import coot_utils import coot_gui_api from gi.repository import Gtk import coot import gi gi.require_version('Gtk', '4.0') import coot_gui def res_name_from_atom_spec(atom_spec): imol = atom_spec[1] res_name = coot.residue_name(imol, atom_spec[2], atom_spec[3], atom_spec[4]) return res_name def user_defined_add_single_bond_restraint(): m = "Click on 2 atoms to define the additional bond restraint" coot.add_status_bar_text(m) def make_restr(*args): atom_spec_1 = args[0] atom_spec_2 = args[1] imol = atom_spec_1[1] print("BL DEBUG:: imol: %s spec 1: %s and 2: %s" % (imol, atom_spec_1, atom_spec_2)) coot.add_extra_bond_restraint(imol, atom_spec_1[2], atom_spec_1[3], atom_spec_1[4], atom_spec_1[5], atom_spec_1[6], atom_spec_2[2], atom_spec_2[3], atom_spec_2[4], atom_spec_2[5], atom_spec_2[6], 1.54, 0.02) # generic distance?! coot.user_defined_click_py(2, make_restr) def user_defined_add_arbitrary_length_bond_restraint(bond_length=2.0): # maybe make a generic one.... def make_restr(text_list, continue_qm): s = "Now click on 2 atoms to define the additional bond restraint" coot.add_status_bar_text(s) dist = text_list[0] try: bl = float(dist) except: bl = False coot.add_status_bar_text( "Must define a number for the bond length") if bl: # save distance for future use?! def make_restr_dist(*args): atom_spec_1 = args[0] atom_spec_2 = args[1] imol = atom_spec_1[1] print("BL DEBUG:: imol: %s spec 1: %s and 2: %s" % (imol, atom_spec_1, atom_spec_2)) coot.add_extra_bond_restraint(imol, atom_spec_1[2], atom_spec_1[3], atom_spec_1[4], atom_spec_1[5], atom_spec_1[6], atom_spec_2[2], atom_spec_2[3], atom_spec_2[4], atom_spec_2[5], atom_spec_2[6], bl, 0.035) coot.user_defined_click(2, make_restr_dist) if continue_qm: user_defined_add_arbitrary_length_bond_restraint(bl) def stay_open(*args): pass # generic_single_entry("Add a User-defined extra distance restraint", # "2.0", # "OK...", # lambda text: make_restr(text)) coot_gui.generic_multiple_entries_with_check_button( [["Add a User-defined extra distance restraint", str(bond_length)]], ["Stay open?", lambda active_state: stay_open(active_state)], "OK...", lambda text, stay_open_qm: make_restr(text, stay_open_qm)) # spec_1 and spec_2 are 7-element coot_utils.atom_specs # def add_base_restraint(imol, spec_1, spec_2, atom_name_1, atom_name_2, dist): """ spec_1 and spec_2 are 7-element coot_utils.atom_specs """ print("add_base_restraint", imol, spec_1, spec_2, atom_name_1, atom_name_2, dist) coot.add_extra_bond_restraint(imol, spec_1[2], spec_1[3], spec_1[4], atom_name_1, spec_1[6], spec_2[2], spec_2[3], spec_2[4], atom_name_2, spec_2[6], dist, 0.035) def a_u_restraints(spec_1, spec_2): imol = spec_1[1] print("BL DEBUG:: add_base_restraint a u", imol, spec_1, spec_2, " N6 ", " O4 ", 3.12) add_base_restraint(imol, spec_1, spec_2, " N6 ", " O4 ", 3.12) add_base_restraint(imol, spec_1, spec_2, " N1 ", " N3 ", 3.05) add_base_restraint(imol, spec_1, spec_2, " C2 ", " O2 ", 3.90) add_base_restraint(imol, spec_1, spec_2, " N3 ", " O2 ", 5.12) add_base_restraint(imol, spec_1, spec_2, " C6 ", " O4 ", 3.92) add_base_restraint(imol, spec_1, spec_2, " C4 ", " C6 ", 8.38) def g_c_restraints(spec_1, spec_2): imol = spec_1[1] print("BL DEBUG:: add_base_restraint gc", imol, spec_1, spec_2, " O6 ", " N4 ", 3.08) add_base_restraint(imol, spec_1, spec_2, " N6 ", " O4 ", 3.12) add_base_restraint(imol, spec_1, spec_2, " N1 ", " N3 ", 3.04) add_base_restraint(imol, spec_1, spec_2, " N2 ", " O2 ", 3.14) add_base_restraint(imol, spec_1, spec_2, " C4 ", " N1 ", 7.73) add_base_restraint(imol, spec_1, spec_2, " C5 ", " C5 ", 7.21) def dna_a_t_restraints(spec_1, spec_2): imol = spec_1[1] add_base_restraint(imol, spec_1, spec_2, " C2 ", " O2 ", 3.49) add_base_restraint(imol, spec_1, spec_2, " N1 ", " N3 ", 2.85) add_base_restraint(imol, spec_1, spec_2, " N6 ", " O4 ", 3.23) add_base_restraint(imol, spec_1, spec_2, " C6 ", " C8 ", 9.94) add_base_restraint(imol, spec_1, spec_2, " N1 ", " O2 ", 3.52) def dna_g_c_restraints(spec_1, spec_2): imol = spec_1[1] add_base_restraint(imol, spec_1, spec_2, " O6 ", " N4 ", 2.72) add_base_restraint(imol, spec_1, spec_2, " N1 ", " N3 ", 2.81) add_base_restraint(imol, spec_1, spec_2, " N2 ", " O2 ", 2.83) add_base_restraint(imol, spec_1, spec_2, " N9 ", " N1 ", 8.83) def user_defined_RNA_A_form(): def make_restr(*args): spec_1 = args[0] spec_2 = args[1] print("BL DEBUG:: have specs", spec_1, spec_2) res_name_1 = res_name_from_atom_spec(spec_1) res_name_2 = res_name_from_atom_spec(spec_2) print("BL DEBUG:: have resnames", res_name_1, res_name_2) # just check the first letter, should be save if (res_name_1[0] == "G" and res_name_2[0] == "C"): g_c_restraints(spec_1, spec_2) if (res_name_1[0] == "C" and res_name_2[0] == "G"): g_c_restraints(spec_2, spec_1) if (res_name_1[0] == "A" and res_name_2[0] == "U"): a_u_restraints(spec_1, spec_2) if (res_name_1[0] == "U" and res_name_2[0] == "A"): a_u_restraints(spec_2, spec_1) coot.user_defined_click_py(2, make_restr) def user_defined_DNA_B_form(): def make_restr(*args): spec_1 = args[0] spec_2 = args[1] res_name_1 = res_name_from_atom_spec(spec_1) res_name_2 = res_name_from_atom_spec(spec_2) if (res_name_1 == "DG" and res_name_2 == "DC"): dna_g_c_restraints(spec_1, spec_2) if (res_name_1 == "DC" and res_name_2 == "DG"): dna_g_c_restraints(spec_2, spec_1) if (res_name_1 == "DA" and res_name_2 == "DT"): dna_a_t_restraints(spec_1, spec_2) if (res_name_1 == "DT" and res_name_2 == "DA"): dna_a_t_restraints(spec_2, spec_1) coot.user_defined_click_py(2, make_restr) def user_defined_add_helix_restraints(): def make_restr(*args): spec_1 = args[0] spec_2 = args[1] chain_id_1 = spec_1[2] chain_id_2 = spec_2[2] res_no_1 = spec_1[3] res_no_2 = spec_2[3] imol = spec_1[1] if (chain_id_1 == chain_id_2): # if backwards, swap 'em if res_no_2 < res_no_1: tmp = res_no_1 res_no_1 = res_no_2 res_no_2 = tmp for rn in range(res_no_1, res_no_2 - 2): coot.add_extra_bond_restraint(imol, chain_id_1, rn, "", " O ", "", chain_id_1, rn + 3, "", " N ", "", 3.18, 0.035) if (rn + 4 <= res_no_2): coot.add_extra_bond_restraint(imol, chain_id_1, rn, "", " O ", "", chain_id_1, rn + 4, "", " N ", "", 2.91, 0.035) coot.user_defined_click_py(2, make_restr) def user_defined_delete_restraint(): def del_restr(*args): spec_1 = args[0] spec_2 = args[1] imol = spec_1[1] coot.delete_extra_restraint_py(imol, ["bond", spec_1[2:], spec_2[2:]]) coot.user_defined_click_py(2, del_restr) # exte dist first chain A resi 19 ins . atom N second chain A resi 19 ins . atom OG value 2.70618 sigma 0.4 # def extra_restraints2refmac_restraints_file(imol, file_name): restraints = list_extra_restraints(imol) if restraints: fin = open(file_name, 'w') for restraint in restraints: if (restraint[0] == 'bond'): chain_id_1 = restraint[1][1] resno_1 = restraint[1][2] inscode_1 = restraint[1][3] atom_1 = restraint[1][4] chain_id_2 = restraint[2][1] resno_2 = restraint[2][2] inscode_2 = restraint[2][3] atom_2 = restraint[2][4] value = restraint[3] esd = restraint[4] fin.write("EXTE DIST FIRST CHAIN %s RESI %i INS %s ATOM %s " % (chain_id_1 if (chain_id_1 != "" and chain_id_1 != " ") else ".", resno_1, inscode_1 if ( inscode_1 != "" and inscode_1 != " ") else ".", atom_1)) fin.write(" SECOND CHAIN %s RESI %i INS %s ATOM %s " % (chain_id_2 if (chain_id_2 != "" and chain_id_2 != " ") else ".", resno_2, inscode_2 if ( inscode_2 != "" and inscode_2 != " ") else ".", atom_2)) fin.write("VALUE %f SIGMA %f\n" % (value, esd)) fin.close() def res_name2plane_atom_name_list(res_name): if not (isinstance(res_name, str)): return False else: if (res_name == "DG"): return ["N1", "C6", "O6", "C2", "N2", "N3", "C5", "C4", "N9", "N7", "C8", "C1'"] elif (res_name == "DA"): return ["N1", "C6", "C2", "N6", "N3", "C5", "C4", "N9", "N7", "C8", "C1'"] elif (res_name == "DT"): return ["N3", "C2", "O2", "C4", "O4", "C5", "C7", "C6", "N1", "C1'"] elif (res_name == "DC"): return ["N3", "C2", "O2", "C4", "N4", "C5", "C6", "N1", "C1'"] elif (res_name == "G"): return ["N1", "C6", "O6", "C2", "N2", "N3", "C5", "C4", "N9", "N7", "C8", "C1'"] elif (res_name == "A"): return ["N1", "C6", "C2", "N6", "N3", "C5", "C4", "N9", "N7", "C8", "C1'"] elif (res_name == "T"): return ["N3", "C2", "O2", "C4", "O4", "C5", "C7", "C6", "N1", "C1'"] elif (res_name == "U"): return ["N3", "C2", "O2", "C4", "O4", "C5", "C6", "N1", "C1'"] elif (res_name == "C"): return ["N3", "C2", "O2", "C4", "N4", "C5", "C6", "N1", "C1'"] else: return [] # example? # exte stac plan 1 firs resi 99 chai A atoms { CB CG CD1 CD2 CE1 CE2 CZ OH } plan 2 firs resi 61 chai B atoms { CB CG CD1 CD2 CE1 CE2 CZ } dist 3.4 sddi 0.2 sdan 6.0 type 1 # def write_refmac_parallel_plane_restraint(file_name, res_spec_0, res_spec_1, atom_list_0, atom_list_1): fout = open(file_name, 'w') fout.write("EXTE STACK PLAN 1 FIRST RESIDUE ") fout.write(str(coot_utils.residue_spec_to_res_no(res_spec_0))) fout.write(" INS . ") # hack fout.write(" CHAIN ") fout.write(coot_utils.residue_spec_to_chain_id(res_spec_0)) fout.write(" ATOMS { ") for atom_name in atom_list_0: fout.write(" " + atom_name + " ") fout.write(" } PLAN 2 FIRST RESIDUE ") fout.write(str(coot_utils.residue_spec_to_res_no(res_spec_1))) fout.write(" INS . ") # hack fout.write(" CHAIN ") fout.write(coot_utils.residue_spec_to_chain_id(res_spec_1)) fout.write(" ATOMS { ") for atom_name in atom_list_1: fout.write(" " + atom_name + " ") fout.write(" } DIST 3.4 SDDI 0.2 SDAN 6.0 TYPE 1 \n") fout.close() # maybe some return value that it worked to write at some point def add_parallel_planes_restraint(imol, rs_0, rs_1): print("in add_parallel_planes_restraint: rs_0: %s rs_1 %s" % (rs_0, rs_1)) rn_0 = coot_utils.residue_spec_to_residue_name(imol, rs_0) rn_1 = coot_utils.residue_spec_to_residue_name(imol, rs_1) atom_ls_0 = res_name2plane_atom_name_list(rn_0) atom_ls_1 = res_name2plane_atom_name_list(rn_1) write_refmac_parallel_plane_restraint( "tmp.rst", rs_0, rs_1, atom_ls_0, atom_ls_1) coot.add_refmac_extra_restraints(imol, "tmp.rst") def user_defined_add_planes_restraint(): coot.add_status_bar_text( "Click on 2 atoms to define the additional parallel planes restraint") def make_restr(*args): atom_0 = args[0] atom_1 = args[1] rs_0 = coot_utils.atom_spec_to_residue_spec(atom_0) rs_1 = coot_utils.atom_spec_to_residue_spec(atom_1) imol = coot_utils.atom_spec_to_imol(atom_0) rn_0 = coot.residue_name(imol, res_spec_utils.residue_spec_to_chain_id( coot_utils.atom_spec_to_residue_spec(atom_0)), res_spec_utils.residue_spec_to_res_no( coot_utils.atom_spec_to_residue_spec(atom_0)), coot_utils.residue_spec_to_ins_code(coot_utils.atom_spec_to_residue_spec(atom_0))) rn_1 = coot.residue_name(imol, res_spec_utils.residue_spec_to_chain_id( coot_utils.atom_spec_to_residue_spec(atom_1)), res_spec_utils.residue_spec_to_res_no( coot_utils.atom_spec_to_residue_spec(atom_1)), coot_utils.residue_spec_to_ins_code(coot_utils.atom_spec_to_residue_spec(atom_1))) print("BL DEBUG:: got resname 0", rn_0) print("BL DEBUG:: got resname 1", rn_1) atom_ls_0 = res_name2plane_atom_name_list(rn_0) atom_ls_1 = res_name2plane_atom_name_list(rn_1) write_refmac_parallel_plane_restraint("tmp.rst", rs_0, rs_1, atom_ls_0, atom_ls_1) coot.add_refmac_extra_restraints(imol, "tmp.rst") coot.user_defined_click_py(2, make_restr) if True: if coot_gui_api.main_menubar(): menu = coot_gui.coot_menubar_menu("Restraints") coot_gui.add_simple_coot_menu_menuitem( menu, "Add Simple C-C Single Bond Restraint...", lambda func: user_defined_add_single_bond_restraint()) coot_gui.add_simple_coot_menu_menuitem( menu, "Add Distance Restraint...", lambda func: user_defined_add_arbitrary_length_bond_restraint()) coot_gui.add_simple_coot_menu_menuitem( menu, "Add Helix Restraints...", lambda func: user_defined_add_helix_restraints()) coot_gui.add_simple_coot_menu_menuitem( menu, "RNA A form bond restraints...", lambda func: user_defined_RNA_A_form()) coot_gui.add_simple_coot_menu_menuitem( menu, "DNA B form bond restraints...", lambda func: user_defined_DNA_B_form()) def combobox_to_molecule_number(combobox): imol = -1 tree_iter = combobox.get_active_iter() if tree_iter is not None: model = combobox.get_model() it = model[tree_iter] imol = it[0] return imol coot_gui.add_simple_coot_menu_menuitem( menu, "Read Refmac Extra Restraints...", lambda func: coot_gui.generic_chooser_and_file_selector("Apply restraints to molecule", coot_utils.valid_model_molecule_qm, "File:", "", lambda imol, file_name: coot.add_refmac_extra_restraints(imol, file_name))) coot_gui.add_simple_coot_menu_menuitem( menu, "Delete Extra Restraints...", lambda func: coot_gui.molecule_chooser_gui("Delete Extra Restraints for Molecule:", lambda imol: coot.delete_all_extra_restraints(imol))) def set_prosmart_sigma_limit_func(low, high): with coot_utils.UsingActiveAtom() as [aa_imol, aa_chain_id, aa_res_no, aa_ins_code, aa_atom_name, aa_alt_conf]: coot.set_extra_restraints_prosmart_sigma_limits( aa_imol, low, high) # coot_gui.add_simple_coot_menu_menuitem( # menu, # "ProSMART restraints interesting limit to 0.5...", # lambda func: set_prosmart_sigma_limit_func(-0.5, 0.5) # ) # coot_gui.add_simple_coot_menu_menuitem( # menu, # "ProSMART restraints interesting limit to 2.5...", # lambda func: set_prosmart_sigma_limit_func(-2.5, 2.5) # ) # def set_extra_restraints_display_func(state): # with coot_utils.UsingActiveAtom() as [aa_imol, aa_chain_id, aa_res_no, # aa_ins_code, aa_atom_name, aa_alt_conf]: # coot.set_show_extra_restraints(aa_imol, state) # coot_gui.add_simple_coot_menu_menuitem( # menu, # "Undisplay Extra Restraints", # lambda func: set_extra_restraints_display_func(0)) # coot_gui.add_simple_coot_menu_menuitem( # menu, # "Display Extra Restraints", # lambda func: set_extra_restraints_display_func(1)) # def set_prosmart_display_CA_func(state): # with coot_utils.UsingActiveAtom() as [aa_imol, aa_chain_id, aa_res_no, # aa_ins_code, aa_atom_name, aa_alt_conf]: # coot.set_extra_restraints_representation_for_bonds_go_to_CA( # aa_imol, state) # ProSMART menu item - but who needs it? # coot_gui.add_simple_coot_menu_menuitem( # menu, # "Extra Restraints to CA", # lambda func: set_prosmart_display_CA_func(1)) coot_gui.add_simple_coot_menu_menuitem( menu, "Extra Restraints Standard Representation", lambda func: set_prosmart_display_CA_func(0)) coot_gui.add_simple_coot_menu_menuitem( menu, "Delete an Extra Restraint...", lambda func: user_defined_delete_restraint()) def delete_restraints_func(): with coot_utils.UsingActiveAtom() as [aa_imol, aa_chain_id, aa_res_no, aa_ins_code, aa_atom_name, aa_alt_conf]: coot.delete_extra_restraints_for_residue( aa_imol, aa_chain_id, aa_res_no, aa_ins_code) coot_gui.add_simple_coot_menu_menuitem( menu, "Delete Restraints for this residue", lambda func: delete_restraints_func() ) def del_deviant_restr_func(text): try: n = float(text) with coot_utils.UsingActiveAtom() as [aa_imol, aa_chain_id, aa_res_no, aa_ins_code, aa_atom_name, aa_alt_conf]: coot.delete_extra_restraints_worse_than(aa_imol, n) except: print("BL WARNING:: no float given") coot_gui.add_simple_coot_menu_menuitem( menu, "Delete Deviant Extra Restraints...", lambda func: coot_gui.generic_single_entry("Delete Restraints worse than ", "4.0", " Delete Outlying Restraints ", lambda text: del_deviant_restr_func(text)) ) coot_gui.add_simple_coot_menu_menuitem( menu, "Save as REFMAC restraints...", lambda func: coot_gui.generic_chooser_and_file_selector("Save REFMAC restraints for molecule", coot_utils.valid_model_molecule_qm, " Restraints file name: ", "refmac-restraints.txt", lambda imol, file_name: extra_restraints2refmac_restraints_file(imol, file_name))) coot_gui.add_simple_coot_menu_menuitem( menu, "Add Parallel Planes Restraint...", lambda func: user_defined_add_planes_restraint() )