from browser import document import json from visualife.core import CanvasViewport,HtmlViewport from visualife.core.styles import make_brighter from visualife.widget import SequenceViewer, SecondaryStructureViewer, AjaxCommunication, StructureViewer residues_clicked = {} # --- Dictionary stores residues that are currently in "stick" representations first_res_id = 1 N_res = 0 sec, panel3d, ss2_ajax = None, None, None sequence, ss2_str, pdb_name = "", "", "" E, H = [], [] def sse_to_regions(sse_list, ss_name, ss_color): """Creates clickable sequence regions based on a protein's secondary structure""" global sec i = 1 for sse in sse_list: name = "%s %d" % (ss_name, i) sec.add_to_region(name.replace(' ', '-'), first_pos=sse[0], last_pos=sse[1], color=ss_color, tooltip=name, show_in_legend=False, by_residue_id=True) i += 1 def click_on_block(evt): """Function called when you click on a secondary structure block""" global sec, panel3d, sequence # Check which region was clicked pos = int(evt.target.id.split("-")[3]) # evt.target.is is like: "ch-1-show_sequence-15" for pos 15 reg_name, region = sec.region_for_position(pos) if region is None: return color = "red" if reg_name.startswith("helix") else "blue" panel3d.remove_style("1") panel3d.add_style("1", 'cartoon', {"color": "white", "sele": "%d-%d" % (first_res_id, first_res_id + len(sequence))}) if region[0][2] - region[0][1] <= 2: panel3d.add_style("1", 'cartoon', {"color": color, "sele": "%d-%d" % (region[0][1] + first_res_id - 1, region[0][2] + first_res_id + 1)}) else: panel3d.add_style("1", 'cartoon', {"color": color, "sele": "%d-%d" % (region[0][1] + first_res_id, region[0][2] + first_res_id)}) def click_on_aa(evt): """Function called when you click on a letter in amino acid sequence""" global panel3d, sequence, resi_repr pos = int(evt.target.id.split("-")[3]) - 1 # evt.target.id is like: "ch-show_sequence-15" for pos 15 if pos in residues_clicked: evt.target.style.backgroundColor = residues_clicked[pos] panel3d.remove_style("1",resi_repr[pos]) del(residues_clicked[pos]) else: resi_repr[pos] = panel3d.add_style("1", "licorice", {"color": "atomindex", "sele": "%d" % (pos + first_res_id)}) residues_clicked[pos] = evt.target.style.backgroundColor evt.target.style.backgroundColor = "yellow" def binding_site(req): """Gets info about binding sites and creates according regions on SequenceViewer""" global sequence, pdb_name, ss2_str, E, H seq = SequenceViewer("show_sequence", pdb_name, sequence, n_columns_of_ten=4, first_residue_id=first_res_id) seq.secondary_structure = ss2_str seq.set_event_callback("CLICK_ON_LETTER", click_on_aa) seq.regions_palette = "accent" output = json.loads(req.text)[pdb_name] for site in output: desc = site["details"].split() desc_str = "" for i in desc[:4]: desc_str += i.lower() + " " for i in desc[4:]: desc_str += i + " " i = 0 if desc[-3] in ["GOL", "PO4", "SO4", "HOH"]: continue # --- remove obvious buffer compounds from the list of ligands for res in site["site_residues"]: i += 1 aa = res["author_residue_number"] seq.add_to_region(desc_str, first_pos=aa, by_residue_id=True, tooltip=desc_str) def receive_secondary(ss2_req): """Gets secondary structure, creates ss2 string and SecondaryStructureViewer widget""" global N_res, pdb_name, sec, ss2_str, E, H, first_res_id ss_dic = json.loads(ss2_req.text)[pdb_name]["molecules"][0]["chains"][0]["secondary_structure"] for i in ss_dic.get("strands", []): E.append([i["start"]["author_residue_number"], i["end"]["author_residue_number"]]) for i in ss_dic.get("helices", []): H.append([i["start"]["author_residue_number"], i["end"]["author_residue_number"]]) ss2 = ["C" for i in range(N_res)] for i in E: for n in range(i[0], i[1] + 1): ss2[n - first_res_id] = "E" for i in H: for n in range(i[0], i[1] + 1): ss2[n - first_res_id] = "H" ss2_str = "" for i in ss2: ss2_str += i sec = SecondaryStructureViewer("show_secondary", "%s - secondary structure" % pdb_name, ss2_str, n_columns_of_ten=4, first_residue_id=first_res_id) sec.set_event_callback("CLICK_ON_LETTER", click_on_block) sse_to_regions(H, "helix", make_brighter("red", 0.9)) sse_to_regions(E, "strand", make_brighter("blue", 0.9)) def receive_structure(ajax_pdb): """Gets PDB file and creates StructureViewer """ global N_res, panel3d, sequence, ss2_ajax, pdb_name, first_res_id # Definition of menu buttons for the 3D protein viewer menu = {"sticks": "as_sticks", "lines": "as_lines", "cartoon": "as_cartoon", "center": "center"} panel3d = StructureViewer("show_3d", backgroundColor="white", width=350, height=350, menu_buttons=menu) panel3d.add_model("1", ajax_pdb.text) def receive_sequence(ajax): """Sets the sequence and calls download of binding site and secondary structure""" global N_res, sequence, resi_repr, pdb_name d = json.loads(ajax.text) sequence = d[pdb_name][0]["sequence"] N_res = len(sequence) resi_repr = [None for i in range(N_res)] binding = AjaxCommunication("https://www.ebi.ac.uk/pdbe/api/pdb/entry/binding_sites/%s" % pdb_name, binding_site, "GET") ss2_ajax() binding() def set_first_res(req): """Sets the number of first residue in the chain""" global pdb_name, first_res_id data = json.loads(req.text) first_res_id = data[pdb_name]["molecules"][0]["chains"][0]["residues"][0]["author_residue_number"] def receive_protein_description(req): """Gets the description of the protein""" data = json.loads(req.text) description = data[pdb_name][0]["title"] document["loading"].text = description.lower().capitalize() def download_data(evt=None): """Downloads sequence, structure and description of the protein""" global pdb_name, ss2_ajax, panel3d, residues_clicked, first_res_id, N_res, sec, sequence, ss2_str, E, H residues_clicked = {} first_res_id = 1 N_res = 0 sec, panel3d, ss2_ajax = None, None, None sequence, ss2_str, pdb_name = "", "", "" E, H = [], [] if panel3d: panel3d.remove_model("1") document["loading"].text="Downloading structure..." pdb_name = document["name"].value pdb_ajax = AjaxCommunication("https://files.rcsb.org/view/%s.pdb" % pdb_name, receive_structure) pdb_ajax() # --- call the object that has been just created in the line above # --- the remaining AJAX calls in a shorter, single-line syntax AjaxCommunication("https://www.ebi.ac.uk/pdbe/api/pdb/entry/residue_listing/%s" % pdb_name, set_first_res, "GET")() AjaxCommunication("https://www.ebi.ac.uk/pdbe/api/pdb/entry/molecules/%s" % pdb_name, receive_sequence, "GET")() AjaxCommunication("https://www.ebi.ac.uk/pdbe/api/pdb/entry/summary/%s" % pdb_name, receive_protein_description, "GET")() # --- AJAX object for secondary structure will be called later ss2_ajax = AjaxCommunication("https://www.ebi.ac.uk/pdbe/api/pdb/entry/secondary_structure/%s" % pdb_name, receive_secondary, "GET") document["load"].bind("click", download_data)