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cml-cvs
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From: Peter Murray-R. <pe...@us...> - 2006-12-14 09:53:01
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Update of /cvsroot/cml/jumbo53/target/test-outputs/org/xmlcml/cml/tools/PolymerTool In directory sc8-pr-cvs4.sourceforge.net:/tmp/cvs-serv1885/target/test-outputs/org/xmlcml/cml/tools/PolymerTool Added Files: Tag: jumbo-53-beta1 linear3_complete.xml etoac1_explicit.xml linear3_cartesian.xml linear3_intermed.xml linear3_basic.xml etoac1_cartesian.xml etoac1_basic.xml etoac1_complete.xml etoac1_intermed.xml linear3_explicit.xml Log Message: added examples --- NEW FILE: linear3_explicit.xml --- <?xml version="1.0" encoding="UTF-8"?> <molecule id="linear3" convention="cml:PML-explicit" xmlns:g="http://www.xml-cml.org/mols/geom1" xmlns="http://www.xml-cml.org/schema"><molecule role="fragment" id="acetoxy_1"> <atomArray> <atom elementType="R" xFract="0.7232" yFract="0.3453" zFract="0.08396" formalCharge="0" hydrogenCount="0" x3="5.904284388252377" y3="6.9400220825147425" z3="1.3354655365567598" id="acetoxy_1_r1"/> <atom elementType="O" x3="6.393952073348176" y3="7.481432789999999" z3="1.3355287286108608" xFract="0.853" yFract="0.40329" zFract="0.08749" formalCharge="0" hydrogenCount="0" id="acetoxy_1_a70"/> <atom elementType="C" x3="7.470354790502688" y3="7.21912165" z3="2.1153032017509776" xFract="0.9966" yFract="0.38915" zFract="0.12895" formalCharge="0" hydrogenCount="0" id="acetoxy_1_a71"/> <atom elementType="O" x3="7.621770771606594" y3="6.2131009200000005" z3="2.7265105769419966" xFract="1.0168" yFract="0.33492" zFract="0.15894" formalCharge="0" hydrogenCount="0" id="acetoxy_1_a72"/> <atom elementType="C" x3="8.407334871591223" y3="8.375034459999998" z3="2.09259931555679" xFract="1.1216" yFract="0.45146" zFract="0.13125" formalCharge="0" hydrogenCount="0" id="acetoxy_1_a73"/> <atom elementType="H" x3="9.290344900009062" y3="8.0103218" z3="1.9961034580073869" xFract="1.2394" yFract="0.4318" zFract="0.1298" formalCharge="0" hydrogenCount="0" id="acetoxy_1_a74"/> <atom elementType="H" x3="8.339122721687978" y3="8.830276" z3="2.9353942128717265" xFract="1.1125" yFract="0.476" zFract="0.1716" formalCharge="0" hydrogenCount="0" id="acetoxy_1_a75"/> <atom elementType="H" x3="8.236429704800676" y3="8.9953799" z3="1.3798877395986096" xFract="1.0988" yFract="0.4849" zFract="0.0963" formalCharge="0" hydrogenCount="0" id="acetoxy_1_a76"/> </atomArray> <bondArray> <bond order="S" id="acetoxy_1_r1_acetoxy_1_a70" atomRefs2="acetoxy_1_r1 acetoxy_1_a70"/> <bond order="S" id="acetoxy_1_a70_acetoxy_1_a71" atomRefs2="acetoxy_1_a70 acetoxy_1_a71"/> <bond order="D" id="acetoxy_1_a71_acetoxy_1_a72" atomRefs2="acetoxy_1_a71 acetoxy_1_a72"/> <bond order="S" id="acetoxy_1_a71_acetoxy_1_a73" atomRefs2="acetoxy_1_a71 acetoxy_1_a73"/> <bond order="S" id="acetoxy_1_a73_acetoxy_1_a74" atomRefs2="acetoxy_1_a73 acetoxy_1_a74"/> <bond order="S" id="acetoxy_1_a73_acetoxy_1_a75" atomRefs2="acetoxy_1_a73 acetoxy_1_a75"/> <bond order="S" id="acetoxy_1_a73_acetoxy_1_a76" atomRefs2="acetoxy_1_a73 acetoxy_1_a76"/> </bondArray> </molecule><join atomRefs2="g:acetoxy_1_r1 g:eo_2_r1" id="g:acetoxy_1_r1_g:eo_2_r1" order="1"><torsion>60.0</torsion></join><molecule role="fragment" id="eo_2"> <atomArray> <atom elementType="R" x3="1.0927029508094934" y3="0.019313350096244575" z3="-0.04489307394726355" id="eo_2_r1"/> <atom elementType="C" x3="0.703" y3="-0.593" z3="-0.302" id="eo_2_a2"/> <atom elementType="C" x3="-0.703" y3="-0.593" z3="0.302" id="eo_2_a3"/> <atom elementType="O" x3="-1.426" y3="0.543" z3="-0.174" id="eo_2_a4"/> <atom elementType="H" x3="0.631" y3="-0.548" z3="-1.389" id="eo_2_a6"/> <atom elementType="H" x3="1.224" y3="-1.505" z3="-0.01" id="eo_2_a7"/> <atom elementType="H" x3="-1.224" y3="-1.505" z3="0.0090" id="eo_2_a8"/> <atom elementType="H" x3="-0.631" y3="-0.549" z3="1.389" id="eo_2_a9"/> <atom elementType="R" x3="-2.088651624700404" y3="0.5143203169264062" z3="0.1309103147824182" id="eo_2_r2"/> </atomArray> <bondArray> <bond order="1" id="eo_2_r1_eo_2_a2" atomRefs2="eo_2_r1 eo_2_a2"/> <bond order="1" id="eo_2_a2_eo_2_a3" atomRefs2="eo_2_a2 eo_2_a3"/> <bond order="1" id="eo_2_a2_eo_2_a6" atomRefs2="eo_2_a2 eo_2_a6"/> <bond order="1" id="eo_2_a2_eo_2_a7" atomRefs2="eo_2_a2 eo_2_a7"/> <bond order="1" id="eo_2_a3_eo_2_a4" atomRefs2="eo_2_a3 eo_2_a4"/> <bond order="1" id="eo_2_a3_eo_2_a8" atomRefs2="eo_2_a3 eo_2_a8"/> <bond order="1" id="eo_2_a3_eo_2_a9" atomRefs2="eo_2_a3 eo_2_a9"/> <bond order="1" id="eo_2_a4_eo_2_r2" atomRefs2="eo_2_a4 eo_2_r2"/> </bondArray> </molecule><join atomRefs2="g:eo_2_r2 g:et_3_r1" id="g:eo_2_r2_g:et_3_r1" order="1"><torsion>110.0</torsion></join><molecule role="fragment" id="et_3"> <atomArray> <atom elementType="C" x3="1.998" y3="-0.064" z3="-0.0" id="et_3_a1"/> <atom elementType="C" x3="0.757" y3="0.831" z3="-0.0" id="et_3_a2"/> <atom elementType="R" x3="0.12420633514482571" y3="0.3922834882077524" z3="0.0" id="et_3_r1"/> <atom elementType="H" x3="1.992" y3="-0.694" z3="0.89" id="et_3_a6"/> <atom elementType="H" x3="1.992" y3="-0.694" z3="-0.89" id="et_3_a7"/> <atom elementType="H" x3="2.893" y3="0.557" z3="-0.0" id="et_3_a8"/> <atom elementType="H" x3="0.763" y3="1.46" z3="0.89" id="et_3_a9"/> <atom elementType="H" x3="0.763" y3="1.46" z3="-0.89" id="et_3_a10"/> </atomArray> <bondArray> <bond order="1" id="et_3_a1_et_3_a2" atomRefs2="et_3_a1 et_3_a2"/> <bond order="1" id="et_3_a1_et_3_a6" atomRefs2="et_3_a1 et_3_a6"/> <bond order="1" id="et_3_a1_et_3_a7" atomRefs2="et_3_a1 et_3_a7"/> <bond order="1" id="et_3_a1_et_3_a8" atomRefs2="et_3_a1 et_3_a8"/> <bond order="1" id="et_3_a2_et_3_r1" atomRefs2="et_3_a2 et_3_r1"/> <bond order="1" id="et_3_a2_et_3_a9" atomRefs2="et_3_a2 et_3_a9"/> <bond order="1" id="et_3_a2_et_3_a10" atomRefs2="et_3_a2 et_3_a10"/> </bondArray> </molecule></molecule> --- NEW FILE: etoac1_cartesian.xml --- <?xml version="1.0" encoding="UTF-8"?> <molecule id="etoac1" convention="cml:PML-complete" xmlns:g="http://www.xml-cml.org/mols/geom1" xmlns="http://www.xml-cml.org/schema"><atomArray><atom elementType="O" x3="6.393952073348176" y3="7.481432789999999" z3="1.3355287286108608" xFract="0.853" yFract="0.40329" zFract="0.08749" formalCharge="0" hydrogenCount="0" id="acetoxy_1_a70"/><atom elementType="C" x3="7.470354790502688" y3="7.21912165" z3="2.1153032017509776" xFract="0.9966" yFract="0.38915" zFract="0.12895" formalCharge="0" hydrogenCount="0" id="acetoxy_1_a71"/><atom elementType="O" x3="7.621770771606594" y3="6.2131009200000005" z3="2.7265105769419966" xFract="1.0168" yFract="0.33492" zFract="0.15894" formalCharge="0" hydrogenCount="0" id="acetoxy_1_a72"/><atom elementType="C" x3="8.407334871591223" y3="8.375034459999998" z3="2.09259931555679" xFract="1.1216" yFract="0.45146" zFract="0.13125" formalCharge="0" hydrogenCount="0" id="acetoxy_1_a73"/><atom elementType="H" x3="9.290344900009062" y3="8.0103218" z3="1.9961034580073869" xFract="1.2394" yFract="0.4318" zFract="0.1298" formalCharge="0" hydrogenCount="0" id="acetoxy_1_a74"/><atom elementType="H" x3="8.339122721687978" y3="8.830276" z3="2.9353942128717265" xFract="1.1125" yFract="0.476" zFract="0.1716" formalCharge="0" hydrogenCount="0" id="acetoxy_1_a75"/><atom elementType="H" x3="8.236429704800676" y3="8.9953799" z3="1.3798877395986096" xFract="1.0988" yFract="0.4849" zFract="0.0963" formalCharge="0" hydrogenCount="0" id="acetoxy_1_a76"/><atom elementType="C" id="et_2_a1" x3="4.210456513494849" y3="6.746308255256628" z3="0.4339560225271921"/><atom elementType="C" id="et_2_a2" x3="5.387785597123931" y3="6.368945034893308" z3="1.3353988819243519"/><atom elementType="H" id="et_2_a6" x3="3.7442549516581534" y3="7.658542099138979" z3="0.8074818152332051"/><atom elementType="H" id="et_2_a7" x3="4.56922698885097" y3="6.91257545658768" z3="-0.5822501395158677"/><atom elementType="H" id="et_2_a8" x3="3.479986101470585" y3="5.938175251660526" z3="0.43411619694786974"/><atom elementType="H" id="et_2_a9" x3="5.028921467088362" y3="6.203530824006715" z3="2.3510915889034756"/><atom elementType="H" id="et_2_a10" x3="5.853893504281177" y3="5.457564181455413" z3="0.9613596341544026"/></atomArray><bondArray><bond order="S" id="acetoxy_1_a70_acetoxy_1_a71" atomRefs2="acetoxy_1_a70 acetoxy_1_a71"/><bond order="D" id="acetoxy_1_a71_acetoxy_1_a72" atomRefs2="acetoxy_1_a71 acetoxy_1_a72"/><bond order="S" id="acetoxy_1_a71_acetoxy_1_a73" atomRefs2="acetoxy_1_a71 acetoxy_1_a73"/><bond order="S" id="acetoxy_1_a73_acetoxy_1_a74" atomRefs2="acetoxy_1_a73 acetoxy_1_a74"/><bond order="S" id="acetoxy_1_a73_acetoxy_1_a75" atomRefs2="acetoxy_1_a73 acetoxy_1_a75"/><bond order="S" id="acetoxy_1_a73_acetoxy_1_a76" atomRefs2="acetoxy_1_a73 acetoxy_1_a76"/><bond order="1" id="et_2_a1_et_2_a2" atomRefs2="et_2_a1 et_2_a2"/><bond order="1" id="et_2_a1_et_2_a6" atomRefs2="et_2_a1 et_2_a6"/><bond order="1" id="et_2_a1_et_2_a7" atomRefs2="et_2_a1 et_2_a7"/><bond order="1" id="et_2_a1_et_2_a8" atomRefs2="et_2_a1 et_2_a8"/><bond order="1" id="et_2_a2_et_2_a9" atomRefs2="et_2_a2 et_2_a9"/><bond order="1" id="et_2_a2_et_2_a10" atomRefs2="et_2_a2 et_2_a10"/><bond atomRefs2="acetoxy_1_a70 et_2_a2" id="g:acetoxy_1_r1_g:et_2_r1" order="1"/></bondArray><torsion>180.0</torsion></molecule> --- NEW FILE: linear3_cartesian.xml --- <?xml version="1.0" encoding="UTF-8"?> <molecule id="linear3" convention="cml:PML-complete" xmlns:g="http://www.xml-cml.org/mols/geom1" xmlns="http://www.xml-cml.org/schema"><atomArray><atom elementType="O" x3="6.393952073348176" y3="7.481432789999999" z3="1.3355287286108608" xFract="0.853" yFract="0.40329" zFract="0.08749" formalCharge="0" hydrogenCount="0" id="acetoxy_1_a70"/><atom elementType="C" x3="7.470354790502688" y3="7.21912165" z3="2.1153032017509776" xFract="0.9966" yFract="0.38915" zFract="0.12895" formalCharge="0" hydrogenCount="0" id="acetoxy_1_a71"/><atom elementType="O" x3="7.621770771606594" y3="6.2131009200000005" z3="2.7265105769419966" xFract="1.0168" yFract="0.33492" zFract="0.15894" formalCharge="0" hydrogenCount="0" id="acetoxy_1_a72"/><atom elementType="C" x3="8.407334871591223" y3="8.375034459999998" z3="2.09259931555679" xFract="1.1216" yFract="0.45146" zFract="0.13125" formalCharge="0" hydrogenCount="0" id="acetoxy_1_a73"/><atom elementType="H" x3="9.290344900009062" y3="8.0103218" z3="1.9961034580073869" xFract="1.2394" yFract="0.4318" zFract="0.1298" formalCharge="0" hydrogenCount="0" id="acetoxy_1_a74"/><atom elementType="H" x3="8.339122721687978" y3="8.830276" z3="2.9353942128717265" xFract="1.1125" yFract="0.476" zFract="0.1716" formalCharge="0" hydrogenCount="0" id="acetoxy_1_a75"/><atom elementType="H" x3="8.236429704800676" y3="8.9953799" z3="1.3798877395986096" xFract="1.0988" yFract="0.4849" zFract="0.0963" formalCharge="0" hydrogenCount="0" id="acetoxy_1_a76"/><atom elementType="C" id="eo_2_a2" x3="5.387785597123931" y3="6.368945034893308" z3="1.335398881924352"/><atom elementType="C" id="eo_2_a3" x3="4.884347478272546" y3="6.13657769871661" z3="2.7616553390755634"/><atom elementType="O" id="eo_2_a4" x3="4.172359934809556" y3="7.29081895222003" z3="3.2095413364726575"/><atom elementType="H" id="eo_2_a6" x3="4.548426596455828" y3="6.637894643566737" z3="0.6935884924853444"/><atom elementType="H" id="eo_2_a7" x3="5.853413661232006" y3="5.457000297568167" z3="0.9612380849667521"/><atom elementType="H" id="eo_2_a8" x3="4.220880100506592" y3="5.2713385810348585" z3="2.776018760453216"/><atom elementType="H" id="eo_2_a9" x3="5.733324100465195" y3="5.954354093823406" z3="3.420990043751486"/><atom elementType="C" id="et_3_a1" x3="4.492158087675643" y3="7.866016901436913" z3="5.594446103224573"/><atom elementType="C" id="et_3_a2" x3="3.7088997036763622" y3="6.999543958396256" z3="4.6060954858456515"/><atom elementType="H" id="et_3_a6" x3="5.556115828337749" y3="7.642599075139591" z3="5.510099194699318"/><atom elementType="H" id="et_3_a7" x3="4.323907152371222" y3="8.919199552273092" z3="5.367435251618602"/><atom elementType="H" id="et_3_a8" x3="4.15531471373829" y3="7.6542122923637645" z3="6.6085177718012424"/><atom elementType="H" id="et_3_a9" x3="3.8778626379937773" y3="5.947021962935186" z3="4.832868446970858"/><atom elementType="H" id="et_3_a10" x3="2.645653962027252" y3="7.223622440068687" z3="4.690204503890143"/></atomArray><bondArray><bond order="S" id="acetoxy_1_a70_acetoxy_1_a71" atomRefs2="acetoxy_1_a70 acetoxy_1_a71"/><bond order="D" id="acetoxy_1_a71_acetoxy_1_a72" atomRefs2="acetoxy_1_a71 acetoxy_1_a72"/><bond order="S" id="acetoxy_1_a71_acetoxy_1_a73" atomRefs2="acetoxy_1_a71 acetoxy_1_a73"/><bond order="S" id="acetoxy_1_a73_acetoxy_1_a74" atomRefs2="acetoxy_1_a73 acetoxy_1_a74"/><bond order="S" id="acetoxy_1_a73_acetoxy_1_a75" atomRefs2="acetoxy_1_a73 acetoxy_1_a75"/><bond order="S" id="acetoxy_1_a73_acetoxy_1_a76" atomRefs2="acetoxy_1_a73 acetoxy_1_a76"/><bond order="1" id="eo_2_a2_eo_2_a3" atomRefs2="eo_2_a2 eo_2_a3"/><bond order="1" id="eo_2_a2_eo_2_a6" atomRefs2="eo_2_a2 eo_2_a6"/><bond order="1" id="eo_2_a2_eo_2_a7" atomRefs2="eo_2_a2 eo_2_a7"/><bond order="1" id="eo_2_a3_eo_2_a4" atomRefs2="eo_2_a3 eo_2_a4"/><bond order="1" id="eo_2_a3_eo_2_a8" atomRefs2="eo_2_a3 eo_2_a8"/><bond order="1" id="eo_2_a3_eo_2_a9" atomRefs2="eo_2_a3 eo_2_a9"/><bond order="1" id="et_3_a1_et_3_a2" atomRefs2="et_3_a1 et_3_a2"/><bond order="1" id="et_3_a1_et_3_a6" atomRefs2="et_3_a1 et_3_a6"/><bond order="1" id="et_3_a1_et_3_a7" atomRefs2="et_3_a1 et_3_a7"/><bond order="1" id="et_3_a1_et_3_a8" atomRefs2="et_3_a1 et_3_a8"/><bond order="1" id="et_3_a2_et_3_a9" atomRefs2="et_3_a2 et_3_a9"/><bond order="1" id="et_3_a2_et_3_a10" atomRefs2="et_3_a2 et_3_a10"/><bond atomRefs2="acetoxy_1_a70 eo_2_a2" id="g:acetoxy_1_r1_g:eo_2_r1" order="1"/><bond atomRefs2="eo_2_a4 et_3_a2" id="g:eo_2_r2_g:et_3_r1" order="1"/></bondArray><torsion>60.0</torsion><torsion>110.0</torsion></molecule> --- NEW FILE: linear3_intermed.xml --- <?xml version="1.0" encoding="UTF-8"?> <molecule id="linear3" convention="cml:PML-intermediate" xmlns:g="http://www.xml-cml.org/mols/geom1" xmlns="http://www.xml-cml.org/schema"><molecule ref="g:acetoxy"><arg name="idx"><scalar dataType="xsd:string">1</scalar></arg></molecule><join atomRefs2="g:acetoxy_1_r1 g:eo_2_r1" id="g:acetoxy_1_r1_g:eo_2_r1" order="1"><torsion>60.0</torsion></join><molecule ref="g:eo"><arg name="idx"><scalar dataType="xsd:string">2</scalar></arg></molecule><join atomRefs2="g:eo_2_r2 g:et_3_r1" id="g:eo_2_r2_g:et_3_r1" order="1"><torsion>110.0</torsion></join><molecule ref="g:et"><arg name="idx"><scalar dataType="xsd:string">3</scalar></arg></molecule></molecule> --- NEW FILE: linear3_complete.xml --- <?xml version="1.0" encoding="UTF-8"?> <molecule id="linear3" convention="cml:PML-complete" xmlns:g="http://www.xml-cml.org/mols/geom1" xmlns="http://www.xml-cml.org/schema"><atomArray><atom elementType="O" x3="6.393952073348176" y3="7.481432789999999" z3="1.3355287286108608" xFract="0.853" yFract="0.40329" zFract="0.08749" formalCharge="0" hydrogenCount="0" id="acetoxy_1_a70"/><atom elementType="C" x3="7.470354790502688" y3="7.21912165" z3="2.1153032017509776" xFract="0.9966" yFract="0.38915" zFract="0.12895" formalCharge="0" hydrogenCount="0" id="acetoxy_1_a71"/><atom elementType="O" x3="7.621770771606594" y3="6.2131009200000005" z3="2.7265105769419966" xFract="1.0168" yFract="0.33492" zFract="0.15894" formalCharge="0" hydrogenCount="0" id="acetoxy_1_a72"/><atom elementType="C" x3="8.407334871591223" y3="8.375034459999998" z3="2.09259931555679" xFract="1.1216" yFract="0.45146" zFract="0.13125" formalCharge="0" hydrogenCount="0" id="acetoxy_1_a73"/><atom elementType="H" x3="9.290344900009062" y3="8.0103218" z3="1.9961034580073869" xFract="1.2394" yFract="0.4318" zFract="0.1298" formalCharge="0" hydrogenCount="0" id="acetoxy_1_a74"/><atom elementType="H" x3="8.339122721687978" y3="8.830276" z3="2.9353942128717265" xFract="1.1125" yFract="0.476" zFract="0.1716" formalCharge="0" hydrogenCount="0" id="acetoxy_1_a75"/><atom elementType="H" x3="8.236429704800676" y3="8.9953799" z3="1.3798877395986096" xFract="1.0988" yFract="0.4849" zFract="0.0963" formalCharge="0" hydrogenCount="0" id="acetoxy_1_a76"/><atom elementType="C" id="eo_2_a2" x3="5.387785597123931" y3="6.368945034893308" z3="1.335398881924352"/><atom elementType="C" id="eo_2_a3" x3="4.884347478272546" y3="6.13657769871661" z3="2.7616553390755634"/><atom elementType="O" id="eo_2_a4" x3="4.172359934809556" y3="7.29081895222003" z3="3.2095413364726575"/><atom elementType="H" id="eo_2_a6" x3="4.548426596455828" y3="6.637894643566737" z3="0.6935884924853444"/><atom elementType="H" id="eo_2_a7" x3="5.853413661232006" y3="5.457000297568167" z3="0.9612380849667521"/><atom elementType="H" id="eo_2_a8" x3="4.220880100506592" y3="5.2713385810348585" z3="2.776018760453216"/><atom elementType="H" id="eo_2_a9" x3="5.733324100465195" y3="5.954354093823406" z3="3.420990043751486"/><atom elementType="C" id="et_3_a1" x3="4.492158087675643" y3="7.866016901436913" z3="5.594446103224573"/><atom elementType="C" id="et_3_a2" x3="3.7088997036763622" y3="6.999543958396256" z3="4.6060954858456515"/><atom elementType="H" id="et_3_a6" x3="5.556115828337749" y3="7.642599075139591" z3="5.510099194699318"/><atom elementType="H" id="et_3_a7" x3="4.323907152371222" y3="8.919199552273092" z3="5.367435251618602"/><atom elementType="H" id="et_3_a8" x3="4.15531471373829" y3="7.6542122923637645" z3="6.6085177718012424"/><atom elementType="H" id="et_3_a9" x3="3.8778626379937773" y3="5.947021962935186" z3="4.832868446970858"/><atom elementType="H" id="et_3_a10" x3="2.645653962027252" y3="7.223622440068687" z3="4.690204503890143"/></atomArray><bondArray><bond order="S" id="acetoxy_1_a70_acetoxy_1_a71" atomRefs2="acetoxy_1_a70 acetoxy_1_a71"/><bond order="D" id="acetoxy_1_a71_acetoxy_1_a72" atomRefs2="acetoxy_1_a71 acetoxy_1_a72"/><bond order="S" id="acetoxy_1_a71_acetoxy_1_a73" atomRefs2="acetoxy_1_a71 acetoxy_1_a73"/><bond order="S" id="acetoxy_1_a73_acetoxy_1_a74" atomRefs2="acetoxy_1_a73 acetoxy_1_a74"/><bond order="S" id="acetoxy_1_a73_acetoxy_1_a75" atomRefs2="acetoxy_1_a73 acetoxy_1_a75"/><bond order="S" id="acetoxy_1_a73_acetoxy_1_a76" atomRefs2="acetoxy_1_a73 acetoxy_1_a76"/><bond order="1" id="eo_2_a2_eo_2_a3" atomRefs2="eo_2_a2 eo_2_a3"/><bond order="1" id="eo_2_a2_eo_2_a6" atomRefs2="eo_2_a2 eo_2_a6"/><bond order="1" id="eo_2_a2_eo_2_a7" atomRefs2="eo_2_a2 eo_2_a7"/><bond order="1" id="eo_2_a3_eo_2_a4" atomRefs2="eo_2_a3 eo_2_a4"/><bond order="1" id="eo_2_a3_eo_2_a8" atomRefs2="eo_2_a3 eo_2_a8"/><bond order="1" id="eo_2_a3_eo_2_a9" atomRefs2="eo_2_a3 eo_2_a9"/><bond order="1" id="et_3_a1_et_3_a2" atomRefs2="et_3_a1 et_3_a2"/><bond order="1" id="et_3_a1_et_3_a6" atomRefs2="et_3_a1 et_3_a6"/><bond order="1" id="et_3_a1_et_3_a7" atomRefs2="et_3_a1 et_3_a7"/><bond order="1" id="et_3_a1_et_3_a8" atomRefs2="et_3_a1 et_3_a8"/><bond order="1" id="et_3_a2_et_3_a9" atomRefs2="et_3_a2 et_3_a9"/><bond order="1" id="et_3_a2_et_3_a10" atomRefs2="et_3_a2 et_3_a10"/><bond atomRefs2="acetoxy_1_a70 eo_2_a2" id="g:acetoxy_1_r1_g:eo_2_r1" order="1"/><bond atomRefs2="eo_2_a4 et_3_a2" id="g:eo_2_r2_g:et_3_r1" order="1"/></bondArray><torsion>60.0</torsion><torsion>110.0</torsion></molecule> --- NEW FILE: etoac1_intermed.xml --- <?xml version="1.0" encoding="UTF-8"?> <molecule id="etoac1" convention="cml:PML-intermediate" xmlns:g="http://www.xml-cml.org/mols/geom1" xmlns="http://www.xml-cml.org/schema"><molecule ref="g:acetoxy"><arg name="idx"><scalar dataType="xsd:string">1</scalar></arg></molecule><join atomRefs2="g:acetoxy_1_r1 g:et_2_r1" id="g:acetoxy_1_r1_g:et_2_r1" order="1"><torsion>180.0</torsion></join><molecule ref="g:et"><arg name="idx"><scalar dataType="xsd:string">2</scalar></arg></molecule></molecule> --- NEW FILE: etoac1_complete.xml --- <?xml version="1.0" encoding="UTF-8"?> <molecule id="etoac1" convention="cml:PML-complete" xmlns:g="http://www.xml-cml.org/mols/geom1" xmlns="http://www.xml-cml.org/schema"><atomArray><atom elementType="O" x3="6.393952073348176" y3="7.481432789999999" z3="1.3355287286108608" xFract="0.853" yFract="0.40329" zFract="0.08749" formalCharge="0" hydrogenCount="0" id="acetoxy_1_a70"/><atom elementType="C" x3="7.470354790502688" y3="7.21912165" z3="2.1153032017509776" xFract="0.9966" yFract="0.38915" zFract="0.12895" formalCharge="0" hydrogenCount="0" id="acetoxy_1_a71"/><atom elementType="O" x3="7.621770771606594" y3="6.2131009200000005" z3="2.7265105769419966" xFract="1.0168" yFract="0.33492" zFract="0.15894" formalCharge="0" hydrogenCount="0" id="acetoxy_1_a72"/><atom elementType="C" x3="8.407334871591223" y3="8.375034459999998" z3="2.09259931555679" xFract="1.1216" yFract="0.45146" zFract="0.13125" formalCharge="0" hydrogenCount="0" id="acetoxy_1_a73"/><atom elementType="H" x3="9.290344900009062" y3="8.0103218" z3="1.9961034580073869" xFract="1.2394" yFract="0.4318" zFract="0.1298" formalCharge="0" hydrogenCount="0" id="acetoxy_1_a74"/><atom elementType="H" x3="8.339122721687978" y3="8.830276" z3="2.9353942128717265" xFract="1.1125" yFract="0.476" zFract="0.1716" formalCharge="0" hydrogenCount="0" id="acetoxy_1_a75"/><atom elementType="H" x3="8.236429704800676" y3="8.9953799" z3="1.3798877395986096" xFract="1.0988" yFract="0.4849" zFract="0.0963" formalCharge="0" hydrogenCount="0" id="acetoxy_1_a76"/><atom elementType="C" id="et_2_a1" x3="4.210456513494849" y3="6.746308255256628" z3="0.4339560225271921"/><atom elementType="C" id="et_2_a2" x3="5.387785597123931" y3="6.368945034893308" z3="1.3353988819243519"/><atom elementType="H" id="et_2_a6" x3="3.7442549516581534" y3="7.658542099138979" z3="0.8074818152332051"/><atom elementType="H" id="et_2_a7" x3="4.56922698885097" y3="6.91257545658768" z3="-0.5822501395158677"/><atom elementType="H" id="et_2_a8" x3="3.479986101470585" y3="5.938175251660526" z3="0.43411619694786974"/><atom elementType="H" id="et_2_a9" x3="5.028921467088362" y3="6.203530824006715" z3="2.3510915889034756"/><atom elementType="H" id="et_2_a10" x3="5.853893504281177" y3="5.457564181455413" z3="0.9613596341544026"/></atomArray><bondArray><bond order="S" id="acetoxy_1_a70_acetoxy_1_a71" atomRefs2="acetoxy_1_a70 acetoxy_1_a71"/><bond order="D" id="acetoxy_1_a71_acetoxy_1_a72" atomRefs2="acetoxy_1_a71 acetoxy_1_a72"/><bond order="S" id="acetoxy_1_a71_acetoxy_1_a73" atomRefs2="acetoxy_1_a71 acetoxy_1_a73"/><bond order="S" id="acetoxy_1_a73_acetoxy_1_a74" atomRefs2="acetoxy_1_a73 acetoxy_1_a74"/><bond order="S" id="acetoxy_1_a73_acetoxy_1_a75" atomRefs2="acetoxy_1_a73 acetoxy_1_a75"/><bond order="S" id="acetoxy_1_a73_acetoxy_1_a76" atomRefs2="acetoxy_1_a73 acetoxy_1_a76"/><bond order="1" id="et_2_a1_et_2_a2" atomRefs2="et_2_a1 et_2_a2"/><bond order="1" id="et_2_a1_et_2_a6" atomRefs2="et_2_a1 et_2_a6"/><bond order="1" id="et_2_a1_et_2_a7" atomRefs2="et_2_a1 et_2_a7"/><bond order="1" id="et_2_a1_et_2_a8" atomRefs2="et_2_a1 et_2_a8"/><bond order="1" id="et_2_a2_et_2_a9" atomRefs2="et_2_a2 et_2_a9"/><bond order="1" id="et_2_a2_et_2_a10" atomRefs2="et_2_a2 et_2_a10"/><bond atomRefs2="acetoxy_1_a70 et_2_a2" id="g:acetoxy_1_r1_g:et_2_r1" order="1"/></bondArray><torsion>180.0</torsion></molecule> --- NEW FILE: etoac1_explicit.xml --- <?xml version="1.0" encoding="UTF-8"?> <molecule id="etoac1" convention="cml:PML-explicit" xmlns:g="http://www.xml-cml.org/mols/geom1" xmlns="http://www.xml-cml.org/schema"><molecule role="fragment" id="acetoxy_1"> <atomArray> <atom elementType="R" xFract="0.7232" yFract="0.3453" zFract="0.08396" formalCharge="0" hydrogenCount="0" x3="5.904284388252377" y3="6.9400220825147425" z3="1.3354655365567598" id="acetoxy_1_r1"/> <atom elementType="O" x3="6.393952073348176" y3="7.481432789999999" z3="1.3355287286108608" xFract="0.853" yFract="0.40329" zFract="0.08749" formalCharge="0" hydrogenCount="0" id="acetoxy_1_a70"/> <atom elementType="C" x3="7.470354790502688" y3="7.21912165" z3="2.1153032017509776" xFract="0.9966" yFract="0.38915" zFract="0.12895" formalCharge="0" hydrogenCount="0" id="acetoxy_1_a71"/> <atom elementType="O" x3="7.621770771606594" y3="6.2131009200000005" z3="2.7265105769419966" xFract="1.0168" yFract="0.33492" zFract="0.15894" formalCharge="0" hydrogenCount="0" id="acetoxy_1_a72"/> <atom elementType="C" x3="8.407334871591223" y3="8.375034459999998" z3="2.09259931555679" xFract="1.1216" yFract="0.45146" zFract="0.13125" formalCharge="0" hydrogenCount="0" id="acetoxy_1_a73"/> <atom elementType="H" x3="9.290344900009062" y3="8.0103218" z3="1.9961034580073869" xFract="1.2394" yFract="0.4318" zFract="0.1298" formalCharge="0" hydrogenCount="0" id="acetoxy_1_a74"/> <atom elementType="H" x3="8.339122721687978" y3="8.830276" z3="2.9353942128717265" xFract="1.1125" yFract="0.476" zFract="0.1716" formalCharge="0" hydrogenCount="0" id="acetoxy_1_a75"/> <atom elementType="H" x3="8.236429704800676" y3="8.9953799" z3="1.3798877395986096" xFract="1.0988" yFract="0.4849" zFract="0.0963" formalCharge="0" hydrogenCount="0" id="acetoxy_1_a76"/> </atomArray> <bondArray> <bond order="S" id="acetoxy_1_r1_acetoxy_1_a70" atomRefs2="acetoxy_1_r1 acetoxy_1_a70"/> <bond order="S" id="acetoxy_1_a70_acetoxy_1_a71" atomRefs2="acetoxy_1_a70 acetoxy_1_a71"/> <bond order="D" id="acetoxy_1_a71_acetoxy_1_a72" atomRefs2="acetoxy_1_a71 acetoxy_1_a72"/> <bond order="S" id="acetoxy_1_a71_acetoxy_1_a73" atomRefs2="acetoxy_1_a71 acetoxy_1_a73"/> <bond order="S" id="acetoxy_1_a73_acetoxy_1_a74" atomRefs2="acetoxy_1_a73 acetoxy_1_a74"/> <bond order="S" id="acetoxy_1_a73_acetoxy_1_a75" atomRefs2="acetoxy_1_a73 acetoxy_1_a75"/> <bond order="S" id="acetoxy_1_a73_acetoxy_1_a76" atomRefs2="acetoxy_1_a73 acetoxy_1_a76"/> </bondArray> </molecule><join atomRefs2="g:acetoxy_1_r1 g:et_2_r1" id="g:acetoxy_1_r1_g:et_2_r1" order="1"><torsion>180.0</torsion></join><molecule role="fragment" id="et_2"> <atomArray> <atom elementType="C" x3="1.998" y3="-0.064" z3="-0.0" id="et_2_a1"/> <atom elementType="C" x3="0.757" y3="0.831" z3="-0.0" id="et_2_a2"/> <atom elementType="R" x3="0.12420633514482571" y3="0.3922834882077524" z3="0.0" id="et_2_r1"/> <atom elementType="H" x3="1.992" y3="-0.694" z3="0.89" id="et_2_a6"/> <atom elementType="H" x3="1.992" y3="-0.694" z3="-0.89" id="et_2_a7"/> <atom elementType="H" x3="2.893" y3="0.557" z3="-0.0" id="et_2_a8"/> <atom elementType="H" x3="0.763" y3="1.46" z3="0.89" id="et_2_a9"/> <atom elementType="H" x3="0.763" y3="1.46" z3="-0.89" id="et_2_a10"/> </atomArray> <bondArray> <bond order="1" id="et_2_a1_et_2_a2" atomRefs2="et_2_a1 et_2_a2"/> <bond order="1" id="et_2_a1_et_2_a6" atomRefs2="et_2_a1 et_2_a6"/> <bond order="1" id="et_2_a1_et_2_a7" atomRefs2="et_2_a1 et_2_a7"/> <bond order="1" id="et_2_a1_et_2_a8" atomRefs2="et_2_a1 et_2_a8"/> <bond order="1" id="et_2_a2_et_2_r1" atomRefs2="et_2_a2 et_2_r1"/> <bond order="1" id="et_2_a2_et_2_a9" atomRefs2="et_2_a2 et_2_a9"/> <bond order="1" id="et_2_a2_et_2_a10" atomRefs2="et_2_a2 et_2_a10"/> </bondArray> </molecule></molecule> --- NEW FILE: etoac1_basic.xml --- <?xml version="1.0" encoding="UTF-8"?> <molecule id="etoac1" convention="cml:PML-basic" xmlns:g="http://www.xml-cml.org/mols/geom1" xmlns="http://www.xml-cml.org/schema"><join convention="fragmentContainer"><molecule ref="g:acetoxy"><join right="r1"/></molecule><join order="1"><torsion>180.0</torsion></join><molecule ref="g:et"><join left="r1"/></molecule></join></molecule> --- NEW FILE: linear3_basic.xml --- <?xml version="1.0" encoding="UTF-8"?> <molecule id="linear3" convention="cml:PML-basic" xmlns:g="http://www.xml-cml.org/mols/geom1" xmlns="http://www.xml-cml.org/schema"><join convention="fragmentContainer"><molecule ref="g:acetoxy"><join right="r1"/></molecule><join order="1"><torsion>60.0</torsion></join><molecule ref="g:eo"><join left="r1" right="r2"/></molecule><join order="1"><torsion>110.0</torsion></join><molecule ref="g:et"><join left="r1"/></molecule></join></molecule> |
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