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[Joelib-help] Multiple molecules input to Convert
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From: Peter Murray-R. <pm...@ca...> - 2003-06-16 22:24:00
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Greetings,
I'm interested in exploring JOELIB for querying medium numbers of CML files
in a repository. I have issued convert.bat with appropriate parameters for
a file with several CML molecules in a <list> element. I include a small
example at the bottom with just two.
D:\sourceforge\joelib\JOELib-20030519>convert -icml test.cml -osdf junk1.sdf
C:\j2sdk1.4.1/bin/java.exe -cp
.;C:\xml\saxon\saxon7.jar;C:\sourceforge\markup\l
ib\wh2fo.jar;C:\sourceforge\jumbo\lib\jakarta-regexp-1.2.jar;C:\Xindice\java\lib
\Xindice.jar;D:\sourceforge\joelib\JOELib-20030519\build;C:\j2sdk1.4.1\lib\tools
.jar;D:\sourceforge\joelib\JOELib-20030519\build;.;lib\ant.jar;;lib\crimson.jar;
;lib\jaxp.jar;;lib\junit-3.2.jar;;lib\log4j.jar;;lib\xerces.jar;;C:\j2sdk1.4.1\l
ib\tools.jar;D:\sourceforge\joelib\JOELib-20030519\build;.;lib\ant.jar;;lib\crim
son.jar;;lib\jaxp.jar;;lib\junit-3.2.jar;;lib\log4j.jar;;lib\xerces.jar;
joelib.
test.Convert -icml test.cml -osdf junk1.sdf
23:03:40 [INFO ] joelib.data.JOEElementTable - Using element
table:
joelib/data/plain/element.txt
23:03:40 [INFO ] joelib.io.IOTypeHolder - 12 input/output
type
s loaded.
23:03:41 [INFO ] joelib.io.types.ChemicalMarkupLanguage - Using Xerces
XML par
ser.
23:03:41 [INFO ] joelib.io.types.ChemicalMarkupLanguage - Deactivated
validati
on
23:03:41 [INFO ] joelib.test.Convert - Start file
conversio
n ...
23:03:42 [INFO ] joelib.data.JOEAromaticTyper - Using
aromaticity mo
del: joelib/data/plain/aromatic.txt
23:03:42 [INFO ] joelib.data.JOEAtomTyper - Using atom type
mode
l: joelib/data/plain/atomtype.txt
23:03:42 [INFO ] joelib.test.Convert - ... 1 molecules
succ
essful converted in 861 ms.
D:\sourceforge\joelib\JOELib-20030519>dir junk1.sdf
Volume in drive D is data
Volume Serial Number is 7C28-B533
Directory of D:\sourceforge\joelib\JOELib-20030519
16/06/2003 23:03 4,194 junk1.sdf
1 File(s) 4,194 bytes
0 Dir(s) 1,918,160,896 bytes free
The junk1.sdf consists of the two molecules merged together rather than two
separate MOL files in an SDF file. The input was:
<list><molecule title="NSC 1"><atomArray><atom id="a1" elementType="O"
x3="0.0021" y3="-0.0041" z3="0.0020"></atom>
<atom id="a2" elementType="O" x3="-0.0691" y3="5.2414" z3="0.0323"></atom>
<atom id="a3" elementType="C" x3="-0.0144" y3="1.2102" z3="0.0087"></atom>
<atom id="a4" elementType="C" x3="-1.3034" y3="1.9312" z3="0.031"></atom>
<atom id="a5" elementType="C" x3="1.2546" y3="1.9661" z3="6.0E-4"></atom>
<atom id="a6" elementType="C" x3="-1.3215" y3="3.2712" z3="0.0389"></atom>
<atom id="a7" elementType="C" x3="1.2365" y3="3.3061" z3="0.0085"></atom>
<atom id="a8" elementType="C" x3="-0.0526" y3="4.0271" z3="0.0252"></atom>
<atom id="a9" elementType="C" x3="-2.598" y3="1.16" z3="0.0445"></atom>
<atom id="a10" elementType="H" x3="2.1971" y3="1.4389" z3="-0.0112"></atom>
<atom id="a11" elementType="H" x3="-2.2641" y3="3.7984" z3="0.0511"></atom>
<atom id="a12" elementType="H" x3="2.1643" y3="3.8588" z3="-0.0015"></atom>
<atom id="a13" elementType="H" x3="-2.3843" y3="0.0912" z3="0.0355"></atom>
<atom id="a14" elementType="H" x3="-3.1608" y3="1.4105" z3="0.9438"></atom>
<atom id="a15" elementType="H" x3="-3.1853" y3="1.4206" z3="-0.836"></atom>
</atomArray>
<bondArray><bond atomRefs2="a1 a3" id="b1" order="2"></bond>
<bond atomRefs2="a2 a8" id="b2" order="2"></bond>
<bond atomRefs2="a3 a5" id="b3" order="1"></bond>
<bond atomRefs2="a3 a4" id="b4" order="1"></bond>
<bond atomRefs2="a4 a6" id="b5" order="2"></bond>
<bond atomRefs2="a4 a9" id="b6" order="1"></bond>
<bond atomRefs2="a5 a7" id="b7" order="2"></bond>
<bond atomRefs2="a5 a10" id="b8" order="1"></bond>
<bond atomRefs2="a6 a8" id="b9" order="1"></bond>
<bond atomRefs2="a6 a11" id="b10" order="1"></bond>
<bond atomRefs2="a7 a8" id="b11" order="1"></bond>
<bond atomRefs2="a7 a12" id="b12" order="1"></bond>
<bond atomRefs2="a9 a13" id="b13" order="1"></bond>
<bond atomRefs2="a9 a14" id="b14" order="1"></bond>
<bond atomRefs2="a9 a15" id="b15" order="1"></bond>
</bondArray>
</molecule>
<molecule title="NSC 2"><atomArray><atom id="a1" elementType="C"
x3="-0.0165" y3="1.3666" z3="0.0096"></atom>
<atom id="a2" elementType="C" x3="8.2041" y3="6.9305" z3="2.5032"></atom>
<atom id="a3" elementType="C" x3="0.0021" y3="-0.0041" z3="0.0020"></atom>
<atom id="a4" elementType="C" x3="1.1892" y3="2.1056" z3="0.0020"></atom>
<atom id="a5" elementType="C" x3="2.5286" y3="4.0208" z3="-0.0013"></atom>
<atom id="a6" elementType="C" x3="4.7319" y3="5.7338" z3="2.3165"></atom>
<atom id="a7" elementType="C" x3="7.0224" y3="6.1538" z3="2.5156"></atom>
<atom id="a8" elementType="C" x3="9.4205" y3="6.3592" z3="2.7733"></atom>
<atom id="a9" elementType="C" x3="1.1946" y3="-0.7124" z3="-0.0132"></atom>
<atom id="a10" elementType="C" x3="2.384" y3="1.3506" z3="-0.0135"></atom>
<atom id="a11" elementType="C" x3="7.1801" y3="4.7823" z3="2.8185"></atom>
<atom id="a12" elementType="C" x3="9.5376" y3="5.0085" z3="3.0668"></atom>
<atom id="a13" elementType="C" x3="2.393" y3="-0.0213" z3="-0.021"></atom>
<atom id="a14" elementType="C" x3="8.4019" y3="4.2188" z3="3.0869"></atom>
<atom id="a15" elementType="N" x3="5.7567" y3="6.5587" z3="2.2741"></atom>
<atom id="a16" elementType="S" x3="5.5106" y3="4.1804" z3="2.7344"></atom>
<atom id="a17" elementType="S" x3="3.0264" y3="6.0746" z3="2.0342"></atom>
<atom id="a18" elementType="S" x3="2.9255" y3="5.7375" z3="0.0045"></atom>
<atom id="a19" elementType="S" x3="3.6321" y3="2.6151" z3="-0.0192"></atom>
<atom id="a20" elementType="N" x3="1.3439" y3="3.4473" z3="0.0074"></atom>
<atom id="a21" elementType="H" x3="-0.9624" y3="1.8878" z3="0.0169"></atom>
<atom id="a22" elementType="H" x3="8.1482" y3="7.9844" z3="2.274"></atom>
<atom id="a23" elementType="H" x3="-0.9329" y3="-0.5446" z3="0.0084"></atom>
<atom id="a24" elementType="H" x3="10.3079" y3="6.9745" z3="2.757"></atom>
<atom id="a25" elementType="H" x3="1.1876" y3="-1.7924" z3="-0.0186"></atom>
<atom id="a26" elementType="H" x3="10.5055" y3="4.5777" z3="3.2764"></atom>
<atom id="a27" elementType="H" x3="3.3299" y3="-0.5584" z3="-0.0325"></atom>
<atom id="a28" elementType="H" x3="8.4764" y3="3.1655" z3="3.3136"></atom>
</atomArray>
<bondArray><bond atomRefs2="a1 a3" id="b1" order="2"></bond>
<bond atomRefs2="a1 a4" id="b2" order="1"></bond>
<bond atomRefs2="a1 a21" id="b3" order="1"></bond>
<bond atomRefs2="a2 a8" id="b4" order="2"></bond>
<bond atomRefs2="a2 a7" id="b5" order="1"></bond>
<bond atomRefs2="a2 a22" id="b6" order="1"></bond>
<bond atomRefs2="a3 a9" id="b7" order="1"></bond>
<bond atomRefs2="a3 a23" id="b8" order="1"></bond>
<bond atomRefs2="a4 a10" id="b9" order="2"></bond>
<bond atomRefs2="a4 a20" id="b10" order="1"></bond>
<bond atomRefs2="a5 a18" id="b11" order="1"></bond>
<bond atomRefs2="a5 a20" id="b12" order="2"></bond>
<bond atomRefs2="a5 a19" id="b13" order="1"></bond>
<bond atomRefs2="a6 a17" id="b14" order="1"></bond>
<bond atomRefs2="a6 a15" id="b15" order="2"></bond>
<bond atomRefs2="a6 a16" id="b16" order="1"></bond>
<bond atomRefs2="a7 a15" id="b17" order="1"></bond>
<bond atomRefs2="a7 a11" id="b18" order="2"></bond>
<bond atomRefs2="a8 a12" id="b19" order="1"></bond>
<bond atomRefs2="a8 a24" id="b20" order="1"></bond>
<bond atomRefs2="a9 a13" id="b21" order="2"></bond>
<bond atomRefs2="a9 a25" id="b22" order="1"></bond>
<bond atomRefs2="a10 a19" id="b23" order="1"></bond>
<bond atomRefs2="a10 a13" id="b24" order="1"></bond>
<bond atomRefs2="a11 a16" id="b25" order="1"></bond>
<bond atomRefs2="a11 a14" id="b26" order="1"></bond>
<bond atomRefs2="a12 a14" id="b27" order="2"></bond>
<bond atomRefs2="a12 a26" id="b28" order="1"></bond>
<bond atomRefs2="a13 a27" id="b29" order="1"></bond>
<bond atomRefs2="a14 a28" id="b30" order="1"></bond>
<bond atomRefs2="a17 a18" id="b31" order="1"></bond>
</bondArray>
</molecule>
</list>
Hope this makes sense...
P.
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