def add_pyranose_pseudo_ring_plane_restraints(comp_id): def filter_out(plane_name_sub_string, plane_restraints): return plane_restraints restraints = monomer_restraints(comp_id) if (not isinstance(restraints, dict)): print "failed to get %s restraints" %comp_id else: plane_restraints = restraints["_chem_comp_plane_atom"] new_plane_restraints = ["_chem_comp_plane_atom", [["pseudo-ring-1", [" C1 ", " C2 ", " C4 ", " C5 "], 0.01], ["pseudo-ring-2", [" C2 ", " C3 ", " C5 ", " O5 "], 0.01], ["pseudo-ring-3", [" C3 ", " C4 ", " O5 ", " C1 "], 0.01]]] + \ filter_out("pseudo-ring-3", plane_restraints) #should be list already restraints["_chem_comp_plane_atom"] = new_plane_restraints print "BL DEBUG:: new plane restraints", new_plane_restraints set_monomer_restraints(comp_id, restraints) def add_synthetic_carbohydrate_planes(): add_pyranose_pseudo_ring_plane_restraints("NAG") add_pyranose_pseudo_ring_plane_restraints("BMA") add_pyranose_pseudo_ring_plane_restraints("MAN") add_pyranose_pseudo_ring_plane_restraints("GAL") add_pyranose_pseudo_ring_plane_restraints("GLC") def multi_add_linked_residue(imol, res_spec, residues_to_add): set_go_to_atom_molecule(imol) current_matrix = matrix_state() # BL says:: maybe should save # and return to original weight?! set_matrix(8) current_refinement_rate = dragged_refinement_steps_per_frame() current_residue_spec = res_spec for residue_to_add in residues_to_add: set_go_to_atom_from_res_spec(current_residue_spec) set_dragged_refinement_steps_per_frame(300) if (not isinstance(current_residue_spec, list)): print "OOps not a proper res_spec %s with residue_to_add: %s" \ %(current_residue_spec, residue_to_add) return False else: if not residue_to_add: return "done" # odd return?! why? else: if (not isinstance(residue_to_add, list) and \ not len(residue_to_add) == 2): print "Oops - not a residue_link string pair when adding new_res_pair" else: new_res = residue_to_add[0] new_link = residue_to_add[1] print "BL DEBUG:: xxxxxxxxxxxxxxxx calling add_linked_residue xxx" new_res_spec = add_linked_residue(imol, res_spec2chain_id(current_residue_spec), res_spec2res_no(current_residue_spec), res_spec2ins_code(current_residue_spec), new_res, new_link) print "BL DEBUG:: xxxxxxxxxx add_linked_residue returns:", new_res_spec # residues_near_residue takes a 3-part spec and makes 3-part specs ls = residues_near_residue(imol, current_residue_spec, 1.9) with AutoAccept(): refine_residues(imol, [current_residue_spec] + ls) # make the new res the one to add to (remove starting bool) current_residue_spec = new_res_spec[1:] # restore refinement mode and matrix weight set_dragged_refinement_steps_per_frame(current_refinement_rate) set_matrix(current_matrix) def oligomannose_tree(): ret = [["NAG-ASN", "NAG"], ["BETA1-4", "NAG"], ["BETA1-4", "BMA"], [ ["ALPHA1-6", "MAN"], [ ["ALPHA1-6", "MAN"], ["ALPHA1-2", "MAN"] ], [ ["ALPHA1-3", "MAN"], ["ALPHA1-2", "MAN"] ] ], [ ["ALPHA1-3", "MAN"], ["ALPHA1-2", "MAN"], ["ALPHA1-2", "MAN"] ] ] return ret def add_linked_residue_tree(imol, parent, tree): def well_fitting_qm(res_spec): with UsingActiveAtom() as [aa_imol, aa_chain_id, aa_res_no, aa_ins_code, aa_atom_name, aa_alt_conf]: neighbs = residues_near_residue(aa_imol, res_spec, 4) c = map_to_model_correlation(imol, [res_spec], neighbs, 0, imol_refinement_map()) print "######## new residue %s density correlation: %s" %(res_spec, c) if (not isNumber(c)): return False else: return c > 0.5 def delete_residue_by_spec(spec): delete_residue(imol, residue_spec2chain_id(spec), residue_spec2res_no(spec), residue_spec2ins_code(spec)) def func(parent, res_pair): if (not isinstance(parent, list)): print "OOps not a proper res_spec %s with residue_to_add: %s" %(parent, res_pair) return False else: # OK. go go go new_link = res_pair[0] new_res_type = res_pair[1] set_go_to_atom_from_res_spec(parent) print "BL DEBUG:: ============== calling add_linked_residue with args", imol, new_res_type, new_link new_res_spec = add_linked_residue(imol, res_spec2chain_id(parent), res_spec2res_no(parent), res_spec2ins_code(parent), new_res_type, new_link) ls = residues_near_residue(imol, parent, 1.9) local_ls = [parent] + ls with AutoAccept(): refine_residues(imol, local_ls) if (not isinstance(new_res_spec, list)): # badness return False else: # okey!? preped_new_res_spec = new_res_spec[1:] # strip off leading result if well_fitting_qm(preped_new_res_spec): return preped_new_res_spec else: print "----------- That was not well fitting. Deleting:", preped_new_res_spec delete_residue_by_spec(preped_new_res_spec) with AutoAccept(): # Note: may not get rid of screwed up refinement from # adding a carb too much... refine_residues(imol, local_ls) return False def process_tree(parent, tree, proc_func): for branch in tree: if ((len(branch) == 2) and isinstance(branch[0], str) and isinstance(branch[0], str)): # have the link, res pair! new_res = proc_func(parent, branch) if new_res: parent = new_res else: break else: if isinstance(branch, list): process_tree(parent, branch, proc_func) # main line of add_linked_residue_tree set_go_to_atom_molecule(imol) process_tree(parent, tree, func) # graphics... def add_module_carbohydrate(): if (have_coot_python): if coot_python.main_menubar(): menu = coot_menubar_menu("Glyco") def add_carbo_link_func(sugar, link): current_weight = matrix_state() set_matrix(8) with UsingActiveAtom() as [aa_imol, aa_chain_id, aa_res_no, aa_ins_code, aa_atom_name, aa_alt_conf]: add_linked_residue(aa_imol, aa_chain_id, aa_res_no, aa_ins_code, sugar, link) set_matrix(current_weight) add_simple_coot_menu_menuitem( menu, "Add a ASN-NAG NAG", lambda func: add_carbo_link_func("NAG", "NAG-ASN")) add_simple_coot_menu_menuitem( menu, "Add a BETA1-4 NAG", lambda func: add_carbo_link_func("NAG", "BETA1-4")) add_simple_coot_menu_menuitem( menu, "Add a BETA1-4 BMA", lambda func: add_carbo_link_func("BMA", "BETA1-4")) add_simple_coot_menu_menuitem( menu, "Add an ALPHA1-2 MAN", lambda func: add_carbo_link_func("MAN", "ALPHA1-2")) add_simple_coot_menu_menuitem( menu, "Add an ALPHA1-3 MAN", lambda func: add_carbo_link_func("MAN", "ALPHA1-3")) # we should do this only if we are sitting on an SIA. # Attaching a SIA to a MAN (i.e. reverse order) would be a # good test too... add_simple_coot_menu_menuitem( menu, "Add an ALPHA2-3 MAN", lambda func: add_carbo_link_func("MAN", "ALPHA2-3")) # same consideration as above add_simple_coot_menu_menuitem( menu, "Add an ALPHA2-3 GAL", lambda func: add_carbo_link_func("GAL", "ALPHA2-3")) add_simple_coot_menu_menuitem( menu, "Add an ALPHA1-6 MAN", lambda func: add_carbo_link_func("MAN", "ALPHA1-6")) add_simple_coot_menu_menuitem( menu, "Add an ALPHA1-6 FUC", lambda func: add_carbo_link_func("FUC", "ALPHA1-6")) def add_multi_carbo_link_func(link_list): with UsingActiveAtom() as [aa_imol, aa_chain_id, aa_res_no, aa_ins_code, aa_atom_name, aa_alt_conf]: multi_add_linked_residue(aa_imol, [aa_chain_id, aa_res_no, aa_ins_code], link_list) add_simple_coot_menu_menuitem( menu, "N-link add NAG, NAG, BMA", lambda func: add_multi_carbo_link_func([["NAG", "NAG-ASN"], ["NAG", "BETA1-4"], ["BMA", "BETA1-4"]])) add_simple_coot_menu_menuitem( menu, "Auto Fit & Refine On for Link Addition", lambda func: set_add_linked_residue_do_fit_and_refine(1)) add_simple_coot_menu_menuitem( menu, "Auto Fit & Refine Off for Link Addition", lambda func: set_add_linked_residue_do_fit_and_refine(0)) def add_oligo_mannose_func(): with UsingActiveAtom() as [aa_imol, aa_chain_id, aa_res_no, aa_ins_code, aa_atom_name, aa_alt_conf]: make_backup(aa_imol) # switch backup off?! add_linked_residue_tree(aa_imol, [aa_chain_id, aa_res_no, aa_ins_code], oligomannose_tree()) add_simple_coot_menu_menuitem( menu, "Add Oligomannose", lambda func: add_oligo_mannose_func()) def torsion_fit_this_func(refine = False): with UsingActiveAtom() as [aa_imol, aa_chain_id, aa_res_no, aa_ins_code, aa_atom_name, aa_alt_conf]: centre_residue = [aa_chain_id,aa_res_no, aa_ins_code] multi_residue_torsion_fit(aa_imol, [centre_residue], 30000) if refine: with AutoAccept(): refine_residues(aa_imol, [centre_residue]) add_simple_coot_menu_menuitem( menu, "Torsion Fit this residue", lambda func: torsion_fit_this_func()) add_simple_coot_menu_menuitem( menu, "Torsion Fit & Refine this residue", lambda func: torsion_fit_this_func(True)) add_simple_coot_menu_menuitem( menu, "Add synthetic pyranose plane restraints", lambda func: add_synthetic_carbohydrate_planes())