Skip to content

Instantly share code, notes, and snippets.

@greglandrum

greglandrum/fragment_canon.py

Created August 2, 2017 04:21
Show Gist options
  • Star 0 You must be signed in to star a gist
  • Fork 0 You must be signed in to fork a gist
  • Save greglandrum/f4e2f2f2ad311560d8ab36874d503843 to your computer and use it in GitHub Desktop.
Save greglandrum/f4e2f2f2ad311560d8ab36874d503843 to your computer and use it in GitHub Desktop.
Download ZIP
Raw
fragment_canon.py
from rdkit import Chem
m = Chem.RWMol()
for i in range(3):
a = Chem.Atom(6)
m.AddAtom(a)
a = Chem.Atom(0)
m.AddAtom(a)
m.GetAtomWithIdx(0).SetIsAromatic(True) # set atom 0 as aromatic
m.GetAtomWithIdx(0).SetNoImplicit(True)
m.GetAtomWithIdx(2).SetNoImplicit(True)
m.GetAtomWithIdx(0).SetNumExplicitHs(1)
m.GetAtomWithIdx(2).SetNumExplicitHs(2)
m.GetAtomWithIdx(3).SetAtomMapNum(1)
m.AddBond(0, 1, Chem.rdchem.BondType.SINGLE)
m.AddBond(1, 2, Chem.rdchem.BondType.SINGLE)
m.AddBond(1, 3, Chem.rdchem.BondType.SINGLE)
print(Chem.MolToSmiles(m))
#2 ===========
m2 = Chem.RWMol()
for i in range(3):
a = Chem.Atom(6)
m2.AddAtom(a)
a = Chem.Atom(0)
m2.AddAtom(a)
m2.GetAtomWithIdx(2).SetIsAromatic(True) # set atom 2 as aromatic
m2.GetAtomWithIdx(3).SetAtomMapNum(1)
m2.GetAtomWithIdx(0).SetNoImplicit(True)
m2.GetAtomWithIdx(2).SetNoImplicit(True)
m2.GetAtomWithIdx(2).SetNumExplicitHs(1)
m2.GetAtomWithIdx(0).SetNumExplicitHs(2)
m2.AddBond(0, 1, Chem.rdchem.BondType.SINGLE)
m2.AddBond(1, 2, Chem.rdchem.BondType.SINGLE)
m2.AddBond(1, 3, Chem.rdchem.BondType.SINGLE)
print(Chem.MolToSmiles(m2))
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment