add an example and update readme (d48f1622) · Commits · github_fork / ChatMol

.gitignore

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		@@ -134,3 +134,11 @@ test*
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		copilot_public/Project-*
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		@@ -18,6 +18,17 @@ pip install -r requirements.txt
		```bash
		streamlit run main.py
		```

		## Example

		### Example 1: enzyme for toxin degradation

		After the copliot is strateted, change the `Project Name` to `examples/enzyme-for-toxin-degradation`, you will see the history of how copliot:
		- explain the toxin ZEA
		- find the chemical structure of ZEA
		- search the enzyme for ZEA degradation
		- download predicted 3D structure of the enzyme adn run docking

		## Want more funtionality?

		You can easily add more functionality to ChatMol copilot.

+20 −1

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		@@ -345,6 +345,10 @@ class ConversationHandler:
		return response, second_response


		# class GLMConversationHandler(ConversationHandler):
		# from zhipuai import ZhipuAI


		def compose_chat_completion_message(
		role="assistant", content="", tool_call_dict_list=[]
		):
		@@ -365,3 +369,18 @@ def compose_chat_completion_message(
		tool_calls=tool_calls,
		)
		return message

		def extract_function_and_execute(llm_output, messages):
		name = llm_output.choices[0].message.tool_calls[0].function.name
		params = json.loads(llm_output.choices[0].message.tool_calls[0].function.arguments)
		function_to_call = globals().get(name)
		if not function_to_call:
		raise ValueError(f"Function '{name}' not found")

		messages.append(
		{
		"role": "tool",
		"content": str(function_to_call(**params))
		}
		)
		return messages
		No newline at end of file

+8 −6

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		@@ -271,6 +271,7 @@ class ChatmolFN:
		# # print(log)
		# return res_df.to_string()

		@handle_file_not_found_error
		def call_proteinmpnn_api(
		self,
		path_to_pdb: str,
		@@ -308,6 +309,7 @@ class ChatmolFN:
		response = requests.post('https://api.cloudmol.org/protein/proteinmpnn/', params=params, headers=headers, files=files)
		return response.text

		@handle_file_not_found_error
		def compare_protein_structures(self, pdb_file1, pdb_file2):
		"""
		Compare two protein structures using TMalign
		@@ -322,21 +324,21 @@ class ChatmolFN:
		@handle_file_not_found_error
		def protein_single_point_mutation_prediction(self, pdb_file, mutations):
		pythia_res = query_pythia(pdb_file)
		mutation_res = ""
		mutation_res = "Mutation: Energy\n"
		for mutation in pythia_res.split("\n"):
		m, score = mutation.split()
		if m in mutations:
		mutation_res += f"{m} {score}\n"
		mutation_res += f"{m}: {score}\n"
		return mutation_res

		@handle_file_not_found_error
		def recommand_stable_mutations(self, pdb_file, cutoff=-2):
		pythia_res = query_pythia(pdb_file)
		mutation_res = ""
		mutation_res = "Mutation: Energy\n"
		for mutation in pythia_res.split("\n"):
		m, score = mutation.split()
		if float(score) < float(cutoff):
		mutation_res += f"{m} {score}\n"
		mutation_res += f"{m}: {score}\n"
		return mutation_res

		@handle_file_not_found_error

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