def res_name_from_atom_spec(atom_spec): imol = atom_spec[1] res_name = residue_name(imol, atom_spec[2], atom_spec[3], atom_spec[4]) return res_name def user_defined_add_single_bond_restraint(): add_status_bar_text("Click on 2 atoms to define the additional bond restraint") 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) 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?! user_defined_click(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" add_status_bar_text(s) dist = text_list[0] try: bl = float(dist) except: bl = False 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) 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) 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)) 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 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 atom_specs """ print "add_base_restraint", imol, spec_1, spec_2, atom_name_1, atom_name_2, dist 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) user_defined_click(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) user_defined_click(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): 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): add_extra_bond_restraint(imol, chain_id_1, rn , "", " O ", "", chain_id_1, rn + 4, "", " N ", "", 2.91, 0.035) user_defined_click(2, make_restr) def user_defined_delete_restraint(): def del_restr(*args): spec_1 = args[0] spec_2 = args[1] imol = spec_1[1] delete_extra_restraint(imol, ["bond", spec_1[2:], spec_2[2:]]) user_defined_click(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() # target is my molecule, ref is the homologous (high-res) model # # extra arg: include_side_chains=False # def run_prosmart(imol_target, imol_ref, include_side_chains=False): """ target is my molecule, ref is the homologous (high-res) model extra arg: include_side_chains=False """ dir_stub = "coot-ccp4" make_directory_maybe(dir_stub) target_pdb_file_name = os.path.join(dir_stub, molecule_name_stub(imol_target, 0).replace(" ", "_") + \ "-prosmart.pdb") reference_pdb_file_name = os.path.join(dir_stub, molecule_name_stub(imol_ref, 0).replace(" ", "_") + \ "-prosmart-ref.pdb") prosmart_out = os.path.join("ProSMART_Output", molecule_name_stub(imol_target, 0).replace(" ", "_") + \ "-prosmart.txt") write_pdb_file(imol_target, target_pdb_file_name) write_pdb_file(imol_ref, reference_pdb_file_name) prosmart_exe = find_exe("prosmart") if prosmart_exe: l = ["-p1", target_pdb_file_name, "-p2", reference_pdb_file_name] if include_side_chains: l += ["-side"] popen_command(prosmart_exe, l, [], os.path.join(dir_stub, "prosmart.log"), False) if (not os.path.isfile(prosmart_out)): print "file not found", prosmart_out else: print "Reading ProSMART restraints from", prosmart_out add_refmac_extra_restraints(imol_target, prosmart_out) 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(residue_spec2res_no(res_spec_0))) fout.write(" CHAIN ") fout.write(residue_spec2chain_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(residue_spec2res_no(res_spec_1))) fout.write(" CHAIN ") fout.write(residue_spec2chain_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 = residue_spec2residue_name(imol, rs_0) rn_1 = residue_spec2residue_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) add_refmac_extra_restraints(imol, "tmp.rst") def user_defined_add_planes_restraint(): 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 = atom_spec2residue_spec(atom_0) rs_1 = atom_spec2residue_spec(atom_1) imol = atom_spec2imol(atom_0) rn_0 = residue_name(imol, residue_spec2chain_id(atom_spec2residue_spec(atom_0)), residue_spec2res_no(atom_spec2residue_spec(atom_0)), residue_spec2ins_code(atom_spec2residue_spec(atom_0))) rn_1 = residue_name(imol, residue_spec2chain_id(atom_spec2residue_spec(atom_1)), residue_spec2res_no(atom_spec2residue_spec(atom_1)), residue_spec2ins_code(atom_spec2residue_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) add_refmac_extra_restraints(imol, "tmp.rst") user_defined_click(2, make_restr) if (have_coot_python): if coot_python.main_menubar(): menu = coot_menubar_menu("Restraints") add_simple_coot_menu_menuitem( menu, "Add Simple C-C Single Bond Restraint...", lambda func: user_defined_add_single_bond_restraint()) add_simple_coot_menu_menuitem( menu, "Add Distance Restraint...", lambda func: user_defined_add_arbitrary_length_bond_restraint()) add_simple_coot_menu_menuitem( menu, "Add Helix Restraints...", lambda func: user_defined_add_helix_restraints()) add_simple_coot_menu_menuitem( menu, "RNA A form bond restraints...", lambda func: user_defined_RNA_A_form()) add_simple_coot_menu_menuitem( menu, "DNA B form bond restraints...", lambda func: user_defined_DNA_B_form()) def launch_prosmart_gui(): def go_button_cb(*args): imol_tar = get_option_menu_active_molecule(*option_menu_mol_list_pair_tar) imol_ref = get_option_menu_active_molecule(*option_menu_mol_list_pair_ref) do_side_chains = check_button.get_active() run_prosmart(imol_tar, imol_ref, do_side_chains) window.destroy() window = gtk.Window(gtk.WINDOW_TOPLEVEL) hbox = gtk.HBox(False, 0) vbox = gtk.VBox(False, 0) h_sep = gtk.HSeparator() chooser_hint_text_1 = " Target molecule " chooser_hint_text_2 = " Reference (high-res) molecule " go_button = gtk.Button(" ProSMART ") cancel_button = gtk.Button(" Cancel ") check_button = gtk.CheckButton("Include Side-chains") option_menu_mol_list_pair_tar = generic_molecule_chooser(vbox, chooser_hint_text_1) option_menu_mol_list_pair_ref = generic_molecule_chooser(vbox, chooser_hint_text_2) vbox.pack_start(check_button, False, False, 2) vbox.pack_start(h_sep, False, False, 2) vbox.pack_start(hbox, False, False, 2) hbox.pack_start(go_button, False, False, 6) hbox.pack_start(cancel_button, False, False, 6) window.add(vbox) cancel_button.connect("clicked", lambda w: window.destroy()) go_button.connect("clicked", go_button_cb, option_menu_mol_list_pair_tar, option_menu_mol_list_pair_ref) window.show_all() add_simple_coot_menu_menuitem( menu, "ProSMART...", lambda func: launch_prosmart_gui() ) add_simple_coot_menu_menuitem( menu, "Read Refmac Extra Restraints...", lambda func: generic_chooser_and_file_selector("Apply restraints to molecule", valid_model_molecule_qm, "File:", "", lambda imol, file_name: add_refmac_extra_restraints(imol, file_name))) def set_prosmart_sigma_limit_func(low, high): with UsingActiveAtom() as [aa_imol, aa_chain_id, aa_res_no, aa_ins_code, aa_atom_name, aa_alt_conf]: set_extra_restraints_prosmart_sigma_limits(aa_imol, low, high) add_simple_coot_menu_menuitem( menu, "ProSMART restraints interesting limit to 0.5...", lambda func: set_prosmart_sigma_limit_func(-0.5, 0.5) ) 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_prosmart_display_func(state): with UsingActiveAtom() as [aa_imol, aa_chain_id, aa_res_no, aa_ins_code, aa_atom_name, aa_alt_conf]: set_show_extra_restraints(aa_imol, state) add_simple_coot_menu_menuitem( menu, "Undisplay Extra Restraints...", lambda func: set_prosmart_display_func(0) ) add_simple_coot_menu_menuitem( menu, "Display ProSMART Extra Restraints...", lambda func: set_prosmart_display_func(1) ) def set_prosmart_display_CA_func(state): with UsingActiveAtom() as [aa_imol, aa_chain_id, aa_res_no, aa_ins_code, aa_atom_name, aa_alt_conf]: set_extra_restraints_representation_for_bonds_go_to_CA(aa_imol, state) add_simple_coot_menu_menuitem( menu, "Extra Restraints to CA", lambda func: set_prosmart_display_CA_func(1)) add_simple_coot_menu_menuitem( menu, "Extra Restraints Standard Representation", lambda func: set_prosmart_display_CA_func(0)) add_simple_coot_menu_menuitem( menu, "Delete an Extra Restraint...", lambda func: user_defined_delete_restraint()) def delete_restraints_func(): with UsingActiveAtom() as [aa_imol, aa_chain_id, aa_res_no, aa_ins_code, aa_atom_name, aa_alt_conf]: delete_extra_restraints_for_residue(aa_imol, aa_chain_id, aa_res_no, aa_ins_code) 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 UsingActiveAtom() as [aa_imol, aa_chain_id, aa_res_no, aa_ins_code, aa_atom_name, aa_alt_conf]: delete_extra_restraints_worse_than(aa_imol, n) except: print "BL WARNING:: no float given" add_simple_coot_menu_menuitem( menu, "Delete Deviant Extra Restraints...", lambda func: generic_single_entry("Delete Restraints worse than ", "4.0", " Delete Outlying Restraints ", lambda text: del_deviant_restr_func(text)) ) add_simple_coot_menu_menuitem( menu, "Save as REFMAC restraints...", lambda func: generic_chooser_and_file_selector("Save REFMAC restraints for molecule", valid_model_molecule_qm, " Restraints file name: ", "refmac-restraints.txt", lambda imol, file_name: extra_restraints2refmac_restraints_file(imol, file_name))) add_simple_coot_menu_menuitem( menu, "Add Parallel Planes Restraint...", lambda func: user_defined_add_planes_restraint() )