I agree almost 100% with Nick's answer. The one change I would make is to
use Chem.RWMol() instead of Chem.EditableMol(). This is new functionality
in the next release and gives you a bit more flexibility with how you work
with the editable object.
There's more information in the documentation here:
http://www.rdkit.org/docs/GettingStartedInPython.html#editing-molecules
Best,
-greg
On Fri, May 22, 2015 at 4:39 PM, Nicholas Firth <[email protected]>
wrote:
> 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] | *W* www.icr.ac.uk |
> *Twitter* @ICRnews <https://twitter.com/ICRnews>
>
> *Facebook* www.facebook.com/theinstituteofcancerresearch
>
> *Making the discoveries that defeat cancer*
>
>
> On 22 May 2015, at 15:22, Eric Smoll <[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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