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| import re | |
| import time | |
| import py3Dmol | |
| import requests | |
| import stmol | |
| import streamlit as st | |
| st.set_page_config(layout="wide") | |
| st.header("Grid visualization of folded protein sequences") | |
| default_sequences = """MINDLLDISRIISGKMTLDRAEVNLTAIARQVVEEQRQAAEAKSIQLLCSTPDTNHYVFGDFDRLKQTLWNLLSNAVKFTPSGGTVELELGY | |
| MQGDSSISSSNRMFTLCKPLTVANETSTLSTTRNSKSNKRVSKQRVNLAESPERNAPSPASIKTNETEEFSTIKTTNNEVLGYEPNYVSYDF | |
| MSTHVSLENTLASLQATFFSLEARHTALETQLLSTRTELAATKQELVRVQAEISRADAQAQDLKAQILTLKEKADQAEVEAAAATQRAEESQ | |
| MVLLSTGPLPILFLGPSLAELNQKYQVVSDTLLRFTNTVTFNTLKFLGSDS | |
| MNNDEQPFIMSTSGYAGNTTSSMNSTSDFNTNNKSNTWSNRFSNFIAYFSGVGWFIGAISVIFFIIYVIVFLSRKTKPSGQKQYSRTERNNR | |
| MEAVYSFTITETGTGTVEVTPLDRTISGADIVYPPDTACVPLTVQPVINANGTWTLGSGCTGHFSVDTTGHVNCLTGGFGAAGVHTVIYTVE | |
| MGLTTSGGARGFCSLAVLQELVPRPELLFVIDRAFHSGKHAVDMQVVDQEGLGDGVATLLYAHQGLYTCLLQAEARLLGREWAAVPALEPNF | |
| MGLTTSGGARGFCSLAVLQELVPRPELLFVIDRAFHSGKHAVDMQVVDQEGLGDGVATLLYAHQGLYTCLLQAEARLLGREWAAVPALEPNF | |
| MGAAGYTGSLILAALKQNPDIAVYALNRNDEKLKDVCGQYSNLKGQVCDLSNESQVEALLSGPRKTVVNLVGPYSFYGSRVLNACIEANCHY | |
| """ | |
| input_sequences = st.text_area("Sequences separated by a newline (max 400 resis each)", default_sequences) | |
| def get_sequences(sequences_string): | |
| sequences = [] | |
| # Parse and clean input sequences | |
| for seq in sequences_string.split("\n"): | |
| seq = seq.strip() | |
| if len(seq) > 400: | |
| seq = seq[:400] | |
| seq = re.sub("[^ACDEFGHIKLMNPQRSTVWY]", "", seq) | |
| if len(seq) > 0: | |
| sequences.append(seq) | |
| return sequences | |
| sequences = get_sequences(input_sequences) | |
| st.write(f"Found {len(sequences)} valid sequences") | |
| pdb_strings = [] | |
| url = "https://api.esmatlas.com/foldSequence/v1/pdb/" | |
| def get_pdb(sequence): | |
| retries = 0 | |
| pdb_str = None | |
| while retries < 3 and pdb_str is None: | |
| response = requests.post(url, data=sequence) | |
| pdb_str = response.text | |
| if pdb_str == "INTERNAL SERVER ERROR": | |
| retries += 1 | |
| time.sleep(0.1) | |
| pdb_str = None | |
| return pdb_str | |
| # Fold sequences with ESMfold | |
| for seq in sequences: | |
| if pdb := get_pdb(seq): | |
| pdb_strings.append(pdb) | |
| else: | |
| st.write(f"Failed to retrieve PDB structure from ESMFold for {seq}") | |
| num_pdb_structures = len(pdb_strings) | |
| if num_pdb_structures == 0: | |
| grid_columns = 1 | |
| grid_rows = 1 | |
| else: | |
| grid_columns = int(num_pdb_structures ** 0.5) | |
| if grid_columns ** 2 < num_pdb_structures: | |
| grid_columns += 1 | |
| grid_columns = min(grid_columns, 12) | |
| grid_rows = (num_pdb_structures + grid_columns - 1) // grid_columns | |
| # Get the width of the viewer from the sidebar | |
| viewer_width = int(st.sidebar.number_input("Viewer Width", 100, 2000, 900)) | |
| # Calculate the width and height of each grid cell | |
| grid_cell_width = int(viewer_width / grid_columns) | |
| grid_cell_height = grid_cell_width | |
| viewer_height = grid_rows * grid_cell_height | |
| xyzview = py3Dmol.view( | |
| width=viewer_width, | |
| height=viewer_height, | |
| linked=False, | |
| viewergrid=(grid_rows, grid_columns), | |
| ) | |
| for row in range(grid_rows): | |
| for col in range(grid_columns): | |
| index = row * grid_columns + col | |
| pdb_string = pdb_strings[index] if index < len(pdb_strings) else None | |
| if pdb_string: | |
| xyzview.addModel(pdb_string, "pdb", viewer=(row, col)) | |
| xyzview.setStyle({"cartoon": {"color": "spectrum"}}) | |
| # Focus the chains we added | |
| xyzview.zoomTo() | |
| # Draw our grid! | |
| stmol.showmol(xyzview, height=viewer_height, width=viewer_width) |