fix bugs and add protein design tools (28cdccbd) · Commits · github_fork / ChatMol

.gitignore

+3 −1

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		@@ -132,3 +132,5 @@ dmypy.json
		test*
		01d70f7c997c6a7d73e8fc592865b84f7371642b7afdba535726ba70f020183e*
		ce73fb8a1b802e6746c58ac3bf915d79506e2b5edc36e83f1cbfa3f6071a9a92*
		e4f51ecb92f1387f12e6a8f00025990b7c16198bf3643601dc66c55144f0b6f8*
		9d58e5ce6d8c9ed839c7cb7d836581dbd48e4ba916403cbd9644f886fd070d2b*
		No newline at end of file

copilot_public/README.md

+2 −5

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		@@ -71,11 +71,9 @@ You are more than welcome to contribute any function to ChatMol copilot.
		## TODO
		### Analysis tools
		- [ ] Protein Docking Simulation: Develop a simulation tool for docking small molecule ligands to protein targets, exploring potential binding modes.
		- AutoDock Vina (High priority)
		- DiffDock (Low priority)
		- DiffDock

		- [ ] Protein Structure and Sequence Comparison: Build a tool for comparing the structures of multiple proteins, identifying similarities, differences, and motifs.
		- TM-align (High priority)
		- Kalign (Medium priority)
		- MMseqs2 (Low priority)

		@@ -91,8 +89,7 @@ You are more than welcome to contribute any function to ChatMol copilot.


		### visualization tools
		- [ ] Protein-Ligand Interaction Visualization: Create a tool for visualizing and analyzing protein-ligand interactions, focusing on key binding residues.

		- [ ] Protein-Ligand Interaction Visualization: Create a tool for visualizing and analyzing protein-ligand interactions, focusing on key binding residues.(Mol* partically done)

		## Online Version
		We provided an online version for you. [Click here](https://chatmol.org/copilot/) to try it.
		No newline at end of file

copilot_public/build_from_registry.py

+12 −9

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		import json
		import requests
		import pymol
		# import pymol
		import os
		import pandas as pd
		import openai
		import time
		import types
		import urllib.parse
		# import pandas as pd
		# import openai
		# import time
		# import types
		# import urllib.parse
		import pprint
		from datetime import datetime
		from pymol import cmd
		from urllib.parse import quote
		# from datetime import datetime
		# from pymol import cmd
		# from urllib.parse import quote


		os.environ["REGISTRY_HOST_PORT"]="100.89.180.132:9999"
		@@ -21,6 +21,9 @@ registry_host_port = os.getenv("REGISTRY_HOST_PORT")
		#os.environ["REGISTRY_HOST_PORT"]="100.89.180.132:9999"

		# Search for pymol service endpoint
		# print("Registry Host Port = ",registry_host_port)
		# print(requests.get("http://"+registry_host_port+"/registry"))
		# print("END")
		registry = requests.get("http://"+registry_host_port+"/registry").json()
		pymol_endpoint = ""
		for key in registry.keys():

copilot_public/chat_helper.py

+38 −1

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		@@ -246,6 +246,41 @@ class ConversationHandler:
		"required": ["query", "type"],
		},
		},
		{
		"type": "function",
		"function": {
		"name": "call_proteinmpnn_api",
		"description": "Calls the ProteinMPNN API to design protein sequences based on structures",
		"parameters": {
		"type": "object",
		"properties": {
		"path_to_pdb": {"type": "string", "description": "The path to the PDB file."},
		"designed_chain": {"type": "string", "description": "The designed chain identifier."},
		"num_seqs": {"type": "string", "description": "The number of sequences to generate."},
		"homonomer": {"type": "string", "description": "Indicates whether the protein is a homomer or not."},
		"sampling_temp": {"type": "string", "description": "The sampling temperature."},
		"fixed_chain": {"type": "string", "description": "The fixed chain identifier, optional.", "default": None},
		},
		},
		"required": ["path_to_pdb", "designed_chain","num_seqs", "homonomer", "sampling_temp","fixed_chain"],
		}
		},
		{
		"type": "function",
		"function": {
		"name": "compare_protein_structures",
		"description": "Compare the structures of two proteins with TMAlign",
		"parameters": {
		"type": "object",
		"properties": {
		"pdb_file1": {"type": "string", "description": "The file path to a local pdb file of the first protein"},
		"pdb_file2": {"type": "string", "description": "The file path to a local pdb file of the second protein"},
		},
		},
		"required": ["pdb_file1", "pdb_file2"],
		}
		}


		]
		self.available_functions = {
		@@ -261,7 +296,9 @@ class ConversationHandler:
		"get_protein_sequence_from_pdb": self.cfn.get_protein_sequence_from_pdb,
		"search_rcsb": self.cfn.search_rcsb,
		"query_uniprot": self.cfn.query_uniprot,
		"blind_docking": self.cfn.blind_docking
		"blind_docking": self.cfn.blind_docking,
		"call_proteinmpnn_api": self.cfn.call_proteinmpnn_api,
		"compare_protein_structures": self.cfn.compare_protein_structures,
		}

		def setup_workdir(self, work_dir):

copilot_public/chatmol_fn.py

+48 −0

Original line number	Diff line number	Diff line
		@@ -12,6 +12,7 @@ from rdkit import Chem
		from rdkit.Chem import AllChem
		import time
		import pandas as pd
		from tool_utils import StructPair

		from Bio.PDB import PDBParser

		@@ -270,6 +271,53 @@ class ChatmolFN:
		# # print(log)
		# return res_df.to_string()

		def call_proteinmpnn_api(
		self,
		path_to_pdb: str,
		designed_chain: str = "A",
		num_seqs: str = "1", # int,
		homonomer: str ="false", #bool,
		sampling_temp: str = '0.9', #int,
		fixed_chain: str = None,
		):
		"""
		Calls the ProteinMPNN API to design protein sequences based on structures.
		"""
		headers = {'accept': 'application/json'}
		num_seqs = int(num_seqs)
		homonomer = True if homonomer.lower() == "true" else False
		sampling_temp = float(sampling_temp)

		if fixed_chain is None:
		params = {
		'designed_chain': designed_chain,
		'num_seqs': num_seqs,
		'homonomer': homonomer,
		'sampling_temp': sampling_temp,
		}
		else:
		params = {
		'designed_chain': designed_chain,
		'fixed_chain': fixed_chain,
		'num_seqs': num_seqs,
		'homonomer': homonomer,
		'sampling_temp': sampling_temp,
		}

		files = {'uploaded_file': open(path_to_pdb, 'rb')}
		response = requests.post('https://api.cloudmol.org/protein/proteinmpnn/', params=params, headers=headers, files=files)
		return response.text

		def compare_protein_structures(self, pdb_file1, pdb_file2):
		"""
		Compare two protein structures using TMalign
		Parameters:
		- pdb_file1 (str): The path to the first PDB file.
		- pdb_file2 (str): The path to the second PDB file.
		"""
		sp = StructPair(pdb_file1, pdb_file2)
		sp.tmalign()
		return f"Aligned length: {sp.aligned_length}, RMSD: {sp.rmsd}, Identity: {sp.identity}, TM-score of {pdb_file1}: {sp.tmscore_p1}, TM-score of {pdb_file2}: {sp.tmscore_p2}"

		@handle_file_not_found_error
		def protein_single_point_mutation_prediction(self, pdb_file, mutations):

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