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 V20000.1235 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
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