> A question I have is why you want to access the bond wedging. This is very good question so I will begin with answering this. I'm writing a module, which converts *mrv files to molfiles, both ways. In my case, the original mrv file looks like this:
<cml><MDocument><MChemicalStruct><molecule molID="m1"><atomArray><atom id="a1" elementType="C" x2="-3.1249866416667733" y2="-0.5015733293207466"/><atom id="a2" elementType="C" x2="-4.458533297665067" y2="-1.2715733231607467"/><atom id="a3" elementType="C" x2="-4.458533297665067" y2="-2.81175997750592"/><atom id="a4" elementType="C" x2="-3.1249866416667733" y2="-3.58175997134592"/><atom id="a5" elementType="C" x2="-1.7912533190033066" y2="-2.81175997750592"/><atom id="a6" elementType="C" x2="-1.7912533190033066" y2="-1.2715733231607467"/><atom id="a7" elementType="C" x2="-0.45751999633984003" y2="-0.5013866626555733"/><atom id="a8" elementType="O" x2="-0.45751999633984003" y2="1.0384266583592534"/><atom id="a9" elementType="C" x2="0.87583999299328" y2="-1.2713866564955734"/><atom id="a10" elementType="C" x2="0.87583999299328" y2="-2.8113866441755735"/></atomArray><bondArray><bond atomRefs2="a1 a2" order="2"/><bond atomRefs2="a2 a3" order="1"/><bond atomRefs2="a3 a4" order="2"/><bond atomRefs2="a4 a5" order="1"/><bond atomRefs2="a5 a6" order="2"/><bond atomRefs2="a6 a1" order="1"/><bond atomRefs2="a6 a7" order="1"/><bond atomRefs2="a7 a9" order="1"/><bond atomRefs2="a9 a10" order="1"/><bond atomRefs2="a7 a8" order="1"><bondStereo>W</bondStereo></bond></bondArray></molecule></MChemicalStruct></MDocument></cml> It's easy to spot, that the last bond have additional tag - "bondStereo" with value 'W'. Looking at this specification http://download.accelrys.com/freeware/ctfile-formats/ctfile-formats.zip, page 50 I can see that this can be translated into '1' in 4th field in bond block and the field is called 'bond stereo', the same as mrv's bond tag - this is the actual reason why I've used term 'stereo' in my email. So the resulting molfile looks like this: 10 10 0 0 0 0 0 0 0 0999 V2000 -1.6741 -0.2687 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3885 -0.6812 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3885 -1.5063 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6741 -1.9188 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9596 -1.5063 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9596 -0.6812 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2451 -0.2686 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2451 0.5563 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.4692 -0.6811 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4692 -1.5061 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 0 0 0 2 3 1 0 0 0 0 3 4 2 0 0 0 0 4 5 1 0 0 0 0 5 6 2 0 0 0 0 6 1 1 0 0 0 0 6 7 1 0 0 0 0 7 9 1 0 0 0 0 9 10 1 0 0 0 0 7 8 1 1 0 0 0 M END Now imagine I only have this molfile and I want to convert it back to *mrv. I don't want to write my own parser for molfiles when I know that RDKit can already parse it. But I need to extract this 'bond stereo' information from within RDKit somehow. Now when you say that this '1' or 'W' value corresponds to bond direction, I'm guessing that 'direction' can store only two values: up and down so '1' and '6' ('W' and 'H' in marvin terms). So what about other values which this field can have, If for example I have this molfile: 10 10 0 0 0 0 0 0 0 0999 V2000 -1.6741 -0.2687 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3885 -0.6812 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3885 -1.5063 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6741 -1.9188 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9596 -1.5063 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9596 -0.6812 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2451 -0.2686 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2451 0.5563 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.4692 -0.6811 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4692 -1.5061 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 0 0 0 2 3 1 0 0 0 0 3 4 2 0 0 0 0 4 5 1 0 0 0 0 5 6 2 0 0 0 0 6 1 1 0 0 0 0 6 7 1 0 0 0 0 7 9 1 0 0 0 0 9 10 1 0 0 0 0 7 8 1 4 0 0 0 M END So 4 instead of 1, how I will get this information from RDKit? ------------------------------------------------------------------------------ Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/ _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
