jhjensen2

#reproduces the "stats" or "verbose" output from LINEST in Excel or Google Sheets

import numpy as np

data = np.genfromtxt('data.csv', delimiter=',', names=True)

x = data['x']
y = data['y']
n = len(y)
dofreedom = n-2

jhjensen2

import subprocess,sys

filename = sys.argv[1]
input = open(filename, "r+")
output = open(filename+".smiles", "w+")


for line in input:
    words = line.split()
    name = words[0]

jhjensen2

import sys

pKa_ref = 11.4
ref = "heliotridane"

filename = sys.argv[1]
file = open(filename, "r+")
energies = {}
log_files = {}
names = []

jhjensen2

import subprocess

file = open("names", "r+")

for line in file:
    name = line.split()
    subprocess.call(['./name2smiles', name[0]])
    subprocess.call(['echo'])

jhjensen2

smiles = "CCCC"
subst = ["F","Cl"]

l = list(smiles)
print l
s = ""

print l[1]+l[2]+l[3]

for i in range(len(subst)):

jhjensen2

cd /Applications/jmol-11.7.26/models/
background white
frank off
hide all
delay 2
display atomno=8; delay 2
display atomno=8,atomno=4; delay 2
display atomno=8,atomno=4,atomno=2; delay 1
display atomno=8,atomno=4,atomno=2; delay 1
display atomno=8,atomno=4,atomno=2,atomno=1; delay 1

jhjensen2

#!/bin/csh
# Molget: cshell script to get coordinates from chemical name using Babel and Cactus
# usage: ./molget methane
# (remember to "chmod 755 molget)
#
set molecule = $argv[1]
curl https://cactus.nci.nih.gov/chemical/structure/$molecule/smiles -o $molecule.smi
babel -ismi $molecule.smi -oxyz $molecule.xyz --gen3D

jhjensen2

"""
type "python readv2.py *.log" to use
This program finds the last heat of formation in all GAMESS log files
for semiempirical geometry optimizations
"""

import sys

for filename in sys.argv[1:]:

jhjensen2

"""
type "python read.py" to use

This program finds the last heat of formation in all GAMESS log files
for semiempirical geometry optimizations
"""

import string
from glob import glob

jhjensen2

"""\
This python program extracts coordinates and gradients from a GAMESS output
file and creates a .xzy+vib file.  Note that the sign of the gradient is chaged to produce the force

To use it type (assuming opt.py and the output file is in the same directory):

python opt.py x xx > xxx.xyz

where x is the number of atoms in the molecule and xx is the name of the GAMESS output file. xxx is whatever you want to call your xyz file.