Hi Axel, Imagine you are working on open source project which can handle mrv files. In such a case you probably wouldn't like to use external proprietary software and this is exactly my case.
Michał On Fri, Aug 22, 2014 at 10:15 AM, Axel Pahl <chemis...@gmx.de> wrote: > Dear Micha, > > have you considered using the commandline tool molconvert that is part of > MarvinSketch, which can do just that (and many other things): > > molconvert mol mol.mrv -o mol.mol > > > > It should be under bin/ in the Marvin installation > > > > for batch processing you can e.g. use a small shell script: > > for f in *.mrv; do > echo " converting $f..." > BN=$(basename $f .mrv) > molconvert mol $f -o $BN.mol > done > > Hope, this helps. > > > Kind regards, > > Axel > > > >> 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. 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