Help about molecule dimension

Hi ,





This may not be the correct section to post, but could not find any appropriate one.


My query is as follows-





Marvin molecule has 3 dimensions that can be used 0,2 and 3. By default smiles gets the dimension 0 and others I suppose get the dimension as 2.


I would be glad if anyone could explain these 3 dimensions and how they matter in terms of Chirality and parity.





Thanks,





Ameya

I try to answer to your question, but to tell the truth the question is not totally clear for me.


So a molecule can have

0 dimension - no coordinates specified


2 dimension - only the x, y coordinates are specified the z coordinate is 0


3 dimension - x, y , z coordinates are specified

As you see the dimension is strongly connected to the number of variable in the coordinate system.








The parity is specified as follows:

0D use @ or @@


2D use the coordinates and the wedges (this defines atoms above or below the plane)


3D use the coordinates only

All the best


Andras

Hi,





Thanks for the reply. I should have made my question more clear.





I meant that when I form a Molecule with smiles string as an input , the dimension that gets set to the molecule is 0. For a molecule formed from sdf, the default dimension that is set is 2.


So I wanted to clarify how the dimension and chirality, parity are related..





Thanks,





Ameya