour): Add a colour rule for M2T representations.

void add_colour_rules_multi(int imol, const std::string &selections_and_colours_combo_string): add multiple colour rules, combined like the following “//A/1^#cc0000|//A/2^#cb0002|//A/3^#c00007” i.e. “|” is the separator for each rule and “^” is the separator for the selection string and the colour string

void delete_colour_rules(int imol): delete the colour rules for the given molecule

std::vector<std::pair<std::string, std::string>> get_colour_rules(int imol) const: get the colour rules

void print_colour_rules(int imol) const: print the colour rules

void set_use_bespoke_carbon_atom_colour(int imol, bool state): use bespoke carbon atom colour

void set_bespoke_carbon_atom_colour(int imol, const coot::colour_t &col): set bespoke carbon atom colour

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

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

coot::simple_mesh_t get_molecular_representation_mesh(int imol, const std::string &cid, const std::string &colour_scheme, const std::string &style, int secondary_structure_usage_flag)

get ribbon and surface representation

imol is the model molecule index

ecid` is the atom selection CID

colour_scheme should be one of

”colorRampChainsScheme”
”colorBySecondaryScheme”
”Chain”

style should be one of

”Ribbon”
”MolecularSurface”

The secondary_structure_usage_flag should be one of

0 (USE_HEADER),
1 (DONT_USE) or
2 (CALC_SECONDARY_STRUCTURE).

Mode 2 was the (implicit) usage mode until now (20240912).

Returns:: a coot::simple_mesh_t

coot::simple_mesh_t get_gaussian_surface(int imol, float sigma, float contour_level, float box_radius, float grid_scale, float b_factor) const

get a Gaussian surface representation

These values seem to give a reasonable quite smooth surface:

sigma = 4.4
contour_level = 4.0
box_radius = 5.0
grid_scale = 0.7
b_factor = 100.0 (use 0.0 for no FFT-B-factor smoothing)

Returns:: a coot::simple_mesh_t composed of a number of Gaussian surfaces (one for each chain)

coot::simple_mesh_t get_chemical_features_mesh(int imol, const std::string &cid) const

get chemical feaatures for the specified residue

Returns:: a coot::simple_mesh_t

unsigned int get_number_of_atoms(int imol) const

Returns:: the number of atoms in the specified model, or 0 on error

float get_molecule_diameter(int imol) const

Returns:: an estimate of the diameter of the model molecule (-1 on failure)

int get_number_of_hydrogen_atoms(int imol) const

Returns:: the number of hydrogen atoms in the specified model, or -1 on error

std::vector<std::string> get_chains_in_model(int imol) const

Returns:: vector of chain-ids for the given molecule

std::vector<std::vector<std::string>> get_ncs_related_chains(int imol) const

Get the chains that are related by NCS or molecular symmetry:

Returns:: a vector of vector of chain ids, e.g. [[A,C], [B,D]] (for hemoglobin).

std::vector<std::pair<coot::residue_spec_t, std::string>> get_single_letter_codes_for_chain(int imol, const std::string &chain_id) const

Returns:: vector of single letter codes - in a pair with the given residue spec

std::vector<std::string> get_residue_names_with_no_dictionary(int imol) const

Returns:: a list of residue that don’t have a dictionary

std::string get_residue_name(int imol, const std::string &chain_id, int res_no, const std::string &ins_code) const

get residue name

Returns:: the residue name, return a blank string on residue not found.

std::vector<coot::residue_spec_t> residues_with_missing_atoms(int imol)

Returns:: an object that has information about residues without dictionaries and residues with missing atom in the the specified molecule

coot::util::missing_atom_info missing_atoms_info_raw(int imol)

Ths function is not const because missing_atoms() takes a non-const pointer to the geometry.

Returns:: an object that has information about residues without dictionaries and residues with missing atom in the the specified molecule

std::vector<coot::residue_spec_t> get_residues_near_residue(int imol, 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

superpose_results_t SSM_superpose(int imol_ref, const std::string &chain_id_ref, int imol_mov, const std::string &chain_id_mov)

superposition (using SSM)

The specified chain of the moving molecule is superposed onto the chain in the reference molecule (if possible). There is some alignment screen output that would be better added to the return value.

void add_lsq_superpose_match(const std::string &chain_id_ref, int res_no_ref_start, int res_no_ref_end, const std::string &chain_id_mov, int res_no_mov_start, int res_no_mov_end, int match_type): superpose using LSQ - setup the matches @params match_type 0: all, 1: main, 2: CAs, 3: N, CA, C

void clear_lsq_matches(): clear any existing lsq matchers

void lsq_superpose(int imol_ref, int imol_mov): apply the superposition using LSQ

lsq_results_t get_lsq_matrix(int imol_ref, int imol_mov) const: return the transformation matrix in a simple class - dont apply it to the coordinates

std::pair<short int, clipper::RTop_orth> get_lsq_matrix_internal(int imol_ref, int imol_mov) const: make this private

coot::symmetry_info_t get_symmetry(int imol, float symmetry_search_radius, float centre_x, float centre_y, float centre_z) const: symmetry now comes in a simple container that also includes the cell

::api::cell_t get_cell(int imol) const

Get the cell

Check that is_set is true before use.

Returns:: a cell_t

coot::util::map_molecule_centre_info_t get_map_molecule_centre(int imol) const

Get the middle of the “molecule blob” in cryo-EM reconstruction maps

Returns:: a coot::util::map_molecule_centre_info_t.

int undo(int imol)

undo

Returns:: 1 on successful undo, return 0 on failure

int redo(int imol)

redo

Returns:: 1 on successful redo, return 0 on failure

Map Utils

float map_sampling_rate

Return:: the map sampling rate (default is 1.8)

inline void set_map_sampling_rate(float msr): set the map sampling rate (default is 1.8). Higher numbers mean smoother maps, but they take longer to generate, longer to transfer, longer to parse and longer to draw

int read_mtz(const std::string &file_name, const std::string &f, const std::string &phi, const std::string &weight, bool use_weight, bool is_a_difference_map)

Read the given mtz file.

Returns:: the new molecule number or -1 on failure

int replace_map_by_mtz_from_file(int imol, const std::string &file_name, const std::string &f, const std::string &phi, const std::string &weight, bool use_weight): replace map

std::vector<auto_read_mtz_info_t> auto_read_mtz(const std::string &file_name)

Read the given mtz file.

Returns:: a vector of the maps created from reading the file

int read_ccp4_map(const std::string &file_name, bool is_a_difference_map)

Returns:: the new molecule number or -1 on failure

int write_map(int imol, const std::string &file_name) const

write a map. This function was be renamed from writeMap

Returns:: 1 on a successful write, return 0 on failure.

float get_map_mean(int imol) const

Returns:: the mean of the map or -1 is imol_map is not a map molecule index

float get_map_rmsd_approx(int imol_map) const

Returns:: the map rmsd (epsilon testing is not used). -1 is returned if imol_map is not a map molecule index.

coot::molecule_t::histogram_info_t get_map_histogram(int imol, 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).

float get_suggested_initial_contour_level(int imol) const

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

bool is_EM_map(int imol) const

check if a map is an EM map or not

Returns:: the “EM” status of this molecule. Return false on not-a-map.

int sharpen_blur_map(int imol_map, float b_factor, bool in_place_flag)

create a new map that is blurred/sharpened

Returns:: the molecule index of the new map or -1 on failure or if in_place_flag was true.

int sharpen_blur_map_with_resample(int imol_map, float b_factor, float resample_factor, bool in_place_flag)

create a new map that is blurred/sharpened and resampling. Note that resampling can be slow, a resample_factor of 1.5 is about the limit of the trade of of prettiness for speed.

Returns:: the molecule index of the new map or -1 on failure or if in_place_flag was true.

int mask_map_by_atom_selection(int imol_coords, int imol_map, const std::string &cid, float atom_radius, bool invert_flag)

mask map by atom selection (note the argument order is reversed compared to the coot api).

atom_radius is the atom radius (funnily enough). Use a negative number to mean “default”.

the invert_flag changes the parts of the map that are masked, so to highlight the density for a ligand one would pass the cid for the ligand and invert_flag as true, so that the parts of the map that are not the ligand are suppressed.

Returns:: the index of the new map - or -1 on failure

std::vector<int> partition_map_by_chain(int imol_map, int imol_model)

Partition the input map. Each voxel in the map is assigned to the chain to which it is nearest. Unlike masking, the generated maps are not restricted to be “close” to the atoms in the atom selection.

c.f. maskChains for ChimeraX - JiangLab

Returns:: a vector/list of the molecules indices of the newly created maps

int make_mask(int imol_map_ref, int imol_model, const std::string &atom_selection_cid, float radius)

make a masked map

Returns:: the index of the newly created mask. Return -1 on failure.

int flip_hand(int imol_map)

generate a new map which is the hand-flipped version of the input map.

Returns:: the molecule index of the new map, or -1 on failure.

std::vector<int> make_masked_maps_split_by_chain(int imol, int imol_map)

Make a vector of maps that are split by chain-id of the input imol

Returns:: a vector of the map molecule indices.

void set_map_colour(int imol, float r, float g, float b): set the map colour. The next time a map mesh is requested, it will have this colour. This does not affect the colour of the difference maps.

void set_map_is_contoured_with_thread_pool(bool state): set the state of the mode of the threading in map contouring

coot::simple_mesh_t get_map_contours_mesh(int imol, double position_x, double position_y, double position_z, float radius, float contour_level)

get the mesh for the map contours.

This function is not const because the internal state of a coot_molecule_t is changed.

Returns:: a simple_mesh_t for the map contours of the specified map

coot::simple_mesh_t get_map_contours_mesh_using_other_map_for_colours(int imol_ref, int imol_map_for_colouring, double position_x, double position_y, double position_z, float radius, float contour_level, float other_map_for_colouring_min_value, float other_map_for_colouring_max_value, bool invert_colour_ramp)

get the mesh for the map contours using another map for colouring

Returns:: a simple_mesh_t for the map contours of the specified map

void set_map_colour_saturation(int imol, float s): set the map saturation

inline coot::util::sfcalc_genmap_stats_t get_latest_sfcalc_stats() const

get the latest sfcalc stats

Returns:: a sfcalc_genmap_stats_t object

r_factor_stats get_r_factor_stats()

get the R-factors

Returns:: a r_factor_stats object

std::string r_factor_stats_as_string(const r_factor_stats &rfs) const

get the R factor stats as a string

Returns:: a string with the R-factor stats

int average_map(const std::string &imol_maps, std::vector<float> &scales)

bool regen_map(int imol_map, const std::string &imol_maps, const std::vector<float> &scales)

Testing functions

ltj_stats_t long_term_job_stats: long term job

bool interrupt_long_term_job

void testing_start_long_term_job(unsigned int n_seconds)

start a long-term job.

if n_seconds is 0, then run forever (or until interrupted)

void testing_stop_long_term_job(): stop the long-term job runnning (testing function)

inline ltj_stats_t testing_interrogate_long_term_job(): get the stats for the long-term job (testing function)

inline double get_contouring_time() const: get the time for conntouring in milliseconds

void set_max_number_of_threads(unsigned int n_threads): set the maximum number of threads for both the thread pool and the vector of threads

void set_max_number_of_threads_in_thread_pool(unsigned int n_threads): deprecated name for the above function

double test_the_threading(int n_threads): get the time to run a test function in milliseconds

double test_launching_threads(unsigned int n_threads_per_batch, unsigned int n_batches) const

Returns:: the time per batch in microseconds

double test_thread_pool_threads(unsigned int n_threads)

Returns:: time in microsections

inline coot::protein_geometry &get_geometry()

Generic Utils

std::string get_molecule_name(int imol) const

Returns:: the name of the molecule

void set_molecule_name(int imol, const std::string &new_name): set the molecule name

void display_molecule_names_table() const: debugging function: display the table of molecule and names

bool is_valid_model_molecule(int imol) const

Returns:: is this a valid model?

bool is_valid_map_molecule(int imol_map) const

Returns:: is this a valid map?

bool is_a_difference_map(int imol_map) const

Returns:: is this a difference map?

int new_molecule(const std::string &name)

create an empty molecule

Returns:: the index of the new molecule

int close_molecule(int imol)

close the molecule (and delete dynamically allocated memory)

Returns:: 1 on successful closure and 0 on failure to close

void end_delete_closed_molecules()

void pop_back(): delete the most recent/last molecule in the molecule vector

void clear(): delete all molecules

std::vector<double> get_eigenvalues(int imol, const std::string &chain_id, int res_no, const std::string &ins_code)

Returns:: the eigenvalues of the atoms in the specified residue

coot::simple_mesh_t test_origin_cube() const

Returns:: the mesh of a unit solid cube at the origin

inline void fill_rotamer_probability_tables(): fill the rotamer probability tables (currently not ARG and LYS)

void accept_rotamer_probability_tables_compressed_data(const std::string &data_stream): the caller has access to a compressed file that contains the rotamer probabilities. libcootapi will fill the rotamer probabilities tables from this compressed data stream. (placeholder only)

Backup and Saving

inline bool contains_unsaved_models() const

Returns:: a flag of unsaved models state - i.e. if any of them are unsaved, then this returns true.

inline void save_unsaved_model_changes(): Save the unsaved model - this function has not yet been written!

Geometry and Dictionaries

void geometry_init_standard(): read the stardard list of residues

std::vector<std::string> non_standard_residue_types_in_model(int imol) const

Returns:: a vector of non-standard residues (so that they can be used for auxiliary dictionary import)

Coordinates Modelling

int auto_fit_rotamer(int imol, const std::string &chain_id, int res_no, const std::string &ins_code, const std::string &alt_conf, int imol_map)

auto-fit rotamer

Returns:: 1 on successful modification, return 0 on failure

coot::molecule_t::rotamer_change_info_t change_to_next_rotamer(int imol, const std::string &residue_cid, const std::string &alt_conf)

change to the next rotamer (rotamer cycling is implicit if needed)

Returns:: the change information.

coot::molecule_t::rotamer_change_info_t change_to_previous_rotamer(int imol, const std::string &residue_cid, const std::string &alt_conf)

change to the next rotamer (rotamer cycling is implicit if needed)

Returns:: the change information.

coot::molecule_t::rotamer_change_info_t change_to_first_rotamer(int imol, const std::string &residue_cid, const std::string &alt_conf)

change to the first (0th) rotamer

Returns:: a coot::molecule_t::rotamer_change_info_t

std::pair<int, unsigned int> delete_using_cid(int imol, const std::string &cid, const std::string &scope)

delete item

where scope is one of the strings: [“ATOM”,”WATER”,”RESIDUE”,”CHAIN”,”MOLECULE”, “LITERAL”]

Returns:: 1 on successful modification, return 0 on failure

std::pair<int, unsigned int> delete_atom(int imol, const std::string &chain_id, int res_no, const std::string &ins_code, const std::string &atom_name, const std::string &alt_conf)

delete atom

Returns:: 1 on successful deletion, return 0 on failure to delete.

std::pair<int, unsigned int> delete_atom_using_cid(int imol, const std::string &cid)

delete atom using atom cid

Returns:: 1 on successful deletion, return 0 on failure to delete.

std::pair<int, unsigned int> delete_residue(int imol, const std::string &chain_id, int res_no, const std::string &ins_code)

delete residue

Returns:: 1 on successful deletion, return 0 on failure to delete.

std::pair<int, unsigned int> delete_residue_using_cid(int imol, const std::string &cid)

delete residue using cid

Returns:: 1 on successful deletion, return 0 on failure to delete.

std::pair<int, unsigned int> delete_residue_atoms_with_alt_conf(int imol, const std::string &chain_id, int res_no, const std::string &ins_code, const std::string &alt_conf)

delete residue atoms using alt_conf

Returns:: 1 on successful deletion, return 0 on failure to delete.

std::pair<int, unsigned int> delete_residue_atoms_using_cid(int imol, const std::string &cid)

delete residue atoms using cid

Returns:: 1 on successful deletion, return 0 on failure to delete.

std::pair<int, unsigned int> delete_side_chain(int imol, const std::string &chain_id, int res_no, const std::string &ins_code)

delete side chain

Returns:: 1 on successful deletion, return 0 on failure to delete.

std::pair<int, unsigned int> delete_side_chain_using_cid(int imol, const std::string &cid)

delete side chain

Returns:: 1 on successful deletion, return 0 on failure to delete.

std::pair<int, unsigned int> delete_chain_using_cid(int imol, const std::string &cid)

delete chain.

Returns:: 1 on successful deletion, return 0 on failure to delete.

std::pair<int, unsigned int> delete_literal_using_cid(int imol, const std::string &cid)

delete the atoms specified in the CID selection

Returns:: 1 on successful deletion, return 0 on failure to delete.

std::pair<int, std::string> add_terminal_residue_directly(int imol, const std::string &chain_id, int res_no, const std::string &ins_code)

add a residue onto the end of the chain by fitting to density

Returns:: a first of 1 on success. Return a useful message in second if the addition did not work

int add_terminal_residue_directly_using_cid(int imol, const std::string &cid)

the cid is for an atom. This used to return a pair, but I removed it so that I could compile the binding.

Returns:: an status.

int add_terminal_residue_directly_using_bucca_ml_growing_using_cid(int imol, const std::string &cid): the cid is for an atom. buccaneer building

int add_terminal_residue_directly_using_bucca_ml_growing(int imol, const coot::residue_spec_t &spec): buccaneer building, called by the above

inline void set_add_waters_water_to_protein_distance_lim_min(float d): parameter for add_waters() default 2.4

inline void set_add_waters_water_to_protein_distance_lim_max(float d): parameter for add_waters() default 3.4

inline void set_add_waters_variance_limit(float d): parameter for add_waters() - default 0.1

inline void set_add_waters_sigma_cutoff(float d): parameter for add_waters() - default 1.75

int add_waters(int imol_model, int imol_map)

add waters, updating imol_model (of course)

Returns:: the number of waters added on a success, -1 on failure.

int add_hydrogen_atoms(int imol_model)

add hydrogen atoms, updating imol_model (of course)

Returns:: 1 on success, 0 on failure.

int delete_hydrogen_atoms(int imol_model)

delete hydrogen atoms, updating imol_model (of course)

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

int add_alternative_conformation(int imol_model, const std::string &cid)

add an alternative conformation for the specified residue

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

int fill_partial_residue(int imol, const std::string &chain_id, int res_no, const std::string &ins_code)

fill the specified residue

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

int fill_partial_residue_using_cid(int imol, const std::string &cid)

fill the specified residue

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

int fill_partial_residues(int imol)

fill all the the partially-filled residues in the molecule

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

int flip_peptide(int imol, const coot::atom_spec_t &atom_spec, const std::string &alt_conf)

flip peptide

Returns:: 1 on a successful flip

int flip_peptide_using_cid(int imol, const std::string &atom_cid, const std::string &alt_conf)

flip peptide using an atom CID

Returns:: 1 on a successful flip

void eigen_flip_ligand(int imol, const std::string &chain_id, int res_no, const std::string &ins_code): eigen-flip ligand

void eigen_flip_ligand_using_cid(int imol, const std::string &residue_cid): eigen-flip ligand using CID

int mutate(int imol, const std::string &cid, const std::string &new_residue_type)

mutate residue

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

int side_chain_180(int imol, const std::string &atom_cid)

rotate last chi angle of the side chain by 180 degrees

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

std::string jed_flip(int imol, const std::string &atom_cid, bool invert_selection)

JED-Flip the ligand (or residue) at the specified atom.

Returns:: a non-blank message if there is a problem

int move_molecule_to_new_centre(int imol, float x, float y, float z)

move the molecule to the given centre

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

void multiply_residue_temperature_factors(int imol, const std::string &cid, float factor): Interactive B-factor refinement (fun). “factor” might typically be say 0.9 or 1.1

coot::Cartesian get_molecule_centre(int imol) const

get molecule centre

Returns:: the molecule centre

int copy_fragment_using_cid(int imol, const std::string &multi_cid)

copy a fragment given the multi_cid selection string.

Returns:: the new molecule number (or -1 on no atoms selected)

int copy_fragment_for_refinement_using_cid(int imol, const std::string &multi_cid)

copy a fragment - use this in preference to copy_fragment_using_cid() when copying a molecule fragment to make a molten zone for refinement. That is because this version quietly also copies the residues near the residues of the selection. so that those residues can be used for links and non-bonded contact restraints. `multi_cids” is a “||”-separated list of residues CIDs, e.g. “//A/12-52||//A/14-15||/B/56-66”

Returns:: the new molecule number (or -1 on no atoms selected)

int copy_fragment_using_residue_range(int imol, const std::string &chain_id, int res_no_start, int res_no_end)

copy a residue-range fragment

Returns:: the new molecule number (or -1 on no atoms selected)

int apply_transformation_to_atom_selection(int imol, const std::string &atoms_selection_cid, int n_atoms, float m00, float m01, float m02, float m10, float m11, float m12, float m20, float m21, float m22, float c0, float c1, float c2, float t0, float t1, float t2)

apply transformation to atom selection in the given molecule.

Returns:: the number of atoms moved.

int new_positions_for_residue_atoms(int imol, const std::string &residue_cid, std::vector<coot::molecule_t::moved_atom_t> &moved_atoms): update the positions of the atoms in the residue

int new_positions_for_atoms_in_residues(int imol, const std::vector<coot::molecule_t::moved_residue_t> &moved_residues): update the positions of the atoms in the residues

std::pair<int, std::vector<merge_molecule_results_info_t>> merge_molecules(int imol, const std::string &list_of_other_molecules)

list_of_other_molecules is a colon-separated list of molecules, e.g. “2:3:4”

Returns:: the first is a flag set to 1 if a merge occurred (and 0 if it did not) the second is a vector of merge results, i.e. if you merged a ligand, what is the new residue spec of the ligand, and if you merged a (polymer) chain, what is the new chain-id of that chain.

std::pair<int, std::vector<merge_molecule_results_info_t>> merge_molecules(int imol, std::vector<mmdb::Manager*> mols): this is called by the above function and is useful for other non-api functions (such as add_compound()).

int cis_trans_convert(int imol, const std::string &atom_cid)

Convert a cis peptide to a trans or vice versa.

Returns:: 1 on a successful conversion.

void replace_residue(int imol, const std::string &residue_cid, const std::string &new_residue_type, int imol_enc)

Replace a residue.

This has a different meaning of “replace” to replace_fragment. In this function the atoms are not note merely moved/”slotted in to place”, but the residue type is changed - new atoms are introduce and others are deleted (typically).

Change the type of a residue (for example, “TYR” to “PTY”) The algorithm will superpose the mainchain CA, C and N and try to set matching torsion to the angle that they were in the reference structure.

int replace_fragment(int imol_base, int imol_reference, const std::string &atom_selection)

replace a fragment

i.e. replace the atoms of imol_base by those of the atom selection atom_selection in imol_reference (imol_base is the molecule that is modified).

Returns:: the success status

int rigid_body_fit(int imol, const std::string &multi_cid, int imol_map)

Rigid-body fitting

`multi_cids” is a “||”-separated list of residues CIDs, e.g. “//A/12-52||//A/14-15||/B/56-66”

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

change the chain id

Returns:: -1 on a conflict 1 on good. 0 on did nothing return also an information/error message

void associate_sequence(int imol, const std::string &name_or_chain_id, const std::string &sequence): associate a sequence with a molecule

void assign_sequence(int imol_model, int imol_map): assign a sequence to a molecule. Often one might copy out a fragment from a more complete molecule (and then copy it back after the sequence has been added). This runs backrub_rotamer() on the newly assigned residues.

int refine_residues_using_atom_cid(int imol, const std::string &cid, const std::string &mode, int n_cycles)

refine the residues

mode is one of {SINGLE, TRIPLE, QUINTUPLE, HEPTUPLE, SPHERE, BIG_SPHERE, CHAIN, ALL};

Returns:: a value of 1 if the refinement was performed and 0 if it was not.

int refine_residues(int imol, const std::string &chain_id, int res_no, const std::string &ins_code, const std::string &alt_conf, const std::string &mode, int n_cycles)

refine the residues

Returns:: a value of 1 if the refinement was performed and 0 if it was not.

int refine_residue_range(int imol, const std::string &chain_id, int res_no_start, int res_no_end, int n_cycles)

refine residue range

Returns:: a value of 1 if the refinement was performed and 0 if it was not.

std::pair<int, coot::instanced_mesh_t> minimize_energy(int imol, 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)

void fix_atom_selection_during_refinement(int imol, const std::string &atom_selection_cid): fix atoms during refinement. Does nothing at the moment.

void add_target_position_restraint(int imol, const std::string &atom_cid, float pos_x, float pos_y, float pos_z): add or update (if it has a pull restraint already)

void clear_target_position_restraint(int imol, const std::string &atom_cid): clear target_position restraint

void turn_off_when_close_target_position_restraint(int imol): clear target_position restraint if it is (or they are) close to their target position

inline void set_use_rama_plot_restraints(bool state): turn on or off rama restraints

inline bool get_use_rama_plot_restraints() const

get the state of the rama plot restraints usage in refinement.

Returns:: the state

inline void set_rama_plot_restraints_weight(float f): set the Ramachandran plot restraints weight

inline float get_rama_plot_restraints_weight() const

get the Ramachandran plot restraints weight

Returns:: the Ramachandran plot restraints weight

inline void set_use_torsion_restraints(bool state): turn on or off torsion restraints

inline bool get_use_torsion_restraints() const

get the state of the rama plot restraints usage in refinement.

Returns:: the state

inline void set_torsion_restraints_weight(float f): set the Ramachandran plot restraints weight

inline float get_torsion_restraints_weight() const

get the Ramachandran plot restraints weight

Returns:: the Ramachandran plot restraints weight

void init_refinement_of_molecule_as_fragment_based_on_reference(int imol_frag, int imol_ref, int imol_map): initialise the refinement of (all of) molecule imol_frag

std::pair<int, coot::instanced_mesh_t> refine(int imol, int n_cycles)

Run some cycles of refinement and return a mesh. That way we can see the molecule animate as it refines

Returns:: a pair: the first of which is 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); The second is a coot::instanced_mesh_t

coot::instanced_mesh_t add_target_position_restraint_and_refine(int imol, const std::string &atom_cid, float pos_x, float pos_y, float pos_z, int n_cycles)

Create a new position for the given atom and create a new bonds mesh based on that. This is currently “heavyweight” as the bonds mesh is calculated from scratch (it is not (yet) merely a distortion of an internally-stored mesh). n_cycles specifies the number of refinement cyles to run after the target position of the atom has been applied. If n_cycles is -1 then, no cycles are done and the mesh is bonds merely calculated.

Returns:: a coot::instanced_mesh_t

void clear_target_position_restraints(int imol): clear any and all drag-atom target position restraints

void clear_refinement(int imol): call this after molecule refinement has finished (say when the molecule molecule is accepted into the original molecule)

inline void set_refinement_is_verbose(bool state): for debugging the refinement - write out some diagnositics - some might be useful. API change 20240226 - this function now takes a boolean argument

inline void set_refinement_geman_mcclure_alpha(float a): set the refinement Geman-McClure alpha

inline float get_geman_mcclure_alpha() const: set the refinement Geman-McClure alpha

int generate_self_restraints(int imol, float local_dist_max)

generate GM self restraints for the whole molecule

Returns:: nothing useful.

void generate_chain_self_restraints(int imol, float local_dist_max, const std::string &chain_id): generate GM self restraints for the given chain

void generate_local_self_restraints(int imol, float local_dist_max, const std::string &residue_cids): generate GM self restraints for the given residues. `residue_cids” is a “||”-separated list of residues, e.g. “//A/12||//A/14||/B/56”

void add_parallel_plane_restraint(int imol, const std::string &residue_cid_1, const std::string &residue_cid_2): generate parallel plane restraints (for RNA and DNA)

coot::instanced_mesh_t get_extra_restraints_mesh(int imol, int mode): get the mesh for extra restraints currently mode is unused.

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

void clear_extra_restraints(int imol): clear the extra restraints

Coordinates Validation

coot::simple_mesh_t get_rotamer_dodecs(int imol)

get the rotamer dodecs for the model, not const because it regenerates the bonds.

Returns:: a coot::simple_mesh_t

coot::instanced_mesh_t get_rotamer_dodecs_instanced(int imol)

get the rotamer dodecs for the model, not const because it regenerates the bonds.

Returns:: an instanced_mesh_t

coot::simple_mesh_t get_ramachandran_validation_markup_mesh(int imol) const

get the ramachandran validation markup mesh

20221126-PE: the function was renamed from ramachandran_validation_markup_mesh().

Returns:: a coot::simple_mesh_t

std::vector<coot::phi_psi_prob_t> ramachandran_validation(int imol) const

get the data for Ramachandran validation, which importantly contains probability information

Returns:: a vector of phi_psi_prob_t

coot::instanced_mesh_t contact_dots_for_ligand(int imol, const std::string &cid, unsigned int smoothness_factor) const

Recently (20230202) the smoothness factor has been added as an extra argument smoothness_factor is 1, 2 or 3 (3 is the most smooth).

Returns:: the instanced mesh for the specified ligand

coot::instanced_mesh_t all_molecule_contact_dots(int imol, unsigned int smoothness_factor) const

Recently (20230202) the smoothness factor has been added as an extra argument smoothness_factor is 1, 2 or 3 (3 is the most smooth).

Returns:: the instanced mesh for the specified molecule.

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

Returns:: a simple::molecule_t for the specified residue. this function is not const because we pass a pointer to the protein_geometry geom.

generic_3d_lines_bonds_box_t make_exportable_environment_bond_box(int imol, coot::residue_spec_t &spec)

Returns:: a vector of lines for non-bonded contacts and hydrogen bonds

std::vector<moorhen::h_bond> get_h_bonds(int imol, const std::string &cid_str, bool mcdonald_and_thornton_mode) const

mcdonald_and_thornton_mode turns on the McDonald & Thornton algorithm - using explicit hydrogen atoms

Returns:: a vector of hydrogen bonds around the specified residue (typically a ligand)

coot::simple_mesh_t get_mesh_for_ligand_validation_vs_dictionary(int imol, const std::string &ligand_cid): 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.

void get_ligand_validation_vs_dictionary(int imol, const std::string &ligand_cid, bool include_non_bonded_contacts)

ligand validation

Returns:: a vector of interesting geometry

bool match_ligand_torsions(int imol_ligand, int imol_ref, const std::string &chain_id_ref, int resno_ref): match ligand torsions - return the success status

bool match_ligand_position(int imol_ligand, int imol_ref, const std::string &chain_id_ref, int resno_ref): match ligand positions - return the success status

bool match_ligand_torsions_and_position(int imol_ligand, int imol_ref, const std::string &chain_id_ref, int resno_ref)

match ligand torsions and positions

Returns:: the success status.

bool match_ligand_torsions_and_position_using_cid(int imol_ligand, int imol_ref, const std::string &cid): match ligand torsions and positions, different api

coot::atom_overlaps_dots_container_t get_overlap_dots(int imol): not const because it can dynamically add dictionaries

coot::atom_overlaps_dots_container_t get_overlap_dots_for_ligand(int imol, const std::string &cid_ligand): not const because it can dynamically add dictionaries

std::vector<coot::plain_atom_overlap_t> get_overlaps(int imol): not const because it can dynamically add dictionaries

std::vector<coot::plain_atom_overlap_t> get_overlaps_for_ligand(int imol, const std::string &cid_ligand): not const because it can dynamically add dictionaries

Coordinates and Map Validation

coot::validation_information_t density_fit_analysis(int imol_model, int imol_map) const

density fit validation information

Returns:: a coot::validation_information_t

coot::validation_information_t density_correlation_analysis(int imol_model, int imol_map) const

Get the density correlation validation information

Returns:: a coot::validation_information_t object

coot::validation_information_t rotamer_analysis(int imol_model) const

Get the rotamer validation information

Returns:: a coot::validation_information_t object

coot::validation_information_t ramachandran_analysis(int imol_model) const

Get the ramachandran validation information (formatted for a graph, not 3d)

Returns:: a coot::validation_information_t object

coot::validation_information_t ramachandran_analysis_for_chain(int imol_model, const std::string &chain_id) const

ramachandran validation information (formatted for a graph, not 3d) for a given chain in a given molecule 20230127-PE This function does not exist yet.

Returns:: a coot::validation_information_t

coot::validation_information_t peptide_omega_analysis(int imol_model) const

peptide omega validation information

Returns:: a coot::validation_information_t

float get_median_temperature_factor(int imol) const

get the median temperature factor for the model

Returns:: a negative number on failure.

std::vector<coot::molecule_t::interesting_place_t> get_interesting_places(int imol, const std::string &mode) const

get interesting places (does not work yet)

Returns:: a vector of coot::validation_information_t

std::vector<coot::molecule_t::interesting_place_t> difference_map_peaks(int imol_map, int imol_protein, float n_rmsd) const

get difference map peaks

Returns:: a vector of coot::validation_information_t

std::vector<coot::molecule_t::interesting_place_t> pepflips_using_difference_map(int imol_coords, int imol_difference_map, float n_sigma) const

get pepflips based on the difference map

Returns:: a vector of coot::validation_information_t

std::vector<coot::molecule_t::interesting_place_t> unmodelled_blobs(int imol_model, int imol_map) const

unmodelled blobs

Returns:: a vector of coot::validation_information_t

std::vector<coot::atom_spec_t> find_water_baddies(int imol_model, int imol_map, float b_factor_lim, float outlier_sigma_level, float min_dist, float max_dist, bool ignore_part_occ_contact_flag, bool ignore_zero_occ_flag)

Check waters, using implicit logical OR

typical values for b_factor_lim is 60.0 typical values for outlier_sigma_level is 0.8 typical values for min_dist is 2.3 typical values for max_dist is 3.5

Returns:: a vector of atom specifiers Use the string_user_data of the spec for the button label

std::vector<std::pair<double, double>> fourier_shell_correlation(int imol_map_1, int imol_map_2) const

Calculate the MMRRCC for the residues in the chain Multi Masked Residue Range Corellation Coefficient calculate the MMRRCC for the residues in the chain Multi Masked Residue Range Corellation Coefficient Fourier Shell Correlation (FSC) between maps

Returns:: a vector or pairs of graph points (resolution, correlation). The resolution is in inverse Angstroms squared. An empty list is returned on failure

int make_power_scaled_map(int imol_ref, int imol_map_for_scaling)

Make a FSC-scaled map

Returns:: the molecule index of the new map

coot::validation_information_t get_q_score(int imol_model, int imol_map) const

Get the Pintile et al. Q Score

Returns:: a coot::validation_information_t object

Rail Points!

int calculate_new_rail_points()

calling this adds to the rail_points history. Make this pairs when we add model scoring.

Returns:: the new rail points (since last modification)

int rail_points_total() const

the total rail points

Returns:: the sum of all rail points accumulated since the maps were connected.

Updating Maps

void associate_data_mtz_file_with_map(int imol, const std::string &data_mtz_file_name, const std::string &f_col, const std::string &sigf_col, const std::string &free_r_col)

associate a data mtz file with a molecule

call this before calling connect_updating_maps().

int connect_updating_maps(int imol_model, int imol_with_data_info_attached, int imol_map_2fofc, int imol_map_fofc)

reset the rail_points (calls reset_the_rail_points()), updates the maps (using internal/clipper SFC) so, update your contour lines meshes after calling this function.

Returns:: 1 if the connection was successful.

void sfcalc_genmap(int imol_model, int imol_map_with_data_attached, int imol_updating_difference_map): sfcalc and re-generate maps. This is a low-level function - generally one would use the updating maps method rather than this

coot::util::sfcalc_genmap_stats_t sfcalc_genmaps_using_bulk_solvent(int imol_model, int imol_2fofc_map, int imol_updating_difference_map, int imol_map_with_data_attached)

sfcalc and re-generate maps (low-level function). This functions uses bulk solvent.

Call this function after connecting maps for updating maps to set the initial R-factor and store the initial map flatness.

On failure to calculate SFS and generate the maps the returned r_factor in the returned stats will be set to -1.

Returns:: a class of interesting statistics.

bool shift_field_b_factor_refinement(int imol, int imol_with_data_attached)

shift_field B-factor refinement. This function presumes that the Fobs,sigFobs and RFree data have been filled in the imol_map_with_data_attached molecule.

Returns:: success status

float get_density_at_position(int imol_map, float x, float y, float z) const

get density at position

Returns:: density value

std::vector<std::pair<clipper::Coord_orth, float>> get_diff_diff_map_peaks(int imol_diff_map, float screen_centre_x, float screen_centre_y, float screen_centre_z) const

This is a light-weight fetch, the values have already been computed, here were are merely copying them.

Returns:: a vector the position where the differenc map has been flattened. The associated float value is the ammount that the map has been flattened.

std::string get_data_set_file_name(int imol) const: the stored data set file name

Go to Blob

std::pair<bool, clipper::Coord_orth> go_to_blob(float x1, float y1, float z1, float x2, float y2, float z2, float contour_level)

Given a point on the front clipping plane (x1, y1, z1) and a point on the back clipping plane (x2, y2, z2) this function searches imol_refinement_map (if set) to find a the centre of a blob above the contour level. Blobs at the “front” are selected in preference to blobs at the back. If no blob is found, then the first of the pair is false. If it is found, then the second is (obviously) the centre of the blob.

20221022-PE: in future, this function should/will be provided with a list of displayed maps and their contour levels - but for now, it uses (only) imol_refinement_map. Use a string to pass the map information (map index and contour level), something like “0 0.45:1 1.2:2 0.1”

Ligand Functions

std::vector<int> fit_ligand_right_here(int imol_protein, int imol_map, int imol_ligand, float x, float y, float z, float n_rmsd, bool use_conformers, unsigned int n_conformers)

Ligand Fitting

I am not yet clear what extra cut-offs and flags need to be added here. You can expect this to take about 20 seconds.

For trivial (i.e non-flexible) ligands you should instead use the jiggle-fit algorithm, which takes a fraction of a second. (That is the algorithm used for “Add Other Solvent Molecules” in Coot.)

Returns:: a vector of indices of molecules for the best fitting ligands to this blob.

std::vector<fit_ligand_info_t> fit_ligand(int imol_protein, int imol_map, int imol_ligand, float n_rmsd, bool use_conformers, unsigned int n_conformers)

Fit ligand

Returns:: a vector of interesting information about the fitted ligands

std::vector<fit_ligand_info_t> fit_ligand_multi_ligand(int imol_protein, int imol_map, const std::string &multi_ligand_molecule_number_list, float n_rmsd, bool use_conformers, unsigned int n_conformers)

Fit ligands (place-holder) multi_ligand_molecule_number_list is a colon-separated list of molecules, e.g. “2:3:4”

Returns:: an empty vector (at the moment)

float fit_to_map_by_random_jiggle(int imol, const coot::residue_spec_t &res_spec, int n_trials, float translation_scale_factor)

“Jiggle-Fit Ligand” if n_trials is 0, then a sensible default value will be used. if translation_scale_factor is negative then a sensible default value will be used.

Returns:: a value less than -99.9 on failure to fit.

float fit_to_map_by_random_jiggle_using_cid(int imol, const std::string &cid, int n_trials, float translation_scale_factor)

“Jiggle-Fit Ligand” with a different interface - one that can use any atom selection (instead of just a ligand). As above, if n_trials is 0, then a sensible default value will be used. if translation_scale_factor is negative then a sensible default value will be used.

Returns:: a value less than -99.9 on failure to fit.

float fit_to_map_by_random_jiggle_with_blur_using_cid(int imol, int imol_map, const std::string &cid, float b_factor, int n_trials, float translation_scale_factor)

Jiggle fit an atom selection, typically a whole molecule or a chain As above, if n_trials is 0, then a sensible default value will be used. if translation_scale_factor is negative then a sensible default value will be used.

Returns:: a value less than -99.9 on failure to fit.

std::string get_svg_for_residue_type(int imol, const std::string &comp_id, bool use_rdkit_svg, bool dark_background_flag)

This is a ligand function, not really a ligand-fitting function.

It won’t work unless the dictionary for that ligand has been imported. The output renderings are not very good at the moment.

Except for unusual cases, imol will be IMOL_ENC_ANY (-666666)

dark_background_flag returns a representation suitable for rendering on a dark background (funnily enough).

This function is not const because it caches the svgs if it can.

Returns:: the string for the SVG representation.

int add_compound(int imol, const std::string &tlc, int imol_dict, int imol_map, float x, float y, float z)

This function is for adding compounds/molecules like buffer agents and precipitants or anions and cations. i.e. those ligands that can be positioned without need for internal torsion angle manipulation.

tlc is the three-letter-code/compound-id

imol_dict is the molecule to which the ligand is attached (if any). Typically this will be IMOL_ENC_ANY (-666666).

imol_map is the molecule number of the map that will be used for fitting.

Returns:: the success status, 1 or good, 0 for not good.

std::vector<coot::residue_spec_t> get_non_standard_residues_in_molecule(int imol) const

Returns:: a vector of residue specifiers for the ligand residues - the residue name is encoded in the string_user_data data item of the residue specifier

std::vector<int> get_dictionary_conformers(const std::string &comp_id, int imol_enc, bool remove_internal_clash_conformers)

Get the conformers that can be generated by variation around rotatable bonds as described in the dictionary. Torsions that are marked as “const” are excluded from the variation, as are pyranose ring torsions and torsions that rotate hydrogen atoms.

Returns:: a vector of indices of the new molecules

texture_as_floats_t get_map_section_texture(int imol, int section_id, int axis, float data_value_for_bottom, float data_value_for_top) const

The new arguments, data_value_for_top, data_value_for_bottom should be pre-calculated (don’t calculate them for every call to this function).

Returns:: a texture_as_floats_t object for the given section On failure, the image_data vector is empty.

int get_number_of_map_sections(int imol_map, 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.

Other Features

coot::simple_mesh_t make_mesh_from_gltf_file(const std::string &file_name)

Returns:: a simple_mesh_t from the give file.

coot::simple_mesh_t get_octahemisphere(unsigned int n_divisions) const

@params n_divisions is a number divisble by 2, at least 4 (typically 16)

Returns:: a unit-vector end-cap octohemisphere mesh

std::string pae_png(const std::string &pae_file_name) const

Returns:: a string of a png

Functions for Blender Interface

void make_mesh_for_map_contours_for_blender(int imol, float x, float y, float z, float level, float radius)

void make_mesh_for_bonds_for_blender(int imol, const std::string &mode, 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(int imol, const std::string &cid, const std::string &colour_scheme, const std::string &style, int secondary_structure_usage_flag)

void make_mesh_for_gaussian_surface_for_blender(int imol, float sigma, float contour_level, float box_radius, float grid_scale, float b_factor)

void make_mesh_for_goodsell_style_for_blender(int imol, float colour_wheel_rotation_step, float saturation, float goodselliness)

std::vector<float> get_colour_table_for_blender(int imol)

std::vector<float> get_vertices_for_blender(int imol)

std::vector<int> get_triangles_for_blender(int imol)

Public Functions

inline explicit molecules_container_t(bool verbose = true): the one and only constructor

~molecules_container_t()

inline void set_use_gemmi(bool state): Set the state of using gemmi for coordinates parsing. The default is true.

inline bool get_use_gemmi(): get the state of using GEMMI for coordinates parsing

Public Members

int imol_refinement_map: the refinement map - direct access. When refinement is performed, this is the map that will be used. Many (indeed most) of thesee functions explicity take a map. If the map is not known by the calling function then this map can be used as the map molecule index

int imol_difference_map

the difference map - direct access

I am not sure that this is needed - or will ever be.

bool use_gemmi

Private Types

enum moving_atoms_asc_t

Values:

enumerator NEW_COORDS_UNSET

enumerator NEW_COORDS_ADD

enumerator NEW_COORDS_REPLACE

enumerator NEW_COORDS_REPLACE_CHANGE_ALTCONF

enumerator NEW_COORDS_INSERT

enumerator NEW_COORDS_INSERT_CHANGE_ALTCONF

Private Functions

void set_updating_maps_need_an_update(int imol)

void update_updating_maps(int imol): update the updating maps without generating a mesh

std::string adjust_refinement_residue_name(const std::string &resname) const

bool make_last_restraints(const std::vector<std::pair<bool, mmdb::Residue*>> &local_residues, const std::vector<mmdb::Link> &links, const coot::protein_geometry &geom, mmdb::Manager *mol_for_residue_selection, const std::vector<coot::atom_spec_t> &fixed_atom_specs, coot::restraint_usage_Flags flags, bool use_map_flag, const clipper::Xmap<float> *xmap_p)

coot::refinement_results_t refine_residues_vec(int imol, const std::vector<mmdb::Residue*> &residues, const std::string &alt_conf, mmdb::Manager *mol)

int find_serial_number_for_insert(int seqnum_new, const std::string &ins_code_for_new, mmdb::Chain *chain_p) const

atom_selection_container_t make_moving_atoms_asc(mmdb::Manager *residues_mol, const std::vector<mmdb::Residue*> &residues) const

std::pair<int, std::vector<std::string>> check_dictionary_for_residue_restraints(int imol, mmdb::PResidue *SelResidues, int nSelResidues)

std::pair<int, std::vector<std::string>> check_dictionary_for_residue_restraints(int imol, const std::vector<mmdb::Residue*> &residues)

std::pair<mmdb::Manager*, std::vector<mmdb::Residue*>> create_mmdbmanager_from_res_vector(const std::vector<mmdb::Residue*> &residues, int imol, mmdb::Manager *mol_in, std::string alt_conf)

coot::refinement_results_t generate_molecule_and_refine(int imol, const std::vector<mmdb::Residue*> &residues, const std::string &alt_conf, mmdb::Manager *mol, bool use_map_flag = true)

std::vector<std::pair<mmdb::Residue*, std::vector<coot::dict_torsion_restraint_t>>> make_rotamer_torsions(const std::vector<std::pair<bool, mmdb::Residue*>> &local_residues) const

int refine_direct(int imol, std::vector<mmdb::Residue*> rv, const std::string &alt_loc, int n_cycles)

Real space refinement.

the n_cycles parameter allows partial refinement - so for an animated representation one would call this with a small number (10, 20, 100?) and call it again if the refine status is still yet to reach completion GSL_CONTINUE (-2). And then make a call to get the bonds mesh (or other molecular representation). If n_cycles is negative, this means “refine to completion.”

Returns:: success/progress status

double phi_psi_probability(const coot::util::phi_psi_t &phi_psi, const ramachandrans_container_t &rc) const

void read_standard_residues(): read the standard protein, RNA, and DNA dictionaries.

int install_model(const coot::molecule_t &m)

coot::graph_match_info_t overlap_ligands_internal(int imol_ligand, int imol_ref, const std::string &chain_id_ref, int resno_ref, bool apply_rtop_flag)

superpose_results_t superpose_with_atom_selection(atom_selection_container_t asc_ref, atom_selection_container_t asc_mov, int imol_mov, std::string moving_mol_name, std::string referennce_mol_name, bool move_copy_of_imol2_flag)

int valid_labels(const std::string &mtz_file_name, const std::string &f_col, const std::string &phi_col, const std::string &weight_col, int use_weights) const

inline void init()

void debug() const

Private Members

std::vector<coot::molecule_t> molecules

coot::protein_geometry geom

coot::rotamer_probability_tables rot_prob_tables

ramachandrans_container_t ramachandrans_container

bool draw_missing_residue_loops_flag

std::vector<rail_points_t> rail_point_history

updating_maps_info_f updating_maps_info

coot::util::sfcalc_genmap_stats_t latest_sfcalc_stats

float map_weight

float geman_mcclure_alpha

bool use_rama_plot_restraints

float rama_plot_restraints_weight

bool use_torsion_restraints

float torsion_restraints_weight

ctpl::thread_pool thread_pool

bool show_timings

coot::restraints_container_t *last_restraints

bool continue_threaded_refinement_loop

bool refinement_is_quiet

int cif_dictionary_read_number

bool refinement_immediate_replacement_flag = true

int imol_moving_atoms

short int moving_atoms_asc_type

bool particles_have_been_shown_already_for_this_round_flag

std::map<svg_store_key_t, std::string> ligand_svg_store

atom_selection_container_t standard_residues_asc

float ligand_water_to_protein_distance_lim_max

float ligand_water_to_protein_distance_lim_min

float ligand_water_variance_limit

float ligand_water_sigma_cut_off

bool map_is_contoured_using_thread_pool_flag

double contouring_time

Private Static Functions

static void thread_for_refinement_loop_threaded()

static void get_restraints_lock(const std::string &calling_function_name)

static void release_restraints_lock(const std::string &calling_function_name)

static void all_atom_pulls_off()

static void atom_pull_off(const coot::atom_spec_t &spec)

static void atom_pulls_off(const std::vector<coot::atom_spec_t> &specs)

Private Static Attributes

static std::atomic<bool> on_going_updating_map_lock

static clipper::Xmap<float> *dummy_xmap

static std::atomic<bool> restraints_lock

static std::string restraints_locking_function_name

static std::vector<atom_pull_info_t> atom_pulls

class auto_read_mtz_info_t

#include <molecules-container.hh>

class for the information about columns extracted from auto-reading the given mtz file

Public Functions

inline auto_read_mtz_info_t()

inline auto_read_mtz_info_t(int index, const std::string &F_in, const std::string &phi_in)

inline void set_fobs_sigfobs(const std::string &f, const std::string &s)

Public Members

int idx: molecule index

std::string F: F column.

std::string phi: phi column

std::string w: weights column

bool weights_used: flag for weights usage

std::string F_obs: F_obs column. There were not avaliable if the return value is empty.

std::string sigF_obs: sigF_obs column

std::string Rfree: R-Free column. There were not avaliable if the return value is empty.

class fit_ligand_info_t

#include <molecules-container.hh>

Ligand Fitting

Return:: a vector of indices of molecules for the best fitting ligands each of the “possible ligand” blobs.

Public Functions

inline fit_ligand_info_t(int i, int c, int l)

inline fit_ligand_info_t()