Avogadro Batch Render Orbitals

orbitals.py

#!/usr/bin/python

import json
import socket
import struct
import glob
import tempfile
import os
import time

class Connection:
    '''Process a JSON-RPC request'''

    def __init__(self, name="avogadro"):
        """
        Connect to the local named pipe

        :param name: The name of the named pipe.
        """
        # create socket
        self.sock = socket.socket(socket.AF_UNIX, socket.SOCK_STREAM)

        # connect
        self.sock.connect(tempfile.gettempdir() + "/" + name)

    def send_json(self, obj):
        """
        Send a JSON-RPC request to the named pipe.

        :param obj: The JSON-RPC request object.
        """
        self.send_message(json.dumps(obj))

    def send_message(self, msg):
        """
        Send a message to the named pipe

        :param msg: The message to send.
        """
        size = len(msg)
        header = struct.pack(">I", size)
        packet = header + msg.encode("ascii")
        self.sock.send(packet)

    def receive_message(self, size=1024):
        """
        Receive a message from the named pipe.

        :param size: The maximum size of the message to receive.
        """
        packet = self.sock.recv(size)

        return packet[4:]

    def recv_json(self):
        '''Receive a JSON-RPC response'''
        msg = self.recv_message()

        try:
            return json.loads(msg)
        except Exception as exception:
            print("error: " + str(exception))
            return {}

    def close(self):
        '''Close the socket to the named pipe'''
        self.sock.close()

def sendMessage(method, options):
    conn = Connection()
    conn.send_json({"jsonrpc": "2.0", "id": 0, "method": method, "params": options})
    reply = str(conn.receive_message())
    conn.close()
    return reply

if __name__ == "__main__":
    conn = Connection()

    # render the orbital
    options = {
        "orbital": "homo",
        "isovalue": 0.003
    }

    cwd = os.getcwd()
    for fileName in glob.glob("*.fchk"):
        # open the file
        print("Opening " + fileName)
        path = cwd + "/" + fileName
        basename = path[:-5] # strip off the .fchk
        sendMessage("openFile", {"fileName": path})

        sendMessage("renderOrbital", options)
        # wait 1 minute to compute the surface
        # .. adjust as needed
        time.sleep(60)
        print("Saving HOMO")
        sendMessage("saveGraphic", { "fileName": basename + "-homo.png" })
        
        # also render the electron density
        sendMessage("renderElectronDensity", {"isovalue": 0.003})
        # wait 1 minute to compute the surface
        time.sleep(60)
        print("Saving Electron Denisty")
        sendMessage("saveGraphic", { "fileName": basename + "-edens.png" })