Hi Jan,
Thanks, 6 digits is OK! Forcing V3000 did the trick:
sdf_out=Chem.SDWriter(outfile)
sdf_out.SetForceV3000(True)
Best,
Michal
On Fri, 5 Oct 2018 at 12:59, Jan Holst Jensen <j...@biochemfusion.com> wrote:
> Hi Michal,
>
> V2000 format is restricted by its specification to fixed format with 4
> decimals. V3000 output is not restricted to a fixed format, but the current
> code still rounds it in practice as seen below.
>
> To get extra precision you could change the formatting of x, y, and z
> coordinate output in Code/GraphMol/FileParsers/MolFileWriter.cpp, function
> GetV3000MolFileAtomLine(),
> look for the
>
> ss << " " << x << " " << y << " " << z;
>
> line. Adding extra digits to the X, Y, and Z coordinates *should* not
> cause issues for compliant V3000 readers.
>
> Cheers
> -- Jan
>
> >>> import rdkit
> >>> from rdkit import Chem
> >>> from Chem import AllChem
> >>> m = Chem.MolFromSmiles('CC')
> >>> AllChem.Compute2DCoords(m)
> 0
> >>> m.GetConformer(0).SetAtomPosition(0,
> rdkit.Geometry.Point3D(0.123456789, 0.2, 0.3))
> >>>
> print(Chem.MolToMolBlock(m))
> RDKit 2D
>
> 2 1 0 0 0 0 0 0 0 0999 V2000
> 0.1235 0.2000 0.3000 C 0 0 0 0 0 0 0 0 0 0 0 0
> <== 4 decimal digits
> 0.7500 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 1 2 1 0
> M END
>
> >>> print(Chem.MolToMolBlock(m, forceV3000=True))
>
> RDKit 2D
>
> 0 0 0 0 0 0 0 0 0 0999 V3000
> M V30 BEGIN CTAB
> M V30 COUNTS 2 1 0 0 0
> M V30 BEGIN ATOM
> M V30 1 C 0.123457 0.2 0.3 0 <== 6 decimal digits
> M V30 2 C 0.75 -5.55112e-17 0 0
> M V30 END ATOM
> M V30 BEGIN BOND
> M V30 1 1 1 2
> M V30 END BOND
> M V30 END CTAB
> M END
>
> >>>
>
> On 2018-10-05 11:42, Michal Krompiec wrote:
>
> Hello,
> Is it possible to control the number of significant digits of XYZ
> coordinates? I am modifying coordinates of my molecules
> using SetAtomPosition but when I save them into an SDF it seems that the
> precision is limited to 4 digits after the decimal point (I'd like 10
> instead...).
> Best wishes,
> Michal
>
>
>
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
