Sebastian While reading CML files, OB ignores most elements and attributes it does not understand. But the <molecule> element (for the SGroup) embedded within the main <molecule> is not handled properly. I don't think there is an option to bypass this (see obabel -L cml). It seems this issue was recognized but not fixed 11 years ago when the code was written.
Chris On 01/03/2017 10:40, Sebastien wrote: > <?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 ? ------------------------------------------------------------------------------ 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
