Ah, but there is, just a little hidden :-). The source-and-timestamp line of each molfile in the SDF contains that information. The line is the second line of the molfile and you can find the 2D/3D tag as the last two characters of that line. An example:
:MOLFILE_BEGINS: Mol2Comp0618061807*2D* 1 0 0 0 0 0 0 0 0 0999 V2000 10.2967 -1.5283 0.0000 Ar 0 0 0 0 0 0 0 0 0 0 0 0 M END :MOLFILE_ENDS: Cheers -- Jan On 2023-12-13 03:39, Mandar Kulkarni wrote:
Hello,I am using RDKit 2023.9.2's SDMolSupplier to read docked SDF files (V2000 formats, suppl = Chem.SDMolSupplier(sdf_file);) and getting a warning as:Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.I could not figure out how Rdkit is guessing it as 2D structure, as there is no such information in SDF. Is there any more information need to provide SDMolSupplier to make it understand it's a 3D molecule?I kindly look forward to hearing to suggestions. TIhanks in advance, Mandar Kulkarni
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