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Jan H. Jensen jhjensen2

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jhjensen2 / make_product_from_reactant.py
Created December 4, 2017 13:26
from rdkit import Chem
from rdkit.Chem import AllChem
#reactant_smiles = "C12=CC=CC=CC1CC=C2"
#reactant_smiles = "N#CC1(C#N)C2C=CC=CC=C2C=C1C3=CC=CC=C3"
reactant_smiles = "N#CC1(C#N)C2C=CC=C(C=CC=C3)C3=C2C=C1C4=CC=CC=C4"
reactant = Chem.MolFromSmiles(reactant_smiles)
print Chem.MolToSmiles(reactant)
Chem.Kekulize(reactant,clearAromaticFlags=True)
@jhjensen2
jhjensen2 / molecule_generator.py
Last active September 3, 2017 12:26
create molecules using RDKit
from rdkit import Chem
from rdkit.Chem import AllChem
parent_smiles = 'c1ccccc1'
rxn_smarts_list = ['[cX3;H1:1]>>[*:1]F','[cX3;H1:1]>>[*:1]O']
molecule_substitutions = {}
molecules = []
mol = Chem.MolFromSmiles(parent_smiles)
molecule_substitutions[0] = [mol]
molecules.append(mol)
@jhjensen2
jhjensen2 / smiles2png.py
Created November 5, 2016 10:43
Converts a SMILES string to a 2D picture
import sys
sys.path.append("/usr/local/lib/python2.7/site-packages/")
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem import Draw
from rdkit.sping import PIL
filename = sys.argv[1]
file = open(filename, "r+")
@jhjensen2
jhjensen2 / elements.smiles
Created November 5, 2016 08:33
List containing a SMILE string for a closed shell molecules for each element + program that converts the list to a set of sdf files
Hydrogen HCl
Helium He
Lithium LiCl
Beryllium Be
Boron B
Carbon C
Nitrogen N
Oxygen O
Fluorine F
Neon Ne
@jhjensen2
jhjensen2 / stripplotfromcsv.py
Created October 19, 2016 17:49
#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
jhjensen2 / GAMESS_DFTB3-SMD_opt.inp
Created October 17, 2016 09:21
!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
jhjensen2 / MOPAC input file for soln phase optimization
Created October 17, 2016 07:48
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
jhjensen2 / find_ref.py
Last active August 22, 2016 18:19
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
jhjensen2 / conf_search_w_rdkit
Created August 7, 2016 13:35
#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
jhjensen2 / disorder.py
Last active July 21, 2016 10:47
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)]