Hi Mandar,
> On Dec 13, 2023, at 03:39, Mandar Kulkarni <[email protected]>
> wrote:
> I could not figure out how Rdkit is guessing it as 2D structure, as there is
> no such information in SDF.
Line 2 of the SDF record looks something like:
RDKit 2D
This line has the format (quoting from the documentation):
IIPPPPPPPPMMDDYYHHmmddSSssssssssssEEEEEEEEEEEERRRRRR
A2<--A8--><---A10-->A2I2<--F10.5-><---F12.5--><-I6-> )
where "User's first and last initials (l), program name (P), date/time
(M/D/Y,H:m), dimensional codes (d) such as 2D or 3D, scaling factors (S, s),
energy (E) if modeling program input, internal registry number (R)"
In the example I gave, most of these fields are blank, except for the program
name ("RDKit") and the dimension code "2D" in columns 21-22 (if I counted
right). The dimension code indicates the structure is expected to be in 2D.
> Is there any more information need to provide SDMolSupplier to make it
> understand it's a 3D molecule?
It is only a warning. RDKit interprets the molecule as 3D despite the warning.
The file format documentation also says: "The “dimensional code” is maintained
explicitly. Thus “3D” really means 3D, although “2D” will be interpreted as 3D
if any non-zero Z-coordinates are found.
Best regards,
Andrew
[email protected]
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