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[Cml-cvs] schema25/examples/experimental benzene0_intermed.xml, NONE, 1.1 aspirin_intermed.xml, 1.1, 1.2 benzene0_basic.xml, 1.1, 1.2 benzene0_concise.xml, 1.1, 1.2 benzene2_intermed.xml, 1.1, 1.2 copoly_basic.xml, 1.2, 1.3 copoly_concise.xml, 1.2, 1.3 etoac_complete.xml, 1.1, 1.2 etoac_explicit.xml, 1.1, 1.2 etoac_intermed.xml, 1.1, 1.2
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From: Peter Murray-R. <pe...@us...> - 2006-06-23 16:11:39
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Update of /cvsroot/cml/schema25/examples/experimental In directory sc8-pr-cvs4.sourceforge.net:/tmp/cvs-serv31652/examples/experimental Modified Files: aspirin_intermed.xml benzene0_basic.xml benzene0_concise.xml benzene2_intermed.xml copoly_basic.xml copoly_concise.xml etoac_complete.xml etoac_explicit.xml etoac_intermed.xml Added Files: benzene0_intermed.xml Log Message: revised examples Index: etoac_intermed.xml =================================================================== RCS file: /cvsroot/cml/schema25/examples/experimental/etoac_intermed.xml,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** etoac_intermed.xml 21 Jun 2006 12:42:00 -0000 1.1 --- etoac_intermed.xml 23 Jun 2006 16:11:33 -0000 1.2 *************** *** 1,35 **** <?xml version="1.0" encoding="UTF-8"?> - <!-- - <molecule id="etoac" convention="cml:PML-basic" xmlns:g="http://www.xml-cml.org/mols/geom" xmlns="http://www.xml-cml.org/schema"> - <join convention="fragmentContainer"> - <molecule ref="g:acetate"> - <join right="r1"/> - </molecule> - <join order="1"> - <torsion>180.0</torsion> - </join> - <molecule ref="g:et"> - <join left="r1"/> - </molecule> - </join> - </molecule> - --> - <!-- - <?xml version="1.0" encoding="UTF-8"?> - <molecule id="etoac" convention="cml:PML-intermediate" xmlns:g="http://www.xml-cml.org/mols/geom" xmlns="http://www.xml-cml.org/schema"> - <molecule ref="g:acetate"> - <arg name="idx"> - <scalar dataType="xsd:string">1</scalar> - </arg> - </molecule> - <torsion>180.0</torsion> - <join atomRefs2="g:acetate_1_r1 g:et_2_r1" id="g:acetate_1_r1_g:et_2_r1"/> - <molecule ref="g:et"> - <arg name="idx"> - <scalar dataType="xsd:string">2</scalar> - </arg> - </molecule> - </molecule> - --> <molecule id="etoac" convention="cml:PML-intermediate" xmlns:g="http://www.xml-cml.org/mols/geom" xmlns="http://www.xml-cml.org/schema"> <molecule ref="g:acetate"> --- 1,3 ---- *************** *** 39,43 **** </molecule> <join atomRefs2="g:acetate_1_r1 g:et_2_r1" id="g:acetate_1_r1_g:et_2_r1"> ! <torsion>180</torsion> </join> <molecule ref="g:et"> --- 7,11 ---- </molecule> <join atomRefs2="g:acetate_1_r1 g:et_2_r1" id="g:acetate_1_r1_g:et_2_r1"> ! <torsion>180.0</torsion> </join> <molecule ref="g:et"> *************** *** 47,49 **** </molecule> </molecule> - --- 15,16 ---- Index: benzene0_basic.xml =================================================================== RCS file: /cvsroot/cml/schema25/examples/experimental/benzene0_basic.xml,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** benzene0_basic.xml 21 Jun 2006 12:42:00 -0000 1.1 --- benzene0_basic.xml 23 Jun 2006 16:11:33 -0000 1.2 *************** *** 31,41 **** </join> <molecule ref="f:ophenylene"> ! <join left="r5" right="r1"/> </molecule> ! <join order="3"> <torsion>180.0</torsion> </join> <molecule ref="f:br"> ! <join left="r6"/> </molecule> </join> --- 31,41 ---- </join> <molecule ref="f:ophenylene"> ! <join left="r2" right="r1"/> </molecule> ! <join order="1"> <torsion>180.0</torsion> </join> <molecule ref="f:br"> ! <join left="r1"/> </molecule> </join> Index: benzene2_intermed.xml =================================================================== RCS file: /cvsroot/cml/schema25/examples/experimental/benzene2_intermed.xml,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** benzene2_intermed.xml 12 Jun 2006 21:58:37 -0000 1.1 --- benzene2_intermed.xml 23 Jun 2006 16:11:33 -0000 1.2 *************** *** 36,40 **** </arg> </molecule> ! <join atomRefs2="f:benzene_3_r2 f:me_7_r1" id="f:benzene_3_r2_f:me_7_r1"/> <molecule ref="f:me"> <arg name="idx"> --- 36,40 ---- </arg> </molecule> ! <join atomRefs2="f:benzene_1_r2 f:me_7_r1" id="f:benzene_1_r2_f:me_7_r1"/> <molecule ref="f:me"> <arg name="idx"> --- NEW FILE: benzene0_intermed.xml --- <?xml version="1.0" encoding="UTF-8"?> <molecule id="benzene0" convention="cml:PML-intermediate" xmlns:f="http://www.xml-cml.org/mols/frags" xmlns="http://www.xml-cml.org/schema"> <molecule ref="f:me"> <arg name="idx"> <scalar dataType="xsd:string">1</scalar> </arg> </molecule> <join atomRefs2="f:me_1_r1 f:benzene_2_r2" id="f:me_1_r1_f:benzene_2_r2"> <torsion>60.0</torsion> </join> <molecule ref="f:benzene"> <arg name="idx"> <scalar dataType="xsd:string">2</scalar> </arg> </molecule> <join atomRefs2="f:benzene_2_r3 f:cl_3_r3" id="f:benzene_2_r3_f:cl_3_r3"> <torsion>70.0</torsion> </join> <molecule ref="f:cl"> <arg name="idx"> <scalar dataType="xsd:string">3</scalar> </arg> </molecule> <join atomRefs2="f:benzene_2_r4 f:i_4_r4" id="f:benzene_2_r4_f:i_4_r4"> <torsion>80.0</torsion> </join> <molecule ref="f:i"> <arg name="idx"> <scalar dataType="xsd:string">4</scalar> </arg> </molecule> <join atomRefs2="f:benzene_2_r1 f:ophenylene_5_r2" id="f:benzene_2_r1_f:ophenylene_5_r2"> <torsion>90.0</torsion> </join> <molecule ref="f:ophenylene"> <arg name="idx"> <scalar dataType="xsd:string">5</scalar> </arg> </molecule> <join atomRefs2="f:ophenylene_5_r1 f:br_6_r1" id="f:ophenylene_5_r1_f:br_6_r1"> <torsion>180.0</torsion> </join> <molecule ref="f:br"> <arg name="idx"> <scalar dataType="xsd:string">6</scalar> </arg> </molecule> </molecule> Index: aspirin_intermed.xml =================================================================== RCS file: /cvsroot/cml/schema25/examples/experimental/aspirin_intermed.xml,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** aspirin_intermed.xml 12 Jun 2006 21:58:37 -0000 1.1 --- aspirin_intermed.xml 23 Jun 2006 16:11:33 -0000 1.2 *************** *** 6,10 **** </arg> </molecule> ! <join atomRefs2="f:acetate_1_r1 f:ophenylene_2_r1" id="f:acetate_1_r1_f:ophenylene_2_r1"/> <molecule ref="f:ophenylene"> <arg name="idx"> --- 6,12 ---- </arg> </molecule> ! <join atomRefs2="f:acetate_1_r1 f:ophenylene_2_r1" id="f:acetate_1_r1_f:ophenylene_2_r1"> ! <torsion>180.0</torsion> ! </join> <molecule ref="f:ophenylene"> <arg name="idx"> Index: copoly_concise.xml =================================================================== RCS file: /cvsroot/cml/schema25/examples/experimental/copoly_concise.xml,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** copoly_concise.xml 21 Jun 2006 12:42:00 -0000 1.2 --- copoly_concise.xml 23 Jun 2006 16:11:33 -0000 1.3 *************** *** 4,7 **** xmlns:f='http://www.xml-cml.org/mols/frags' convention='cml:PML-concise' ! formula='f:oh}r1-(r1{f:po}r2)*(3)-(r1{f:eo}r2)*(4)-r1{f:me' /> --- 4,7 ---- xmlns:f='http://www.xml-cml.org/mols/frags' convention='cml:PML-concise' ! formula='f:oh}r1-(r1{f:po}r2-[60])*(3)-(r1{f:eo}r2-[180])*(4)-r1{f:me' /> Index: etoac_complete.xml =================================================================== RCS file: /cvsroot/cml/schema25/examples/experimental/etoac_complete.xml,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** etoac_complete.xml 21 Jun 2006 12:42:00 -0000 1.1 --- etoac_complete.xml 23 Jun 2006 16:11:33 -0000 1.2 *************** *** 30,32 **** <length atomRefs2="et_2_a1 et_2_a2">1.54</length> <name>ethyl_2</name> ! </molecule> \ No newline at end of file --- 30,33 ---- <length atomRefs2="et_2_a1 et_2_a2">1.54</length> <name>ethyl_2</name> ! <torsion>180.0</torsion> ! </molecule> Index: benzene0_concise.xml =================================================================== RCS file: /cvsroot/cml/schema25/examples/experimental/benzene0_concise.xml,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** benzene0_concise.xml 21 Jun 2006 12:42:00 -0000 1.1 --- benzene0_concise.xml 23 Jun 2006 16:11:33 -0000 1.2 *************** *** 7,10 **** [r3-[70]r3{f:cl] [r4-[80]r4{f:i] ! }r1-[90]r5{f:ophenylene}r1-[180]r6{f:br' /> --- 7,10 ---- [r3-[70]r3{f:cl] [r4-[80]r4{f:i] ! }r1-[90]r2{f:ophenylene}r1-[180]r1{f:br' /> Index: copoly_basic.xml =================================================================== RCS file: /cvsroot/cml/schema25/examples/experimental/copoly_basic.xml,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** copoly_basic.xml 21 Jun 2006 12:42:00 -0000 1.2 --- copoly_basic.xml 23 Jun 2006 16:11:33 -0000 1.3 *************** *** 5,15 **** <join right="r1"/> </molecule> <molecule ref="f:po" countExpression="*(3)"> <join left="r1" right="r2"/> ! <join order="1"/> <molecule ref=""/> </molecule> <molecule ref="f:eo" countExpression="*(4)"> <join left="r1" right="r2"/> <molecule ref=""/> </molecule> --- 5,21 ---- <join right="r1"/> </molecule> + <join order="1"/> <molecule ref="f:po" countExpression="*(3)"> <join left="r1" right="r2"/> ! <join order="1"> ! <torsion>60.0</torsion> ! </join> <molecule ref=""/> </molecule> <molecule ref="f:eo" countExpression="*(4)"> <join left="r1" right="r2"/> + <join order="1"> + <torsion>180.0</torsion> + </join> <molecule ref=""/> </molecule> Index: etoac_explicit.xml =================================================================== RCS file: /cvsroot/cml/schema25/examples/experimental/etoac_explicit.xml,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** etoac_explicit.xml 21 Jun 2006 12:42:00 -0000 1.1 --- etoac_explicit.xml 23 Jun 2006 16:11:33 -0000 1.2 *************** *** 1,16 **** <molecule id="etoac" convention="cml:PML-explicit" xmlns:g="http://www.xml-cml.org/mols/geom" xmlns="http://www.xml-cml.org/schema"> <molecule role="fragment" id="acetate_1"> <atomArray> ! <atom elementType="C" hydrogenCount="3" id="acetate_1_a1"/> ! <atom elementType="C" hydrogenCount="0" id="acetate_1_a2"/> ! <atom elementType="O" hydrogenCount="0" id="acetate_1_a3"/> ! <atom elementType="O" hydrogenCount="0" id="acetate_1_a4"/> ! <atom elementType="R" id="acetate_1_r1"/> </atomArray> <bondArray> ! <bond order="1" id="acetate_1_a1_acetate_1_a2" atomRefs2="acetate_1_a1 acetate_1_a2"/> ! <bond order="2" id="acetate_1_a2_acetate_1_a3" atomRefs2="acetate_1_a2 acetate_1_a3"/> ! <bond order="1" id="acetate_1_a2_acetate_1_a4" atomRefs2="acetate_1_a2 acetate_1_a4"/> ! <bond order="1" id="acetate_1_a4_acetate_1_r1" atomRefs2="acetate_1_a4 acetate_1_r1"/> </bondArray> <name>acetate_1</name> --- 1,17 ---- + <?xml version="1.0" encoding="UTF-8"?> <molecule id="etoac" convention="cml:PML-explicit" xmlns:g="http://www.xml-cml.org/mols/geom" xmlns="http://www.xml-cml.org/schema"> <molecule role="fragment" id="acetate_1"> <atomArray> ! <atom elementType="C" hydrogenCount="3" id="acetate_1_a1"> </atom> ! <atom elementType="C" hydrogenCount="0" id="acetate_1_a2"> </atom> ! <atom elementType="O" hydrogenCount="0" id="acetate_1_a3"> </atom> ! <atom elementType="O" hydrogenCount="0" id="acetate_1_a4"> </atom> ! <atom elementType="R" id="acetate_1_r1"> </atom> </atomArray> <bondArray> ! <bond order="1" id="acetate_1_a1_acetate_1_a2" atomRefs2="acetate_1_a1 acetate_1_a2"> </bond> ! <bond order="2" id="acetate_1_a2_acetate_1_a3" atomRefs2="acetate_1_a2 acetate_1_a3"> </bond> ! <bond order="1" id="acetate_1_a2_acetate_1_a4" atomRefs2="acetate_1_a2 acetate_1_a4"> </bond> ! <bond order="1" id="acetate_1_a4_acetate_1_r1" atomRefs2="acetate_1_a4 acetate_1_r1"> </bond> </bondArray> <name>acetate_1</name> *************** *** 25,38 **** <torsion atomRefs4="acetate_1_a1 acetate_1_a2 acetate_1_a4 acetate_1_r1">180</torsion> </molecule> ! <join atomRefs2="g:acetate_1_r1 g:et_2_r1" id="g:acetate_1_r1_g:et_2_r1"/> <molecule role="fragment" id="et_2"> <atomArray> ! <atom elementType="C" hydrogenCount="3" id="et_2_a1"/> ! <atom elementType="C" hydrogenCount="2" id="et_2_a2"/> ! <atom elementType="R" id="et_2_r1"/> </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_a2_et_2_r1" atomRefs2="et_2_a2 et_2_r1"/> </bondArray> <name>ethyl_2</name> --- 26,41 ---- <torsion atomRefs4="acetate_1_a1 acetate_1_a2 acetate_1_a4 acetate_1_r1">180</torsion> </molecule> ! <join atomRefs2="g:acetate_1_r1 g:et_2_r1" id="g:acetate_1_r1_g:et_2_r1"> ! <torsion>180.0</torsion> ! </join> <molecule role="fragment" id="et_2"> <atomArray> ! <atom elementType="C" hydrogenCount="3" id="et_2_a1"> </atom> ! <atom elementType="C" hydrogenCount="2" id="et_2_a2"> </atom> ! <atom elementType="R" id="et_2_r1"> </atom> </atomArray> <bondArray> ! <bond order="1" id="et_2_a1_et_2_a2" atomRefs2="et_2_a1 et_2_a2"> </bond> ! <bond order="1" id="et_2_a2_et_2_r1" atomRefs2="et_2_a2 et_2_r1"> </bond> </bondArray> <name>ethyl_2</name> |