Hi Eric,
I don't know if there is a recommended way, but there's an easy way for sure!
from rdkit import Chem
m = Chem.Mol() #creates a blank molecule, can use an existing RDKit molecule
though
em = Chem.EditableMol(m)
idx1 = em.AddAtom(Chem.Atom(6)) #this returns the RDKit index of the atom
you're creating, which is atomic number 6
idx2 = em.AddAtom(Chem.Atom(6))
bondIdx = em.AddBond(idx1,idx2, Chem.BondType.SINGLE) #returns the RDKit index
of the bond you're creating
m = em.GetMol()
Chem.SanitizeMol(m)
from rdkit.Chem import AllChem
AllChem.EmbedMolecule(m)
AllChem.MMFFOptimizeMolecule(m)
print Chem.MolToMolBlock(m)
RDKit 3D
2 1 0 0 0 0 0 0 0 0999 V2000
0.7540 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.7540 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
M END
Best,
Nick
Nicholas C. Firth | PhD Student | Cancer Therapeutics
The Institute of Cancer Research | 15 Cotswold Road | Belmont | Sutton | Surrey
| SM2 5NG
T 020 8722 4033 | E [email protected]<mailto:[email protected]> |
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On 22 May 2015, at 15:22, Eric Smoll
<[email protected]<mailto:[email protected]>> wrote:
Hello RDKIT users,
I have a molecular data structure with the connectivity of all atoms in my
molecule. Is there a recommended way to build a mol object by manually
specifying each atom and each bond perhaps relaxing the coordinates with a
forcefield?
Best,
Eric
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