Hi Michal, The old SDF format (aka V2000 CTAB) is column-based, as things often were in the era of Fortran 77 and punch cards. Not only the precision but also the exact position of each value on the line is specified! Here's what the spec says:
The Atom Block is made up of atom lines, one line per atom with the following format: xxxxx.xxxxyyyyy.yyyyzzzzz.zzzz aaaddcccssshhhbbbvvvHHHrrriiimmmnnneee which explains why you see four digits after the decimal point. Also note that in a huge blow to readability, no spaces are required between the coordinates; if you have coordinates with five digits before the decimal point, the numbers run into each other, and if you have even more digits, the number doesn't even fit! There are also limits in the number of atoms for similar reasons. But I digress... In the newer "V3000", the atom line is not column-based, which I believe gives more freedom to implementers to decide the precision of the coordinates. You can force RDKit to write in this format by calling SetForceV3000(True) on your writer object. I tried it and I get 5 digits after the decimal point instead of 4, so at least that's a start. Looking at the RDKit code (function GetV3000MolFileAtomLine), it just writes the coordinates without setting the precision, so what you get is the default stringstream conversion. Here's where one could in principle adjust this precision, but there's clearly no API to do so at the moment. Hope this helps, Ivan On Fri, Oct 5, 2018 at 5:44 AM Michal Krompiec <michal.kromp...@gmail.com> 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 >
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