Loading chatmol_pkg/chatmol/pymol_server.py +48 −10 Original line number Original line Diff line number Diff line import subprocess import subprocess, threading from xmlrpc import client from xmlrpc import client from .utils import ChatMol from .utils import ChatMol class PymolServer(): class PymolServer(): def __init__(self, default_client:ChatMol): def __init__(self, default_client:ChatMol): self.cm = default_client self.cm = default_client self.start_pymol() self.pymol_console = "" def start_pymol(self): def start_pymol(self, pymol_path='pymol'): # os.system("nohup pymol -R /dev/null 2>&1") """ subprocess.Popen(["pymol", "-R"], stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL) Starts PyMOL using a subprocess and captures its stdout in a non-blocking way. Args: pymol_path (str): Path to the PyMOL executable. Default is 'pymol'. """ # Start PyMOL as a subprocess self.pymol_process = subprocess.Popen( [pymol_path, "-R"], stdout=subprocess.PIPE, stderr=subprocess.PIPE, text=True, bufsize=1, # Line-buffered universal_newlines=True ) self.server = client.ServerProxy(uri="http://localhost:9123/RPC2") self.server = client.ServerProxy(uri="http://localhost:9123/RPC2") return 0 # Check if the process has started correctly if self.pymol_process.stdout is None: print("Failed to start PyMOL process.") return # Start a thread to listen to the output self.stdout_thread = threading.Thread(target=self.get_stdout) self.stdout_thread.start() def get_stdout(self): """ Prints the stdout of the PyMol subprocess continuously. """ # This function runs in a separate thread if self.pymol_process is not None: while True: output = self.pymol_process.stdout.readline() if output == '' and self.pymol_process.poll() is not None: break if output: self.pymol_console += output.strip() # print(output.strip()) self.pymol_process.stdout.close() def chatlite(self, question): def chatlite(self, question): answer = self.cm.chatlite(question) answer = self.cm.chatlite(question) Loading @@ -23,7 +59,7 @@ class PymolServer(): else: else: print(command) print(command) self.server.do(command) self.server.do(command) return commands return answer def chatgpt(self, message, execute:bool=True, lite:bool=False): def chatgpt(self, message, execute:bool=True, lite:bool=False): if lite: if lite: Loading @@ -33,7 +69,7 @@ class PymolServer(): if len(self.cm.stashed_commands) == 0: if len(self.cm.stashed_commands) == 0: print("There is no stashed commands") print("There is no stashed commands") else: else: for command in stashed_commands: for command in self.cm.stashed_commands: self.server.do(command) self.server.do(command) self.cm.clear_stashed_commands() self.cm.clear_stashed_commands() return 0 return 0 Loading Loading @@ -69,6 +105,7 @@ class PymolServer(): self.cm.stashed_commands.append(command) self.cm.stashed_commands.append(command) except Exception as e: except Exception as e: print(f"Error during command execution: {e}") print(f"Error during command execution: {e}") return response def claude(self, message, execute:bool=True): def claude(self, message, execute:bool=True): message = message.strip() message = message.strip() Loading @@ -76,7 +113,7 @@ class PymolServer(): if len(self.cm.stashed_commands) == 0: if len(self.cm.stashed_commands) == 0: print("There is no stashed commands") print("There is no stashed commands") else: else: for command in stashed_commands: for command in self.cm.stashed_commands: self.server.do(command) self.server.do(command) self.cm.clear_stashed_commands() self.cm.clear_stashed_commands() return 0 return 0 Loading Loading @@ -112,3 +149,4 @@ class PymolServer(): self.cm.stashed_commands.append(command) self.cm.stashed_commands.append(command) except Exception as e: except Exception as e: print(f"Error during command execution: {e}") print(f"Error during command execution: {e}") return response No newline at end of file Loading
chatmol_pkg/chatmol/pymol_server.py +48 −10 Original line number Original line Diff line number Diff line import subprocess import subprocess, threading from xmlrpc import client from xmlrpc import client from .utils import ChatMol from .utils import ChatMol class PymolServer(): class PymolServer(): def __init__(self, default_client:ChatMol): def __init__(self, default_client:ChatMol): self.cm = default_client self.cm = default_client self.start_pymol() self.pymol_console = "" def start_pymol(self): def start_pymol(self, pymol_path='pymol'): # os.system("nohup pymol -R /dev/null 2>&1") """ subprocess.Popen(["pymol", "-R"], stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL) Starts PyMOL using a subprocess and captures its stdout in a non-blocking way. Args: pymol_path (str): Path to the PyMOL executable. Default is 'pymol'. """ # Start PyMOL as a subprocess self.pymol_process = subprocess.Popen( [pymol_path, "-R"], stdout=subprocess.PIPE, stderr=subprocess.PIPE, text=True, bufsize=1, # Line-buffered universal_newlines=True ) self.server = client.ServerProxy(uri="http://localhost:9123/RPC2") self.server = client.ServerProxy(uri="http://localhost:9123/RPC2") return 0 # Check if the process has started correctly if self.pymol_process.stdout is None: print("Failed to start PyMOL process.") return # Start a thread to listen to the output self.stdout_thread = threading.Thread(target=self.get_stdout) self.stdout_thread.start() def get_stdout(self): """ Prints the stdout of the PyMol subprocess continuously. """ # This function runs in a separate thread if self.pymol_process is not None: while True: output = self.pymol_process.stdout.readline() if output == '' and self.pymol_process.poll() is not None: break if output: self.pymol_console += output.strip() # print(output.strip()) self.pymol_process.stdout.close() def chatlite(self, question): def chatlite(self, question): answer = self.cm.chatlite(question) answer = self.cm.chatlite(question) Loading @@ -23,7 +59,7 @@ class PymolServer(): else: else: print(command) print(command) self.server.do(command) self.server.do(command) return commands return answer def chatgpt(self, message, execute:bool=True, lite:bool=False): def chatgpt(self, message, execute:bool=True, lite:bool=False): if lite: if lite: Loading @@ -33,7 +69,7 @@ class PymolServer(): if len(self.cm.stashed_commands) == 0: if len(self.cm.stashed_commands) == 0: print("There is no stashed commands") print("There is no stashed commands") else: else: for command in stashed_commands: for command in self.cm.stashed_commands: self.server.do(command) self.server.do(command) self.cm.clear_stashed_commands() self.cm.clear_stashed_commands() return 0 return 0 Loading Loading @@ -69,6 +105,7 @@ class PymolServer(): self.cm.stashed_commands.append(command) self.cm.stashed_commands.append(command) except Exception as e: except Exception as e: print(f"Error during command execution: {e}") print(f"Error during command execution: {e}") return response def claude(self, message, execute:bool=True): def claude(self, message, execute:bool=True): message = message.strip() message = message.strip() Loading @@ -76,7 +113,7 @@ class PymolServer(): if len(self.cm.stashed_commands) == 0: if len(self.cm.stashed_commands) == 0: print("There is no stashed commands") print("There is no stashed commands") else: else: for command in stashed_commands: for command in self.cm.stashed_commands: self.server.do(command) self.server.do(command) self.cm.clear_stashed_commands() self.cm.clear_stashed_commands() return 0 return 0 Loading Loading @@ -112,3 +149,4 @@ class PymolServer(): self.cm.stashed_commands.append(command) self.cm.stashed_commands.append(command) except Exception as e: except Exception as e: print(f"Error during command execution: {e}") print(f"Error during command execution: {e}") return response No newline at end of file
