Hello, We are converting CML files into SDFiles using this command : cmd>obabel example.cml -O example.sdf
That works fine. But in a few cases, the conversion is not done. The problem happens when there is data on a atom. For example, <http://forums.openbabel.org/file/n4659781/example.png> In this case, the CML looks like : <?xml version='1.0' encoding='windows-1252'?><cml xmlns="http://www.chemaxon.com"; xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"; xsi:schemaLocation="http://www.chemaxon.com/marvin/schema/mrvSchema_14_8_4.xsd"; version="ChemAxon file format v14.8.4, generated by v14.9.8.0"> <MDocument> <MChemicalStruct> <molecule molID="m1"> <atomArray atomID="a1 a2 a3 a4 a5 a6 a7" elementType="C C C C C N C" mrvStereoGroup="0 or1 0 0 0 0 0" lonePair="0 0 0 0 0 1 0" sgroupRef="0 sg1 0 0 0 0 0" x2="1.333679121828039 1.3336791218280368 2.6673582436560745 2.6673582436560714 1.3336791218280346 0.0 1.3322676295501878E-15" y2="3.850000000000002 2.310000000000002 1.5399999999999978 -2.220446049250313E-15 -0.77 1.9984014443252818E-15 1.5400000000000018" /> <bondArray> <bond id="b1" atomRefs2="a2 a1" order="1"> <bondStereo>W</bondStereo> </bond> <bond id="b2" atomRefs2="a2 a3" order="1" /> <bond id="b3" atomRefs2="a3 a4" order="1" /> <bond id="b4" atomRefs2="a4 a5" order="1" /> <bond id="b5" atomRefs2="a5 a6" order="1" /> <bond id="b6" atomRefs2="a6 a7" order="1" /> <bond id="b7" atomRefs2="a2 a7" order="1" /> </bondArray> <molecule id="sg1" role="DataSgroup" molID="m2" atomRefs="a2" fieldName="[DUP]" x="0.000000000000000" y="0.000000000000000" placement="Relative" unitsDisplayed="Unit displayed" context="Atom" fieldData="Enantiomer1" /> </molecule> </MChemicalStruct> <MElectronContainer id="o2" occupation="0 0" radical="0"> <MElectron atomRefs="m1.a6" difLoc="0.0 0.0 0.0" /> <MElectron atomRefs="m1.a6" difLoc="0.0 0.0 0.0" /> </MElectronContainer> </MDocument> </cml> Is there a parameter to add in the command line for making the conversion works in such case ? Can we ignore the data which is added on the atom ? Thanks, Sebastien. -- View this message in context: http://forums.openbabel.org/Conversion-CML-to-SDF-tp4659781.html Sent from the General discussion mailing list archive at Nabble.com. ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
