Nicolas Vervelle wrote: >Hi again, > >there are still some problems with the readers (and some that weren't >here yesterday). >When running the tests, the CML, Gaussian and MolPro tests fail (MolPro >was working before). > >Error: ERROR IN XmlReader.parseReaderXML - java.lang.NullPointerException >Error: ERROR IN XmlReader.parseReaderXML - org.xml.sax.SAXParseException >- The element type "molecule" must be terminated by the matching end-tag >"</molecule>". > > checkFile (cml/ci6455_I_symm.cml) :No atoms in file
that file is broken: <molecule id="ci6455_I" xmlns="http://www.xml-cml.org/schema/cml2/core"; xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"; xsi:schemaLocation="http://www.xml-cml.org/schema/cml2/core cmlAll.xsd">> note the two >> and, later, <crystal> <scalar dictRef="cif:_cell_length_a">8.781 </scalar> <scalar dictRef="cif:_cell_length_b">8.845 </scalar> <scalar dictRef="cif:_cell_length_c">10.171 </scalar> <scalar dictRef="cif:_cell_angle_alpha">90.00 </scalar> <scalar dictRef="cif:_cell_angle_beta">101.34 </scalar> <scalar dictRef="cif:_cell_angle_gamma">90.00 </scalar> <symmetry> <matrix rows="3" columns="4" dataType="xsd:float">1.0 0.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 0.0 1.0 0.0 </matrix> <matrix rows="3" columns="4" dataType="xsd:float">-1.0 0.0 0.0 0.0 0.0 1.0 0.0 0.5 0.0 0.0 -1.0 0.5 </matrix> <matrix rows="3" columns="4" dataType="xsd:float">-1.0 0.0 0.0 0.0 0.0 -1.0 0.0 0.0 0.0 0.0 -1.0 0.0 </matrix> <matrix rows="3" columns="4" dataType="xsd:float">1.0 0.0 0.0 0.0 0.0 -1.0 0.0 -0.5 0.0 0.0 1.0 -0.5 </matrix> </symmetry> </crystal> Problems here: 1) I can't find cif:_cell_angle_alpha in the xsd. Is this genuine? 2) Jmol isn't set up to read the operator matrices like this. (Although it can reconstruct the Jones Faithful notation from them if it did.) CML should support Jones Faithful -- people should not be required to convert this simple-to-parse information into matrix format. Besides, it's more precise in its more mathematically correct fractional form: "x-5/6". Removal of that > (and possibly my recent fixes) reads this file just fine, sans symmetry. >Error: java.lang.ArrayIndexOutOfBoundsException - 6 >Error: Could not read file - java.lang.ArrayIndexOutOfBoundsException - 5 >checkFile (gaussian/tms.log) :Could not read >file:java.lang.ArrayIndexOutOfBoundsException: 5 > > I've escaped that one -- not supporting reading Gaussian 94 MOs. >Error: ERROR IN XmlReader.parseReaderXML - java.lang.NullPointerException >checkFile (molpro/vib.xml) :No atoms in file > > > ok, that's fixed. >Nico > > >------------------------------------------------------------------------- >Using Tomcat but need to do more? Need to support web services, security? >Get stuff done quickly with pre-integrated technology to make your job easier >Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo >http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 >_______________________________________________ >Jmol-developers mailing list >[email protected] >https://lists.sourceforge.net/lists/listinfo/jmol-developers > > ------------------------------------------------------------------------- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
