User 9b0b2c1b48
25-06-2014 15:46:15
When I export a reaction that contains curved arrows to mrv file, the atomRefs are not correct. For example the following reaction was drawn on the demo marvinjs on chemaoxn site. Below are the MEFlow arrow tags I extracted from the mrv file. Shouldn't the second MEFlow arrow refer to m2 instead of m1?
<MEFlow id="o1" arcAngle="270"><MAtomSetPoint atomRefs="m1.a1 m1.a2"/><MAtomSetPoint atomRefs="m1.a2 m1.a3"/></MEFlow>
<MEFlow id="o2" arcAngle="270"><MAtomSetPoint atomRefs="m1.a7 m1.a8"/><MAtomSetPoint atomRefs="m1.a6 m1.a7"/></MEFlow>
ChemAxon 996dedebe0
30-06-2014 10:31:13
Dear carl,
Thank you for your feedback. If chemaxon webservices are set properly while using MarvinJS, this problem will not occur.
Explanation:
client side MRV export stores arrows as "graphical objects", not reaction symbols. Therefore there is still only one molecule in your document.
Example without webservice:
<cml><MDocument><MChemicalStruct><molecule molID="m1"><atomArray><atom id="a1" elementType="C" x2="-11.536551666665922" y2="-1.4413649907607469"/><atom id="a2" elementType="C" x2="-12.870098322664212" y2="-0.6713649969207469"/><atom id="a3" elementType="C" x2="-12.870098322664212" y2="0.8684483240940799"/><atom id="a4" elementType="C" x2="-10.202818344002456" y2="0.8684483240940799"/><atom id="a5" elementType="C" x2="-10.202818344002456" y2="-0.6713649969207469"/><atom id="a6" elementType="C" x2="-1.8750933333325848" y2="2.191134987679253"/><atom id="a7" elementType="C" x2="-3.2086399893308792" y2="1.421134993839254"/><atom id="a8" elementType="C" x2="-3.2086399893308792" y2="-0.11905166050591998"/><atom id="a9" elementType="C" x2="-1.8750933333325848" y2="-0.8890516543459199"/><atom id="a10" elementType="C" x2="-0.5413600106691203" y2="-0.11905166050591998"/><atom id="a11" elementType="C" x2="-0.5413600106691203" y2="1.421134993839254"/></atomArray><bondArray><bond atomRefs2="a1 a2" order="1"/><bond atomRefs2="a1 a5" order="1"/><bond atomRefs2="a2 a3" order="1"/><bond atomRefs2="a3 a4" order="1"/><bond atomRefs2="a4 a5" order="1"/><bond atomRefs2="a6 a7" order="2"/><bond atomRefs2="a11 a6" order="1"/><bond atomRefs2="a7 a8" order="1"/><bond atomRefs2="a8 a9" order="2"/><bond atomRefs2="a9 a10" order="1"/><bond atomRefs2="a10 a11" order="2"/></bondArray></molecule></MChemicalStruct><MEFlow id="o1" arcAngle="270" headFlags="4"><MAtomSetPoint atomRefs="m1.a1 m1.a2"/><MAtomSetPoint atomRefs="m1.a2 m1.a3"/></MEFlow><MEFlow id="o2" arcAngle="270" headFlags="2"><MAtomSetPoint atomRefs="m1.a6 m1.a7"/><MAtomSetPoint atomRefs="m1.a11 m1.a6"/></MEFlow><MPolyline headLength="0.6" headWidth="0.4" id="o3"><MPoint x="-8.489583333333334" y="0.3125"/><MPoint x="-5.074548630351613" y="0.3125"/></MPolyline></MDocument></cml>
same molecule with ws:
<?xml version="1.0" encoding="UTF-8"?><cml xmlns="http://www.chemaxon.com" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.chemaxon.com/marvin/help/formats/schema/mrvSchema_6_2_0.xsd" version="ChemAxon file format v6.2, generated by v6.3.0"><MDocument><MChemicalStruct><reaction><arrow type="DEFAULT" x1="-1.7838541666666679" y1="-0.06238499845925305" x2="1.6311805363150533" y2="-0.06238499845925305"></arrow><reactantList><molecule molID="m1"><atomArray atomID="a1 a2 a3 a4 a5" elementType="C C C C C" x2="-4.830822499999256 -6.164369155997546 -6.164369155997546 -3.4970891773357895 -3.4970891773357895" y2="-1.81624998922 -1.04624999538 0.49356332563482685 0.49356332563482685 -1.04624999538"></atomArray><bondArray><bond id="b1" atomRefs2="a1 a2" order="1"></bond><bond id="b2" atomRefs2="a1 a5" order="1"></bond><bond id="b3" atomRefs2="a2 a3" order="1"></bond><bond id="b4" atomRefs2="a3 a4" order="1"></bond><bond id="b5" atomRefs2="a4 a5" order="1"></bond></bondArray></molecule></reactantList><productList><molecule molID="m2"><atomArray atomID="a1 a2 a3 a4 a5 a6" elementType="C C C C C C" x2="4.830635833334082 3.497089177335787 3.497089177335787 4.830635833334082 6.164369155997546 6.164369155997546" y2="1.81624998922 1.0462499953800009 -0.493936658965173 -1.263936652805173 -0.493936658965173 1.0462499953800009"></atomArray><bondArray><bond id="b1" atomRefs2="a1 a2" order="2"></bond><bond id="b2" atomRefs2="a6 a1" order="1"></bond><bond id="b3" atomRefs2="a2 a3" order="1"></bond><bond id="b4" atomRefs2="a3 a4" order="2"></bond><bond id="b5" atomRefs2="a4 a5" order="1"></bond><bond id="b6" atomRefs2="a5 a6" order="2"></bond></bondArray></molecule></productList></reaction></MChemicalStruct><MEFlow id="o2" arcAngle="270.0" headFlags="4" headLength="0.6" headWidth="0.5" baseElectronContainerIndex="-1" baseElectronIndexInContainer="0"><MAtomSetPoint atomRefs="m1.a1 m1.a2"></MAtomSetPoint><MAtomSetPoint atomRefs="m1.a2 m1.a3"></MAtomSetPoint></MEFlow><MEFlow id="o3" arcAngle="270.0" headFlags="2" headLength="0.6" headWidth="0.5" baseElectronContainerIndex="-1" baseElectronIndexInContainer="0"><MAtomSetPoint atomRefs="m2.a1 m2.a2"></MAtomSetPoint><MAtomSetPoint atomRefs="m2.a6 m2.a1"></MAtomSetPoint></MEFlow></MDocument></cml>
If our web service is used, set properly, and kept up to date, MarvinJS will automatically convert the structure to "reaction", and the electron flow arrows will refer to the appropriate fragment.
I encourage you to use our web services, and please contact us, if you have difficulties in usage or configuration.
All the best,
Janos