jhjensen2

import sys

pKa_ref = 11.4
ref = "heliotridane"

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

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

#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 numpy as np

models = 20
res = 166
filename = "lis"

file = open(filename,'r')

ave = [[0 for x in xrange(3)] for x in xrange(res)]
stdev = [[0 for x in xrange(3)] for x in xrange(res)]

jhjensen2

#conformer search with RDKIT
import sys
sys.path.append("/usr/local/lib/python2.7/site-packages/")
from rdkit import Chem
from rdkit.Chem import AllChem

m = Chem.AddHs(Chem.MolFromSmiles('CCCO')) #creates molecule from smiles and adds H's
AllChem.EmbedMultipleConfs(m,20) #makes 20 3D conformations
_=AllChem.MMFFOptimizeMoleculeConfs(m,maxIters=1000) #MMFF geometry optimization

jhjensen2

import sys
sys.path.append("/usr/local/lib/python2.7/site-packages/")
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit import DataStructs

m = Chem.MolFromSmiles('NCCc1c[nH]cn1')
mp_A = Chem.MolFromSmiles('[NH3+]CCc1c[nH]cn1')
mp_B = Chem.MolFromSmiles('NCCc1c[nH]c[nH+]1')
mpp = Chem.MolFromSmiles('[NH3+]CCc1c[nH]c[nH+]1')

jhjensen2

pm6-dh+ eps=78.4 cycles=200 charge=1


C  -1.80630 1 -1.29240 1 -0.04450 1
C  -1.07800 1 -0.22540 1  0.75060 1
N  -0.23770 1  0.65500 1 -0.15110 1
C   0.26310 1  1.87190 1  0.58650 1
C   0.85450 1 -0.04100 1 -0.93790 1
C   1.87420 1 -0.73340 1 -0.05330 1
H  -2.50750 1 -1.82630 1  0.60510 1

jhjensen2

 !GAMESS input file for DFTB3/SMD optimization
 $contrl runtyp=optimize icharg=1 nprint=-5 nzvar=1 $end
 $system mwords=20 $end
 $zmat dlc=.t. auto=.t. $end
 $scf npunch=0 $end
 $statpt nstep=200 opttol=0.0005 $end
 $pcm solvnt=water smd=.t. $end
 $system modio=31 $end
 $basis gbasis=dftb $end
 $dftb ndftb=3 dampxh=.t. dampex=4.0 $end

jhjensen2

#making a strip plot from a csv file using seaborn
import matplotlib.pyplot as plt
import seaborn as sns
import pandas as pd
import csv
import sys

filename = sys.argv[1]
reader = csv.DictReader(open(filename))

jhjensen2

Hydrogen	HCl
Helium	He
Lithium	LiCl
Beryllium	Be
Boron	B
Carbon	C
Nitrogen	N
Oxygen	O
Fluorine	F
Neon	Ne