#! /usr/bin/env python
import sys
import re
import numpy as np
import readarc
fileprefix = sys.argv[1]
cutoff = float(sys.argv[2])
filename = fileprefix + '.arc'
ljoname = fileprefix + '.ljo'
arc = readarc.readarc(filename)
n = arc[0]
atomname = arc[1]
x = arc[2]
y = arc[3]
z = arc[4]
atomtype = arc[5]
bonds = arc[6]
ljofile = open(ljoname, 'r')
nsolatoms = int(re.split('\s+',ljofile.readline().strip())[0])
ljofile.close()
newatomname = []
newx = []
newy = []
newz = []
import os
import sys
import math
import re
import readarc
import numpy as np
fileprefix = sys.argv[1]
keywords = '$rem\nJOBTYPE SP\nEXCHANGE omegaB97X-D\nBASIS GENERAL\nPURECART 2222\nEFP TRUE\nCHELPG TRUE\n$end\n\n'
arcname = fileprefix + '.arc'
ljoname = fileprefix + '.ljo'
arc = readarc.readarc(arcname)
ljofile = open(ljoname, 'r')
nsolatoms = int(re.split('\s+',ljofile.readline().strip())[0])
charge = re.split('\s+',ljofile.readline().strip())[0]
ljofile.close()
n = arc[0]
x = arc[2]
y = arc[3]
z = arc[4]
atomtype = arc[5]
symbols = {900:'C', 901:'C', 902:'C', 910:'H', 911:'H', 912:'H', 920:'Cl',
921:'Cl', 922:'Cl', 930:'O', 931:'O', 932:'O', 940:'H', 941:'H', 942:'H',
55:'O', 56:'H', 57:''}
weight_e = 15.19562
weight_f = 1.293817
weight_t = 1.0
fileprefix = sys.argv[1]
atom_tinker = {901:'C', 911:'H', 921:'Cl', 55:'O', 56:'H', 57:''}
atom_gauss = {1:'H', 6:'C', 8:'O', 17:'Cl'}
mass = {'H':1.008,'C':12.000,'O':15.999,'Cl':35.453}
arcname = fileprefix + '.arc'
keyname = fileprefix + '.key'
ljoname = fileprefix + '.ljo'
outname = fileprefix + '.out'
arcdata = readarc.readarc(arcname)
n = arcdata[0]
x = arcdata[2]
y = arcdata[3]
z = arcdata[4]
atomtype = arcdata[5]
bonds = arcdata[6]
keydata = readkey.readkey(keyname)
prm_sigma = keydata[0]
prm_ep = keydata[1]
prm_ch = keydata[2]
conv = keydata[3]
ljofile = open(ljoname, 'r')
