82 #define BEGIN_C_DECLS extern "C" {
94 #define COOT_SCHEME_DIR "COOT_SCHEME_DIR"
95 #define COOT_PYTHON_DIR "COOT_PYTHON_DIR"
101 void try_load_scheme_extras_dir();
104 void try_load_python_extras_dir();
233 int file_chooser_selector_state();
234 void set_file_chooser_overwrite(
int istate);
235 int file_chooser_overwrite_state();
300 PyObject *python_representation_kk(
int imol);
315 chain_id_py(
int imol,
int ichain);
395 SCM residue_centre_scm(
int imol,
const char *chain_id,
int resno,
const char *ins_code);
399 PyObject *remarks_py(
int imol);
400 PyObject *residue_centre_py(
int imol,
const char *chain_id,
int resno,
const char *ins_code);
407 SCM model_composition_statistics_scm(
int imol);
410 PyObject *model_composition_statistics_py(
int imol);
438 void write_header_secondary_structure_info(
int imol,
const char *file_name);
458 const char *chain_id_ligand_new,
459 int resno_ligand_new,
461 const char *chain_id_ligand_current,
462 int resno_ligand_current);
490 SCM coot_sys_build_type_scm();
493 PyObject *coot_sys_build_type_py();
521 gboolean coot_checked_exit(
int retval);
540 void run_clear_backups_py(
int retval);
631 int molecule_has_hydrogens_raw(
int imol);
637 int own_molecule_number(
int imol);
645 double get_idle_function_rock_target_angle();
696 int recentre_on_read_pdb_flag);
714 int hetify_residue(
int imol,
const char * chain_id,
int resno,
const char *ins_code);
741 int replace_fragment(
int imol_target,
int imol_fragment,
const char *atom_selection);
747 int imol_reference,
const char *chain_id_reference,
748 int resno_range_start,
int resno_range_end);
756 SCM residue_specs_list_ref_scm);
760 int replace_residues_from_mol_py(
int imol_target,
762 PyObject *residue_specs_list_ref_py);
770 const char *file_name);
813 float get_solid_density_surface_opacity(
int imol);
828 SCM test_internal_scm();
829 SCM test_internal_single_scm();
832 PyObject *test_internal_py();
833 PyObject *test_internal_single_py();
873 float get_view_matrix_element(
int row,
int col);
889 const char *current_chain,
890 const char *next_ncs_chain,
891 short int forward_flag);
931 int suck_model_fit_dialog_bl();
945 void set_accept_reject_dialog_docked(
int state);
956 void set_model_toolbar_style(
int state);
957 int model_toolbar_style_state();
960 void set_main_toolbar_style(
int state);
961 int main_toolbar_style_state();
1181 const char *sigf_col,
1189 const char *sigf_col,
1197 int imol_map_with_data_attached,
1204 void sfcalc_genmap(
int imol_model,
int imol_map_with_data_attached,
int imol_updating_difference_map);
1211 gdouble* get_map_colour(
int imol);
1215 SCM get_map_colour_scm(
int imol);
1218 PyObject *get_map_colour_py(
int imol);
1250 void set_map_colour(
int imol,
float red,
float green,
float blue);
1285 int export_map(
int imol,
const char *filename);
1287 int export_map_fragment(
int imol,
float x,
float y,
float z,
float radius,
const char *filename);
1302 int transform_map_raw(
int imol,
1303 double r00,
double r01,
double r02,
1304 double r10,
double r11,
double r12,
1305 double r20,
double r21,
double r22,
1306 double t0,
double t1,
double t2,
1307 double pt0,
double pt1,
double pt2,
1308 double box_half_size,
1309 const char *ref_space_group,
1310 double cell_a,
double cell_b,
double cell_c,
1311 double alpha,
double beta,
double gamma);
1328 int smooth_map(
int map_no,
float sampling_multiplier);
1358 char* get_text_for_iso_level_increment_entry(
int imol);
1359 char* get_text_for_diff_map_iso_level_increment_entry(
int imol);
1367 float get_iso_level_increment();
1368 void set_iso_level_increment_from_text(
const char *text,
int imol);
1394 char* get_text_for_map_sampling_rate_text();
1459 const char *f_col,
const char *phi_col,
1461 int use_weights,
int is_diff_map);
1470 const char *a,
const char *b,
const char *weight,
1471 int use_weights,
int is_diff_map,
1472 short int have_refmac_params,
1473 const char *fobs_col,
1474 const char *sigfobs_col,
1475 const char *r_free_col,
1476 short int sensible_f_free_col);
1483 const char *a,
const char *b,
1485 int use_weights,
int is_diff_map,
1486 short int have_refmac_params,
1487 const char *fobs_col,
1488 const char *sigfobs_col,
1489 const char *r_free_col,
1490 short int sensible_f_free_col,
1491 short int is_anomalous,
1492 short int use_reso_limits,
1493 float low_reso_limit,
1494 float high_reso_lim);
1500 const char *f_col,
const char *phi_col,
1502 int use_weights,
int is_diff_map);
1505 void stop_updating_molecule(
int imol);
1509 SCM refmac_parameters_scm(
int imol);
1513 PyObject *refmac_parameters_py(
int imol);
1521 const char *phi_col,
1522 const char *weight_col,
1536 void wrapped_auto_read_make_and_draw_maps(
const char *filename);
1538 void set_auto_read_do_difference_map_too(
int i);
1552 int is_for_diff_map_flag);
1556 char* get_text_for_density_size_widget();
1557 void set_density_size_from_widget(
const char *text);
1560 char *get_text_for_density_size_em_widget();
1561 void set_density_size_em_from_widget(
const char *text);
1572 void set_map_radius_slider_max(
float f);
1597 int swap_difference_map_colours_state();
1727 int resno_start,
int resno_end,
1728 const char *filename);
1731 int write_chain_to_pdb_file(
int imol,
const char *chainid,
const char *filename);
1790 SCM get_refmac_sad_atom_info_scm();
1793 PyObject *get_refmac_sad_atom_info_py();
1814 int refmac_runs_with_nolabels(
void);
1824 char* get_text_for_symmetry_size_widget();
1827 void set_symmetry_size_from_widget(
const char *text);
1830 double* get_symmetry_bonds_colour(
int imol);
1874 void add_symmetry_on_to_preferences_and_apply();
1892 const char *filename,
1897 int pre_shift_to_origin_na,
1898 int pre_shift_to_origin_nb,
1899 int pre_shift_to_origin_nc);
1915 double m11,
double m12,
double m13,
1916 double m21,
double m22,
double m23,
1917 double m31,
double m32,
double m33,
1918 double tx,
double ty,
double tz,
1919 int pre_shift_to_origin_na,
1920 int pre_shift_to_origin_nb,
1921 int pre_shift_to_origin_nc);
1940 const char *mmdb_atom_selection_string,
1941 double m11,
double m12,
double m13,
1942 double m21,
double m22,
double m23,
1943 double m31,
double m32,
double m33,
1944 double tx,
double ty,
double tz,
1945 int pre_shift_to_origin_na,
1946 int pre_shift_to_origin_nb,
1947 int pre_shift_to_origin_nc);
1954 int pre_shift_to_origin_na,
1955 int pre_shift_to_origin_nb,
1956 int pre_shift_to_origin_nc);
1964 int move_reference_chain_to_symm_chain_position();
1981 void setup_save_symmetry_coords();
2034 SCM save_coords_name_suggestion_scm(
int imol);
2040 PyObject *save_coords_name_suggestion_py(
int imol);
2113 const char *save_state_file_name_raw();
2124 void run_state_file_py();
2140 #define VT_SPHERICAL 2
2188 void set_unit_cell_colour(
float red,
float green,
float blue);
2199 void set_symmetry_colour_merge(
float v);
2224 int get_colour_map_rotation_on_read_pdb_c_only_flag();
2270 void set_aniso_limit_size_from_widget(
const char *text);
2276 char *get_text_for_aniso_limit_radius_entry();
2325 void set_dti_stereo_mode(
short int state);
2334 void set_model_display_radius(
int state,
float radius);
2373 void set_smooth_scroll_steps_str(
const char * t);
2382 char *get_text_for_smooth_scroll_steps();
2385 void set_smooth_scroll_limit_str(
const char *t);
2391 char *get_text_for_smooth_scroll_limit();
2429 void set_rotation_centre_size_from_widget(
const gchar *text);
2433 gchar *get_text_for_rotation_centre_cube_size();
2443 void set_rotation_centre_internal(
float x,
float y,
float z);
2444 float rotation_centre_position(
int axis);
2451 PyObject *go_to_ligand_py();
2476 void set_draw_axes(
int i);
2488 int atom_index(
int imol,
const char *chain_id,
int iresno,
const char *atom_id);
2491 int atom_index_full(
int imol,
const char *chain_id,
int iresno,
const char *inscode,
const char *atom_id,
const char *altconf);
2496 int atom_index_first_atom_in_residue(
int imol,
const char *chain_id,
2497 int iresno,
const char *ins_code);
2501 int atom_index_first_atom_in_residue_with_altconf(
int imol,
2502 const char *chain_id,
2504 const char *ins_code,
2505 const char *alt_conf);
2515 char *centre_of_mass_string(
int imol);
2517 char *centre_of_mass_string_py(
int imol);
2534 void set_temperature_factors_for_atoms_in_residue_scm(
int imol, SCM residue_spec_scm,
float bf);
2541 int set_atom_attribute(
int imol,
const char *chain_id,
int resno,
const char *ins_code,
const char *atom_name,
const char*alt_conf,
const char *attribute_name,
float val);
2546 int set_atom_string_attribute(
int imol,
const char *chain_id,
int resno,
const char *ins_code,
const char *atom_name,
const char*alt_conf,
const char *attribute_name,
const char *attribute_value);
2555 int set_atom_attributes_py(PyObject *attribute_expression_list);
2560 void set_residue_name(
int imol,
const char *chain_id,
int res_no,
const char *ins_code,
const char *new_residue_name);
2570 void skel_greer_on();
2571 void skel_greer_off();
2586 void set_initial_map_for_skeletonize();
2604 gchar *get_text_for_skeletonization_level_entry();
2607 void set_skeletonization_level_from_widget(
const char *txt);
2610 gchar *get_text_for_skeleton_box_size_entry();
2613 void set_skeleton_box_size_from_widget(
const char *txt);
2637 int save_molecule_number_from_option_menu();
2640 void set_save_molecule_number(
int imol);
2676 read_phs_and_make_map_using_cell_symm_from_mol_using_implicit_phs_filename(
int imol);
2681 const char *hm_spacegroup,
float a,
float b,
float c,
2682 float alpha,
float beta,
float gamma);
2697 float reso_lim_low,
float reso_lim_high);
2705 graphics_store_phs_filename(
const gchar *phs_filename);
2707 short int possible_cell_symm_for_phs_file();
2710 gchar *get_text_for_phs_cell_chooser(
int imol,
char *field);
2729 float m11,
float m12,
float m13,
2730 float m21,
float m22,
float m23,
2731 float m31,
float m32,
float m33,
2732 float x,
float y,
float z);
2736 void transform_zone(
int imol,
const char *chain_id,
int resno_start,
int resno_end,
const char *ins_code,
2737 float m11,
float m12,
float m13,
2738 float m21,
float m22,
float m23,
2739 float m31,
float m32,
float m33,
2740 float x,
float y,
float z);
2777 const char *t3_atom_name);
2789 const char *ins_code,
2790 const char *atom_name,
2791 const char *alt_conf);
2794 short int make_the_move_flag);
2796 int set_go_to_atom_chain_residue_atom_name_strings(
const gchar *t1,
2808 void update_go_to_atom_residue_list(
int imol);
2816 const char *inscode,
const char *atom_name,
2817 const char *altloc);
2826 void update_go_to_atom_window_on_other_molecule_chosen(
int imol);
2851 void unset_go_to_atom_widget();
2864 void autobuild_ca_off();
2866 void test_fragment();
2868 void do_skeleton_prune();
2870 int test_function(
int i,
int j);
2874 SCM test_function_scm(SCM i, SCM j);
2877 PyObject *test_function_py(PyObject *i, PyObject *j);
2883 void glyco_tree_test();
2887 SCM glyco_tree_scm(
int imol, SCM active_residue_scm);
2888 SCM glyco_tree_residues_scm(
int imol, SCM active_residue_scm);
2889 SCM glyco_tree_internal_distances_fn_scm(
int imol, SCM residue_spec,
const std::string &file_name);
2890 SCM glyco_tree_residue_id_scm(
int imol, SCM residue_spec_scm);
2891 SCM glyco_tree_compare_trees_scm(
int imol_1, SCM res_spec_1,
int imol_2, SCM res_spec_2);
2892 SCM glyco_tree_matched_residue_pairs_scm(
int imol_1, SCM res_spec_1,
int imol_2, SCM res_spec_2);
2897 PyObject *glyco_tree_internal_distances_fn_py(
int imol, PyObject *residue_spec,
const std::string &file_name);
2898 PyObject *glyco_tree_residue_id_py(
int imol, PyObject *residue_spec_py);
2899 PyObject *glyco_tree_compare_trees_py(
int imol_1, PyObject *res_spec_1,
int imol_2, PyObject *res_spec_2);
2900 PyObject *glyco_tree_matched_residue_pairs_py(
int imol_1, PyObject *res_spec_1,
int imol_2, PyObject *res_spec_2);
2916 void add_map_display_control_widgets();
2917 void add_mol_display_control_widgets();
2918 void add_map_and_mol_display_control_widgets();
2920 void reset_graphics_display_control_window();
2921 void close_graphics_display_control_window();
2945 void display_maps_py(PyObject *pyo);
2985 PyObject *space_group_py(
int imol);
3005 SCM symmetry_operators_to_xHM_scm(SCM symmetry_operators);
3014 PyObject *symmetry_operators_to_xHM_py(PyObject *symmetry_operators);
3038 void set_merge_molecules_ligand_spec_scm(SCM ligand_spec_scm);
3042 PyObject *merge_molecules_py(PyObject *add_molecules,
int imol);
3043 void set_merge_molecules_ligand_spec_py(PyObject *ligand_spec_py);
3056 void align_and_mutate(
int imol,
const char *chain_id,
const char *fasta_maybe,
short int renumber_residues_flag);
3064 SCM alignment_results_scm(
int imol,
const char* chain_id,
const char *seq);
3072 PyObject *alignment_results_py(
int imol,
const char* chain_id,
const char *seq);
3090 int start_res,
int last_res,
int offset);
3095 int change_residue_number(
int imol,
const char *chain_id,
int current_resno,
const char *current_inscode,
int new_resno,
const char *new_inscode);
3106 void change_chain_id(
int imol,
const char *from_chain_id,
const char *to_chain_id,
3107 short int use_res_range_flag,
int from_resno,
int to_resno);
3111 SCM change_chain_id_with_result_scm(
int imol,
const char *from_chain_id,
const char *to_chain_id,
3112 short int use_res_range_flag,
int from_resno,
int to_resno);
3115 PyObject *change_chain_id_with_result_py(
int imol,
const char *from_chain_id,
const char *to_chain_id,
short int use_res_range_flag,
int from_resno,
int to_resno);
3134 int probe_available_p_py();
3147 void run_command_line_scripts();
3149 void set_guile_gui_loaded_flag();
3150 void set_python_gui_loaded_flag();
3151 void set_found_coot_gui();
3152 void set_found_coot_python_gui();
3164 int get_monomer_for_molecule_by_index(
int dict_idx,
int imol_enc);
3190 short int allow_minimal_descriptions_flag);
3219 short int allow_minimal_descriptions_flag);
3237 void do_regularize(
short int state);
3238 void do_refine(
short int state);
3241 void do_regularize_kill_delete_dialog();
3259 int planar_peptide_restraints_state();
3306 void clear_up_moving_atoms();
3307 void clear_moving_atoms_object();
3335 SCM refine_residues_with_alt_conf_scm(
int imol, SCM r,
const char *alt_conf);
3336 SCM refine_residues_with_modes_with_alt_conf_scm(
int imol, SCM residues_spec_list_scm,
3337 const char *alt_conf,
3341 SCM regularize_residues_scm(
int imol, SCM r);
3342 SCM regularize_residues_with_alt_conf_scm(
int imol, SCM r,
const char *alt_conf);
3349 PyObject *refine_residues_with_modes_with_alt_conf_py(
int imol, PyObject *r,
const char *alt_conf,
3353 PyObject *refine_residues_with_alt_conf_py(
int imol, PyObject *r,
const char *alt_conf);
3354 PyObject *regularize_residues_py(
int imol, PyObject *r);
3355 PyObject *regularize_residues_with_alt_conf_py(
int imol, PyObject *r,
const char *alt_conf);
3360 void stop_refinement_internal();
3362 void set_refinement_use_soft_mode_nbc_restraints(
short int flag);
3399 float estimate_map_weight(
int imol_map);
3423 void refine_zone(
int imol,
const char *chain_id,
int resno1,
int resno2,
const char *altconf);
3428 SCM refine_zone_with_score_scm(
int imol,
const char *chain_id,
int resno1,
int resno2,
const char *altconf);
3429 SCM regularize_zone_with_score_scm(
int imol,
const char *chain_id,
int resno1,
int resno2,
const char *altconf);
3432 PyObject *refine_zone_with_score_py(
int imol,
const char *chain_id,
int resno1,
int resno2,
const char *altconf);
3433 PyObject *regularize_zone_with_score_py(
int imol,
const char *chain_id,
int resno1,
int resno2,
const char *altconf);
3440 void refine_auto_range(
int imol,
const char *chain_id,
int resno1,
const char *altconf);
3446 int regularize_zone(
int imol,
const char *chain_id,
int resno1,
int resno2,
const char *altconf);
3482 void set_refine_ramachandran_torsion_angles(
int state);
3497 void set_torsion_restraints_weight(
double w);
3504 void set_refinement_geman_mcclure_alpha_from_text(
int combobox_item_idx,
const char *t);
3505 void set_refinement_lennard_jones_epsilon_from_text(
int combobox_item_idx,
const char *t);
3506 void set_refinement_ramachandran_restraints_weight_from_text(
int combobox_item_idx,
const char *t);
3507 void set_refinement_overall_weight_from_text(
const char *t);
3508 void set_refinement_torsion_weight_from_text(
int combobox_item_index,
const char *t);
3509 void set_refine_params_dialog_more_control_frame_is_active(
int state);
3512 int refine_ramachandran_angles_state();
3514 void set_numerical_gradients(
int istate);
3516 void set_debug_refinement(
int state);
3531 SCM chiral_volume_errors_scm(
int imol);
3534 PyObject *chiral_volume_errors_py(
int imol);
3591 int add_extra_bond_restraint(
int imol,
const char *chain_id_1,
int res_no_1,
const char *ins_code_1,
const char *atom_name_1,
const char *alt_conf_1,
const char *chain_id_2,
int res_no_2,
const char *ins_code_2,
const char *atom_name_2,
const char *alt_conf_2,
double bond_dist,
double esd);
3603 int add_extra_geman_mcclure_restraint(
int imol,
const char *chain_id_1,
int res_no_1,
const char *ins_code_1,
const char *atom_name_1,
const char *alt_conf_1,
const char *chain_id_2,
int res_no_2,
const char *ins_code_2,
const char *atom_name_2,
const char *alt_conf_2,
double bond_dist,
double esd);
3606 int add_extra_bond_restraints_scm(
int imol, SCM extra_bond_restraints_scm);
3609 int add_extra_bond_restraints_py(
int imol, PyObject *extra_bond_restraints_py);
3612 int add_extra_angle_restraint(
int imol,
3613 const char *chain_id_1,
int res_no_1,
const char *ins_code_1,
const char *atom_name_1,
const char *alt_conf_1,
3614 const char *chain_id_2,
int res_no_2,
const char *ins_code_2,
const char *atom_name_2,
const char *alt_conf_2,
3615 const char *chain_id_3,
int res_no_3,
const char *ins_code_3,
const char *atom_name_3,
const char *alt_conf_3,
3616 double torsion_angle,
double esd);
3617 int add_extra_torsion_restraint(
int imol,
3618 const char *chain_id_1,
int res_no_1,
const char *ins_code_1,
const char *atom_name_1,
const char *alt_conf_1,
3619 const char *chain_id_2,
int res_no_2,
const char *ins_code_2,
const char *atom_name_2,
const char *alt_conf_2,
3620 const char *chain_id_3,
int res_no_3,
const char *ins_code_3,
const char *atom_name_3,
const char *alt_conf_3,
3621 const char *chain_id_4,
int res_no_4,
const char *ins_code_4,
const char *atom_name_4,
const char *alt_conf_4,
3622 double torsion_angle,
double esd,
int period);
3623 int add_extra_start_pos_restraint(
int imol,
const char *chain_id_1,
int res_no_1,
const char *ins_code_1,
const char *atom_name_1,
const char *alt_conf_1,
double esd);
3625 int add_extra_target_position_restraint(
int imol,
3626 const char *chain_id,
3628 const char *ins_code,
3629 const char *atom_name,
3630 const char *alt_conf,
float x,
float y,
float z,
float weight);
3640 void delete_extra_restraints_for_residue_spec_scm(
int imol, SCM residue_spec_in);
3643 void delete_extra_restraints_for_residue_spec_py(
int imol, PyObject *residue_spec_in_py);
3644 #endif // USE_PYTHON
3645 #endif // __cplusplus
3647 void delete_extra_restraints_worse_than(
int imol,
float n_sigma);
3652 void set_show_extra_restraints(
int imol,
int state);
3653 int extra_restraints_are_shown(
int imol);
3670 void generate_local_self_restraints_by_residues_py(
int imol, PyObject *residue_specs,
float local_dist_max);
3671 #endif // USE_PYTHON
3672 #endif // __cplusplus
3683 int interpolation_mode);
3685 void set_show_parallel_plane_restraints(
int imol,
int state);
3686 int parallel_plane_restraints_are_shown(
int imol);
3687 void add_parallel_plane_restraint(
int imol,
3688 const char *chain_id_1,
int re_no_1,
const char *ins_code_1,
3689 const char *chain_id_2,
int re_no_2,
const char *ins_code_2);
3690 void set_extra_restraints_representation_for_bonds_go_to_CA(
int imol,
short int state);
3698 void delete_extra_restraint_scm(
int imol, SCM restraint_spec);
3699 SCM list_extra_restraints_scm(
int imol);
3705 void delete_extra_restraint_py(
int imol, PyObject *restraint_spec);
3706 PyObject *list_extra_restraints_py(
int imol);
3715 void clear_all_atom_pull_restraints();
3716 void set_auto_clear_atom_pull_restraint(
int state);
3717 int get_auto_clear_atom_pull_restraint_state();
3779 const char *ins_code,
const char *atname,
3780 const char *altconf);
3791 void do_residue_info_dialog();
3794 void output_residue_info_dialog (
int imol,
int atom_index);
3797 void residue_info_dialog(
int imol,
const char *chain_id,
int resno,
const char *ins_code);
3798 int residue_info_dialog_is_displayed();
3799 void output_residue_info_as_text(
int atom_index,
int imol);
3802 void do_distance_define();
3803 void do_angle_define();
3804 void do_torsion_define();
3805 void residue_info_apply_all_checkbutton_toggled();
3806 void clear_residue_info_edit_list();
3809 void unset_residue_info_widget();
3810 void clear_simple_distances();
3811 void clear_last_simple_distance();
3822 void do_edit_copy_molecule();
3823 void do_edit_copy_fragment();
3824 void do_edit_replace_residue();
3825 void do_edit_replace_fragment();
3868 double add_geometry_distance(
int imol_1,
float x_1,
float y_1,
float z_1,
int imol_2,
float x_2,
float y_2,
float z_2);
3871 double add_atom_geometry_distance_scm(
int imol_1, SCM atom_spec_1,
int imol_2, SCM atom_spec_2);
3874 double add_atom_geometry_distance_py(
int imol_1, PyObject *atom_spec_1,
int imol_2, PyObject *atom_spec_2);
3894 #endif // USE_PYTHON
3922 void scale_zoom_internal(
float f);
3932 float smooth_scroll_zoom_limit();
3933 void set_smooth_scroll_zoom_limit(
float f);
3934 void set_zoom(
float f);
3951 int handle_cns_data_file_with_cell(
const char *filename,
int imol,
float a,
float b,
float c,
float alpha,
float beta,
float gamma,
const char *spg_info);
3961 int auto_read_cif_data_with_phases(
const char *filename);
3962 int read_cif_data_with_phases_sigmaa(
const char *filename);
3963 int read_cif_data_with_phases_diff_sigmaa(
const char *filename);
3964 int read_cif_data(
const char *filename,
int imol_coords);
3965 int read_cif_data_2fofc_map(
const char *filename,
int imol_coords);
3966 int read_cif_data_fofc_map(
const char *filename,
int imol_coords);
3967 int read_cif_data_with_phases_fo_fc(
const char *filename);
3968 int read_cif_data_with_phases_2fo_fc(
const char *filename);
3969 int read_cif_data_with_phases_nfo_fc(
const char *filename,
3971 int read_cif_data_with_phases_fo_alpha_calc(
const char *filename);
3976 int handle_cif_dictionary(
const char *filename);
3980 int read_cif_dictionary(
const char *filename);
3989 int handle_cif_dictionary_for_molecule(
const char *filename,
int imol_enc,
short int new_molecule_from_dictionary_cif_checkbutton_state);
3991 int write_connectivity(
const char* monomer_name,
const char *filename);
4008 void import_all_refmac_cifs();
4010 int read_small_molecule_cif(
const char *file_name);
4012 int read_small_molecule_data_cif(
const char *file_name);
4014 int read_small_molecule_data_cif_and_make_map_using_coords(
const char *file_name,
4030 int handle_shelx_fcf_file_internal(
const char *filename);
4039 int is_shelx_molecule(
int imol);
4047 void add_shelx_string_to_molecule(
int imol,
const char *
string);
4057 void deviant_geometry(
int imol);
4058 short int is_valid_model_molecule(
int imol);
4059 short int is_valid_map_molecule(
int imol);
4071 void difference_map_peaks(
int imol,
int imol_coords,
float level,
float max_closeness,
int do_positive_level_flag,
int do_negative_level_flag,
int around_model_only_flag);
4078 void set_difference_map_peaks_max_closeness(
float m);
4079 float difference_map_peaks_max_closeness();
4081 void clear_diff_map_peaks();
4088 void gln_asn_b_factor_outliers_py(
int imol);
4098 PyObject *map_peaks_near_point_py(
int imol_map,
float n_sigma,
float x,
float y,
float z,
float radius);
4099 PyObject *map_peaks_near_point_from_list_py(
int imol_map, PyObject *peak_list,
float x,
float y,
float z,
float radius);
4100 PyObject *map_peaks_around_molecule_py(
int imol_map,
float sigma,
int negative_also_flag,
int imol_coords);
4103 PyObject *screen_vectors_py();
4112 SCM map_peaks_near_point_scm(
int imol_map,
float n_sigma,
float x,
float y,
float z,
float radius);
4118 SCM get_torsion_scm(
int imol, SCM atom_spec_1, SCM atom_spec_2, SCM atom_spec_3, SCM atom_spec_4);
4122 SCM
set_torsion_scm(
int imol,
const char *chain_id,
int res_no,
const char *insertion_code,
4123 const char *alt_conf,
4124 const char *atom_name_1,
4125 const char *atom_name_2,
4126 const char *atom_name_3,
4127 const char *atom_name_4,
double tors);
4137 PyObject *get_torsion_py(
int imol, PyObject *atom_spec_1, PyObject *atom_spec_2, PyObject *atom_spec_3, PyObject *atom_spec_4);
4141 PyObject *
set_torsion_py(
int imol,
const char *chain_id,
int res_no,
const char *insertion_code,
4142 const char *alt_conf,
4143 const char *atom_name_1,
4144 const char *atom_name_2,
4145 const char *atom_name_3,
4146 const char *atom_name_4,
double tors);
4157 void clear_multi_residue_torsion_mode();
4158 void set_multi_residue_torsion_reverse_mode(
short int mode);
4159 void show_multi_residue_torsion_dialog();
4160 void setup_multi_residue_torsion();
4163 float atom_overlap_score(
int imol);
4187 void add_on_rama_choices();
4201 int ramachandran_psi_axis_mode();
4203 void set_moving_atoms(
double phi,
double psi);
4205 void accept_phi_psi_moving_atoms();
4206 void setup_edit_phi_psi(
short int state);
4210 void setup_dynamic_distances(
short int state);
4212 void destroy_edit_backbone_rama_plot();
4219 const char *a_chain,
const char *b_chain);
4247 void add_on_sequence_view_choices();
4254 void change_peptide_carbonyl_by(
double angle);
4255 void change_peptide_peptide_by(
double angle);
4256 void execute_setup_backbone_torsion_edit(
int imol,
int atom_index);
4257 void setup_backbone_torsion_edit(
short int state);
4259 void set_backbone_torsion_peptide_button_start_pos(
int ix,
int iy);
4260 void change_peptide_peptide_by_current_button_pos(
int ix,
int iy);
4261 void set_backbone_torsion_carbonyl_button_start_pos(
int ix,
int iy);
4262 void change_peptide_carbonyl_by_current_button_pos(
int ix,
int iy);
4273 int add_atom_label(
int imol,
char *chain_id,
int iresno,
char *atom_id);
4274 int remove_atom_label(
int imol,
char *chain_id,
int iresno,
char *atom_id);
4275 void remove_all_atom_labels();
4277 void set_label_on_recentre_flag(
int i);
4279 int centre_atom_label_status();
4316 void spin_zoom_trans(
int axis,
int nstep,
float stepsize,
float zoom_by,
4317 float x_rel,
float y_rel,
float z_rel);
4346 int add_view_raw(
float rcx,
float rcy,
float rcz,
float quat1,
float quat2,
4347 float quat3,
float quat4,
float zoom,
const char *
view_name);
4349 void remove_this_view();
4356 int go_to_first_view(
int snap_to_view_flag);
4357 int go_to_view_number(
int view_number,
int snap_to_view_flag);
4358 int add_spin_view(
const char *
view_name,
int n_steps,
float degrees_total);
4378 float views_play_speed();
4379 void set_views_play_speed(
float f);
4387 SCM view_description(
int view_number);
4388 void go_to_view(SCM view);
4395 PyObject *view_description_py(
int view_number);
4396 void go_to_view_py(PyObject *view);
4411 void set_movie_file_name_prefix(
const char *file_name);
4412 void set_movie_frame_number(
int frame_number);
4415 SCM movie_file_name_prefix();
4418 PyObject *movie_file_name_prefix_py();
4421 int movie_frame_number();
4422 void set_make_movie_mode(
int make_movies_flag);
4466 void set_ligand_verbose_reporting(
int i);
4475 void set_find_ligand_do_real_space_refinement(
short int state);
4522 void execute_ligand_search();
4526 SCM execute_ligand_search_scm();
4529 PyObject *execute_ligand_search_py();
4532 void add_ligand_clear_ligands();
4558 SCM
overlap_ligands(
int imol_ligand,
int imol_ref,
const char *chain_id_ref,
int resno_ref);
4559 SCM analyse_ligand_differences(
int imol_ligand,
int imol_ref,
const char *chain_id_ref,
4561 SCM compare_ligand_atom_types_scm(
int imol_ligand,
int imol_ref,
const char *chain_id_ref,
4564 void match_ligand_torsions(
int imol_ligand,
int imol_ref,
const char *chain_id_ref,
int resno_ref);
4566 PyObject *overlap_ligands_py(
int imol_ligand,
int imol_ref,
const char *chain_id_ref,
int resno_ref);
4567 PyObject *analyse_ligand_differences_py(
int imol_ligand,
int imol_ref,
const char *chain_id_ref,
int resno_ref);
4568 PyObject *compare_ligand_atom_types_py(
int imol_ligand,
int imol_ref,
const char *chain_id_ref,
int resno_ref);
4579 void match_ligand_atom_names(
int imol_ligand,
const char *chain_id_ligand,
int resno_ligand,
const char *ins_code_ligand,
4580 int imol_reference,
const char *chain_id_reference,
int resno_reference,
const char *ins_code_reference);
4617 int exchange_ligand(
int imol_lig,
const char *chain_id_lig,
int resno_lig,
const char *ins_code_lig);
4624 void flip_ligand(
int imol,
const char *chain_id,
int resno);
4626 void jed_flip(
int imol,
const char *chain_id,
int res_no,
const char *ins_code,
const char *atom_name,
const char *alt_conf,
short int invert_selection);
4646 int imol_for_protein,
4647 short int new_waters_mol_flag,
4648 float rmsd_cut_off);
4650 void find_waters(
int imol_for_map,
4651 int imol_for_protein,
4652 short int new_waters_mol_flag,
4654 short int show_blobs_dialog);
4672 char *get_text_for_find_waters_sigma_cut_off();
4673 void set_value_for_find_waters_sigma_cut_off(
float f);
4688 void set_write_peaksearched_waters();
4691 void execute_find_blobs(
int imol_model,
int imol_for_map,
float cut_off,
short int interactive_flag);
4705 void split_water(
int imol,
const char *chain_id,
int res_no,
const char *ins_code);
4740 void set_unbonded_atom_star_size(
float f);
4831 void set_draw_moving_atoms_restraints(
int state);
4837 const char *atom_selection_str,
4838 float bond_thickness,
float sphere_size,
4839 int do_spheres_flag);
4844 void set_show_additional_representation(
int imol,
int representation_number,
int on_off_flag);
4847 void set_show_all_additional_representations(
int imol,
int on_off_flag);
4851 void all_additional_representations_off_except(
int imol,
int representation_number,
4852 short int ball_and_sticks_off_too_flag);
4856 void delete_additional_representation(
int imol,
int representation_number);
4860 int representation_type,
4863 int draw_hydrogens_flag);
4884 int resno_start,
int resno_end,
4885 const char *ins_code,
4886 int representation_type,
4889 int draw_hydrogens_flag);
4895 SCM additional_representation_info_scm(
int imol);
4899 PyObject *additional_representation_info_py(
int imol);
4909 void set_flev_idle_ligand_interactions(
int state);
4912 void toggle_flev_idle_ligand_interactions();
4928 const char *atom_selection_str,
4929 const char *dots_object_name,
4930 float dot_density,
float sphere_size_scale);
4961 void do_pepflip(
short int state);
4964 void pepflip(
int imol,
const char *chain_id,
int resno,
const char *inscode,
4965 const char *altconf);
4966 int pepflip_intermediate_atoms();
4967 int pepflip_intermediate_atoms_other_peptide();
4971 SCM pepflip_using_difference_map_scm(
int imol_coords,
int imol_difference_map,
float n_sigma);
4974 PyObject *pepflip_using_difference_map_py(
int imol_coords,
int imol_difference_map,
float n_sigma);
4986 void do_rigid_body_refine(
short int state);
4994 const char *chain_id,
int imol);
4997 rigid_body_refine_by_atom_selection(
int imol,
4998 const char *atom_selection_string);
5016 void execute_rigid_body_refine(
short int auto_range_flag);
5033 void toggle_dynamic_map_display_size();
5034 void toggle_dynamic_map_sampling();
5036 void set_dynamic_map_size_display_on();
5037 void set_dynamic_map_size_display_off();
5038 int get_dynamic_map_size_display();
5039 void set_dynamic_map_sampling_on();
5040 void set_dynamic_map_sampling_off();
5041 int get_dynamic_map_sampling();
5042 void set_dynamic_map_zoom_offset(
int i);
5052 void do_add_terminal_residue(
short int state);
5057 void set_add_terminal_residue_n_phi_psi_trials(
int n);
5060 void set_add_terminal_residue_add_other_residue_flag(
int i);
5061 void set_add_terminal_residue_do_rigid_body_refine(
short int v);
5062 void set_terminal_residue_do_rigid_body_refine(
short int v);
5063 void set_add_terminal_residue_debug_trials(
short int debug_state);
5064 int add_terminal_residue_immediate_addition_state();
5077 const char *residue_type,
int immediate_add);
5092 const char *residue_type,
float phi,
float psi);
5104 SCM find_terminal_residue_type(
int imol,
const char *chain_id,
int resno);
5107 PyObject *find_terminal_residue_type_py(
int imol,
const char *chain_id,
int resno);
5127 int add_residue_with_atoms_py(
int imol, PyObject *residue_spec,
const std::string &res_name, PyObject *list_of_atoms);
5141 void delete_atom_by_atom_index(
int imol,
int index,
short int do_delete_dialog);
5142 void delete_residue_by_atom_index(
int imol,
int index,
short int do_delete_dialog);
5143 void delete_residue_hydrogens_by_atom_index(
int imol,
int index,
short int do_delete_dialog);
5149 void delete_residue(
int imol,
const char *chain_id,
int resno,
const char *inscode);
5165 void delete_atom(
int imol,
const char *chain_id,
int resno,
const char *ins_code,
const char *at_name,
const char *altloc);
5168 short int do_delete_dialog);
5190 void post_delete_item_dialog();
5195 void set_delete_atom_mode();
5196 void set_delete_residue_mode();
5197 void set_delete_residue_zone_mode();
5198 void set_delete_residue_hydrogens_mode();
5199 void set_delete_water_mode();
5200 void set_delete_sidechain_mode();
5201 void set_delete_sidechain_range_mode();
5202 void set_delete_chain_mode();
5203 short int delete_item_mode_is_atom_p();
5204 short int delete_item_mode_is_residue_p();
5205 short int delete_item_mode_is_water_p();
5206 short int delete_item_mode_is_sidechain_p();
5207 short int delete_item_mode_is_sidechain_range_p();
5208 short int delete_item_mode_is_chain_p();
5209 void clear_pending_delete_item();
5210 void clear_delete_item_widget();
5211 void store_delete_item_widget_position();
5212 short int delete_item_widget_is_being_shown();
5213 short int delete_item_widget_keep_active_on();
5217 void delete_object_handle_delete_dialog(
short int do_delete_dialog);
5226 void do_rot_trans_setup(
short int state);
5227 void rot_trans_reset_previous();
5228 void set_rotate_translate_zone_rotates_about_zone_centre(
int istate);
5229 void set_rot_trans_object_type(
short int rt_type);
5230 int get_rot_trans_object_type();
5235 void do_cis_trans_conversion_setup(
int istate);
5236 void cis_trans_convert(
int imol,
const char *chain_id,
int resno,
const char *altconf);
5244 SCM twisted_trans_peptides(
int imol);
5251 PyObject *twisted_trans_peptides_py(
int imol);
5267 void do_db_main(
short int state);
5276 const char *chain_id,
5279 const char *direction);
5319 void setup_rotamers(
short int state);
5323 void do_rotamers(
int atom_index,
int imol);
5325 void show_rotamers_dialog(
int imol,
const char *chain_id,
int resno,
const char *ins_code,
const char *altconf);
5343 const char *insertion_code,
5344 const char *chain_id,
int imol_coords,
int imol_map,
5345 int clash_flag,
float lowest_probability);
5354 float rotamer_score(
int imol,
const char *chain_id,
int res_no,
const char *insertion_code,
5355 const char *alt_conf);
5356 void setup_auto_fit_rotamer(
short int state);
5361 int n_rotamers(
int imol,
const char *chain_id,
int resno,
const char *ins_code);
5364 const char *alt_conf,
int rotamer_number);
5373 const char *alt_conf,
const char *rotamer_name);
5377 SCM get_rotamer_name_scm(
int imol,
const char *chain_id,
int resno,
const char *ins_code);
5380 PyObject *get_rotamer_name_py(
int imol,
const char *chain_id,
int resno,
const char *ins_code);
5391 void fill_partial_residue(
int imol,
const char *chain_id,
int resno,
const char* inscode);
5401 SCM missing_atom_info_scm(
int imol);
5404 PyObject *missing_atom_info_py(
int imol);
5435 const char *inscode,
const char *altconf);
5437 void setup_180_degree_flip(
short int state);
5440 int side_chain_flip_180_intermediate_atoms();
5453 void setup_mutate(
short int state);
5459 void do_mutation(
const char *type,
short int is_stub_flag);
5466 short int progressive_residues_in_chain_check(
const char *chain_id,
int imol);
5473 int mutate(
int imol,
const char *chain_id,
int ires,
const char *inscode,
const char *target_res_type);
5476 int mutate_base(
int imol,
const char *chain_id,
int res_no,
const char *ins_code,
const char *res_type);
5486 int nudge_residue_sequence(
int imol,
char *chain_id,
int res_no_range_start,
int res_no_range_end,
int nudge_by,
short int nudge_residue_numbers_also);
5522 const char *chain_id,
5523 int imol,
char target_res_type);
5525 int mutate_single_residue_by_seqno(
int ires,
const char *inscode,
5526 const char *chain_id,
5527 int imol,
char target_res_type);
5531 void do_base_mutation(
const char *type);
5537 void handle_residue_type_chooser_entry_chose_type(
const char *entry_text,
short int stub_mode);
5550 short int alt_conf_split_type_number();
5551 void set_add_alt_conf_split_type_number(
short int i);
5559 SCM
add_alt_conf_scm(
int imol,
const char *chain_id,
int res_no,
const char *ins_code,
5560 const char *alt_conf,
int rotamer_number);
5567 PyObject *
add_alt_conf_py(
int imol,
const char*chain_id,
int res_no,
const char *ins_code,
5568 const char *alt_conf,
int rotamer_number);
5572 void unset_add_alt_conf_dialog();
5574 void unset_add_alt_conf_define();
5576 void set_add_alt_conf_new_atoms_occupancy(
float f);
5577 float get_add_alt_conf_new_atoms_occupancy();
5578 void set_show_alt_conf_intermediate_atoms(
int i);
5579 int show_alt_conf_intermediate_atoms_state();
5580 void zero_occupancy_residue_range(
int imol,
const char *chain_id,
int ires1,
int ires2);
5581 void fill_occupancy_residue_range(
int imol,
const char *chain_id,
int ires1,
int ires2);
5582 void set_occupancy_residue_range(
int imol,
const char *chain_id,
int ires1,
int ires2,
float occ);
5583 void set_b_factor_residue_range(
int imol,
const char *chain_id,
int ires1,
int ires2,
float bval);
5584 void reset_b_factor_residue_range(
int imol,
const char *chain_id,
int ires1,
int ires2);
5595 void place_atom_at_pointer();
5597 void place_atom_at_pointer_by_window();
5598 void place_typed_atom_at_pointer(
const char *type);
5601 void set_pointer_atom_is_dummy(
int i);
5602 void display_where_is_pointer();
5609 void set_pointer_atom_molecule(
int imol);
5655 void reverse_direction_of_fragment(
int imol,
const char *chain_id,
int resno);
5656 void setup_reverse_direction(
short int i);
5666 short int add_OXT_to_residue(
int imol,
const char *chain_id,
int reso,
const char *insertion_code);
5680 short int draw_crosshairs_state();
5690 void setup_edit_chi_angles(
short int state);
5692 void rotate_chi(
float am);
5700 void set_graphics_edit_current_chi(
int ichi);
5701 void unset_moving_atom_move_chis();
5702 void set_moving_atom_move_chis();
5709 const char *ins_code,
const char *altconf);
5711 int set_show_chi_angle_bond(
int imode);
5715 void set_edit_chi_angles_reverse_fragment_state(
short int istate);
5722 void toggle_torsion_general_reverse();
5724 void setup_residue_partial_alt_locs(
short int state);
5736 int backrub_rotamer(
int imol,
const char *chain_id,
int res_no,
5737 const char *ins_code,
const char *alt_conf);
5784 void set_check_waters_b_factor_limit(
float f);
5785 void set_check_waters_map_sigma_limit(
float f);
5786 void set_check_waters_min_dist_limit(
float f);
5787 void set_check_waters_max_dist_limit(
float f);
5792 float map_sigma_lim,
5793 float min_dist,
float max_dist,
5794 short int part_occ_contact_flag,
5795 short int zero_occ_flag,
5796 short int logical_operator_and_or_flag);
5799 void check_waters_by_difference_map(
int imol_waters,
int imol_diff_map,
5800 int interactive_flag);
5803 float check_waters_by_difference_map_sigma_level_state();
5804 void set_check_waters_by_difference_map_sigma_level(
float f);
5816 SCM metal_coordination_scm(
int imol,
float dist_max);
5825 PyObject *metal_coordination_py(
int imol,
float dist_max);
5838 void clear_lsq_matches();
5839 void add_lsq_match(
int reference_resno_start,
5840 int reference_resno_end,
5841 const char *chain_id_reference,
5842 int moving_resno_start,
5843 int moving_resno_end,
5844 const char *chain_id_moving,
5851 void add_lsq_atom_pair_scm(SCM atom_spec_ref, SCM atom_spec_moving);
5854 void add_lsq_atom_pair_py(PyObject *atom_spec_ref, PyObject *atom_spec_moving);
5864 SCM get_lsq_matrix_scm(
int imol_reference,
int imol_moving);
5868 PyObject *apply_lsq_matches_py(
int imol_reference,
int imol_moving);
5869 PyObject *get_lsq_matrix_py(
int imol_reference,
int imol_moving);
5874 int apply_lsq_matches_simple(
int imol_reference,
int imol_moving);
5877 void setup_lsq_deviation(
int state);
5878 void setup_lsq_plane_define(
int state);
5879 void unset_lsq_plane_dialog();
5880 void remove_last_lsq_plane_atom();
5896 float map_level,
int delete_or_zero_occ_flag);
5909 void raster3d(
const char *rd3_filename);
5910 void povray(
const char *filename);
5911 void renderman(
const char *rib_filename);
5914 void make_image_raster3d(
const char *filename);
5915 void make_image_povray(
const char *filename);
5917 void make_image_raster3d_py(
const char *filename);
5918 void make_image_povray_py(
const char *filename);
5942 void raster_screen_shot_py();
5949 void citation_notice_off();
5963 void superpose(
int imol1,
int imol2,
short int move_imol2_flag);
5972 const char *chain_imol1,
5973 const char *chain_imol2,
5974 int chain_used_flag_imol1,
5975 int chain_used_flag_imol2,
5976 short int move_imol2_copy_flag);
5990 const char *mmdb_atom_sel_str_1,
5991 const char *mmdb_atom_sel_str_2,
5992 short int move_imol2_copy_flag);
6015 int overwrite_maps_of_same_name_flag);
6016 void make_ncs_ghosts_maybe(
int imol);
6018 void add_ncs_matrix(
int imol,
const char *this_chain_id,
const char *target_chain_id,
6019 float m11,
float m12,
float m13,
6020 float m21,
float m22,
float m23,
6021 float m31,
float m32,
float m33,
6022 float t1,
float t2,
float t3);
6024 void clear_ncs_ghost_matrices(
int imol);
6030 const char *this_chain_id,
6031 const char *target_chain_id,
6032 float m11,
float m12,
float m13,
6033 float m21,
float m22,
float m23,
6034 float m31,
float m32,
float m33,
6035 float t1,
float t2,
float t3);
6036 int add_strict_ncs_from_mtrix_from_self_file(
int imol);
6048 void copy_chain(
int imol,
const char *from_chain,
const char *to_chain);
6058 int residue_range_start,
int residue_range_end);
6068 void copy_residue_range_from_ncs_master_to_chains_scm(
int imol,
const char *master_chain_id,
6069 int residue_range_start,
int residue_range_end,
6076 PyObject *ncs_master_chains_py(
int imol);
6077 void copy_residue_range_from_ncs_master_to_chains_py(
int imol,
const char *master_chain_id,
6078 int residue_range_start,
int residue_range_end,
6079 PyObject *chain_id_list);
6080 void copy_from_ncs_master_to_chains_py(
int imol,
const char *master_chain_id,
6081 PyObject *chain_id_list);
6092 void set_ncs_matrix_type(
int flag);
6093 int get_ncs_matrix_state();
6104 SCM ncs_chain_differences_scm(
int imol,
const char *master_chain_id);
6123 PyObject *ncs_chain_differences_py(
int imol,
const char *master_chain_id);
6160 #define FIND_SECSTRUC_NORMAL 0
6161 #define FIND_SECSTRUC_STRICT 1
6162 #define FIND_SECSTRUC_HI_RES 2
6163 #define FIND_SECSTRUC_LO_RES 3
6191 void set_place_helix_here_fudge_factor(
float ff);
6226 short int use_helix,
int helix_length,
int helix_target,
6227 short int use_strand,
int strand_length,
int strand_target );
6236 short int use_helix,
int helix_length,
int helix_target,
6237 short int use_strand,
int strand_length,
int strand_target,
6284 float r,
short int allow_partial_residues);
6312 set_axis_orientation_matrix(
float m11,
float m12,
float m13,
6313 float m21,
float m22,
float m23,
6314 float m31,
float m32,
float m33);
6317 set_axis_orientation_matrix_usage(
int state);
6338 short int single_stranged_flag,
6339 const char *sequence);
6354 SCM
pucker_info_scm(
int imol, SCM residue_spec,
int do_pukka_pucker_check);
6365 PyObject *
pucker_info_py(
int imol, PyObject *residue_spec,
int do_pukka_pucker_check);
6376 void setup_base_pairing(
int state);
6394 short int pir_format,
6395 short int file_output,
6396 const char *file_name);
6405 void assign_sequence(
int imol_model,
int imol_map,
const char *chain_id);
6466 int molecule_is_drawn_as_surface_int(
int imol);
6483 void set_electrostatic_surface_charge_range(
float v);
6484 float get_electrostatic_surface_charge_range();
6519 void set_coot_listener_socket_state_internal(
int sock_state);
6526 void set_remote_control_port(
int port_number);
6527 int get_remote_control_port_number();
6531 void set_tip_of_the_day_flag(
int state);
6599 void set_do_coot_probe_dots_during_refine(
short int state);
6638 void sharpen(
int imol,
float b_factor);
6639 void sharpen_with_gompertz_scaling(
int imol,
float b_factor,
short int try_gompertz,
float gompertz_factor);
6647 float optimal_B_kurtosis(
int imol);
6658 SCM drag_intermediate_atom_scm(SCM atom_spec, SCM position);
6661 PyObject *drag_intermediate_atom_py(PyObject *atom_spec, PyObject *position);
6672 PyObject *add_target_position_restraints_for_intermediate_atoms_py(PyObject *atom_spec_position_list);
6685 SCM mark_atom_as_fixed_scm(
int imol, SCM atom_spec,
int state);
6686 int mark_multiple_atoms_as_fixed_scm(
int imol, SCM atom_spec_list,
int state);
6689 PyObject *mark_atom_as_fixed_py(
int imol, PyObject *atom_spec,
int state);
6690 int mark_multiple_atoms_as_fixed_py(
int imol, PyObject *atom_spec_list,
int state);
6694 void setup_fixed_atom_pick(
short int ipick,
short int is_unpick);
6698 void clear_fixed_atoms_all();
6701 void set_debug_atom_picking(
int istate);
6723 int scale_cell(
int imol_map,
float fac_u,
float fac_v,
float fac_w);
6728 void segment_map(
int imol_map,
float low_level);
6730 void segment_map_multi_scale(
int imol_map,
float low_level,
float b_factor_inc,
int n_rounds);
6732 void map_histogram(
int imol_map);
6770 void delete_dipole(
int imol,
int dipole_number);
6777 SCM
add_dipole_scm(
int imol,
const char* chain_id,
int res_no,
const char *ins_code);
6781 PyObject *
add_dipole_py(
int imol,
const char* chain_id,
int res_no,
6782 const char *ins_code);
6798 const char *sigf_col);
6804 const char *sigi_col);
6829 PyObject *get_pkgdatadir_py();
6833 SCM get_pkgdatadir_scm();
6872 int place_text(
const char*text,
float x,
float y,
float z,
int size);
6877 void edit_text(
int text_handle,
const char *new_text);
6906 SCM handle_pisa_interfaces_scm(SCM interfaces_description_scm);
6909 SCM pisa_molecule_record_residues(SCM molecule_record_1);
6910 SCM pisa_molecule_record_chain_id(SCM molecule_record_1);
6911 void add_pisa_interface_bond_scm(
int imol_1,
int imol_2, SCM pisa_bond_scm,
6912 int interface_number);
6916 void pisa_clear_interfaces();
6931 PyObject *handle_pisa_interfaces_py(PyObject *interfaces_description_py);
6936 void add_pisa_interface_bond_py(
int imol_1,
int imol_2, PyObject *pisa_bond_py,
6937 int interface_number);
6940 void pisa_clear_interfaces();
6956 int n_trials,
float jiggle_scale_factor);
7020 int add_linked_residue(
int imol,
const char *chain_id,
int resno,
const char *ins_code,
7021 const char *new_residue_comp_id,
const char *link_type,
int n_trials);
7025 SCM add_linked_residue_scm(
int imol,
const char *chain_id,
int resno,
const char *ins_code,
7026 const char *new_residue_comp_id,
const char *link_type,
int mode);
7029 PyObject *add_linked_residue_py(
int imol,
const char *chain_id,
int resno,
const char *ins_code,
7030 const char *new_residue_comp_id,
const char *link_type,
int mode);
7033 void set_add_linked_residue_do_fit_and_refine(
int state);
7040 void fle_view_internal(
int imol,
const char *chain_id,
int res_no,
7041 const char *ins_code,
7042 int imol_ligand_fragment,
7043 const char *prodrg_output_flat_mol_file_name,
7044 const char *prodrg_output_flat_pdb_file_name,
7045 const char *prodrg_output_3d_pdb_file_name,
7046 const char *prodrg_output_dict_cif_file_name);
7048 void fle_view_internal_to_png(
int imol,
const char *chain_id,
int res_no,
7049 const char *ins_code,
7050 int imol_ligand_fragment,
7051 const char *prodrg_output_flat_mol_file_name,
7052 const char *prodrg_output_flat_pdb_file_name,
7053 const char *prodrg_output_3d_pdb_file_name,
7054 const char *prodrg_output_dict_cif_file_name,
7055 int output_to_png_file_flag,
7056 const char *png_file_name);
7058 void fle_view_with_rdkit(
int imol,
const char *chain_id,
int res_no,
const char *ins_code,
float residues_near_radius);
7059 void fle_view_with_rdkit_to_png(
int imol,
const char *chain_id,
int res_no,
const char *ins_code,
float residues_near_radius,
const char *png_file_name);
7060 void fle_view_with_rdkit_to_svg(
int imol,
const char *chain_id,
int res_no,
const char *ins_code,
float residues_near_radius,
const char *svg_file_name);
7062 void fle_view_with_rdkit_internal(
int imol,
const char *chain_id,
int res_no,
const char *ins_code,
float residues_near_radius,
const char *file_format,
const char *file_name);
7079 int sprout_hydrogens(
int imol,
const char *chain_id,
int res_no,
const char *ins_code);
7100 void lsq_improve(
int imol_ref,
const char *ref_selection,
7101 int imol_moving,
const char *moving_selection,
7102 int n_res,
float dist_crit);
7113 void toolbar_multi_refine_stop();
7114 void toolbar_multi_refine_continue();
7115 void toolbar_multi_refine_cancel();
7116 void set_visible_toolbar_multi_refine_stop_button(
short int state);
7117 void set_visible_toolbar_multi_refine_continue_button(
short int state);
7118 void set_visible_toolbar_multi_refine_cancel_button(
short int state);
7121 void toolbar_multi_refine_button_set_sensitive(
const char *button_type,
short int state);
7154 void run_update_self_maybe();
7159 void show_go_to_residue_keyboarding_mode_window();
7160 void handle_go_to_residue_keyboarding_mode(
const gchar *text);
7180 void add_ligand_builder_menu_item_maybe();
7187 SCM all_molecule_rotamer_score(
int imol);
7188 SCM all_molecule_ramachandran_score(
int imol);
7191 PyObject *all_molecule_rotamer_score_py(
int imol);
7192 PyObject *all_molecule_ramachandran_score_py(
int imol);
7193 PyObject *all_molecule_ramachandran_region_py(
int imol);
7222 void user_defined_click_py(
int n_clicks, PyObject *func);
7228 void full_screen(
int mode);
void apply_ncs_to_view_orientation_and_screen_centre(int imol, const char *current_chain, const char *next_ncs_chain, short int forward_flag)
as above, but shift the screen centre also.
void run_script(const char *filename)
run script file
void set_raster3d_water_sphere(int istate)
set the flag to show waters as spheres for the Raster3D representation. 1 show as spheres...
int read_pdb(const char *filename)
read coordinates from filename
int quick_save()
save all modified coordinates molecules to the default names and save the state too.
PyObject * sequence_info_py(int imol)
return the sequence info that has been assigned to molecule number imol. return as a list of dotted p...
void set_do_anti_aliasing(int state)
set the bond lines to be antialiased
void change_chain_id(int imol, const char *from_chain_id, const char *to_chain_id, short int use_res_range_flag, int from_resno, int to_resno)
change the chain id of the specified residue
int set_imol_refinement_map(int imol)
set the molecule number of the map to be used for refinement/fitting.
int backup_state(int imol)
return the backup state for molecule number imol
void set_ligand_cluster_sigma_level(float f)
set the default sigma level that the map is searched to find potential ligand sites ...
void do_ramachandran_plot(int imol)
Ramachandran plot for molecule number imol.
void set_symmetry_molecule_rotate_colour_map(int imol, int state)
set the colour map rotation (i.e. the hue) for the symmetry atoms of molecule number imol ...
int set_unit_cell_and_space_group(int imol, float a, float b, float c, float alpha, float beta, float gamma, const char *space_group)
set the unit cell for a given model molecule
int assign_hetatms(int imol)
some programs produce PDB files with ATOMs where there should be HETATMs. This is a function to assig...
void redraw_background()
re draw the background colour when switching between mono and stereo
int mmcif_sfs_to_mtz(const char *cif_file_name, const char *mtz_file_name)
convert the structure factors in cif_file_name to an mtz file.
void set_model_fit_refine_dialog_stays_on_top(int istate)
model-fit-refine dialog stays on top
void set_only_last_model_molecule_displayed()
only display the last model molecule
void set_dragged_refinement_steps_per_frame(int v)
set the number of refinement steps applied to the intermediate atoms each frame of graphics...
void write_restraints_cif_dictionary(const char *monomer_type, const char *file_name)
write cif restraints for monomer
void set_convert_to_v2_atom_names(short int state)
shall we convert nucleotides to match the old dictionary names?
int apply_redo()
apply redo - the "Redo" button callback
float get_map_sampling_rate()
return the map sampling rate
void set_hardware_stereo_angle_factor(float f)
how much should the eyes be separated in stereo mode?
void do_clipped_surface_scm(int imol, SCM residue_specs)
draw the surface of the imolth molecule clipped to the residues given by residue_specs.
void remove_view(int view_number)
the given view number
int mutate_single_residue_by_serial_number(int ires_ser, const char *chain_id, int imol, char target_res_type)
an alternate interface to mutation of a singe residue.
void graphics_to_ca_plus_ligands_sec_struct_representation(int imol)
draw molecule number imol with CA bonds in secondary structure representation and ligands ...
void set_fffear_angular_resolution(float f)
set and return the fffear angular resolution in degrees
void translate_scene_z(int nsteps)
translate rotation centre relative to screen axes for nsteps
void set_colour_by_molecule(int imol)
colour molecule number imol by molecule
void set_raster3d_density_thickness(float f)
set the density line thickness for the Raster3D representation
void handle_read_draw_probe_dots(const char *dots_file)
pass a filename that contains molprobity's probe output in XtalView format
void set_alignment_gap_and_space_penalty(float wgap, float wspace)
set the penalty for affine gap and space when aligning, defaults -3.0 and -0.4
void delete_sidechains_for_chain(int imol, const char *chain_id)
delete the side chains in the chain
void delete_residues_scm(int imol, SCM residue_specs_scm)
delete residues in the residue spec list
float auto_fit_best_rotamer(int resno, const char *altloc, const char *insertion_code, const char *chain_id, int imol_coords, int imol_map, int clash_flag, float lowest_probability)
auto fit by rotamer search.
void c_accept_moving_atoms()
accept the new positions of the regularized or refined residues
void ramachandran_plot_differences(int imol1, int imol2)
2 molecule ramachandran plot (NCS differences) a.k.a. A Kleywegt Plot.
int make_and_draw_patterson(const char *mtz_file_name, const char *f_col, const char *sigf_col)
Make a patterson molecule.
short int set_space_group(int imol, const char *spg)
set the space group for a coordinates molecule
void write_interpolated_extra_restraints(int imol_1, int imol_2, int n_steps, char *file_name_stub)
proSMART interpolated restraints for model morphing
void info_dialog_with_markup(const char *txt)
as above, create a dialog with information
int draw_ncs_ghosts_state(int imol)
return the drawing state of NCS ghosts for molecule number imol. Return -1 on imol is a bad molecule ...
void set_filter_fileselection_filenames(int istate)
on opening a file selection dialog, pre-filter the files.
void set_pick_cursor_index(int icursor_index)
let the user have a different pick cursor
SCM overlap_ligands(int imol_ligand, int imol_ref, const char *chain_id_ref, int resno_ref)
Overlap residue with "template"-based matching.
int n_chains(int imol)
number of chains in molecule number imol
int map_from_mtz_by_calc_phases(const char *mtz_file_name, const char *f_col, const char *sigf_col, int imol_coords)
Calculate SFs from an MTZ file and generate a map.
PyObject * rigid_body_refine_by_residue_ranges_py(int imol, PyObject *residue_ranges)
rigid body refine using residue ranges. residue_ranges is a list of residue ranges. A residue range is [chain_id, resno_start, resno_end].
void set_ligand_water_to_protein_distance_limits(float f1, float f2)
set ligand to protein distance limits
int try_set_draw_baton(short int i)
draw the baton or not
void rotate_y_scene(int nsteps, float stepsize)
rotate view round y axis stepsize degrees for nstep such steps
int delete_restraints(const char *comp_id)
delete the restraints for the given comp_id (i.e. residue name)
float matrix_state()
return the relative weight of the geometric terms to the map terms.
void make_backup(int imol)
make backup for molecule number imol
void set_find_hydrogen_torsions(short int state)
show torsions that rotate hydrogens in the torsion angle manipulation dialog. Note that this may be n...
void print_all_history_in_scheme()
print the history in scheme format
void add_ligand_search_ligand_molecule(int imol_ligand)
add a rigid ligand molecule to the list of ligands to search for in ligand searching ...
void symmetry_as_calphas(int mol_no, short int state)
display symmetry as CAs?
void set_file_chooser_selector(int istate)
this flag set chooser as default for windows, otherwise use selector 0 is selector 1 is chooser ...
void set_environment_distances_label_atom(int state)
Label the atom on Environment Distances start/change.
void set_clipping_back(float v)
set clipping plane back
void ligand_expert()
this sets the flag to have expert option ligand entries in the Ligand Searching dialog ...
int backup_compress_files_state()
return the state for compression of backup files
void post_other_modelling_tools_dialog()
display the Other Modelling Tools dialog
int find_helices()
autobuild helices
void hide_main_toolbar()
hide the horizontal main toolbar in the GTK2 version
void set_use_trans_peptide_restraints(short int on_off_state)
add a restraint on peptides to keep trans peptides trans
int first_unsaved_coords_imol()
What is the molecule number of first unsaved coordinates molecule?
void shiftfield_b_factor_refinement(int imol)
shiftfield B-factor refinement
short int mtz_use_weight_for_map(int imol_map)
return flag for whether weights were used that was use to generate the map
void align_and_mutate(int imol, const char *chain_id, const char *fasta_maybe, short int renumber_residues_flag)
align and mutate the given chain to the given sequence
void set_rotation_centre_size(float f)
set rotoation centre marker size
void set_map_radius_em(float radius)
set the extent of the box/radius of electron density contours for EM map
SCM symmetry_operators_scm(int imol)
return a list of symmetry operators as strings - or scheme false if that is not possible.
void run_clear_backups(int retval)
run clear-backups
int add_terminal_residue_using_phi_psi(int imol, const char *chain_id, int res_no, const char *residue_type, float phi, float psi)
Add a terminal residue using given phi and psi angles.
void set_swap_difference_map_colours(int i)
not everone likes coot's default difference map colouring.
void add_coordinates_glob_extension(const char *ext)
add an extension to be treated as coordinate files
void set_show_origin_marker(int istate)
set a flag: is the origin marker to be shown? 1 for yes, 0 for no.
int rotamer_auto_fit_do_post_refine_state()
what is the value of the previous flag?
int set_go_to_atom_chain_residue_atom_name_full(const char *chain_id, int resno, const char *ins_code, const char *atom_name, const char *alt_conf)
set the go to (full) atom specification
int git_revision_count()
return the git revision count for for this build.
void vt_surface(int mode)
How should the mouse move the view?
PyObject * cis_peptides_py(int imol)
return cis_peptide info for imol.
int make_and_draw_map(const char *mtz_file_name, const char *f_col, const char *phi_col, const char *weight, int use_weights, int is_diff_map)
make a map from an mtz file (simple interface)
SCM ncs_ghosts_scm(int imol)
get the NCS ghost description
int seqnum_from_serial_number(int imol, const char *chain_id, int serial_num)
a residue seqnum (normal residue number) from a residue serial number
int read_phs_and_make_map_using_cell_symm_from_previous_mol(const char *phs_filename)
read a phs file, the cell and symm information is from previously read (most recently read) coordinat...
void unset_model_fit_refine_dialog()
unset model/fit/refine dialog
int set_atom_string_attribute(int imol, const char *chain_id, int resno, const char *ins_code, const char *atom_name, const char *alt_conf, const char *attribute_name, const char *attribute_value)
set a string attibute to the atom with the given specifier.
PyObject * nearest_residue_by_sequence_py(int imol, const char *chain_id, int resno, const char *ins_code)
return the residue spec of the nearest residue by sequence numbering. Return Python False if not poss...
PyObject * map_peaks_py(int imol_map, float n_sigma)
return a list of map peaks of molecule number imol_map above n_sigma. There will be cluster filtering...
void set_show_modelling_toolbar(short int state)
void graphics_to_b_factor_cas_representation(int imol)
draw molecule number imol coloured by B-factor, CA + ligands
void set_bond_thickness(int imol, float t)
set the thickness of the bonds in molecule number imol to t pixels
int set_go_to_atom_chain_residue_atom_name(const char *t1_chain_id, int iresno, const char *t3_atom_name)
set the go to atom specification
void set_go_to_atom_molecule(int imol)
set the molecule for the Go To Atom
void set_show_paths_in_display_manager(int i)
Show Paths in Display Manager?
SCM comp_id_to_name_scm(const char *comp_id)
return the monomer name
void toggle_idle_spin_function()
Spin spin spin (or not)
int scroll_by_wheel_mouse_state()
return the internal state of the scroll-wheel map contouring
int set_b_factor_bonds_scale_factor(int imol, float f)
scale the colours for colour by b factor representation
int dots(int imol, const char *atom_selection_str, const char *dots_object_name, float dot_density, float sphere_size_scale)
display dotted surface
void post_scheme_scripting_window()
pop-up a scripting window for scheming
char * unmangle_hydrogen_name(const char *pdb_hydrogen_name)
make an attempt to convert pdb hydrogen name to the name used in Coot (and the refmac dictionary...
int set_map_is_difference_map(int imol, short int bool_flag)
post-hoc set the map of molecule number imol to be a difference map
void add_view_description(int view_number, const char *description)
Add a view description/annotation to the give view number.
int single_model_view_this_model_number(int imol)
the current model number being displayed
char * insertion_code_from_serial_number(int imol, const char *chain_id, int serial_num)
the insertion code of the residue.
void add_planar_peptide_restraints()
add a restraint on peptides to make them planar
void set_diff_map_iso_level_increment(float val)
set the contour scroll step for difference map (in absolute e/A3) to val
SCM ncs_chain_ids_scm(int imol)
Return the ncs chains id for the given molecule.
SCM molecule_name_stub_scm(int imol, int include_path_flag)
return the molecule name without file extension
void save_state_file(const char *filename)
save the current state to file filename
int difference_map(int imol1, int imol2, float map_scale)
make a difference map, taking map_scale * imap2 from imap1, on the grid of imap1. Return the new mole...
SCM map_parameters_scm(int imol)
return the parameter that made the map,
PyObject * save_state_file_name_py()
the save state file name
void graphics_to_ca_plus_ligands_and_sidechains_representation(int imol)
draw molecule number imol as CA + ligands + sidechains
int stereo_mode_state()
what is the stero state?
PyObject * molecule_name_stub_py(int imol, int include_path_flag)
return the molecule name without file extension
void set_refine_with_torsion_restraints(int istate)
turn on (or off) torsion restraints
void set_contour_level_absolute(int imol_map, float level)
set the contour level, direct control
int make_dynamically_transformed_ncs_maps(int imol_model, int imol_map, int overwrite_maps_of_same_name_flag)
make NCS map
int do_anti_aliasing_state()
return the flag for antialiasing the bond lines
PyObject * highly_coordinated_waters_py(int imol, int coordination_number, float dist_max)
return a list first of waters, second metals that are coordinated with at least coordination_number o...
int set_atom_attribute(int imol, const char *chain_id, int resno, const char *ins_code, const char *atom_name, const char *alt_conf, const char *attribute_name, float val)
set a numberical attibute to the atom with the given specifier.
void set_refine_ramachandran_angles(int state)
turn on Ramachandran angles refinement in refinement and regularization
int imol_refinement_map()
the molecule number of the map used for refinement
void write_ccp4mg_picture_description(const char *filename)
write a ccp4mg picture description file
void set_default_representation_type(int type)
set the default representation type (default 1).
void set_console_display_commands_state(short int istate)
set a flag to show the text command equivalent of gui commands in the console as they happen...
float fffear_angular_resolution()
return the fffear angular resolution in degrees
void write_interpolated_models_and_extra_restraints(int imol_1, int imol_2, int n_steps, char *file_name_stub, int interpolation_mode)
proSMART interpolated restraints for model morphing and write interpolated model
void remove_text(int text_handle)
Remove "3d" text item.
int mutate_base(int imol, const char *chain_id, int res_no, const char *ins_code, const char *res_type)
mutate a base. return success status, 1 for a good mutate.
void remove_planar_peptide_restraints()
remove restraints on peptides to make them planar.
void set_smooth_scroll_flag(int v)
set smooth scrolling
void set_residue_selection_flash_frames_number(int i)
set the number of frames for which the selected residue range flashes
void set_stop_scroll_iso_map_level(float f)
set the actual map level changing limit
void move_hetgroups_to_around_protein(int imol)
move all hetgroups (including waters) of molecule number imol so that they are around the protein...
SCM map_peaks_scm(int imol_map, float n_sigma)
return a list of map peaks of molecule number imol_map above n_sigma. There will be cluster filtering...
void set_map_radius(float f)
set the extent of the box/radius of electron density contours for x-ray maps
SCM sequence_info(int imol)
return the sequence info that has been assigned to molecule number imol. return as a list of dotted p...
void set_socket_string_waiting(const char *s)
feed the main thread a scheme script to evaluate
SCM set_torsion_scm(int imol, const char *chain_id, int res_no, const char *insertion_code, const char *alt_conf, const char *atom_name_1, const char *atom_name_2, const char *atom_name_3, const char *atom_name_4, double tors)
set the given torsion the given residue. tors is in degrees. Return the resulting torsion (also in de...
PyObject * user_mods_py(const char *file_name)
return the parsed user mod fields from the PDB file file_name (output by reduce most likely) ...
SCM matching_compound_names_from_sbase_scm(const char *compound_name_fragment)
return a list of compoundIDs of in SBase of which the given string is a substring of the compound nam...
void print_view_matrix()
print the view matrix to the console, useful for molscript, perhaps
void simple_fill_partial_residues(int imol)
Fill amino acid residues.
void nsv(int imol)
display the sequence view for molecule number imol
void update_go_to_atom_window_on_changed_mol(int imol)
update the Go To Atom window
void set_model_fit_refine_dialog_position(int x_pos, int y_pos)
set position of Model/Fit/Refine dialog
int single_model_view_next_model_number(int imol)
change the representation to the next model number to be displayed
void undo_last_move()
undo last move
int have_unsaved_changes_p(int imol)
does molecule number imol have unsaved changes?
int draw_hydrogens_state(int imol)
the state of draw hydrogens for molecule number imol.
void set_ligand_flexible_ligand_n_samples(int i)
set the number of conformation samples
void print_sequence_chain(int imol, const char *chain_id)
Print the sequence to the console of the given molecule.
void set_view_quaternion(float i, float j, float k, float l)
Set the view quaternion.
int residue_has_hetatms(int imol, const char *chain_id, int resno, const char *ins_code)
residue has HETATMs?
void update_go_to_atom_window_on_new_mol()
update the Go To Atom window. This updates the option menu for the molecules.
int fix_nomenclature_errors(int imol)
fix nomenclature errors in molecule number imol
void assign_pir_sequence(int imol, const char *chain_id_in, const char *seq)
Assign a PIR sequence to a given chain in the molecule. If the chain of the molecule already had a ch...
int export_map(int imol, const char *filename)
export (write to disk) the map of molecule number imol to filename.
int decoloned_backup_file_names_state()
return the state for adding paths to backup file names
void set_find_ligand_multi_solutions_per_cluster(float lim_1, float lim_2)
allow multiple ligand solutions per cluster.
void remove_omega_torsion_restriants()
remove omega restraints on CIS and TRANS linked residues.
int set_atom_attributes(SCM attribute_expression_list)
set lots of atom attributes at once by-passing the rebonding and redrawing of the above 2 functions ...
int add_nucleotide(int imol, const char *chain_id, int res_no)
Add a terminal nucleotide.
void set_rotamer_selection_dialog_position(int x_pos, int y_pos)
set rotamer selection dialog position
void set_show_environment_distances_as_solid(int state)
show the environment distances with solid modelling
float get_molecule_bonds_colour_map_rotation(int imol)
Get the colour map rotation for molecule number imol.
void set_grey_carbon_colour(int imol, float r, float g, float b)
set the colour for the carbon atoms
PyObject * select_atom_under_pointer_py()
return Python false or a list of molecule number and an atom spec
void set_show_unit_cells_all(short int istate)
set the state of show unit cell for all molecules
void set_rotamer_lowest_probability(float f)
For Dunbrack rotamers, set the lowest probability to be considered. Set as a percentage i...
int average_map_py(PyObject *map_number_and_scales)
make an average map from the map_number_and_scales (which is a list of pairs map_number, scale_factor. The output map is in the same grid as the first (valid) map. Return -1 on failure to make an averaged map, otherwise return the new map molecule number.
void graphics_to_rainbow_representation(int imol)
draw molecule number imol in Jones' Rainbow
void set_run_state_file_status(short int istat)
set run state file status
int map_is_difference_map(int imol)
map is difference map?
void set_all_models_displayed_and_active(int on_or_off)
if on_or_off is 0 turn off all models displayed and active, for other values of on_or_off turn on all...
void set_draw_solid_density_surface(int imol, short int state)
sets the density map of the given molecule to be drawn as a (transparent) solid surface.
void refine_auto_range(int imol, const char *chain_id, int resno1, const char *altconf)
refine a zone using auto-range
short int python_at_prompt_at_startup_state()
is the python interpreter at the prompt?
int n_residues(int imol)
return the number of residues in the molecule,
void set_find_ligand_mask_waters(int istate)
how shall we treat the waters during ligand fitting?
void set_show_environment_distances_bumps(int state)
show bumps environment distances. If state is 0, bump distances are turned off, otherwise bump distan...
void show_set_undo_molecule_chooser()
show the Undo Molecule chooser - i.e. choose the molecule to which the "Undo" button applies...
void remove_map_glob_extension(const char *ext)
remove an extension to be treated as geometry map files
void fle_view_set_water_dist_max(float dist_max)
set the maximum considered distance to water
int get_fps_flag()
set the state of show frames-per-second flag
void set_backup_compress_files(int state)
set if backup files will be compressed or not using gzip
void set_dots_colour(int imol, float r, float g, float b)
set the colour of the surface dots of the imol-th molecule to be the given single colour ...
int place_text(const char *text, float x, float y, float z, int size)
Put text at x,y,z.
int rotamer_search_mode_state()
SCM rigid_body_refine_by_residue_ranges_scm(int imol, SCM residue_ranges)
rigid body refine using residue ranges. residue_ranges is a list of residue ranges. A residue range is (list chain-id resno-start resno-end).
void remove_non_auto_load_residue_name(const char *s)
remove residue name from the list of residue names that don't get auto-loaded from the Refmac diction...
float median_temperature_factor(int imol)
return the median temperature factor for imol
void set_recentre_on_read_pdb(short int)
set the recentre-on-pdb state
void translate_scene_x(int nsteps)
translate rotation centre relative to screen axes for nsteps
void assign_sequence_from_string(int imol, const char *chain_id_in, const char *seq)
Assign a sequence to a given molecule from a simple string.
SCM save_state_file_name_scm()
the save state file name
void baton_tip_try_another()
move the baton tip position - another prime candidate for a key binding
void set_fix_chiral_volumes_before_refinement(int istate)
correct the sign of chiral volumes before commencing refinement?
int set_residue_to_rotamer_name(int imol, const char *chain_id, int resno, const char *ins_code, const char *alt_conf, const char *rotamer_name)
set the residue specified to the rotamer name specified.
void set_add_terminal_residue_immediate_addition(int i)
set immediate addition of terminal residue
void make_tight_planar_peptide_restraints()
make the planar peptide restraints tight
void set_rotamer_auto_fit_do_post_refine(short int istate)
Do you want Coot to automatically run a refinement after every rotamer autofit?
void show_select_map_dialog()
display the Display Manager dialog
void single_model_view_model_number(int imol, int imodel)
put molecule number imol to display only model number imodel
int create_pointer_atom_molecule_maybe()
Return the current pointer atom molecule, create a pointer atom molecule if necessary (i...
void difference_map_peaks(int imol, int imol_coords, float level, float max_closeness, int do_positive_level_flag, int do_negative_level_flag, int around_model_only_flag)
generate a list of difference map peaks
void set_smooth_scroll_steps(int i)
set the number of steps in the smooth scroll
int export_map_fragment_to_plain_file(int imol, float x, float y, float z, float radius, const char *filename)
tmp interface for Hamish
void show_main_toolbar()
show the horizontal main toolbar in the GTK2 version (the toolbar is shown by default) ...
void mutate_active_residue()
display a dialog that allows the choice of residue type to which to mutate
int n_dots_sets(int imol)
return the number of dots sets for molecule number imol
void hide_modelling_toolbar()
hide the vertical modelling toolbar in the GTK2 version
float fit_molecule_to_map_by_random_jiggle_and_blur(int imol, int n_trials, float jiggle_scale_factor, float map_blur_factor)
jiggle fit the molecule to the current refinment map. return < -100 if not possible, else return the new best fit for this molecule - create a map that is blurred by the given factor for fitting
void spin_zoom_trans(int axis, int nstep, float stepsize, float zoom_by, float x_rel, float y_rel, float z_rel)
Bells and whistles rotation.
void post_go_to_atom_window()
Post the Go To Atom Window.
void raster_screen_shot()
run raster3d and display the resulting image.
void calc_phases_generic(const char *mtz_file_name)
fire up a GUI, which asks us which model molecule we want to calc phases from. On "OK" button there...
int show_origin_marker_state()
return the origin marker shown? state
int add_extra_bond_restraint(int imol, const char *chain_id_1, int res_no_1, const char *ins_code_1, const char *atom_name_1, const char *alt_conf_1, const char *chain_id_2, int res_no_2, const char *ins_code_2, const char *atom_name_2, const char *alt_conf_2, double bond_dist, double esd)
add a user-define bond restraint
void set_show_environment_distances(int state)
show environment distances. If state is 0, distances are turned off, otherwise distances are turned o...
void rotate_z_scene(int nsteps, float stepsize)
rotate view round z axis stepsize degrees for nstep such steps
int db_mainchains_fragment(int imol, const char *chain_id, int res_no)
CA-Zone to Mainchain for a fragment based on the given residue.
int do_GL_lighting_state()
return the flag for GL lighting
void set_auto_fit_best_rotamer_clash_flag(int i)
set the clash flag for rotamer search
int auto_load_dictionary(const char *comp_id)
try to auto-load the dictionary for comp_id from the refmac monomer library.
void delete_residue_hydrogens(int imol, const char *chain_id, int resno, const char *inscode, const char *altloc)
delete hydrogen atoms in residue
void set_max_skeleton_search_depth(int v)
set the skeleton search depth, used in baton building
void do_180_degree_side_chain_flip(int imol, const char *chain_id, int resno, const char *inscode, const char *altconf)
rotate 180 degrees around the last chi angle
int symmetry_molecule_rotate_colour_map_state(int imol)
should there be colour map rotation (i.e. the hue) change for the symmetry atoms of molecule number i...
void post_display_control_window()
display the Display Constrol window
void set_accept_reject_dialog_docked_show(int state)
set the accept/reject dialog docked show state
void set_interactive_probe_dots_molprobity_radius(float r)
set the radius over which we can run interactive probe, bigger is better but slower.
void set_brief_atom_labels(int istat)
use brief atom names for on-screen labels
void change_model_molecule_representation_mode(int up_or_down)
change the representation of the model molecule closest to the centre of the screen ...
int change_residue_number(int imol, const char *chain_id, int current_resno, const char *current_inscode, int new_resno, const char *new_inscode)
change chain id, residue number or insertion code for given residue
void toggle_idle_rock_function()
Rock (not roll) (self-timed)
PyObject * comp_id_to_name_py(const char *comp_id)
return the monomer name
void set_accept_reject_dialog_position(int x_pos, int y_pos)
set position of the Accept/Reject dialog
SCM matching_compound_names_from_dictionary_scm(const char *compound_name_fragment, short int allow_minimal_descriptions_flag)
return a list of compoundIDs in the dictionary of which the given string is a substring of the compou...
void renumber_waters(int imol)
Renumber the waters of molecule number imol with consecutive numbering.
void transform_zone(int imol, const char *chain_id, int resno_start, int resno_end, const char *ins_code, float m11, float m12, float m13, float m21, float m22, float m23, float m31, float m32, float m33, float x, float y, float z)
transform fragment of molecule number imol by the given rotation matrix, then translate by (x...
int get_auto_recontour_map()
return the auto-recontour state
int read_phs_and_make_map_using_cell_symm(const char *phs_file_name, const char *hm_spacegroup, float a, float b, float c, float alpha, float beta, float gamma)
read phs file use coords to use cell and symm to make map
int fffear_search(int imol_model, int imol_map)
fffear search model in molecule number imol_model in map number imol_map
void set_reset_b_factor_moved_atoms(int state)
reset temperature factor for all moved atoms to the default for new atoms (usually 30) ...
int secondary_structure_restraints_type()
return the secondary structure restraints type
void set_symmetry_size(float f)
set the size of the displayed symmetry
const char * mtz_phi_for_map(int imol_map)
return the phases column in mtz file that was use to generate the map
void raster3d(const char *rd3_filename)
create a r3d file for the current view
void display_only_active()
display only the active mol and the refinement map
void set_density_size(float f)
another (old) way of setting the radius of the map
void refine_zone(int imol, const char *chain_id, int resno1, int resno2, const char *altconf)
refine a zone
int place_strand_here(int n_residues, int n_sample_strands)
add a strands
void set_contour_level_in_sigma(int imol_map, float level)
set the contour level, direct control in r.m.s.d. (if you like that sort of thing) ...
SCM add_alt_conf_scm(int imol, const char *chain_id, int res_no, const char *ins_code, const char *alt_conf, int rotamer_number)
add an alternative conformer to a residue. Add it in conformation rotamer number rotamer_number.
int get_font_size()
return the font size
int background_is_black_p()
is the background black (or nearly black)?
void set_decoloned_backup_file_names(int state)
set the state for adding paths to backup file names
int reset_view()
"Reset" the view
int find_nucleic_acids_local(float radius)
autobuild nucleic acid chains
int model_fit_refine_dialog_stays_on_top_state()
return the state model-fit-refine dialog stays on top
float get_contour_level_absolute(int imol)
get the contour level
void delete_residue_with_full_spec(int imol, int imodel, const char *chain_id, int resno, const char *inscode, const char *altloc)
delete residue with altconf
void set_rotamer_search_mode(int mode)
set the mode of rotamer search, options are (ROTAMERSEARCHAUTOMATIC), (ROTAMERSEARCHLOWRES) (aka...
void set_use_stroke_characters(int state)
set use stroke characters
void set_show_pointer_distances(int istate)
turn on (or off) the pointer distance by passing 1 (or 0).
float fit_molecule_to_map_by_random_jiggle(int imol, int n_trials, float jiggle_scale_factor)
jiggle fit the molecule to the current refinment map. return < -100 if not possible, else return the new best fit for this molecule.
void ncs_control_display_chain(int imol, int ichain, int state)
display the NCS master chain
int superpose_with_atom_selection(int imol1, int imol2, const char *mmdb_atom_sel_str_1, const char *mmdb_atom_sel_str_2, short int move_imol2_copy_flag)
detailed interface to superposition.
SCM user_mods_scm(const char *file_name)
return the parsed user mod fields from the PDB file file_name (output by reduce most likely) ...
void manage_column_selector(const char *filename)
given a filename, try to read it as a data file
void set_fps_flag(int t)
set show frame-per-second flag
void match_ligand_atom_names_to_comp_id(int imol_ligand, const char *chain_id_ligand, int resno_ligand, const char *ins_code_ligand, const char *comp_id_ref)
Match ligand atom names to a reference ligand type (comp_id)
void set_draw_map_standard_lines(int imol, short int state)
toggle for standard lines representation of map.
void do_clipped_surface_py(int imol, PyObject *residue_specs)
draw the surface of the imolth molecule clipped to the residues given by residue_specs ...
int get_write_conect_record_state()
return the state of the write_conect_records_flag.
void set_add_terminal_residue_default_residue_type(const char *type)
set the residue type of an added terminal residue.
void set_stop_scroll_diff_map_level(float f)
set the actual difference map level changing limit
int backrub_rotamer_intermediate_atoms()
apply rotamer backrub to the active atom of the intermediate atoms
void set_show_symmetry_master(short int state)
set display symmetry, master controller
int control_key_for_rotate_state()
return the control key rotate state
void set_water_check_spherical_variance_limit(float f)
set the limit of interesting variance, above which waters are listed (otherwise ignored) ...
int replace_fragment(int imol_target, int imol_fragment, const char *atom_selection)
replace the parts of molecule number imol that are duplicated in molecule number imol_frag ...
void copy_from_ncs_master_to_chains_scm(int imol, const char *master_chain_id, SCM chain_id_list)
Copy chain from master to a list of NCS chains.
int move_waters_to_around_protein(int imol)
move waters of molecule number imol so that they are around the protein.
void set_seg_ids_in_atom_labels(int istat)
set if brief atom labels should have seg-ids also
void set_unpathed_backup_file_names(int state)
set the state for adding paths to backup file names
int hetify_residue(int imol, const char *chain_id, int resno, const char *ins_code)
if this is not a standard group, then turn the atoms to HETATMs.
PyObject * map_parameters_py(int imol)
return the parameter of the molecule, something like (45 46 47 90 90 120), angles in degress ...
void export_map_fragment_with_text_radius(int imol, const char *radius_text, const char *filename)
void set_sticky_sort_by_date()
sort files in the file selection by date?
float get_electrostatic_surface_opacity(int imol)
return 1.0 for non transparent and 0.5 if screendoor transparency has been turned on...
void delete_residues_py(int imol, PyObject *residue_specs_py)
delete residues in the residue spec list
void sfcalc_genmap(int imol_model, int imol_map_with_data_attached, int imol_updating_difference_map)
Calculate structure factors from the model and update the given difference map accordingly.
void delete_all_extra_restraints(int imol)
clear out all the extra/user-defined restraints for molecule number imol
void refine_zone_atom_index_define(int imol, int ind1, int ind2)
refine a zone based on atom indexing
int chain_n_residues(const char *chain_id, int imol)
the number of residues in chain chain_id and molecule number imol
int set_residue_to_rotamer_number(int imol, const char *chain_id, int resno, const char *ins_code, const char *alt_conf, int rotamer_number)
set the residue specified to the rotamer number specifed.
void pick_cursor_maybe()
pick cursor maybe
void set_all_maps_displayed(int on_or_off)
if on_or_off is 0 turn off all maps displayed, for other values of on_or_off turn on all maps ...
void label_atoms_in_residue()
Label the atoms in the central residue.
int is_mtz_file_p(const char *filename)
is the given filename an mtz file?
void mono_mode()
try to turn on mono mode
int copy_residue_range(int imol_target, const char *chain_id_target, int imol_reference, const char *chain_id_reference, int resno_range_start, int resno_range_end)
copy the given residue range from the reference chain to the target chain
void save_symmetry_coords(int imol, const char *filename, int symop_no, int shift_a, int shift_b, int shift_c, int pre_shift_to_origin_na, int pre_shift_to_origin_nb, int pre_shift_to_origin_nc)
save the symmetry coordinates of molecule number imol to filename
void remove_data_glob_extension(const char *ext)
remove an extension to be treated as data (reflection) files
void set_default_temperature_factor_for_new_atoms(float new_b)
set the default temperature factor for newly created atoms (initial default 20)
void set_ncs_homology_level(float flev)
At what level of homology should we say that we can't see homology for NCS calculation? (default 0.8)
void set_map_mask_atom_radius(float rad)
set the atom radius for map masking
void set_default_initial_contour_level_for_map(float n_sigma)
set the default inital contour for 2FoFc-style map
void show_restraints_editor_by_index(int menu_item_index)
show restraints editor using residue type index
int text_index_near_position(float x, float y, float z, float r)
return the closest text that is with r A of the given position. If no text item is close...
float get_view_quaternion_internal(int element)
internal function to get an element of the view quaternion. The whole quaternion is returned by the s...
void set_mol_active(int imol, int state)
make the coordinates molecule active/inactve (clickable), 0 for off, 1 for on
void set_rigid_body_fit_acceptable_fit_fraction(float f)
set rigid body fraction of atoms in positive density
int does_residue_exist_p(int imol, char *chain_id, int resno, char *inscode)
Does the residue exist? (Raw function)
void go_to_ligand()
centre on the ligand of the "active molecule", if we are already there, centre on the next hetgroup (...
int copy_molecule(int imol)
copy molecule imol
int cis_trans_convert_intermediate_atoms()
cis-trans convert the active residue of the active atom in the inermediate atoms, and continue with t...
short int get_show_unit_cell(int imol)
return the stage of show unit cell for molecule number imol
void show_remarks_browswer()
show the remarks browser
void set_model_fit_refine_rotate_translate_zone_label(const char *txt)
Allow the changing of Model/Fit/Refine button label from "Rotate/Translate Zone". ...
void set_active_map_drag_flag(int t)
set the state of immediate map upate on map drag.
int another_level()
Add another contour level for the last added map.
int refinement_move_atoms_with_zero_occupancy_state()
return the state of "shall atoms with zero occupancy be moved when refining?"
void trim_molecule_by_map(int imol_coords, int imol_map, float map_level, int delete_or_zero_occ_flag)
cut off (delete or give zero occupancy) atoms in the given molecule if they are below the given map (...
int pointer_atom_molecule()
Return the current pointer atom molecule.
void show_partial_charge_info(int imol, const char *chain_id, int resno, const char *ins_code)
show the partial charges for the residue of the given specs (charges are read from the dictionary) ...
void set_map_colour(int imol, float red, float green, float blue)
set the colour of the imolth map
PyObject * refine_residues_py(int imol, PyObject *r)
refine the residues in the given residue spec list
void set_bond_colour_rotation_for_molecule(int imol, float f)
set bond colour for molecule
int brief_atom_labels_state()
the brief atom label state
void set_matrix(float f)
set the relative weight of the geometric terms to the map terms
void normal_cursor()
normal cursor
void set_display_control_dialog_position(int x_pos, int y_pos)
set position of Display Control dialog
void set_save_coordinates_in_original_directory(int i)
set save coordinates in the starting directory
float get_map_radius()
return the extent of the box/radius of electron density contours
short int get_symmetry_as_calphas_state(int imol)
what is state of display CAs for molecule number mol_no?
int cns_file_has_phases_p(const char *cns_file_name)
does the given file have cns phases?
int handle_read_draw_molecule(const char *filename)
a synonym for read-pdb. Read the coordinates from filename (can be pdb, cif or shelx format) ...
void set_display_intro_string(const char *str)
Give me this nice message str when I start coot.
void multi_residue_torsion_py(int imol, PyObject *residues_specs_py)
create a multi-residue torsion dialog (user manipulation of torsions)
void info_dialog(const char *txt)
create a dialog with information
short int refinement_already_ongoing_p()
If there is a refinement on-going already, we don't want to start a new one.
void add_data_glob_extension(const char *ext)
add an extension to be treated as data (reflection) files
void shorten_baton()
shorten the baton length
char * go_to_atom_ins_code()
the go-to-atom insertion code
void set_graphics_window_size(int x_size, int y_size)
set the window size
void superpose(int imol1, int imol2, short int move_imol2_flag)
simple interface to superposition.
int add_terminal_residue_do_post_refine_state()
what is the value of the previous flag?
void set_map_displayed(int imol, int state)
make the map displayed/undisplayed, 0 for off, 1 for on
void store_graphics_window_position(int x_pos, int y_pos)
store the graphics window position
int find_secondary_structure(short int use_helix, int helix_length, int helix_target, short int use_strand, int strand_length, int strand_target)
autobuild secondary structure
void set_refinement_immediate_replacement(int istate)
set immediate replacement mode for refinement and regularization. You need this (call with istate=1) ...
PyObject * het_group_residues_py(int imol)
get the specs for hetgroups - waters are not counted as het-groups.
int keep_map_colour_after_refmac_state()
the keep-map-colour-after-refmac internal state
int map_line_width_state()
return the width in which density contours are drawn
void update_sequence_view_current_position_highlight_from_active_atom()
update the sequnce view current position highlight based on active atom
void add_status_bar_text(const char *s)
Put text s into the status bar.
void remove_coordinates_glob_extension(const char *ext)
remove an extension to be treated as coordinate files
void set_show_chiral_volume_errors_dialog(short int istate)
For experienced Cooters who don't like Coot nannying about chiral volumes during refinement.
void set_baton_build_params(int istart_resno, const char *chain_id, const char *direction)
set the parameters for the start of a new baton-built fragment. direction can either be "forwards" or...
int delete_waters(int imol)
delete all waters in molecule,
int filter_fileselection_filenames_state()
, return the state of the above variable
int exchange_chain_ids_for_seg_ids(int imol)
Experimental interface for Ribosome People.
int new_molecule_by_sphere_selection(int imol, float x, float y, float z, float r, short int allow_partial_residues)
create a new molecule that consists of only the atoms within the given radius (r) of the given positi...
int new_molecule_by_residue_specs_py(int imol, PyObject *residue_spec_list_py)
create a new molecule that consists of only the atoms of the specified list of residues ...
void fit_residue_range_to_map_by_simplex(int res1, int res2, char *altloc, char *chain_id, int imol, int imol_for_map)
refine residue range using simplex optimization
SCM chain_id_for_shelxl_residue_number(int imol, int resno)
float molecule_centre_internal(int imol, int iaxis)
internal function for molecule centre
void remarks_dialog(int imol)
a gui dialog showing remarks header info (for a model molecule).
void run_python_script(const char *filename)
run python script file
void set_prefer_python()
tell coot that you prefer to run python scripts if/when there is an option to do so.
void set_add_terminal_residue_do_post_refine(short int istat)
set a flag to run refine zone on terminal residues after an addition.
SCM remarks_scm(int imol)
return a list of the remarks of hte molecule number imol
int unskeletonize_map(int imol)
undisplay the skeleton on molecule number imol
void set_ligand_water_n_cycles(int i)
set the number of cycles of water searching
SCM cell_scm(int imol)
return the parameter that made the map,
PyObject * set_torsion_py(int imol, const char *chain_id, int res_no, const char *insertion_code, const char *alt_conf, const char *atom_name_1, const char *atom_name_2, const char *atom_name_3, const char *atom_name_4, double tors)
set the given torsion the given residue. tors is in degrees. Return the resulting torsion (also in de...
void user_defined_click_scm(int n_clicks, SCM func)
run a user defined function
void execute_find_waters_real(int imol_for_map, int imol_for_protein, short int new_waters_mol_flag, float rmsd_cut_off)
find waters
void set_nomenclature_errors_on_read(const char *mode)
set way nomenclature errors should be handled on reading coordinates.
PyObject * add_dipole_py(int imol, const char *chain_id, int res_no, const char *ins_code)
generate a dipole from all atoms in the given residues.
int full_atom_spec_to_atom_index(int imol, const char *chain, int resno, const char *inscode, const char *atom_name, const char *altloc)
what is the atom index of the given atom?
int n_rotamers(int imol, const char *chain_id, int resno, const char *ins_code)
return the number of rotamers for this residue - return -1 on no residue found.
void clear_all_fixed_atoms(int imol)
clear all fixed atoms
int map_from_mtz_by_refmac_calc_phases(const char *mtz_file_name, const char *f_col, const char *sigf_col, int imol_coords)
Calculate SFs (using refmac optionally) from an MTZ file and generate a map. Get F and SIGF automatic...
void set_use_grey_carbons_for_molecule(int imol, short int state)
make the carbon atoms for molecule imol be grey
int regularize_zone(int imol, const char *chain_id, int resno1, int resno2, const char *altconf)
regularize a zone
void set_scroll_by_wheel_mouse(int istate)
Some people (like Phil Evans) don't want to scroll their map with the mouse-wheel.
void set_colour_by_chain_goodsell_mode(int imol)
colour molecule number imol by chain type, goodsell-like colour scheme
float get_bond_colour_rotation_for_molecule(int imol)
get the bond colour for molecule.
float fit_to_map_by_random_jiggle(int imol, const char *chain_id, int resno, const char *ins_code, int n_trials, float jiggle_scale_factor)
jiggle fit to the current refinment map. return < -100 if not possible, else return the new best fit ...
void run_state_file()
run the state file (reading from default filenname)
const char * mtz_weight_for_map(int imol_map)
return the weight column in the mtz file that was use to generate the map
void set_do_probe_dots_on_rotamers_and_chis(short int state)
shall we run molprobity for on edit chi angles intermediate atoms?
int get_default_bond_thickness()
get the default thickness for bonds
void set_kleywegt_plot_n_diffs(int n_diffs)
set the number of biggest difference arrows on the Kleywegt plot.
void set_use_only_extra_torsion_restraints_for_torsions(short int state)
set use only extra torsion restraints for torsions
void set_idle_function_rotate_angle(float f)
how far should we rotate when (auto) spinning? Fast computer? set this to 0.1
void unset_dots_colour(int imol)
no longer set the dots of molecule imol to a single colour
void set_rotate_translate_dialog_position(int x_pos, int y_pos)
set position of the Rotate/Translate Residue Range dialog
void ncs_control_change_ncs_master_to_chain_id(int imol, const char *chain_id)
change the NCS master chain (by chain_id)
int make_and_draw_patterson_using_intensities(const char *mtz_file_name, const char *i_col, const char *sigi_col)
Make a patterson molecule.
void delete_all_sequences_from_molecule(int imol)
Delete all the sequences from a given molecule.
void globularize(int imol)
globularize the molecule.
void set_draw_missing_residues_loops(short int state)
set the state for drawing missing resiude loops
void set_ramachandran_plot_dialog_position(int x_pos, int y_pos)
set position of the Ramachadran Plot dialog
int another_level_from_map_molecule_number(int imap)
Add another contour level for the given map.
void set_undo_molecule(int imol)
set the molecule to which undo operations are done to molecule number imol
void set_symmetry_shift_search_size(int shift)
set the cell shift search size for symmetry searching.
void set_stop_scroll_diff_map(int i)
create a lower limit to the "Fo-Fc-style" map contour level changing
void set_delete_dialog_position(int x_pos, int y_pos)
set position of Delete dialog
void set_draw_stick_mode_atoms(int imol, short int state)
draw little coloured balls on atoms
void coot_no_state_real_exit(int retval)
exit without writing a state file
int mol_is_displayed(int imol)
return the display state of molecule number imol
void sequence_view_old_style(int imol)
show old style sequence view
int smooth_map(int map_no, float sampling_multiplier)
make a new map (a copy of map_no) that is in the cell, spacegroup and a multiple of the sampling of t...
void rotate_cursor()
rotate cursor
int make_directory_maybe(const char *dir)
make a directory dir (if it doesn't exist) and return error code
void reattach_modelling_toolbar()
reattach the modelling toolbar to the last attached position
SCM highly_coordinated_waters_scm(int imol, int coordination_number, float dist_max)
return an improper list first is list of metals, second is list of waters that are coordinated with a...
int scroll_wheel_map()
the contouring of which map is altered when the scroll wheel changes?
void set_skeleton_box_size(float f)
the box size (in Angstroms) for which the skeleton is displayed
void open_coords_dialog()
display the open coordinates dialog
SCM origin_pre_shift_scm(int imol)
return the pre-shift (the shift that translates the centre of the molecule as close as possible to th...
void save_state_file_py(const char *filename)
save the current state to file filename
int scale_cell(int imol_map, float fac_u, float fac_v, float fac_w)
Scale the cell, for use with EM maps, where the cell needs to be adjusted. Use like: (scale-cell 2 1...
SCM merge_molecules(SCM add_molecules, int imol)
merge molecules
void sort_residues(int imol)
sort the residues of the imol-th molecule
int show_pointer_distances_state()
show the state of display of the pointer distances
void set_symmetry_colour(float r, float g, float b)
set the symmetry colour base
void wrapped_create_find_waters_dialog()
create a dialog for water fitting
void set_go_to_atom_window_position(int x_pos, int y_pos)
set position of Go To Atom dialog
void generate_local_self_restraints_by_residues_scm(int imol, SCM residue_specs, float local_dist_max)
generate external distance self restraints for selected residues
int export_map_fragment_with_origin_shift(int imol, float x, float y, float z, float radius, const char *filename)
export a fragment of the map about (x,y,z)
void show_restraints_editor(const char *monomer_type)
show restraints editor
SCM refine_residues_scm(int imol, SCM r)
refine residues, r is a list of residue specs.
int set_go_to_atom_chain_residue_atom_name_no_redraw(const char *t1, int iresno, const char *t3, short int make_the_move_flag)
set go to atom but don't redraw
void unset_refine_params_dialog()
unset refine params dialog
void set_smooth_scroll_do_zoom(int i)
set smooth scroll with zoom
void shiftfield_xyz_factor_refinement(int imol)
shiftfield xyz refinement
void side_by_side_stereo_mode(short int use_wall_eye_mode)
turn on side bye side stereo mode
int clear_and_update_model_molecule_from_file(int molecule_number, const char *file_name)
replace pdb. Fail if molecule_number is not a valid model molecule. Return -1 on failure. Else return molecule_number
int insert_action_view_after_view(int view_number, const char *view_name, const char *action_function)
add an action view after the view of the given view number
void graphics_to_user_defined_atom_colours_all_atoms_representation(int imol)
draw molecule number imol all atoms coloured by user-defined atom colours
const char * mtz_fp_for_map(int imol_map)
return the FP column in the file that was use to generate the map
int write_cif_file(int imol, const char *file_name)
write molecule number imol as a mmCIF to file file_name
int make_ball_and_stick(int imol, const char *atom_selection_str, float bond_thickness, float sphere_size, int do_spheres_flag)
make a ball and stick representation of imol given atom selection
void add_ncs_matrix(int imol, const char *this_chain_id, const char *target_chain_id, float m11, float m12, float m13, float m21, float m22, float m23, float m31, float m32, float m33, float t1, float t2, float t3)
Add NCS matrix.
void set_refine_rotamers(int state)
set the state for using rotamer restraints "drive" mode
float map_mask_atom_radius()
get the atom radius for map masking
SCM space_group_scm(int imol)
return the spacegroup as a string, return scheme false if unable to do so.
PyObject * matching_compound_names_from_sbase_py(const char *compound_name_fragment)
return a list of compoundIDs of in SBase of which the given string is a substring of the compound nam...
void hardware_stereo_mode()
try to turn on stereo mode
int is_protein_chain_p(int imol, const char *chain_id)
is this a protein chain? [Raw function]
void label_neighbours()
Label the atoms in the residues around the central residue.
int valid_labels(const char *mtz_file_name, const char *f_col, const char *phi_col, const char *weight_col, int use_weights)
does the mtz file have the columms that we want it to have?
void set_display_lists_for_maps(int i)
Should display lists be used for maps? It may speed things up if these are turned on (or off) - depen...
void ramachandran_plot_differences_by_chain(int imol1, int imol2, const char *a_chain, const char *b_chain)
A chain-specific Kleywegt Plot.
void check_chiral_volumes(int imol)
query the state of the above option
short int do_probe_dots_post_refine_state()
show the state of shall we run molprobity after a refinement has happened?
void set_show_symmetry_molecule(int mol_no, short int state)
set display symmetry for molecule number mol_no
void load_tutorial_model_and_data()
load tutorial model and data
void flip_ligand(int imol, const char *chain_id, int resno)
flip the ligand (usually active residue) around its eigen vectors to the next flip number...
SCM nearest_residue_by_sequence_scm(int imol, const char *chain_id, int resno, const char *ins_code)
return the residue spec of the nearest residue by sequence numbering.
float hardware_stereo_angle_factor_state()
return the hardware stereo angle factor
void execute_find_blobs(int imol_model, int imol_for_map, float cut_off, short int interactive_flag)
find blobs
void set_button_label_for_external_refinement(const char *button_label)
set the button label of the external Refinement program
int find_secondary_structure_local(short int use_helix, int helix_length, int helix_target, short int use_strand, int strand_length, int strand_target, float radius)
autobuild secondary structure
void graphics_window_size_and_position_to_preferences()
store the graphics window position and size to zenops-graphics-window-size-and-postion.scm in the preferences directory.
void set_molecule_bonds_colour_map_rotation(int imol, float theta)
set the colour map rotation for molecule number imol
int refinement_immediate_replacement_state()
query the state of the immediate replacement mode
void set_show_aniso(int state)
set show aniso atoms
void transform_molecule_by(int imol, float m11, float m12, float m13, float m21, float m22, float m23, float m31, float m32, float m33, float x, float y, float z)
transform molecule number imol by the given rotation matrix, then translate by (x,y,z) in Angstroms
PyObject * active_residue_py()
Return a list of [imol, chain-id, resno, ins-code, atom-name, alt-conf] for atom that is closest to t...
int accept_reject_dialog_docked_state()
the accept/reject dialog docked state
void run_guile_script(const char *filename)
guile run script file
void clear_dots_by_name(int imol, const char *dots_object_name)
clear the first dots object for imol with given name
void set_last_map_colour(double f1, double f2, double f3)
set the colour of the last (highest molecule number) map
void print_sequence_chain_general(int imol, const char *chain_id, short int pir_format, short int file_output, const char *file_name)
optionally write the sequence to the file for the given molecule, optionally in PIR format ...
float interactive_probe_dots_molprobity_radius()
return the radius over which we can run interactive probe.
void set_flat_shading_for_solid_density_surface(short int state)
set the flag to do flat shading rather than smooth shading for solid density surface.
void set_solid_density_surface_opacity(int imol, float opacity)
set the opacity of density surface representation of the given map.
void set_raster3d_atom_radius(float f)
set the atom radius for the Raster3D representation
short int recentre_on_read_pdb()
return the recentre-on-pdb state
void set_display_only_model_mol(int imol)
from all the model molecules, display only imol
int mutate_auto_fit_do_post_refine_state()
what is the value of the previous flag?
void set_background_colour(double red, double green, double blue)
set the background colour
int new_molecule_by_symop(int imol, const char *symop_string, int pre_shift_to_origin_na, int pre_shift_to_origin_nb, int pre_shift_to_origin_nc)
create a new molecule (molecule number is the return value) from imol.
void set_last_map_contour_level_by_sigma(float n_sigma)
set the contour level of the map with the highest molecule number to n_sigma sigma ...
void accept_baton_position()
accept the baton tip position - a prime candidate for a key binding
void set_map_sampling_rate(float r)
set the map sampling rate (default 1.5)
void open_cif_dictionary_file_selector_dialog()
open the cif dictionary file selector dialog
void add_dictionary_glob_extension(const char *ext)
add an extension to be treated as geometry dictionary files
void set_colour_map_rotation_on_read_pdb(float f)
set the hue change step on reading a new molecule
void delete_sequence_by_chain_id(int imol, const char *chain_id_in)
Delete the sequence for a given chain_id from a given molecule.
SCM add_dipole_for_residues_scm(int imol, SCM residue_specs)
generate a dipole from all atoms in the given residues. Return the dipole description ...
char * go_to_atom_atom_name()
the go-to-atom atom name
void generate_local_self_restraints(int imol, const char *chain_id, float local_dist_max)
generate external distance local self restraints
void set_ncs_ghost_bond_thickness(int imol, float f)
set bond thickness of NCS ghosts for molecule number imol
void repeat_refine_zone()
repeat the previous (user-selected) refine zone
int sprout_hydrogens(int imol, const char *chain_id, int res_no, const char *ins_code)
Add hydrogens to specificied residue.
int edit_chi_angles(int imol, const char *chain_id, int resno, const char *ins_code, const char *altconf)
display the edit chi angles gui for the given residue
void set_transparent_electrostatic_surface(int imol, float opacity)
simple on/off screendoor transparency at the moment, an opacity > 0.0 will turn on screendoor transpa...
void show_model_toolbar_all_icons()
show all available icons in the modelling toolbar (same as MFR dialog)
void set_refine_ramachandran_restraints_type(int type)
change the target function type
int refinement_refine_per_frame_state()
query the state of the above option
void post_model_fit_refine_dialog()
display the Model/Fit/Refine dialog
void start_ligand_builder_gui()
display the ligand builder dialog
void close_molecule(int imol)
close the molecule
void set_raster3d_bone_thickness(float f)
set the bone (skeleton) thickness for the Raster3D representation
int write_shelx_ins_file(int imol, const char *filename)
write a SHELXL .ins file for molecule number imol
int db_mainchain(int imol, const char *chain_id, int iresno_start, int iresno_end, const char *direction)
CA -> mainchain conversion.
short int file_type_coords(const char *file_name)
is the given file name suitable to be read as coordinates?
int delete_hydrogens(int imol)
delete all hydrogens in molecule,
int show_environment_distances_state()
show the state of display of the environment distances
void do_surface(int imol, int istate)
draw surface of molecule number imol
int remove_named_view(const char *view_name)
the view with the given name
void set_residue_name(int imol, const char *chain_id, int res_no, const char *ins_code, const char *new_residue_name)
set the residue name of the specified residue
char * show_spacegroup(int imol)
return the spacegroup of molecule number imol . Deprecated.
void translate_scene_y(int nsteps)
translate rotation centre relative to screen axes for nsteps
int add_strict_ncs_matrix(int imol, const char *this_chain_id, const char *target_chain_id, float m11, float m12, float m13, float m21, float m22, float m23, float m31, float m32, float m33, float t1, float t2, float t3)
add an NCS matrix for strict NCS molecule representation
int add_view_raw(float rcx, float rcy, float rcz, float quat1, float quat2, float quat3, float quat4, float zoom, const char *view_name)
return the view number
int new_molecule_by_symmetry(int imol, const char *name, double m11, double m12, double m13, double m21, double m22, double m23, double m31, double m32, double m33, double tx, double ty, double tz, int pre_shift_to_origin_na, int pre_shift_to_origin_nb, int pre_shift_to_origin_nc)
create a new molecule (molecule number is the return value) from imol.
int refine_with_torsion_restraints_state()
return the state of above
int map_is_displayed(int imol)
return the display state of molecule number imol
void add_header_secondary_structure_info(int imol)
add secondary structure info to the internal representation of the model
void set_colour_map_rotation_on_read_pdb_flag(short int i)
shall the hue change step be used?
int handle_cns_data_file(const char *filename, int imol)
read CNS data (currently only a placeholder)
void add_non_auto_load_residue_name(const char *s)
add residue name to the list of residue names that don't get auto-loaded from the Refmac dictionary...
void set_extra_restraints_prosmart_sigma_limits(int imol, double limit_high, double limit_low)
often we don't want to see all prosmart restraints, just the (big) violations
void set_ramachandran_plot_background_block_size(float blocksize)
set the ramachandran plot background block size.
void set_auto_updating_sfcalc_genmap(int imol_model, int imol_map_with_data_attached, int imol_updating_difference_map)
As above, calculate structure factors from the model and update the given difference map accordingly ...
int unpathed_backup_file_names_state()
return the state for adding paths to backup file names
PyObject * add_alt_conf_py(int imol, const char *chain_id, int res_no, const char *ins_code, const char *alt_conf, int rotamer_number)
add an alternative conformer to a residue. Add it in conformation rotamer number rotamer_number.
void zalman_stereo_mode()
try to turn on Zalman stereo mode
void set_renderer_show_atoms(int istate)
set the flag to show atoms for the Raster3D representation
int first_small_coords_imol()
molecule number of first small (<400 atoms) molecule.
short int get_show_aniso()
return show-aniso-atoms state
void graphics_to_bonds_no_waters_representation(int imol)
draw molecule number imol with no waters
void set_reorienting_next_residue_mode(int state)
rotate the view so that the next main-chain atoms are oriented in the same direction as the previous ...
void set_rocking_factors(float width_scale, float frequency_scale)
Settings for the inevitable discontents who dislike the default rocking rates (defaults 1 and 1) ...
int save_coordinates(int imol, const char *filename)
save coordinates of molecule number imol in filename
int average_map_scm(SCM map_number_and_scales)
make an average map from the map_number_and_scales (which is a list of pairs (list map-number scale-f...
void set_scroll_wheel_map(int imap)
set the map that is moved by changing the scroll wheel and change_contour_level().
void graphics_to_user_defined_atom_colours_representation(int imol)
draw molecule number imol in CA+Ligands mode coloured by user-defined atom colours ...
int handle_read_draw_molecule_with_recentre(const char *filename, int recentre_on_read_pdb_flag)
read coordinates from filename with option to not recentre.
void recover_session()
recover session
void set_map_sharpening_scale_limit(float f)
set the limit of the b-factor map sharpening slider (default 30)
void set_smooth_scroll_limit(float lim)
do not scroll for distances greater this limit
float get_aniso_probability()
get aniso probability
void print_header_secondary_structure_info(int imol)
simply print secondary structure info to the terminal/console. In future, this could/should return th...
void set_mol_displayed(int imol, int state)
make the coordinates molecule displayed/undisplayed, 0 for off, 1 for on
float model_resolution(int imol)
return the resolution set in the header of the model/coordinates file. If this number is not availabl...
void graphics_to_sec_struct_bonds_representation(int imol)
draw molecule number imol with bonds in secondary structure representation
SCM non_standard_residue_names_scm(int imol)
non-standard residue/monomer names (note HOH is not non-standard).
void baton_build_delete_last_residue()
delete the most recently build CA position
int mutate(int imol, const char *chain_id, int ires, const char *inscode, const char *target_res_type)
mutate a given residue
void set_last_map_sigma_step(float f)
set the sigma step of the last map to f sigma
void set_find_ligand_n_top_ligands(int n)
search the top n sites for ligands.
void set_ligand_search_map_molecule(int imol_map)
set the map molecule for ligand searching
short int do_probe_dots_on_rotamers_and_chis_state()
return the state of if run molprobity for on edit chi angles intermediate atoms?
float max_water_distance(int imol)
return the maximum minimum distance of any water atom to any protein atom - used in validation of mov...
int new_molecule_by_atom_selection(int imol, const char *atom_selection)
create a new molecule that consists of only the atoms specified by the mmdb atoms selection string in...
int go_to_atom_residue_number()
the go-to-atom residue number
int delete_hydrogen_atoms(int imol)
delete all hydrogens in molecule,
void assign_sequence_from_file(int imol, const char *file)
Assign a sequence to a given molecule from (whatever) sequence file.
void set_residue_type_chooser_stub_state(short int istat)
set a flag saying that the residue chosen by mutate or auto-fit mutate should only be added as a stub...
short int get_show_symmetry()
is symmetry master display control on?
void accept_regularizement()
a hideous alias for the above
short int get_active_map_drag_flag()
return the state of the dragged map flag
void set_map_line_width(int w)
draw the lines of the chickenwire density in width w
void set_save_state_file_name(const char *filename)
set the default state file name (default 0-coot.state.scm)
void set_draw_hydrogens(int imol, int istat)
set the hydrogen drawing state. istat = 0 is hydrogens off, istat = 1: show hydrogens ...
float default_new_atoms_b_factor()
return the default temperature factor for newly created atoms
void post_python_scripting_window()
pop-up a scripting window for pythoning
void set_limit_aniso(short int state)
set the aniso atom limit
int add_ligand_delete_residue_copy_molecule(int imol_ligand_new, const char *chain_id_ligand_new, int resno_ligand_new, int imol_current, const char *chain_id_ligand_current, int resno_ligand_current)
Copy a molecule with addition of a ligand and a deletion of current ligand.
void set_refine_ramachandran_restraints_weight(float w)
change the target function weight
int get_sbase_monomer(const char *comp_id)
same as above but using old name for back-compatibility
void start_graphics_interface()
start Gtk (and graphics)
int place_helix_here()
add a helix
void split_water(int imol, const char *chain_id, int res_no, const char *ins_code)
split the given water and fit to map.
int first_molecule_with_symmetry_displayed()
return the molecule number.
int new_molecule_by_residue_specs_scm(int imol, SCM residue_spec_list_scm)
create a new molecule that consists of only the atoms of the specified list of residues ...
void set_molecule_name(int imol, const char *new_name)
set the molecule name of the imol-th molecule
void make_socket_listener_maybe()
try to make socket listener
void set_nsv_canvas_pixel_limit(int cpl)
set the pixel limit for sequence view windows
void set_have_unsaved_changes(int imol)
set the molecule number imol to be marked as having unsaved changes
int esoteric_depth_cue_state()
native depth cueing system
void set_do_GL_lighting(int state)
turn the GL lighting on (state = 1) or off (state = 0)
void print_all_history_in_python()
print the history in python format
int reinterp_map(int map_no, int reference_map_no)
make a new map (a copy of map_no) that is in the cell, spacegroup and gridding of the map in referenc...
void copy_chain(int imol, const char *from_chain, const char *to_chain)
Copy single NCS chain.
void set_last_map_contour_level(float level)
set the contour level of the map with the highest molecule number to level
void add_omega_torsion_restriants()
add restraints on the omega angle of the peptides
PyObject * alignment_mismatches_py(int imol)
do a internal alignment of all the assigned sequences, return a list of mismatches that need to be ma...
SCM het_group_residues_scm(int imol)
get the specs for hetgroups - waters are not counted as het-groups.
void browser_url(const char *url)
try to open given url in Web browser
int make_updating_map(const char *mtz_file_name, const char *f_col, const char *phi_col, const char *weight, int use_weights, int is_diff_map)
make a map molecule from the give file name.
void set_refine_auto_range_step(int i)
change the +/- step for autoranging (default is 1)
int read_phs_and_make_map_using_cell_symm_from_mol(const char *phs_filename, int imol)
read phs file and use a previously read molecule to provide the cell and symmetry information ...
void set_model_fit_refine_place_atom_at_pointer_label(const char *txt)
Allow the changing of Model/Fit/Refine button label from "Place Atom at Pointer". ...
char * go_to_atom_chain_id()
the go-to-atom chain-id
void turn_on_backup(int imol)
turn on backups for molecule number imol
int import_python_module(const char *module_name, int use_namespace)
import python module
void update_go_to_atom_from_current_position()
update the Go To Atom widget entries to atom closest to screen centre.
char * go_to_atom_alt_conf()
the go-to-atom alt conf
void setup_mutate_auto_fit(short int state)
Mutate then fit to map.
PyObject * non_standard_residue_names_py(int imol)
non-standard residue/monomer names (note HOH is not non-standard).
void coot_real_exit(int retval)
exit from coot, give return value retval back to invoking process.
int reload_dictionary(const char *comp_id)
as above, but dictionary is cleared and re-read if it already exists
int add_terminal_residue(int imol, const char *chain_id, int residue_number, const char *residue_type, int immediate_add)
Add a terminal residue.
SCM apply_lsq_matches(int imol_reference, int imol_moving)
apply the LSQ matches
void set_environment_distances_distance_limits(float min_dist, float max_dist)
min and max distances for the environment distances
float idle_function_rotate_angle()
what is the idle function rotation angle?
int n_atoms(int imol)
return the atoms of residues in the molecule,
int mol_is_active(int imol)
return the active state of molecule number imol
int handle_cns_data_file_with_cell(const char *filename, int imol, float a, float b, float c, float alpha, float beta, float gamma, const char *spg_info)
read CNS data (currently only a placeholder)
float average_temperature_factor(int imol)
return the average temperature factor for the atoms in imol
int dragged_refinement_steps_per_frame()
return the number of steps per frame in dragged refinement
void set_refinement_move_atoms_with_zero_occupancy(int state)
shall atoms with zero occupancy be moved when refining? (default 1, yes)
int read_shelx_ins_file(const char *filename, short int recentre_flag)
read a SHELXL .ins file
void set_symmetry_atom_labels_expanded(int state)
set use expanded symmetry atom labels
int add_extra_geman_mcclure_restraint(int imol, const char *chain_id_1, int res_no_1, const char *ins_code_1, const char *atom_name_1, const char *alt_conf_1, const char *chain_id_2, int res_no_2, const char *ins_code_2, const char *atom_name_2, const char *alt_conf_2, double bond_dist, double esd)
add a user-define GM distance restraint
SCM add_dipole_scm(int imol, const char *chain_id, int res_no, const char *ins_code)
return the dipole number
void set_mutate_auto_fit_do_post_refine(short int istate)
Do you want Coot to automatically run a refinement after every mutate and autofit?
void fill_partial_residues(int imol)
fill all the residues of molecule number imol that have missing atoms.
PyObject * rotamer_graphs_py(int imol)
Activate rotamer graph analysis for molecule number imol.
float residue_density_fit_scale_factor()
return the scale factor for the Residue Density fit analysis
int new_molecule_by_symmetry_with_atom_selection(int imol, const char *name, const char *mmdb_atom_selection_string, double m11, double m12, double m13, double m21, double m22, double m23, double m31, double m32, double m33, double tx, double ty, double tz, int pre_shift_to_origin_na, int pre_shift_to_origin_nb, int pre_shift_to_origin_nc)
create a new molecule (molecule number is the return value) from imol, but only for atom that match t...
PyObject * chain_id_for_shelxl_residue_number_py(int imol, int resno)
void do_find_ligands_dialog()
display the find ligands dialog
void residue_info_dialog(int imol, const char *chain_id, int resno, const char *ins_code)
show residue info dialog for given residue
void save_previous_map_colour(int imol)
save previous colour map for molecule number imol
void set_main_window_title(const char *s)
set the main window title.
void match_ligand_atom_names(int imol_ligand, const char *chain_id_ligand, int resno_ligand, const char *ins_code_ligand, int imol_reference, const char *chain_id_reference, int resno_reference, const char *ins_code_reference)
Match ligand atom names.
int blob_under_pointer_to_screen_centre()
Put the blob under the cursor to the screen centre. Check only positive blobs. Useful function if bou...
void graphics_to_ca_plus_ligands_representation(int imol)
draw molecule number imol as CA + ligands
int undo_symmetry_view()
Undo symmetry view. Translate back to main molecule from this symmetry position.
int is_solvent_chain_p(int imol, const char *chain_id)
is this a solvent chain? [Raw function]
int n_models(int imol)
return the number of models in molecule number imol
void lengthen_baton()
lengthen the baton
int find_strands()
autobuild strands
void setup_torsion_general(short int state)
beloved torsion general at last makes an entrance onto the Coot scene...
void set_secondary_structure_restraints_type(int itype)
set the type of secondary structure restraints
void set_auto_recontour_map(int state)
turn off (0) or on (1) auto recontouring (on screen centre change) (default it on) ...
void set_esoteric_depth_cue(int istate)
not everone likes coot's esoteric depth cueing system
void copy_residue_range_from_ncs_master_to_others(int imol, const char *master_chain_id, int residue_range_start, int residue_range_end)
Copy residue range to all related NCS chains.
void coot_clear_backup_or_real_exit(int retval)
exit coot doing clear-backup maybe
void check_for_dark_blue_density()
give a warning dialog if density it too dark (blue)
void set_draw_stick_mode_atoms_default(short int state)
set default for the drawing of atoms in stick mode (default is on (1))
void quanta_buttons()
quanta-like buttons
int read_phs_and_make_map_with_reso_limits(int imol, const char *phs_file_name, float reso_lim_low, float reso_lim_high)
read a phs file and use the cell and symm in molecule number imol and use the resolution limits reso_...
int is_nucleotide_chain_p(int imol, const char *chain_id)
is this a nucleic acid chain? [Raw function]
int watson_crick_pair_for_residue_range(int imol, const char *chain_id, int resno_start, int resno_end)
add base pairs for the given residue range, modify molecule imol by creating a new chain ...
int single_model_view_prev_model_number(int imol)
change the representation to the previous model number to be displayed
int pisa_interaction(int imol_1, int imol_2)
return the molecule number of the interacting residues. Return -1 if no new model was created...
void show_model_toolbar_main_icons()
show only a selection of icons in the modelling toolbar
PyObject * matching_compound_names_from_dictionary_py(const char *compound_name_fragment, short int allow_minimal_descriptions_flag)
return a list of compoundIDs in the dictionary which the given string is a substring of the compound ...
PyObject * ncs_ghosts_py(int imol)
Get the NCS ghosts description.
void set_model_toolbar_docked_position(int state)
to swap sides of the Model/Fit/Refine toolbar 0 (default) is right, 1 is left, 2 is top...
void set_refine_max_residues(int n)
set the heuristic fencepost for the maximum number of residues in the refinement/regularization resid...
void apply_ncs_to_view_orientation(int imol, const char *current_chain, const char *next_ncs_chain)
Given that we are in chain current_chain, apply the NCS operator that maps current_chain on to next_n...
void set_font_colour(float red, float green, float blue)
set the colour of the atom label font - the arguments are in the range 0->1
void set_baton_mode(short int i)
toggle so that mouse movement moves the baton not rotates the view.
PyObject * calculate_maps_and_stats_py(int imol_model, int imol_map_with_data_attached, int imol_map_2fofc, int imol_map_fofc)
Calculate structure factors and make a 2FoFC map and a Fo-Fc map updating the given molecule numbers ...
int set_unit_cell_and_space_group_using_molecule(int imol, int imol_from)
set the unit cell for a given model molecule using the cell of moecule imol_from
void copy_from_ncs_master_to_others(int imol, const char *chain_id)
Copy chain from master to all related NCS chains.
void set_default_bond_thickness(int t)
set the default thickness for bonds (e.g. in ~/.coot)
void set_iso_level_increment(float val)
set the contour scroll step (in absolute e/A3) for 2Fo-Fc-style maps to val
void clear_pending_picks()
clear pending picks (stop coot thinking that the user is about to pick an atom).
void set_find_ligand_here_cluster(int state)
Allow the user a scripting means to find ligand at the rotation centre.
PyObject * pucker_info_py(int imol, PyObject *residue_spec, int do_pukka_pucker_check)
return False if residue not found, otherwise [[phosphate_distance, puckered_atom, out_of_plane_distan...
void set_show_unit_cell(int imol, short int istate)
set the state of show unit cell for the particular molecule number imol
void set_edit_chi_angles_dialog_position(int x_pos, int y_pos)
set edit chi angles dialog position
void add_refmac_extra_restraints(int imol, const char *file_name)
void set_raster3d_bond_thickness(float f)
set the bond thickness for the Raster3D representation
int atom_spec_to_atom_index(int mol, char *chain, int resno, char *atom_name)
what is the atom index of the given atom?
void set_draw_cis_peptide_markups(int status)
set status of drawing cis-peptide markups
void turn_off_backup(int imol)
turn off backups for molecule number imol
void sharpen(int imol, float b_factor)
Sharpen map imol by b_factor (note (of course) that positive numbers blur the map).
void run_state_file_maybe()
run the state file depending on the state variables
void scale_zoom(float f)
scale the view by f
void set_write_conect_record_state(int state)
set the flag to write (or not) conect records to the PDB file.
void set_go_to_ligand_n_atoms_limit(int n_atom_min)
go to the ligand that has more than n_atom_min atoms
void set_font_size(int i)
set the font size
void set_ligand_search_protein_molecule(int imol)
set the protein molecule for ligand searching
void set_symmetry_colour_by_symop(int imol, int state)
set symmetry colour by symop mode
void set_browser_interface(const char *browser)
set command to open the web browser,
int clear_ball_and_stick(int imol)
clear ball and stick representation of molecule number imol
int accept_reject_dialog_docked_show_state()
what is the accept/reject dialog docked show state?
const char * molecule_name(int imol)
return the name of molecule number imol
int vt_surface_status()
return the mouse view status mode
int ideal_nucleic_acid(const char *RNA_or_DNA, const char *form, short int single_stranged_flag, const char *sequence)
create a molecule of idea nucleotides
int probe_available_p()
Can we run probe (was the executable variable set properly?) (predicate).
int make_updating_model_molecule(const char *filename)
make a model molecule from the give file name.
PyObject * get_pointer_position_frac_py()
return the [x,y] position of the pointer in fractional coordinates.
int prefer_python()
the python-prefered mode.
float get_map_weight()
return the relative weight of the geometric terms to the map terms.
int mtz_file_has_phases_p(const char *mtz_file_name)
does the mtz file have phases?
void set_rotation_centre(float x, float y, float z)
set the rotation centre
void set_contour_by_sigma_step_by_mol(float f, short int state, int imol)
set the contour level step
float get_limit_aniso()
get the aniso radius limit
float get_contour_level_in_sigma(int imol)
get the contour level in rmd above 0.
void set_residue_density_fit_scale_factor(float f)
set the scale factor for the Residue Density fit analysis
int additional_representation_by_attributes(int imol, const char *chain_id, int resno_start, int resno_end, const char *ins_code, int representation_type, int bonds_box_type, float bond_width, int draw_hydrogens_flag)
return the index of the additional representation.
void rigid_body_refine_zone(int reso_start, int resno_end, const char *chain_id, int imol)
setup rigid body refine zone
void pepflip(int imol, const char *chain_id, int resno, const char *inscode, const char *altconf)
pepflip the given residue
void save_views(const char *view_file_name)
save views to view_file_name
void set_graphics_window_position(int x_pos, int y_pos)
set the graphics window position
void handle_read_draw_probe_dots_unformatted(const char *dots_file, int imol, int show_clash_gui_flag)
pass a filename that contains molprobity's probe output in unformatted format
short int use_graphics_interface_state()
shall we start up the Gtk and the graphics window?
void set_ramachandran_psi_axis_mode(int mode)
set the psi axis for the ramachandran plot. Default (0) from -180 to 180. Alternative (1) from -120 t...
void set_rotamer_check_clashes(int i)
set a flag: 0 is off, 1 is on
void set_do_probe_dots_post_refine(short int state)
shall we run molprobity after a refinement has happened?
void baton_tip_previous()
move the baton tip to the previous position
void remove_dictionary_glob_extension(const char *ext)
remove an extension to be treated as geometry dictionary files
PyObject * symmetry_operators_py(int imol)
return a list of symmetry operators as strings - or Python False if that is not possible.
void change_contour_level(short int is_increment)
change the contour level of the current map by a step
void set_sequence_view_is_docked(short int state)
control where the sequence view is displayed
void set_colour_map_rotation_for_map(float f)
set the colour map rotation (hue change) for maps
void display_maps_scm(SCM maps_list)
maps_list is a list of integers (map molecule numbers).
void set_colour_by_chain(int imol)
colour molecule number imol by chain type
void set_raster3d_font_size(const char *size_in)
set the font size (as a string) for raster3d
void generate_self_restraints(int imol, float local_dist_max)
generate external distance all-molecule self restraints
void lsq_improve(int imol_ref, const char *ref_selection, int imol_moving, const char *moving_selection, int n_res, float dist_crit)
an slightly-modified implementation of the "lsq_improve" algorithm of Kleywegt and Jones (1997)...
int has_unit_cell_state(int imol)
molecule number imol has a unit cell?
void add_map_glob_extension(const char *ext)
add an extension to be treated as geometry map files
void coot_save_state_and_exit(int retval, int save_state_flag)
exit coot, write a state file
void set_use_variable_bond_thickness(short int state)
allow lines that are further away to be thinner
void handle_online_coot_search_request(const char *entry_text)
the search interface
int mask_map_by_atom_selection(int map_mol_no, int coords_mol_no, const char *mmdb_atom_selection, short int invert_flag)
mask map by atom selection
int add_view_here(const char *view_name)
return the view number
void delete_residue_sidechain(int imol, const char *chain_id, int resno, const char *ins_code, short int do_delete_dialog)
delete all atoms in residue that are not main chain or CB
void multi_residue_torsion_scm(int imol, SCM residues_specs_scm)
create a multi-residue torsion dialog (user manipulation of torsions)
void set_ramachandran_plot_contour_levels(float level_prefered, float level_allowed)
set the contour levels for the ramachandran plot, default values are 0.02 (prefered) 0...
void set_refinement_refine_per_frame(int istate)
allow refinement of intermediate atoms after dragging, before displaying (default: 0...
void set_bond_thickness_intermediate_atoms(float t)
set the thickness of the bonds of the intermediate atoms to t pixels
void set_symmetry_whole_chain(int imol, int state)
set symmetry colour for the chain
void set_colour_map_rotation_on_read_pdb_c_only_flag(short int i)
shall the colour map rotation apply only to C atoms?
int go_to_atom_molecule_number()
the go-to-atom molecule number
void set_auto_read_column_labels(const char *fwt, const char *phwt, int is_for_diff_map_flag)
set the expected MTZ columns for Auto-reading MTZ file.
int renumber_residue_range(int imol, const char *chain_id, int start_res, int last_res, int offset)
renumber the given residue range by offset residues
int replace_residues_from_mol_scm(int imol_target, int imol_ref, SCM residue_specs_list_ref_scm)
replace the given residues from the reference molecule to the target molecule
void set_console_display_commands_hilights(short int bold_flag, short int colour_flag, int colour_index)
set a flag to show the text command equivalent of gui commands in the console as they happen in bold ...
void graphics_to_occupancy_representation(int imol)
draw molecule number imol coloured by occupancy
void clear_all_views()
Clear the view list.
void set_ligand_acceptable_fit_fraction(float f)
set the fraction of atoms which must be in positive density after a ligand fit
void set_draw_ncs_ghosts(int imol, int istate)
set drawing state of NCS ghosts for molecule number imol
SCM view_name(int view_number)
return the name of the given view, if view_number does not specify a view return scheme value False ...
void ncs_update_ghosts(int imol)
update ghosts for molecule number imol
int handle_read_draw_molecule_and_move_molecule_here(const char *filename)
read coordinates from filename and recentre the new molecule at the screen rotation centre...
int svn_revision()
an alias to git_revision_count() for backwards compatibility
SCM ccp4i_projects_scm()
return a list of pairs of strings, the project names and the directory. Include aliases.
int het_group_n_atoms(const char *comp_id)
return the number of non-hydrogen atoms in the given het-group (comp-id).
void post_scripting_window()
do nothing - compatibility function
void set_diff_map_iso_level_increment_from_text(const char *text, int imol)
set the difference maps iso-map level increment
void set_scrollable_map(int imol)
return the molecule number to which the mouse scroll wheel is attached
int display_lists_for_maps_state()
return the state of display_lists_for_maps.
int first_coords_imol()
What is the molecule number of first coordinates molecule?
void set_refinement_drag_elasticity(float e)
the elasticity of the dragged atom in refinement mode.
SCM select_atom_under_pointer_scm()
return scheme false or a list of molecule number and an atom spec
SCM cis_peptides(int imol)
return cis_peptide info for imol.
void set_aniso_probability(float f)
set aniso probability
void set_add_ccp4i_projects_to_file_dialogs(short int state)
allow the user to not add ccp4i directories to the file choosers
int smooth_scroll_do_zoom()
return the state of the above system
void save_state()
save the current state to the default filename
float density_at_point(int imol_map, float x, float y, float z)
return the density at the given point for the given map. Return 0 for bad imol
void allow_duplicate_sequence_numbers()
enable reading PDB/pdbx files with duplicate sequence numbers
void do_smiles_gui()
display the SMILES string dialog
SCM rotamer_graphs(int imol)
Activate rotamer graph analysis for molecule number imol.
void set_control_key_for_rotate(int state)
Alternate mode for rotation.
int suck_model_fit_dialog()
reparent the Model/Fit/Refine dialog so that it becomes part of the main window, next to the GL graph...
void set_draw_crosshairs(short int i)
draw the distance crosshairs, 0 for off, 1 for on.
void gln_asn_b_factor_outliers(int imol)
Make a gui for GLN adn ASN B-factor outiers, compairing the O and N temperatur factors difference to ...
int auto_read_do_difference_map_too_state()
return the flag to do a difference map (too) on auto-read MTZ
int use_only_extra_torsion_restraints_for_torsions_state()
return only-use-extra-torsion-restraints-for-torsions state
void do_sequence_view(int imol)
display the sequence view dialog for molecule number imol
void assign_fasta_sequence(int imol, const char *chain_id_in, const char *seq)
Assign a FASTA sequence to a given chain in the molecule.
float refine_ramachandran_restraints_weight()
void set_socket_python_string_waiting(const char *s)
feed the main thread a python script to evaluate
void set_map_sampling_rate_text(const char *text)
sampling rate
void restore_previous_map_colour(int imol)
restore previous colour map for molecule number imol
float get_diff_map_iso_level_increment()
return difference maps iso-map level increment
void delete_chain(int imol, const char *chain_id)
delete the chain
int get_reset_b_factor_moved_atoms_state()
return the state if temperature factors shoudl be reset for moved atoms
void sort_chains(int imol)
sort the chain ids of the imol-th molecule in lexographical order
int apply_undo()
apply undo - the "Undo" button callback
void info_dialog_and_text(const char *txt)
create a dialog with information and print to console
void set_raster3d_shadows_enabled(int state)
turn off shadows for raster3d output - give argument 0 to turn off
int write_pdb_file(int imol, const char *file_name)
write molecule number imol as a PDB to file file_name
void set_refmac_counter(int imol, int refmac_count)
set counter for runs of refmac so that this can be used to construct a unique filename for new output...
std::string mtz_file_name(int imol)
presumes that imol_Refinement_Map has been set
float fit_chain_to_map_by_random_jiggle_and_blur(int imol, const char *chain_id, int n_trials, float jiggle_scale_factor, float map_blur_factor)
jiggle fit the chain to the current refinment map
void graphics_to_bonds_representation(int mol)
draw molecule number imol with normal bonds
void set_draw_zero_occ_markers(int status)
set status of drawing zero occupancy markers.
void place_strand_here_dialog()
show the strand placement gui.
void graphics_to_b_factor_representation(int imol)
draw molecule number imol coloured by B-factor
void show_modelling_toolbar()
show the vertical modelling toolbar in the GTK2 version (the toolbar is shown by default) ...
short int get_show_limit_aniso()
get show the aniso limit
int n_symops(int imol)
return the number of symmetry operators for the given molecule
void delete_extra_restraints_for_residue(int imol, const char *chain_id, int res_no, const char *ins_code)
clear out all the extra/user-defined restraints for this residue in molecule number imol ...
int make_and_draw_map_with_refmac_params(const char *mtz_file_name, const char *a, const char *b, const char *weight, int use_weights, int is_diff_map, short int have_refmac_params, const char *fobs_col, const char *sigfobs_col, const char *r_free_col, short int sensible_f_free_col)
as the above function, execpt set refmac parameters too
int get_ccp4srs_monomer_and_dictionary(const char *comp_id)
return the new molecule number of the monomer.
void fle_view_set_h_bond_dist_max(float h_bond_dist_max)
set the maximum considered hydrogen bond distance
void read_phs_and_coords_and_make_map(const char *pdb_filename)
read phs file use coords to get cell and symm to make map
void delete_residue_range(int imol, const char *chain_id, int resno_start, int end_resno)
delete residue range
void set_show_graphics_ligand_view(int state)
set the graphics ligand view state
void superpose_with_chain_selection(int imol1, int imol2, const char *chain_imol1, const char *chain_imol2, int chain_used_flag_imol1, int chain_used_flag_imol2, short int move_imol2_copy_flag)
chain-based interface to superposition.
int show_paths_in_display_manager_state()
return the internal state
void delete_atom(int imol, const char *chain_id, int resno, const char *ins_code, const char *at_name, const char *altloc)
delete atom in residue
void add_ligand_search_wiggly_ligand_molecule(int imol_ligand)
add a flexible ligand molecule to the list of ligands to search for in ligand searching ...
float fit_chain_to_map_by_random_jiggle(int imol, const char *chain_id, int n_trials, float jiggle_scale_factor)
jiggle fit the chain to the current refinment map. return < -100 if not possible, else return the new...
void set_stop_scroll_iso_map(int i)
create a lower limit to the "2Fo-Fc-style" map contour level changing
double add_geometry_distance(int imol_1, float x_1, float y_1, float z_1, int imol_2, float x_2, float y_2, float z_2)
Add a geometry distance between points in a given molecule.
int additional_representation_by_string(int imol, const char *atom_selection, int representation_type, int bonds_box_type, float bond_width, int draw_hydrogens_flag)
return the index of the additional representation. Return -1 on error
PyObject * origin_pre_shift_py(int imol)
return the pre-shift (the shift that translates the centre of the molecule as close as possible to th...
void graphics_to_ca_representation(int imol)
draw molecule number imol as CAs
void graphics_draw()
draw a frame
void set_show_environment_distances_h_bonds(int state)
show H-bond environment distances. If state is 0, bump distances are turned off, otherwise H-bond dis...
void set_refine_hydrogen_bonds(int state)
add or remove auto H-bond restraints
int get_smooth_scroll()
return the smooth scrolling state
void screendump_image(const char *filename)
dump the current screen image to a file. Format ppm
void fleur_cursor()
fleur cursor
PyObject * add_dipole_for_residues_py(int imol, PyObject *residue_specs)
add a dipole given a set of residues. Return a dipole description.
void ncs_control_change_ncs_master_to_chain(int imol, int ichain)
change the NCS master chain (by number)
void set_keep_map_colour_after_refmac(int istate)
flag to enable above
PyObject * add_target_position_restraint_for_intermediate_atom_py(PyObject *atom_spec, PyObject *position)
add a target position for an intermediate atom and refine
void quanta_like_zoom()
quanta-like zoom buttons
int make_masked_maps_split_by_chain(int imol, int imol_map)
make chain masked maps
int skeletonize_map(int imol, short int prune_flag)
skeletonize molecule number imol
void set_default_initial_contour_level_for_difference_map(float n_sigma)
set the default inital contour for FoFc-style map
void delete_checked_waters_baddies(int imol, float b_factor_lim, float map_sigma_lim, float min_dist, float max_dist, short int part_occ_contact_flag, short int zero_occ_flag, short int logical_operator_and_or_flag)
Delete waters that are fail to meet the given criteria.
const char * mtz_hklin_for_map(int imol_map)
return the mtz file that was use to generate the map
void swap_map_colours(int imol1, int imol2)
swap the colours of maps
PyObject * ccp4i_projects_py()
return a list of pairs of strings, the project names and the directory. Include aliases.
SCM alignment_mismatches_scm(int imol)
do a internal alignment of all the assigned sequences, return a list of mismatches that need to be ma...
SCM ncs_master_chains_scm(int imol)
Copy residue range to selected NCS chains.
int make_and_draw_map_with_reso_with_refmac_params(const char *mtz_file_name, const char *a, const char *b, const char *weight, int use_weights, int is_diff_map, short int have_refmac_params, const char *fobs_col, const char *sigfobs_col, const char *r_free_col, short int sensible_f_free_col, short int is_anomalous, short int use_reso_limits, float low_reso_limit, float high_reso_lim)
as the above function, except set expert options too.
int new_molecule_by_residue_type_selection(int imol, const char *residue_type)
create a new molecule that consists of only the residue of type residue_type in molecule number imol ...
void unset_sticky_sort_by_date()
do not sort files in the file selection by date?
int mask_map_by_molecule(int map_mol_no, int coord_mol_no, short int invert_flag)
generate a new map that has been masked by some coordinates
void set_show_strict_ncs(int imol, int state)
set display state of NCS ghost molecules for molecule number imol
void set_clipping_front(float v)
set clipping plane front
float score_residue_range_fit_to_map(int res1, int res2, char *altloc, char *chain_id, int imol, int imol_for_map)
simply score the residue range fit to map
int export_map_fragment(int imol, float x, float y, float z, float radius, const char *filename)
export a fragment of the map about (x,y,z)
void clear_dots(int imol, int dots_handle)
clear dots in imol with dots_handle
int graphics_molecule_bond_type(int imol)
what is the bond drawing state of molecule number imol
void rotate_x_scene(int nsteps, float stepsize)
rotate view round x axis stepsize degrees for nstep such steps
PyObject * ncs_chain_ids_py(int imol)
Return the ncs chains id for the given molecule.
float data_resolution(int imol)
return the resolution of the data for molecule number imol. Return negative number on error...
SCM chain_id_scm(int imol, int ichain)
the chain_id (string) of the ichain-th chain molecule number imol
int graphics_n_molecules()
return the number of molecules (coordinates molecules and map molecules combined) that are currently ...
void translate_molecule_by(int imol, float x, float y, float z)
translate molecule number imol by (x,y,z) in Angstroms
int show_strict_ncs_state(int imol)
return the state of NCS ghost molecules for molecule number imol
SCM pucker_info_scm(int imol, SCM residue_spec, int do_pukka_pucker_check)
get the pucker info for the specified residue
int watson_crick_pair(int imol, const char *chain_id, int resno)
Return a molecule that contains a residue that is the WC pair partner of the clicked/picked/selected ...
int add_action_view(const char *view_name, const char *action_function)
add a view (not add to an existing view) that does something (e.g. displays or undisplays a molecule)...
void delete_residue(int imol, const char *chain_id, int resno, const char *inscode)
delete residue
PyObject * view_name_py(int view_number)
return the name of the given view, if view_number does not specify a view return Python value False ...
void output_atom_info_as_text(int imol, const char *chain_id, int resno, const char *ins_code, const char *atname, const char *altconf)
output to the terminal the Atom Info for the give atom specs
int write_residue_range_to_pdb_file(int imol, const char *chainid, int resno_start, int resno_end, const char *filename)
write molecule number imol's residue range as a PDB to file file_name
PyObject * cell_py(int imol)
return the parameter that made the map,
float standard_deviation_temperature_factor(int imol)
return the standard deviation of the atom temperature factors for imol
float zoom_factor()
return the current zoom factor
int laplacian(int imol)
Create the "Laplacian" (-ve second derivative) of the given map.
