update repo

## Requirements

- PyMOL

- OpenAI Python package: To install, enter `pip install openai` in the PyMOL command line.

- Install other dependencies: `pip install flask flask-cors chardet` in PyMOL command line.

![img](./assets/install.png)

## Installation

            self.end_headers()

            self.wfile.write(str(e).encode())

    def do_GET(self):

        if self.path == "/":

            self.send_response(HTTPStatus.OK)

            self._send_cors_headers()

            self.send_header("Content-Type", "text/html")

            self.end_headers()

            self.wfile.write(b'Hello, this is the local Pymol server.')

            return

        self.send_response(HTTPStatus.NOT_FOUND)

        self.end_headers()

def start_server():

    httpd = http.server.HTTPServer(('localhost', 8101), PyMOLCommandHandler)

    httpd.serve_forever()

# Save API Key in ~/.PyMOL/apikey.txt

API_KEY_FILE = os.path.expanduser('~')+"/.PyMOL/apikey.txt"

OPENAI_KEY_ENV = "OPENAI_API_KEY"

GPT_MODEL = "gpt-3.5-turbo"

def set_api_key(api_key):

    api_key = api_key.strip()

                  f" or by environment variable '{OPENAI_KEY_ENV}'.")

def chat_with_gpt(message):

def chat_with_gpt(message, max_history=10):

    global conversation_history

    conversation_history += f"User: {message}\nChatGPT:"

        messages = [

            {"role": "system", "content": "You are an AI language model specialized in providing command line code solutions related to PyMOL. Generate clear and effective solutions in a continuous manner. When providing demos or examples, try to use 'fetch' if object name is not provided. Prefer academic style visulizations. Code within triple backticks, comment and code should not in the same line."}

        ]

        message_parts = conversation_history.strip().split("\n")

        # Keep only the max_history latest exchanges to avoid making the conversation too long

        message_parts = conversation_history.strip().split("\n")[-2 * max_history:]

        for i, part in enumerate(message_parts):

            role = "user" if i % 2 == 0 else "assistant"

            messages.append({"role": role, "content": part})

        response = openai.ChatCompletion.create(

            model="gpt-3.5-turbo",

            model=GPT_MODEL,

            messages=messages,

            max_tokens=1024,

            max_tokens=256,

            n=1,

            temperature=0,

        )

        answer = response.choices[0].message['content'].strip()

        conversation_history += f"{answer}\n"

        else:

            print(command)

def start_chatgpt_cmd(message, execute:bool=True, lite:bool=True):

def start_chatgpt_cmd(message, execute:bool=True, lite:bool=False):

    if lite == True:

        chatlite(message)

        return 0

cmd.extend("set_api_key", set_api_key)

cmd.extend("chat", start_chatgpt_cmd)

cmd.extend("chatlite", chatlite)

 No newline at end of file

def launch_pymol():

    """start a new process to launch PyMOL

    Only tested on MacOS, may be different on other OS

    """

    process = subprocess.Popen(["pymol", "pymol_server.py"], stdout=subprocess.PIPE, stderr=subprocess.PIPE)

    stdout, stderr = process.communicate()

from pymol import cmd

import urllib.parse

import threading

import requests

class PyMOLCommandHandler(http.server.BaseHTTPRequestHandler):

    def _send_cors_headers(self):

            self.end_headers()

            self.wfile.write(str(e).encode())

    def do_GET(self):

        if self.path == "/":

            self.send_response(HTTPStatus.OK)

            self._send_cors_headers()

            self.send_header("Content-Type", "text/html")

            self.end_headers()

            self.wfile.write(b'Hello, this is the local Pymol server.')

            return

        self.send_response(HTTPStatus.NOT_FOUND)

        self.end_headers()

def start_server():

    httpd = http.server.HTTPServer(('localhost', 8101), PyMOLCommandHandler)

    httpd.serve_forever()

def is_http_server_running():

    url = f'http://localhost:8101'

    try:

        response = requests.get(url)

        return True

    except requests.ConnectionError:

        return False

if not is_http_server_running():

    server_thread = threading.Thread(target=start_server)

    server_thread.start()

    print("Server started")