jhjensen2

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

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

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

from rdkit import Chem
from rdkit.Chem import AllChem
from itertools import islice

smiles_list = ['C12=CC=CC=CC1CC=C2']
#smiles_list = ['C1=CC2CC=CC2=c2ccccc2=C1']
rxn_smarts_list = ['[CX3,cX3;H1:1]~[CX3,cX3;H1:2]>>[c:1]1[c:2]cccc1']
molecules = []
mol = Chem.MolFromSmiles(smiles_list[0])
molecules.append(mol)

jhjensen2

from rdkit import Chem
import itertools

atoms = ["C","N","O","F","Si","P","S","Cl","Br","I"]
bonds = ["","=","#"]

raw_smiles = []
mols = []
smiles_list = []

jhjensen2

from rdkit import Chem
from rdkit.Chem import AllChem
from itertools import islice


raw_smiles = ['NCCN']
smiles_list = ['NCCN']
rxn_smarts_list = ['[C:1][*:2][C:3]>>[C:1]1[*:2][C:3]1','[C:1][C:2]>>[C:1][C][C:2]']
molecules = []
mol = Chem.MolFromSmiles(smiles_list[0])

jhjensen2

#!/usr/bin/env python

import copy
import numpy as np
import matplotlib as mpl
import matplotlib.pyplot as plt
import matplotlib.animation as animation


"""

jhjensen2

import numpy as np
import matplotlib.pyplot as plt
from IPython.display import clear_output
import time

n_particles = 100

for x in range(50):
  clear_output(wait=True)
  positions_x = [np.random.random() for i in range(n_particles)]

jhjensen2

from rdkit import Chem
from rdkit.Chem import Draw
from rdkit.Chem.Draw import IPythonConsole
import string

filename_smiles = "/Users/jan/Desktop/diels_alder.smiles"

molecules = []
names = []

jhjensen2

from rdkit import Chem
import itertools

smiles = 'CNCC[NH+](C)CC(F)C'

mol = Chem.MolFromSmiles(smiles)

N_atoms = mol.GetSubstructMatches(Chem.MolFromSmarts('N([*])[*]'))
chiral = Chem.FindMolChiralCenters(mol, includeUnassigned=True)