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From: Stefan K. <sh...@us...> - 2006-10-12 14:34:26
|
Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/webservices In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv14380/src/java/org/openscience/nmrshiftdb/webservices Modified Files: NMRShiftDBServiceBindingImpl.java Log Message: changes in lab system Index: NMRShiftDBServiceBindingImpl.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/webservices/NMRShiftDBServiceBindingImpl.java,v retrieving revision 1.22 retrieving revision 1.23 diff -C2 -r1.22 -r1.23 *** NMRShiftDBServiceBindingImpl.java 9 Oct 2006 13:24:38 -0000 1.22 --- NMRShiftDBServiceBindingImpl.java 12 Oct 2006 14:34:13 -0000 1.23 *************** *** 239,244 **** ValueTriple vt=new ValueTriple(); vt.value1=(float)peak.getXValue(); ! vt.value2=(float)peak.getYValue(); ! String[] atomrefs=peak.getAtomRefs(); if(atomrefs!=null){ for(int l=0;l<atomrefs.length;l++){ --- 239,246 ---- ValueTriple vt=new ValueTriple(); vt.value1=(float)peak.getXValue(); ! if(!Double.isNaN(peak.getYValue())){ ! vt.value2=(float)peak.getYValue(); ! } ! String[] atomrefs=peak.getAtomRefs(); if(atomrefs!=null){ for(int l=0;l<atomrefs.length;l++){ |
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From: Stefan K. <sh...@us...> - 2006-10-12 14:34:19
|
Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/conf/jetspeed/WEB-INF/templates/vm/screens/html In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv14380/src/conf/jetspeed/WEB-INF/templates/vm/screens/html Modified Files: NewAccount.vm Log Message: changes in lab system Index: NewAccount.vm =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/conf/jetspeed/WEB-INF/templates/vm/screens/html/NewAccount.vm,v retrieving revision 1.14 retrieving revision 1.15 diff -C2 -r1.14 -r1.15 *** NewAccount.vm 15 Sep 2006 14:06:40 -0000 1.14 --- NewAccount.vm 12 Oct 2006 14:34:12 -0000 1.15 *************** *** 53,87 **** </tr> <tr bgcolor="#F8F8F8"> <td> Address: </td> <td align=right><input name="address" type="TEXT" value="$!data.Parameters.getString("address")" /> </td> </tr> ! <tr> <td> City: </td> <td align=right><input name="city" type="TEXT" value="$!data.Parameters.getString("city")" /> </td> </tr> <tr bgcolor="#F8F8F8"> ! <td> State: </td> <td align=right><input name="state" type="TEXT" value="$!data.Parameters.getString("state")" /> </td> </tr> <tr> - <td> ZIP Code: </td> - <td align=right><input name="zipcode" type="TEXT" value="$!data.Parameters.getString("zipcode")" /> </td> - </tr> - <tr bgcolor="#F8F8F8"> <td> Country: </td> <td align=right><input name="country" type="TEXT" value="$!data.Parameters.getString("country")" /> </td> </tr> ! <tr> <td> $l10n.USERFORM_EMAILMSG </td> <td align=right><input name="email" type="TEXT" value="$!data.Parameters.getString("email")" /> </td> </tr> ! <tr bgcolor="#F8F8F8"> <td> Web Page: </td> <td align=right><input name="webpage" type="TEXT" value="$!data.Parameters.getString("webpage")" /> </td> </tr> - <tr> - <td> Affiliation: </td> - <td align=right><input name="affiliation" type="TEXT" value="$!data.Parameters.getString("affiliation")" /> </td> - </tr> <tr bgcolor="#F8F8F8"> <td> I want to become a contributor </td> --- 53,87 ---- </tr> <tr bgcolor="#F8F8F8"> + <td> Affiliation/Institute: </td> + <td align=right><input name="affiliation" type="TEXT" value="$!data.Parameters.getString("affiliation")" /> </td> + </tr> + <tr> <td> Address: </td> <td align=right><input name="address" type="TEXT" value="$!data.Parameters.getString("address")" /> </td> </tr> ! <tr bgcolor="#F8F8F8"> ! <td> ZIP Code: </td> ! <td align=right><input name="zipcode" type="TEXT" value="$!data.Parameters.getString("zipcode")" /> </td> ! </tr> ! <tr> <td> City: </td> <td align=right><input name="city" type="TEXT" value="$!data.Parameters.getString("city")" /> </td> </tr> <tr bgcolor="#F8F8F8"> ! <td> State/Province/Land etc.: </td> <td align=right><input name="state" type="TEXT" value="$!data.Parameters.getString("state")" /> </td> </tr> <tr> <td> Country: </td> <td align=right><input name="country" type="TEXT" value="$!data.Parameters.getString("country")" /> </td> </tr> ! <tr bgcolor="#F8F8F8"> <td> $l10n.USERFORM_EMAILMSG </td> <td align=right><input name="email" type="TEXT" value="$!data.Parameters.getString("email")" /> </td> </tr> ! <tr> <td> Web Page: </td> <td align=right><input name="webpage" type="TEXT" value="$!data.Parameters.getString("webpage")" /> </td> </tr> <tr bgcolor="#F8F8F8"> <td> I want to become a contributor </td> |
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From: Stefan K. <sh...@us...> - 2006-10-11 16:54:43
|
Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv30462/src/java/org/openscience/nmrshiftdb Modified Files: NmrshiftdbServlet.java Log Message: the rss now includes inchis Index: NmrshiftdbServlet.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/NmrshiftdbServlet.java,v retrieving revision 1.93 retrieving revision 1.94 diff -C2 -r1.93 -r1.94 *** NmrshiftdbServlet.java 9 Oct 2006 13:24:37 -0000 1.93 --- NmrshiftdbServlet.java 11 Oct 2006 16:54:34 -0000 1.94 *************** *** 45,48 **** --- 45,49 ---- import nu.xom.Element; import nu.xom.Node; + import nu.xom.Text; import org.apache.fop.apps.FOUserAgent; *************** *** 154,157 **** --- 155,166 ---- rssWriter.getCreatormap().put(cdkmol,mol.getNmrshiftdbUser().getUserName()); rssWriter.setCreator(GeneralUtils.getAdminEmail(getServletConfig())); + Vector v = mol.getDBCanonicalNames(); + for (int k = 0; k < v.size(); k++) { + DBCanonicalName canonName = (DBCanonicalName)v.get(k); + if (canonName.getDBCanonicalNameType().getCanonicalNameType()=="INChI") { + rssWriter.getInchimap().put(cdkmol,canonName.getName()); + break; + } + } rssWriter.setTitle("NMRShiftDB"); rssWriter.setLink("http://www.nmrshiftdb.org"); |
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From: Stefan K. <sh...@us...> - 2006-10-11 16:54:38
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/lib In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv30462/lib Modified Files: cdk-libio-cml.jar Log Message: the rss now includes inchis Index: cdk-libio-cml.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/lib/cdk-libio-cml.jar,v retrieving revision 1.40 retrieving revision 1.41 diff -C2 -r1.40 -r1.41 Binary files /tmp/cvsY87Hhh and /tmp/cvs7kr6HX differ |
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From: Stefan K. <sh...@us...> - 2006-10-11 16:32:02
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv20802/src/vmtemplates Modified Files: details.vm Log Message: avoids double inchi= with inchi display Index: details.vm =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/details.vm,v retrieving revision 1.160 retrieving revision 1.161 diff -C2 -r1.160 -r1.161 *** details.vm 10 Oct 2006 15:20:32 -0000 1.160 --- details.vm 11 Oct 2006 16:32:00 -0000 1.161 *************** *** 268,272 **** #end #foreach($canname in $mol.getDBCanonicalNames()) ! <li>#if($canname.getDBCanonicalNameType().getCanonicalNameType()=="INChI") INChI=#end$genutil.getShort($canname.getName()) ($canname.getDBCanonicalNameType().getCanonicalNameType())</li> #end </ul></td></tr> --- 268,272 ---- #end #foreach($canname in $mol.getDBCanonicalNames()) ! <li>$genutil.getShort($canname.getName()) ($canname.getDBCanonicalNameType().getCanonicalNameType())</li> #end </ul></td></tr> |
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From: Stefan K. <sh...@us...> - 2006-10-11 12:25:17
|
Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/portlets/html In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv13190/src/vmtemplates/portlets/html Modified Files: worker-order.vm Log Message: same for machine Index: worker-order.vm =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/portlets/html/worker-order.vm,v retrieving revision 1.21 retrieving revision 1.22 diff -C2 -r1.21 -r1.22 *** worker-order.vm 11 Oct 2006 12:24:07 -0000 1.21 --- worker-order.vm 11 Oct 2006 12:25:14 -0000 1.22 *************** *** 39,43 **** <img src="$image"><br> #end ! Spectrometer: $sample.getDBMachine() ($sample.getDBMachine().getDBCondition().getValue()<br> $sample.getWishedSpectrum()<br> Other nuclei (please specify): $sample.getOtherNuclei()<br> --- 39,43 ---- <img src="$image"><br> #end ! Spectrometer: $sample.getDBMachine().getName() ($sample.getDBMachine().getDBCondition().getValue() Mhz)<br> $sample.getWishedSpectrum()<br> Other nuclei (please specify): $sample.getOtherNuclei()<br> |
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From: Stefan K. <sh...@us...> - 2006-10-11 12:24:09
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/portlets/html In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv12423/src/vmtemplates/portlets/html Modified Files: user-order.vm worker-order.vm Log Message: correct display of solvent in workers portlet of the lab system Index: user-order.vm =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/portlets/html/user-order.vm,v retrieving revision 1.41 retrieving revision 1.42 diff -C2 -r1.41 -r1.42 *** user-order.vm 6 Oct 2006 20:12:11 -0000 1.41 --- user-order.vm 11 Oct 2006 12:24:07 -0000 1.42 *************** *** 199,203 **** </select> #else ! : $sample.getDBMachine().getName() ($sample.getDBMachine().getDBCondition().getValue() #end <br> --- 199,203 ---- </select> #else ! : $sample.getDBMachine().getName() ($sample.getDBMachine().getDBCondition().getValue() Mhz) #end <br> Index: worker-order.vm =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/portlets/html/worker-order.vm,v retrieving revision 1.20 retrieving revision 1.21 diff -C2 -r1.20 -r1.21 *** worker-order.vm 6 Oct 2006 20:12:11 -0000 1.20 --- worker-order.vm 11 Oct 2006 12:24:07 -0000 1.21 *************** *** 35,39 **** Sample I. D.: $sample.getUsersId()<br> Date: $date<br> ! Solvent: $sample.getDBConditionRelated().getValue()<br> #if($image) <img src="$image"><br> --- 35,39 ---- Sample I. D.: $sample.getUsersId()<br> Date: $date<br> ! Solvent: $sample.getDBCondition().getValue()<br> #if($image) <img src="$image"><br> |
Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/html In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv31919/src/html Modified Files: jchempaint-applet-Jama.jar jchempaint-applet-com_ozten.jar jchempaint-applet-core.jar jchempaint-applet-editor-opts.jar jchempaint-applet-editor.jar jchempaint-applet-jas.jar jchempaint-applet-javax_media.jar jchempaint-applet-javax_vecmath.jar jchempaint-applet-nu.jar jchempaint-applet-org.jar jchempaint-applet-org_3pq.jar jchempaint-applet-org_apache.jar jchempaint-applet-org_omegahat.jar jchempaint-applet-org_openscience.jar jchempaint-applet-org_openscience_cdk.jar jchempaint-applet-org_openscience_cdk_applications.jar jchempaint-applet-org_openscience_cdk_applications_jchempaint.jar jchempaint-applet-org_openscience_cdk_config.jar jchempaint-applet-org_openscience_cdk_dict.jar jchempaint-applet-org_openscience_cdk_io.jar jchempaint-applet-org_openscience_cdk_iupac.jar jchempaint-applet-org_openscience_cdk_math.jar jchempaint-applet-org_openscience_cdk_nonotify.jar jchempaint-applet-org_openscience_cdk_qsar.jar jchempaint-applet-org_openscience_cdk_structgen.jar jchempaint-applet-org_openscience_cdk_tools.jar jchempaint-applet-org_w3c.jar jchempaint-applet-org_xmlcml.jar jchempaint-applet-others.jar jchempaint-applet-resources.jar jchempaint-applet-viewer-opts.jar marvin.js Log Message: i do not fully understand this Index: jchempaint-applet-Jama.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-Jama.jar,v retrieving revision 1.18 retrieving revision 1.19 diff -C2 -r1.18 -r1.19 Binary files /tmp/cvsNIvknS and /tmp/cvsLYKm3z differ Index: jchempaint-applet-com_ozten.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-com_ozten.jar,v retrieving revision 1.18 retrieving revision 1.19 diff -C2 -r1.18 -r1.19 Binary files /tmp/cvsXX2a62 and /tmp/cvsLvseiL differ Index: jchempaint-applet-core.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-core.jar,v retrieving revision 1.47 retrieving revision 1.48 diff -C2 -r1.47 -r1.48 Binary files /tmp/cvsI0z646 and /tmp/cvsBDAttP differ Index: jchempaint-applet-editor-opts.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-editor-opts.jar,v retrieving revision 1.45 retrieving revision 1.46 diff -C2 -r1.45 -r1.46 Binary files /tmp/cvsneLZFn and /tmp/cvslSs0u6 differ Index: jchempaint-applet-editor.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-editor.jar,v retrieving revision 1.48 retrieving revision 1.49 diff -C2 -r1.48 -r1.49 Binary files /tmp/cvsmQAvqt and /tmp/cvsXvSKoc differ Index: jchempaint-applet-jas.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-jas.jar,v retrieving revision 1.18 retrieving revision 1.19 diff -C2 -r1.18 -r1.19 Binary files /tmp/cvsN3KV0x and /tmp/cvsBHvk6g differ Index: jchempaint-applet-javax_media.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-javax_media.jar,v retrieving revision 1.18 retrieving revision 1.19 diff -C2 -r1.18 -r1.19 Binary files /tmp/cvspWqbiG and /tmp/cvsOBb0yp differ Index: jchempaint-applet-javax_vecmath.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-javax_vecmath.jar,v retrieving revision 1.18 retrieving revision 1.19 diff -C2 -r1.18 -r1.19 Binary files /tmp/cvs0qwoRL and /tmp/cvsYrSTjv differ Index: jchempaint-applet-nu.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-nu.jar,v retrieving revision 1.18 retrieving revision 1.19 diff -C2 -r1.18 -r1.19 Binary files /tmp/cvscmNDzR and /tmp/cvsP17p8A differ Index: jchempaint-applet-org.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org.jar,v retrieving revision 1.44 retrieving revision 1.45 diff -C2 -r1.44 -r1.45 Binary files /tmp/cvs8XG4MT and /tmp/cvsdyT2sD differ Index: jchempaint-applet-org_3pq.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_3pq.jar,v retrieving revision 1.18 retrieving revision 1.19 diff -C2 -r1.18 -r1.19 Binary files /tmp/cvswlNITZ and /tmp/cvsscI2KJ differ Index: jchempaint-applet-org_apache.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_apache.jar,v retrieving revision 1.18 retrieving revision 1.19 diff -C2 -r1.18 -r1.19 Binary files /tmp/cvs9YN4re and /tmp/cvsengv2Y differ Index: jchempaint-applet-org_omegahat.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_omegahat.jar,v retrieving revision 1.18 retrieving revision 1.19 diff -C2 -r1.18 -r1.19 Binary files /tmp/cvsBQNU4q and /tmp/cvsegPnSb differ Index: jchempaint-applet-org_openscience.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_openscience.jar,v retrieving revision 1.44 retrieving revision 1.45 diff -C2 -r1.44 -r1.45 Binary files /tmp/cvsenlhyu and /tmp/cvsG9sGsf differ Index: jchempaint-applet-org_openscience_cdk.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_openscience_cdk.jar,v retrieving revision 1.44 retrieving revision 1.45 diff -C2 -r1.44 -r1.45 Binary files /tmp/cvsf51QDC and /tmp/cvs5GtsLn differ Index: jchempaint-applet-org_openscience_cdk_applications.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_openscience_cdk_applications.jar,v retrieving revision 1.44 retrieving revision 1.45 diff -C2 -r1.44 -r1.45 Binary files /tmp/cvsEum9pK and /tmp/cvsuyZiHv differ Index: jchempaint-applet-org_openscience_cdk_applications_jchempaint.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_openscience_cdk_applications_jchempaint.jar,v retrieving revision 1.48 retrieving revision 1.49 diff -C2 -r1.48 -r1.49 Binary files /tmp/cvsOFDOJO and /tmp/cvsXhMc8z differ Index: jchempaint-applet-org_openscience_cdk_config.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_openscience_cdk_config.jar,v retrieving revision 1.17 retrieving revision 1.18 diff -C2 -r1.17 -r1.18 Binary files /tmp/cvs9bloXP and /tmp/cvsos0irB differ Index: jchempaint-applet-org_openscience_cdk_dict.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_openscience_cdk_dict.jar,v retrieving revision 1.17 retrieving revision 1.18 diff -C2 -r1.17 -r1.18 Binary files /tmp/cvs5r1rZW and /tmp/cvsEKcZAI differ Index: jchempaint-applet-org_openscience_cdk_io.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_openscience_cdk_io.jar,v retrieving revision 1.17 retrieving revision 1.18 diff -C2 -r1.17 -r1.18 Binary files /tmp/cvs8kXd11 and /tmp/cvsjo1QQN differ Index: jchempaint-applet-org_openscience_cdk_iupac.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_openscience_cdk_iupac.jar,v retrieving revision 1.17 retrieving revision 1.18 diff -C2 -r1.17 -r1.18 Binary files /tmp/cvsqnzZPq and /tmp/cvstIgQxd differ Index: jchempaint-applet-org_openscience_cdk_math.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_openscience_cdk_math.jar,v retrieving revision 1.17 retrieving revision 1.18 diff -C2 -r1.17 -r1.18 Binary files /tmp/cvsVgd6px and /tmp/cvs2J53fk differ Index: jchempaint-applet-org_openscience_cdk_nonotify.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_openscience_cdk_nonotify.jar,v retrieving revision 1.5 retrieving revision 1.6 diff -C2 -r1.5 -r1.6 Binary files /tmp/cvsc5CmDH and /tmp/cvsl9k1Lu differ Index: jchempaint-applet-org_openscience_cdk_qsar.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_openscience_cdk_qsar.jar,v retrieving revision 1.17 retrieving revision 1.18 diff -C2 -r1.17 -r1.18 Binary files /tmp/cvsbG5WWM and /tmp/cvsYaTXdA differ Index: jchempaint-applet-org_openscience_cdk_structgen.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_openscience_cdk_structgen.jar,v retrieving revision 1.17 retrieving revision 1.18 diff -C2 -r1.17 -r1.18 Binary files /tmp/cvszmsUeR and /tmp/cvsfkw1BE differ Index: jchempaint-applet-org_openscience_cdk_tools.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_openscience_cdk_tools.jar,v retrieving revision 1.17 retrieving revision 1.18 diff -C2 -r1.17 -r1.18 Binary files /tmp/cvsdl0QVU and /tmp/cvsztLgtI differ Index: jchempaint-applet-org_w3c.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_w3c.jar,v retrieving revision 1.18 retrieving revision 1.19 diff -C2 -r1.18 -r1.19 Binary files /tmp/cvsbHkaH5 and /tmp/cvsP511rT differ Index: jchempaint-applet-org_xmlcml.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_xmlcml.jar,v retrieving revision 1.18 retrieving revision 1.19 diff -C2 -r1.18 -r1.19 Binary files /tmp/cvszzyyEb and /tmp/cvsor7XUZ differ Index: jchempaint-applet-others.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-others.jar,v retrieving revision 1.48 retrieving revision 1.49 diff -C2 -r1.48 -r1.49 Binary files /tmp/cvsuaNkjj and /tmp/cvsuTuA27 differ Index: jchempaint-applet-resources.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-resources.jar,v retrieving revision 1.45 retrieving revision 1.46 diff -C2 -r1.45 -r1.46 Binary files /tmp/cvs3aPtQE and /tmp/cvsszzKNt differ Index: jchempaint-applet-viewer-opts.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-viewer-opts.jar,v retrieving revision 1.44 retrieving revision 1.45 diff -C2 -r1.44 -r1.45 Binary files /tmp/cvsrBNaCF and /tmp/cvsGWHcEu differ Index: marvin.js =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/marvin.js,v retrieving revision 1.25 retrieving revision 1.26 diff -C2 -r1.25 -r1.26 *** marvin.js 10 Oct 2006 15:20:27 -0000 1.25 --- marvin.js 11 Oct 2006 11:53:56 -0000 1.26 *************** *** 362,366 **** function msketch_begin(codebase, width, height) { ! document.write("<a target=\"_new\" href=\"nmrshiftdbhtml/userhelp_jcp/jcp.html\">Help for JChemPaint</a><br>"); var archive, code; var jvm = marvin_jvm0; --- 362,366 ---- function msketch_begin(codebase, width, height) { ! //document.write("<a target=\"_new\" href=\"nmrshiftdbhtml/userhelp_jcp/jcp.html\">Help for JChemPaint</a><br>"); var archive, code; var jvm = marvin_jvm0; |
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From: Stefan K. <sh...@us...> - 2006-10-11 11:53:59
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/util In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv31919/src/java/org/openscience/nmrshiftdb/util Modified Files: ParseUtils.java Log Message: i do not fully understand this Index: ParseUtils.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/util/ParseUtils.java,v retrieving revision 1.15 retrieving revision 1.16 diff -C2 -r1.15 -r1.16 *** ParseUtils.java 4 Aug 2005 21:55:43 -0000 1.15 --- ParseUtils.java 11 Oct 2006 11:53:56 -0000 1.16 *************** *** 141,145 **** } } ! figures.value2 = (new Float(intensitynew.trim())).floatValue(); } int addTo = -1; --- 141,147 ---- } } ! if(!intensitynew.trim().equals("")){ ! figures.value2 = (new Float(intensitynew.trim())).floatValue(); ! } } int addTo = -1; |
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From: Stefan K. <sh...@us...> - 2006-10-10 15:20:55
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Update of /cvsroot/nmrshiftdb/nmrshiftdb In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv12846 Modified Files: CHANGELOG Log Message: highlighting now also works for the table Index: CHANGELOG =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/CHANGELOG,v retrieving revision 1.115 retrieving revision 1.116 diff -C2 -r1.115 -r1.116 *** CHANGELOG 21 Sep 2006 12:22:11 -0000 1.115 --- CHANGELOG 10 Oct 2006 15:20:18 -0000 1.116 *************** *** 11,14 **** --- 11,15 ---- * The CML export now contains Hs if exported with a proton spectrum * Saving multiple bookmarks for the same molecule no longer gives an exception + * Thanks to new cdk algorithm the bond orders in aromatic rings should now be ok 1.2.1 Release |
Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/html In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv12846/src/html Modified Files: jchempaint-applet-Jama.jar jchempaint-applet-com_ozten.jar jchempaint-applet-core.jar jchempaint-applet-editor-opts.jar jchempaint-applet-editor.jar jchempaint-applet-jas.jar jchempaint-applet-javax_media.jar jchempaint-applet-javax_vecmath.jar jchempaint-applet-nu.jar jchempaint-applet-org.jar jchempaint-applet-org_3pq.jar jchempaint-applet-org_apache.jar jchempaint-applet-org_omegahat.jar jchempaint-applet-org_openscience.jar jchempaint-applet-org_openscience_cdk.jar jchempaint-applet-org_openscience_cdk_applications.jar jchempaint-applet-org_openscience_cdk_applications_jchempaint.jar jchempaint-applet-org_openscience_cdk_config.jar jchempaint-applet-org_openscience_cdk_dict.jar jchempaint-applet-org_openscience_cdk_io.jar jchempaint-applet-org_openscience_cdk_iupac.jar jchempaint-applet-org_openscience_cdk_math.jar jchempaint-applet-org_openscience_cdk_nonotify.jar jchempaint-applet-org_openscience_cdk_qsar.jar jchempaint-applet-org_openscience_cdk_structgen.jar jchempaint-applet-org_openscience_cdk_tools.jar jchempaint-applet-org_w3c.jar jchempaint-applet-org_xmlcml.jar jchempaint-applet-others.jar jchempaint-applet-resources.jar jchempaint-applet-viewer-opts.jar marvin.js spectrumapplet.jar Log Message: highlighting now also works for the table Index: jchempaint-applet-Jama.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-Jama.jar,v retrieving revision 1.17 retrieving revision 1.18 diff -C2 -r1.17 -r1.18 Binary files /tmp/cvsSjXmRe and /tmp/cvsWYeKE4 differ Index: jchempaint-applet-com_ozten.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-com_ozten.jar,v retrieving revision 1.17 retrieving revision 1.18 diff -C2 -r1.17 -r1.18 Binary files /tmp/cvsvwE2Jz and /tmp/cvsk2RiRp differ Index: jchempaint-applet-core.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-core.jar,v retrieving revision 1.46 retrieving revision 1.47 diff -C2 -r1.46 -r1.47 Binary files /tmp/cvsSTJBbK and /tmp/cvs9Wn3BA differ Index: jchempaint-applet-editor-opts.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-editor-opts.jar,v retrieving revision 1.44 retrieving revision 1.45 diff -C2 -r1.44 -r1.45 Binary files /tmp/cvsYrHgMZ and /tmp/cvsZreTzQ differ Index: jchempaint-applet-editor.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-editor.jar,v retrieving revision 1.47 retrieving revision 1.48 diff -C2 -r1.47 -r1.48 Binary files /tmp/cvsqZ24ab and /tmp/cvsCwKuf2 differ Index: jchempaint-applet-jas.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-jas.jar,v retrieving revision 1.17 retrieving revision 1.18 diff -C2 -r1.17 -r1.18 Binary files /tmp/cvsHzajrj and /tmp/cvsOIOLYa differ Index: jchempaint-applet-javax_media.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-javax_media.jar,v retrieving revision 1.17 retrieving revision 1.18 diff -C2 -r1.17 -r1.18 Binary files /tmp/cvs0bGqzF and /tmp/cvsZKk3Kx differ Index: jchempaint-applet-javax_vecmath.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-javax_vecmath.jar,v retrieving revision 1.17 retrieving revision 1.18 diff -C2 -r1.17 -r1.18 Binary files /tmp/cvss43qOR and /tmp/cvsvjeojK differ Index: jchempaint-applet-nu.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-nu.jar,v retrieving revision 1.17 retrieving revision 1.18 diff -C2 -r1.17 -r1.18 Binary files /tmp/cvsnfXJm3 and /tmp/cvsyVwB9V differ Index: jchempaint-applet-org.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org.jar,v retrieving revision 1.43 retrieving revision 1.44 diff -C2 -r1.43 -r1.44 Binary files /tmp/cvsgoypPf and /tmp/cvs8QHPf9 differ Index: jchempaint-applet-org_3pq.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_3pq.jar,v retrieving revision 1.17 retrieving revision 1.18 diff -C2 -r1.17 -r1.18 Binary files /tmp/cvskiMr0s and /tmp/cvs4h5bIm differ Index: jchempaint-applet-org_apache.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_apache.jar,v retrieving revision 1.17 retrieving revision 1.18 diff -C2 -r1.17 -r1.18 Binary files /tmp/cvs2g2peC and /tmp/cvsyD79hw differ Index: jchempaint-applet-org_omegahat.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_omegahat.jar,v retrieving revision 1.17 retrieving revision 1.18 diff -C2 -r1.17 -r1.18 Binary files /tmp/cvskkF7yO and /tmp/cvstoqqUI differ Index: jchempaint-applet-org_openscience.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_openscience.jar,v retrieving revision 1.43 retrieving revision 1.44 diff -C2 -r1.43 -r1.44 Binary files /tmp/cvsXTmGE8 and /tmp/cvswKWZM3 differ Index: jchempaint-applet-org_openscience_cdk.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_openscience_cdk.jar,v retrieving revision 1.43 retrieving revision 1.44 diff -C2 -r1.43 -r1.44 Binary files /tmp/cvsvnXbRs and /tmp/cvsGEOzvo differ Index: jchempaint-applet-org_openscience_cdk_applications.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_openscience_cdk_applications.jar,v retrieving revision 1.43 retrieving revision 1.44 diff -C2 -r1.43 -r1.44 Binary files /tmp/cvsMfVRmH and /tmp/cvsYYjLnD differ Index: jchempaint-applet-org_openscience_cdk_applications_jchempaint.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_openscience_cdk_applications_jchempaint.jar,v retrieving revision 1.47 retrieving revision 1.48 diff -C2 -r1.47 -r1.48 Binary files /tmp/cvsEng8pQ and /tmp/cvsj3xpHM differ Index: jchempaint-applet-org_openscience_cdk_config.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_openscience_cdk_config.jar,v retrieving revision 1.16 retrieving revision 1.17 diff -C2 -r1.16 -r1.17 Binary files /tmp/cvs4NRxYX and /tmp/cvs33QpqU differ Index: jchempaint-applet-org_openscience_cdk_dict.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_openscience_cdk_dict.jar,v retrieving revision 1.16 retrieving revision 1.17 diff -C2 -r1.16 -r1.17 Binary files /tmp/cvsmKjXV1 and /tmp/cvsVMioyY differ Index: jchempaint-applet-org_openscience_cdk_io.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_openscience_cdk_io.jar,v retrieving revision 1.16 retrieving revision 1.17 diff -C2 -r1.16 -r1.17 Binary files /tmp/cvs9Lgxj8 and /tmp/cvs9hJi84 differ Index: jchempaint-applet-org_openscience_cdk_iupac.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_openscience_cdk_iupac.jar,v retrieving revision 1.16 retrieving revision 1.17 diff -C2 -r1.16 -r1.17 Binary files /tmp/cvsbzwE3g and /tmp/cvsbwrC1d differ Index: jchempaint-applet-org_openscience_cdk_math.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_openscience_cdk_math.jar,v retrieving revision 1.16 retrieving revision 1.17 diff -C2 -r1.16 -r1.17 Binary files /tmp/cvsBPaMOm and /tmp/cvscQGTbk differ Index: jchempaint-applet-org_openscience_cdk_nonotify.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_openscience_cdk_nonotify.jar,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -r1.4 -r1.5 Binary files /tmp/cvsLVEH3t and /tmp/cvsKZ0GCr differ Index: jchempaint-applet-org_openscience_cdk_qsar.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_openscience_cdk_qsar.jar,v retrieving revision 1.16 retrieving revision 1.17 diff -C2 -r1.16 -r1.17 Binary files /tmp/cvsD2cj1y and /tmp/cvs61C3Jw differ Index: jchempaint-applet-org_openscience_cdk_structgen.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_openscience_cdk_structgen.jar,v retrieving revision 1.16 retrieving revision 1.17 diff -C2 -r1.16 -r1.17 Binary files /tmp/cvsHsL57C and /tmp/cvsGIrl0A differ Index: jchempaint-applet-org_openscience_cdk_tools.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_openscience_cdk_tools.jar,v retrieving revision 1.16 retrieving revision 1.17 diff -C2 -r1.16 -r1.17 Binary files /tmp/cvsIIjGiN and /tmp/cvsfC64nL differ Index: jchempaint-applet-org_w3c.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_w3c.jar,v retrieving revision 1.17 retrieving revision 1.18 diff -C2 -r1.17 -r1.18 Binary files /tmp/cvsKAeOQR and /tmp/cvs08t76P differ Index: jchempaint-applet-org_xmlcml.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_xmlcml.jar,v retrieving revision 1.17 retrieving revision 1.18 diff -C2 -r1.17 -r1.18 Binary files /tmp/cvswfGgTY and /tmp/cvspeyQrX differ Index: jchempaint-applet-others.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-others.jar,v retrieving revision 1.47 retrieving revision 1.48 diff -C2 -r1.47 -r1.48 Binary files /tmp/cvsjZhJVb and /tmp/cvsKWsYbb differ Index: jchempaint-applet-resources.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-resources.jar,v retrieving revision 1.44 retrieving revision 1.45 diff -C2 -r1.44 -r1.45 Binary files /tmp/cvsYLBiOP and /tmp/cvsYgSnSP differ Index: jchempaint-applet-viewer-opts.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-viewer-opts.jar,v retrieving revision 1.43 retrieving revision 1.44 diff -C2 -r1.43 -r1.44 Binary files /tmp/cvsudCgnR and /tmp/cvs5CpvxR differ Index: marvin.js =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/marvin.js,v retrieving revision 1.24 retrieving revision 1.25 diff -C2 -r1.24 -r1.25 *** marvin.js 27 Jun 2006 14:29:17 -0000 1.24 --- marvin.js 10 Oct 2006 15:20:27 -0000 1.25 *************** *** 345,349 **** code = "org.openscience.nmrshiftdb.spectrumapplet.SpectrumView.class"; applet_begin(jvm, codebase, archive, code, width, height, spectrumapplet_name, ! false); } --- 345,349 ---- code = "org.openscience.nmrshiftdb.spectrumapplet.SpectrumView.class"; applet_begin(jvm, codebase, archive, code, width, height, spectrumapplet_name, ! true); } Index: spectrumapplet.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/spectrumapplet.jar,v retrieving revision 1.45 retrieving revision 1.46 diff -C2 -r1.45 -r1.46 Binary files /tmp/cvsBQqyw4 and /tmp/cvsiGKcZ4 differ |
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From: Stefan K. <sh...@us...> - 2006-10-10 15:20:36
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv12846/src/java/org/openscience/nmrshiftdb/om Modified Files: BaseDBCondition.java BaseDBMachine.java BaseDBMachinePeer.java BaseDBMolecule.java BaseDBSample.java BaseDBSamplePeer.java BaseNmrshiftdbUser.java DBLabGroup.java DBMachine.java DBMachinePeer.java DBSpectrum.java Log Message: highlighting now also works for the table Index: BaseDBCondition.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/BaseDBCondition.java,v retrieving revision 1.9 retrieving revision 1.10 diff -C2 -r1.9 -r1.10 *** BaseDBCondition.java 6 Oct 2006 20:12:10 -0000 1.9 --- BaseDBCondition.java 10 Oct 2006 15:20:31 -0000 1.10 *************** *** 2,14 **** ! import java.util.*; ! import java.math.*; ! import org.apache.turbine.om.*; import org.apache.turbine.om.peer.BasePeer; - import org.apache.turbine.util.db.Criteria; import org.apache.turbine.util.ObjectUtils; ! import org.apache.turbine.util.StringUtils; ! import org.apache.turbine.util.ParameterParser; ! import org.apache.turbine.util.Log; import org.apache.turbine.util.db.pool.DBConnection; --- 2,16 ---- ! import java.util.List; ! import java.util.Vector; ! ! import org.apache.turbine.om.BaseObject; ! import org.apache.turbine.om.NumberKey; ! import org.apache.turbine.om.ObjectKey; ! import org.apache.turbine.om.Persistent; ! import org.apache.turbine.om.Retrievable; import org.apache.turbine.om.peer.BasePeer; import org.apache.turbine.util.ObjectUtils; ! import org.apache.turbine.util.db.Criteria; import org.apache.turbine.util.db.pool.DBConnection; Index: BaseDBMachine.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/BaseDBMachine.java,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -r1.1 -r1.2 *** BaseDBMachine.java 6 Oct 2006 20:18:37 -0000 1.1 --- BaseDBMachine.java 10 Oct 2006 15:20:31 -0000 1.2 *************** *** 2,14 **** ! import java.util.*; ! import java.math.*; ! import org.apache.turbine.om.*; import org.apache.turbine.om.peer.BasePeer; - import org.apache.turbine.util.db.Criteria; import org.apache.turbine.util.ObjectUtils; ! import org.apache.turbine.util.StringUtils; ! import org.apache.turbine.util.ParameterParser; ! import org.apache.turbine.util.Log; import org.apache.turbine.util.db.pool.DBConnection; --- 2,16 ---- ! import java.util.List; ! import java.util.Vector; ! ! import org.apache.turbine.om.BaseObject; ! import org.apache.turbine.om.NumberKey; ! import org.apache.turbine.om.ObjectKey; ! import org.apache.turbine.om.Persistent; ! import org.apache.turbine.om.Retrievable; import org.apache.turbine.om.peer.BasePeer; import org.apache.turbine.util.ObjectUtils; ! import org.apache.turbine.util.db.Criteria; import org.apache.turbine.util.db.pool.DBConnection; Index: BaseDBMachinePeer.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/BaseDBMachinePeer.java,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -r1.1 -r1.2 *** BaseDBMachinePeer.java 6 Oct 2006 20:18:37 -0000 1.1 --- BaseDBMachinePeer.java 10 Oct 2006 15:20:31 -0000 1.2 *************** *** 1,19 **** package org.openscience.nmrshiftdb.om; ! import java.util.*; ! import java.math.*; ! import java.sql.*; ! import com.workingdogs.village.*; ! import org.apache.turbine.om.*; ! import org.apache.turbine.om.peer.*; ! import org.apache.turbine.util.*; ! import org.apache.turbine.util.db.*; ! import org.apache.turbine.util.db.map.*; ! import org.apache.turbine.util.db.pool.DBConnection; import org.apache.turbine.services.db.TurbineDB; ! import org.apache.turbine.util.TurbineException; ! // Local classes ! import org.openscience.nmrshiftdb.om.map.*; /** --- 1,19 ---- package org.openscience.nmrshiftdb.om; ! import java.util.Vector; ! ! import org.apache.turbine.om.NumberKey; ! import org.apache.turbine.om.ObjectKey; ! import org.apache.turbine.om.peer.BasePeer; import org.apache.turbine.services.db.TurbineDB; ! import org.apache.turbine.util.Log; ! import org.apache.turbine.util.db.Criteria; ! import org.apache.turbine.util.db.map.MapBuilder; ! import org.apache.turbine.util.db.map.TableMap; ! import org.apache.turbine.util.db.pool.DBConnection; ! import org.openscience.nmrshiftdb.om.map.DBMachineMapBuilder; ! import com.workingdogs.village.QueryDataSet; ! import com.workingdogs.village.Record; /** Index: BaseDBMolecule.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/BaseDBMolecule.java,v retrieving revision 1.40 retrieving revision 1.41 diff -C2 -r1.40 -r1.41 *** BaseDBMolecule.java 6 Oct 2006 20:12:10 -0000 1.40 --- BaseDBMolecule.java 10 Oct 2006 15:20:31 -0000 1.41 *************** *** 2,14 **** ! import java.util.*; ! import java.math.*; ! import org.apache.turbine.om.*; import org.apache.turbine.om.peer.BasePeer; - import org.apache.turbine.util.db.Criteria; import org.apache.turbine.util.ObjectUtils; ! import org.apache.turbine.util.StringUtils; ! import org.apache.turbine.util.ParameterParser; ! import org.apache.turbine.util.Log; import org.apache.turbine.util.db.pool.DBConnection; --- 2,17 ---- ! import java.util.Date; ! import java.util.List; ! import java.util.Vector; ! ! import org.apache.turbine.om.BaseObject; ! import org.apache.turbine.om.NumberKey; ! import org.apache.turbine.om.ObjectKey; ! import org.apache.turbine.om.Persistent; ! import org.apache.turbine.om.Retrievable; import org.apache.turbine.om.peer.BasePeer; import org.apache.turbine.util.ObjectUtils; ! import org.apache.turbine.util.db.Criteria; import org.apache.turbine.util.db.pool.DBConnection; Index: BaseDBSample.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/BaseDBSample.java,v retrieving revision 1.7 retrieving revision 1.8 diff -C2 -r1.7 -r1.8 *** BaseDBSample.java 6 Oct 2006 20:12:10 -0000 1.7 --- BaseDBSample.java 10 Oct 2006 15:20:31 -0000 1.8 *************** *** 2,14 **** ! import java.util.*; ! import java.math.*; ! import org.apache.turbine.om.*; import org.apache.turbine.om.peer.BasePeer; - import org.apache.turbine.util.db.Criteria; import org.apache.turbine.util.ObjectUtils; ! import org.apache.turbine.util.StringUtils; ! import org.apache.turbine.util.ParameterParser; ! import org.apache.turbine.util.Log; import org.apache.turbine.util.db.pool.DBConnection; --- 2,17 ---- ! import java.util.Date; ! import java.util.List; ! import java.util.Vector; ! ! import org.apache.turbine.om.BaseObject; ! import org.apache.turbine.om.NumberKey; ! import org.apache.turbine.om.ObjectKey; ! import org.apache.turbine.om.Persistent; ! import org.apache.turbine.om.Retrievable; import org.apache.turbine.om.peer.BasePeer; import org.apache.turbine.util.ObjectUtils; ! import org.apache.turbine.util.db.Criteria; import org.apache.turbine.util.db.pool.DBConnection; Index: BaseDBSamplePeer.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/BaseDBSamplePeer.java,v retrieving revision 1.6 retrieving revision 1.7 diff -C2 -r1.6 -r1.7 *** BaseDBSamplePeer.java 6 Oct 2006 20:12:10 -0000 1.6 --- BaseDBSamplePeer.java 10 Oct 2006 15:20:31 -0000 1.7 *************** *** 1,19 **** package org.openscience.nmrshiftdb.om; ! import java.util.*; ! import java.math.*; ! import java.sql.*; ! import com.workingdogs.village.*; ! import org.apache.turbine.om.*; ! import org.apache.turbine.om.peer.*; ! import org.apache.turbine.util.*; ! import org.apache.turbine.util.db.*; ! import org.apache.turbine.util.db.map.*; ! import org.apache.turbine.util.db.pool.DBConnection; import org.apache.turbine.services.db.TurbineDB; ! import org.apache.turbine.util.TurbineException; ! // Local classes ! import org.openscience.nmrshiftdb.om.map.*; /** --- 1,19 ---- package org.openscience.nmrshiftdb.om; ! import java.util.Vector; ! ! import org.apache.turbine.om.NumberKey; ! import org.apache.turbine.om.ObjectKey; ! import org.apache.turbine.om.peer.BasePeer; import org.apache.turbine.services.db.TurbineDB; ! import org.apache.turbine.util.Log; ! import org.apache.turbine.util.db.Criteria; ! import org.apache.turbine.util.db.map.MapBuilder; ! import org.apache.turbine.util.db.map.TableMap; ! import org.apache.turbine.util.db.pool.DBConnection; ! import org.openscience.nmrshiftdb.om.map.DBSampleMapBuilder; ! import com.workingdogs.village.QueryDataSet; ! import com.workingdogs.village.Record; /** Index: BaseNmrshiftdbUser.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/BaseNmrshiftdbUser.java,v retrieving revision 1.23 retrieving revision 1.24 diff -C2 -r1.23 -r1.24 *** BaseNmrshiftdbUser.java 6 Oct 2006 20:12:10 -0000 1.23 --- BaseNmrshiftdbUser.java 10 Oct 2006 15:20:31 -0000 1.24 *************** *** 2,15 **** ! import java.util.*; ! import java.math.*; ! import org.apache.turbine.om.*; ! import org.apache.turbine.om.peer.BasePeer; import org.apache.turbine.util.db.Criteria; - import org.apache.turbine.util.ObjectUtils; - import org.apache.turbine.util.StringUtils; - import org.apache.turbine.util.ParameterParser; - import org.apache.turbine.util.Log; - import org.apache.turbine.util.db.pool.DBConnection; /** --- 2,9 ---- ! import java.util.Vector; ! ! import org.apache.turbine.om.Retrievable; import org.apache.turbine.util.db.Criteria; /** Index: DBLabGroup.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/DBLabGroup.java,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -r1.3 -r1.4 *** DBLabGroup.java 20 Sep 2006 11:35:47 -0000 1.3 --- DBLabGroup.java 10 Oct 2006 15:20:31 -0000 1.4 *************** *** 3,11 **** // JDK classes import org.apache.turbine.om.Persistent; import org.apache.turbine.util.db.Criteria; - import java.util.Vector; - /** * You should add additional methods to this class to meet the --- 3,11 ---- // JDK classes + import java.util.Vector; + import org.apache.turbine.om.Persistent; import org.apache.turbine.util.db.Criteria; /** * You should add additional methods to this class to meet the Index: DBMachine.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/DBMachine.java,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -r1.1 -r1.2 *** DBMachine.java 6 Oct 2006 20:18:37 -0000 1.1 --- DBMachine.java 10 Oct 2006 15:20:31 -0000 1.2 *************** *** 3,17 **** // JDK classes ! import java.util.*; ! ! // Turbine classes ! import org.apache.turbine.om.*; ! import org.apache.turbine.om.peer.BasePeer; ! import org.apache.turbine.util.db.Criteria; ! import org.apache.turbine.util.ObjectUtils; ! import org.apache.turbine.util.StringUtils; ! import org.apache.turbine.util.ParameterParser; ! import org.apache.turbine.util.Log; ! import org.apache.turbine.util.db.pool.DBConnection; /** --- 3,7 ---- // JDK classes ! import org.apache.turbine.om.Persistent; /** Index: DBMachinePeer.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/DBMachinePeer.java,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -r1.1 -r1.2 *** DBMachinePeer.java 6 Oct 2006 20:18:37 -0000 1.1 --- DBMachinePeer.java 10 Oct 2006 15:20:31 -0000 1.2 *************** *** 2,19 **** // JDK classes - import java.util.*; - - // Village classes - import com.workingdogs.village.*; - - // Turbine classes - import org.apache.turbine.om.peer.*; - import org.apache.turbine.util.*; - import org.apache.turbine.util.db.*; - import org.apache.turbine.util.db.map.*; - import org.apache.turbine.util.db.pool.DBConnection; - - // Local classes - import org.openscience.nmrshiftdb.om.map.*; /** --- 2,5 ---- Index: DBSpectrum.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/DBSpectrum.java,v retrieving revision 1.189 retrieving revision 1.190 diff -C2 -r1.189 -r1.190 *** DBSpectrum.java 9 Oct 2006 13:24:37 -0000 1.189 --- DBSpectrum.java 10 Oct 2006 15:20:31 -0000 1.190 *************** *** 25,29 **** import org.apache.turbine.util.db.pool.DBConnection; import org.openscience.cdk.exception.CDKException; - import org.openscience.cdk.interfaces.IAtom; import org.openscience.cdk.interfaces.IMolecule; import org.openscience.nmrshiftdb.util.AtomUtils; --- 25,28 ---- |
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From: Stefan K. <sh...@us...> - 2006-10-10 15:20:34
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/util In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv12846/src/java/org/openscience/nmrshiftdb/util Modified Files: UrlTool.java Log Message: highlighting now also works for the table Index: UrlTool.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/util/UrlTool.java,v retrieving revision 1.17 retrieving revision 1.18 diff -C2 -r1.17 -r1.18 *** UrlTool.java 6 Oct 2006 14:27:48 -0000 1.17 --- UrlTool.java 10 Oct 2006 15:20:31 -0000 1.18 *************** *** 5,9 **** import java.io.StringWriter; import java.net.URL; - import java.sql.ResultSet; import java.util.HashMap; import java.util.List; --- 5,8 ---- |
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From: Stefan K. <sh...@us...> - 2006-10-10 15:20:34
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv12846/src/java/org/openscience/nmrshiftdb Modified Files: AdminPanel.java Log Message: highlighting now also works for the table Index: AdminPanel.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/AdminPanel.java,v retrieving revision 1.234 retrieving revision 1.235 diff -C2 -r1.234 -r1.235 *** AdminPanel.java 9 Oct 2006 13:24:37 -0000 1.234 --- AdminPanel.java 10 Oct 2006 15:20:30 -0000 1.235 *************** *** 20,24 **** import java.text.SimpleDateFormat; import java.util.Date; - import java.util.Enumeration; import java.util.HashMap; import java.util.Iterator; --- 20,23 ---- *************** *** 62,68 **** import org.openscience.cdk.io.iterator.IteratingMDLReader; import org.openscience.cdk.isomorphism.UniversalIsomorphismTester; - import org.openscience.cdk.isomorphism.matchers.QueryAtomContainer; - import org.openscience.cdk.isomorphism.matchers.QueryAtomContainerCreator; - import org.openscience.cdk.isomorphism.matchers.smarts.AnyOrderQueryBond; import org.openscience.cdk.isomorphism.mcss.RMap; import org.openscience.cdk.ringsearch.AllRingsFinder; --- 61,64 ---- |
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From: Stefan K. <sh...@us...> - 2006-10-10 15:20:34
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv12846/src/vmtemplates Modified Files: details.vm Log Message: highlighting now also works for the table Index: details.vm =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/details.vm,v retrieving revision 1.159 retrieving revision 1.160 diff -C2 -r1.159 -r1.160 *** details.vm 22 Aug 2006 12:58:17 -0000 1.159 --- details.vm 10 Oct 2006 15:20:32 -0000 1.160 *************** *** 125,128 **** --- 125,129 ---- mview_param("spectrumRenderer","Spectrum$velocityCount"); mview_param("detachable","true"); + mview_param("highlightTable","true"); mview_end(); </script> *************** *** 180,184 **** </tr> #end ! <tr #if($greyorwhite==0) bgcolor="#D3D3D3" --- 181,185 ---- </tr> #end ! <tr id="tableid$option.getValue().intValue()" #if($greyorwhite==0) bgcolor="#D3D3D3" *************** *** 187,196 **** onMouseover=" #if($coords=="3d") ! jmolScript('select atomno=$option.getValueAsIntPlus1();set display selected;',0);document.Spectrum${outercounter}.paintLine($option.getValueAsInt()) #else #set($atomnumber=$option.getValue().intValue()) ! select($atomnumber,document.Spectrum$outercounter,document.JcpViewer$outercounter) #end ! " #end > --- 188,197 ---- onMouseover=" #if($coords=="3d") ! jmolScript('select atomno=$option.getValueAsIntPlus1();set display selected;',0);document.Spectrum${outercounter}.paintLine($option.getValueAsInt()); #else #set($atomnumber=$option.getValue().intValue()) ! select($atomnumber,document.Spectrum$outercounter,document.JcpViewer$outercounter); #end ! style.backgroundColor='red';" onmouseout="style.backgroundColor='#if($greyorwhite==0) #D3D3D3 #else white #end';" #end > *************** *** 231,234 **** --- 232,236 ---- spectrumapplet_param("spectrum","$spectrum.getSpectrumForAppletNewFormat()"); spectrumapplet_param("spectrumTyp","$spectrum.getDBSpectrumType().getNameAsString()"); + mview_param("highlightTable","true"); #if($spectrum.getConditionType()=="m" && !$spectrum.getMeasurementConditionWithName("Field Strength [MHz]").getValue().equals("unknown") && !$spectrum.getMeasurementConditionWithName("Field Strength [MHz]").getValue().equals("Unreported")) spectrumapplet_param("frequency","$spectrum.getMeasurementConditionWithName("Field Strength [MHz]").getValue()"); |
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From: Stefan K. <sh...@us...> - 2006-10-10 15:20:34
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/map In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv12846/src/java/org/openscience/nmrshiftdb/om/map Modified Files: DBMachineMapBuilder.java DBSampleMapBuilder.java Log Message: highlighting now also works for the table Index: DBMachineMapBuilder.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/map/DBMachineMapBuilder.java,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -r1.1 -r1.2 *** DBMachineMapBuilder.java 6 Oct 2006 20:22:30 -0000 1.1 --- DBMachineMapBuilder.java 10 Oct 2006 15:20:31 -0000 1.2 *************** *** 1,10 **** package org.openscience.nmrshiftdb.om.map; - import java.util.*; - import java.math.*; - import org.apache.turbine.services.db.PoolBrokerService; import org.apache.turbine.services.db.TurbineDB; - import org.apache.turbine.util.db.map.MapBuilder; import org.apache.turbine.util.db.map.DatabaseMap; import org.apache.turbine.util.db.map.TableMap; --- 1,7 ---- package org.openscience.nmrshiftdb.om.map; import org.apache.turbine.services.db.TurbineDB; import org.apache.turbine.util.db.map.DatabaseMap; + import org.apache.turbine.util.db.map.MapBuilder; import org.apache.turbine.util.db.map.TableMap; Index: DBSampleMapBuilder.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/map/DBSampleMapBuilder.java,v retrieving revision 1.7 retrieving revision 1.8 diff -C2 -r1.7 -r1.8 *** DBSampleMapBuilder.java 6 Oct 2006 20:12:11 -0000 1.7 --- DBSampleMapBuilder.java 10 Oct 2006 15:20:31 -0000 1.8 *************** *** 1,10 **** package org.openscience.nmrshiftdb.om.map; ! import java.util.*; ! import java.math.*; ! import org.apache.turbine.services.db.PoolBrokerService; import org.apache.turbine.services.db.TurbineDB; - import org.apache.turbine.util.db.map.MapBuilder; import org.apache.turbine.util.db.map.DatabaseMap; import org.apache.turbine.util.db.map.TableMap; --- 1,9 ---- package org.openscience.nmrshiftdb.om.map; ! import java.util.Date; ! import org.apache.turbine.services.db.TurbineDB; import org.apache.turbine.util.db.map.DatabaseMap; + import org.apache.turbine.util.db.map.MapBuilder; import org.apache.turbine.util.db.map.TableMap; |
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From: Stefan K. <sh...@us...> - 2006-10-10 15:16:17
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Update of /cvsroot/nmrshiftdb/spectrumapplet/src/java/org/openscience/nmrshiftdb/spectrumapplet/util In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv11540/src/java/org/openscience/nmrshiftdb/spectrumapplet/util Modified Files: SpectrumApplet.java Log Message: highlights table as well Index: SpectrumApplet.java =================================================================== RCS file: /cvsroot/nmrshiftdb/spectrumapplet/src/java/org/openscience/nmrshiftdb/spectrumapplet/util/SpectrumApplet.java,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -r1.1 -r1.2 *** SpectrumApplet.java 28 Jun 2005 14:41:38 -0000 1.1 --- SpectrumApplet.java 10 Oct 2006 15:15:35 -0000 1.2 *************** *** 54,58 **** */ public void highlightAtomsInStructur(int[] atomNumbers); ! /** --- 54,59 ---- */ public void highlightAtomsInStructur(int[] atomNumbers); ! ! public void highlightRowsInTable(int[] atomNumbers); /** |
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From: Stefan K. <sh...@us...> - 2006-10-10 15:15:47
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Update of /cvsroot/nmrshiftdb/spectrumapplet/src/java/org/openscience/nmrshiftdb/spectrumapplet/renderer In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv11540/src/java/org/openscience/nmrshiftdb/spectrumapplet/renderer Modified Files: SpectrumNavigation.java Log Message: highlights table as well Index: SpectrumNavigation.java =================================================================== RCS file: /cvsroot/nmrshiftdb/spectrumapplet/src/java/org/openscience/nmrshiftdb/spectrumapplet/renderer/SpectrumNavigation.java,v retrieving revision 1.5 retrieving revision 1.6 diff -C2 -r1.5 -r1.6 *** SpectrumNavigation.java 22 Aug 2006 12:41:02 -0000 1.5 --- SpectrumNavigation.java 10 Oct 2006 15:15:35 -0000 1.6 *************** *** 573,576 **** --- 573,577 ---- ((JApplet) applet).requestFocus(); } + applet.highlightRowsInTable(atomNumbers); } else { |
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From: Stefan K. <sh...@us...> - 2006-10-10 15:15:46
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Update of /cvsroot/nmrshiftdb/spectrumapplet/src/java/org/openscience/nmrshiftdb/spectrumapplet In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv11540/src/java/org/openscience/nmrshiftdb/spectrumapplet Modified Files: SpectrumView.java SpectrumViewNoRenderer.java Log Message: highlights table as well Index: SpectrumView.java =================================================================== RCS file: /cvsroot/nmrshiftdb/spectrumapplet/src/java/org/openscience/nmrshiftdb/spectrumapplet/SpectrumView.java,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -r1.2 -r1.3 *** SpectrumView.java 5 Jul 2005 08:01:02 -0000 1.2 --- SpectrumView.java 10 Oct 2006 15:15:30 -0000 1.3 *************** *** 21,24 **** --- 21,27 ---- import java.applet.*; + + import netscape.javascript.JSObject; + import org.openscience.nmrshiftdb.spectrumapplet.data.nmr.*; import org.openscience.nmrshiftdb.spectrumapplet.util.*; *************** *** 33,36 **** --- 36,40 ---- public class SpectrumView extends SpectrumViewNoRenderer { private StructureApplet structureApplet; + int[] oldnumbers=null; /** *************** *** 54,58 **** } } ! private void getStructureApplet() { --- 58,86 ---- } } ! ! ! public void highlightRowsInTable(int[] atomNumbers){ ! if(getParameter("highlightTable")==null || getParameter("highlightTable").equals("false")) ! return; ! if(atomNumbers==null) ! return; ! JSObject win = JSObject.getWindow(this); ! for(int i=0;i<atomNumbers.length;i++){ ! JSObject tr = (JSObject) win.eval("document.getElementById(\"tableid"+(atomNumbers[i]-1)+"\")"); ! if(tr!=null){ ! tr.setMember("bgColor","red"); ! } ! } ! if(oldnumbers!=null){ ! for(int i=0;i<oldnumbers.length;i++){ ! JSObject tr = (JSObject) win.eval("document.getElementById(\"tableid"+(oldnumbers[i]-1)+"\")"); ! if((oldnumbers[i]+1)%2==0) ! tr.setMember("bgColor","#D3D3D3"); ! else ! tr.setMember("bgColor","white"); ! } ! } ! oldnumbers=atomNumbers; ! } private void getStructureApplet() { Index: SpectrumViewNoRenderer.java =================================================================== RCS file: /cvsroot/nmrshiftdb/spectrumapplet/src/java/org/openscience/nmrshiftdb/spectrumapplet/SpectrumViewNoRenderer.java,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -r1.2 -r1.3 *** SpectrumViewNoRenderer.java 21 Aug 2006 15:18:41 -0000 1.2 --- SpectrumViewNoRenderer.java 10 Oct 2006 15:15:30 -0000 1.3 *************** *** 138,141 **** --- 138,144 ---- public void highlightAtomsInStructur(int[] atomNumbers) { } + + public void highlightRowsInTable(int[] atomNumbers){ + } |
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From: Stefan K. <sh...@us...> - 2006-10-09 13:24:48
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv21218/src/java/org/openscience/nmrshiftdb/om Modified Files: DBAtom.java DBMolecule.java DBSpectrum.java Log Message: this uses new cdk and new saturation stuff. should resolve a long standing problem Index: DBAtom.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/DBAtom.java,v retrieving revision 1.54 retrieving revision 1.55 diff -C2 -r1.54 -r1.55 *** DBAtom.java 29 Aug 2006 16:10:05 -0000 1.54 --- DBAtom.java 9 Oct 2006 13:24:37 -0000 1.55 *************** *** 78,82 **** setHoseCodeWithRings(""); } ! if(atom.getSymbol().equals("H") && !ac.getConnectedAtoms(atom)[0].equals("C")){ this.setHetero("true"); } --- 78,82 ---- setHoseCodeWithRings(""); } ! if(atom.getSymbol().equals("H") && !((IAtom)ac.getConnectedAtomsList(atom).get(0)).getSymbol().equals("C")){ this.setHetero("true"); } *************** *** 130,136 **** for (int i = 0; i < dbatoms.length; i++) { if(this.getAtomId().equals(dbatoms[i].getAtomId())){ ! IAtom[] connectedatoms=mol.getConnectedAtoms(mol.getAtom(i)); ! for(int k=0;k<connectedatoms.length;k++){ ! connecteddbatoms.add(dbatoms[mol.getAtomNumber(connectedatoms[k])]); } return connecteddbatoms; --- 130,136 ---- for (int i = 0; i < dbatoms.length; i++) { if(this.getAtomId().equals(dbatoms[i].getAtomId())){ ! List connectedatoms=mol.getConnectedAtomsList(mol.getAtom(i)); ! for(int k=0;k<connectedatoms.size();k++){ ! connecteddbatoms.add(dbatoms[mol.getAtomNumber((IAtom)connectedatoms.get(k))]); } return connecteddbatoms; Index: DBMolecule.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/DBMolecule.java,v retrieving revision 1.187 retrieving revision 1.188 diff -C2 -r1.187 -r1.188 *** DBMolecule.java 28 Aug 2006 14:33:58 -0000 1.187 --- DBMolecule.java 9 Oct 2006 13:24:37 -0000 1.188 *************** *** 48,53 **** import org.openscience.cdk.libio.cml.Convertor; import org.openscience.cdk.ringsearch.AllRingsFinder; import org.openscience.cdk.tools.MFAnalyser; - import org.openscience.cdk.tools.SaturationChecker; import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; import org.openscience.nmrshiftdb.util.AtomUtils; --- 48,53 ---- import org.openscience.cdk.libio.cml.Convertor; import org.openscience.cdk.ringsearch.AllRingsFinder; + import org.openscience.cdk.smiles.DeduceBondSystemTool; import org.openscience.cdk.tools.MFAnalyser; import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; import org.openscience.nmrshiftdb.util.AtomUtils; *************** *** 1546,1550 **** promol.getBond(i).setFlag(CDKConstants.ISAROMATIC, false); } ! new SaturationChecker().newSaturate(promol.getBonds(), promol); for (int i = promol.getAtomCount() - 1; i > -1; i--) { if (!visibility[i]) { --- 1546,1551 ---- promol.getBond(i).setFlag(CDKConstants.ISAROMATIC, false); } ! DeduceBondSystemTool dbot=new DeduceBondSystemTool(); ! dbot.fixAromaticBondOrders(promol); for (int i = promol.getAtomCount() - 1; i > -1; i--) { if (!visibility[i]) { Index: DBSpectrum.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/DBSpectrum.java,v retrieving revision 1.188 retrieving revision 1.189 diff -C2 -r1.188 -r1.189 *** DBSpectrum.java 21 Sep 2006 07:24:23 -0000 1.188 --- DBSpectrum.java 9 Oct 2006 13:24:37 -0000 1.189 *************** *** 322,329 **** IMolecule cdkMolWithOutH = getDBMolecule().getAsCDKMoleculeWithoutH(); StringBuffer comment = new StringBuffer(); ! IAtom[] atoms = getDBMolecule().getAsCDKMolecule(1).getAtoms(); int l=k; for(int m=0;m<k;m++){ ! if(atoms[m].getSymbol().equals("H")) l--; } --- 322,329 ---- IMolecule cdkMolWithOutH = getDBMolecule().getAsCDKMoleculeWithoutH(); StringBuffer comment = new StringBuffer(); ! Iterator atoms = getDBMolecule().getAsCDKMolecule(1).atoms(); int l=k; for(int m=0;m<k;m++){ ! if(getDBMolecule().getAsCDKMolecule(1).getAtom(m).getSymbol().equals("H")) l--; } |
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From: Stefan K. <sh...@us...> - 2006-10-09 13:24:46
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/portlets In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv21218/src/java/org/openscience/nmrshiftdb/portlets Modified Files: PredictPortlet.java SubmitPortlet.java Log Message: this uses new cdk and new saturation stuff. should resolve a long standing problem Index: PredictPortlet.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/portlets/PredictPortlet.java,v retrieving revision 1.173 retrieving revision 1.174 diff -C2 -r1.173 -r1.174 *** PredictPortlet.java 14 Sep 2006 17:08:26 -0000 1.173 --- PredictPortlet.java 9 Oct 2006 13:24:38 -0000 1.174 *************** *** 203,210 **** double[] statistics=null; if(predictAtomType.equals("H")){ ! IAtom[] connatoms=molh.getConnectedAtoms(molh.getAtom(i)); ! for(int k=0;k<connatoms.length;k++){ ! if(connatoms[k].getSymbol().equals("H")){ ! hatom=connatoms[k]; hoseCode=new StringBuffer(); statistics = AtomUtils.predictRange(molh, hatom , calculated, measured, null, comment, true, false, null, predictionValuesForAppletMap, ((Integer) session.getAttribute("choosennumber")).intValue(), true, hoseCode, ((Boolean)session.getAttribute("trueonly")).booleanValue()); --- 203,210 ---- double[] statistics=null; if(predictAtomType.equals("H")){ ! List connatoms=molh.getConnectedAtomsList(molh.getAtom(i)); ! for(int k=0;k<connatoms.size();k++){ ! if(((IAtom)connatoms.get(k)).getSymbol().equals("H")){ ! hatom=(IAtom)connatoms.get(k); hoseCode=new StringBuffer(); statistics = AtomUtils.predictRange(molh, hatom , calculated, measured, null, comment, true, false, null, predictionValuesForAppletMap, ((Integer) session.getAttribute("choosennumber")).intValue(), true, hoseCode, ((Boolean)session.getAttribute("trueonly")).booleanValue()); *************** *** 338,356 **** StringBuffer hoseCode = new StringBuffer(); if(predictbyhose){ ! hoseCode.append(hcg.getHOSECode(mol, mol.getConnectedAtoms(mol.getAtoms()[l])[0], 10,true)); }else{ hoseCode.append(mn[l]+""); } ! IAtom heavyatom=mol.getConnectedAtoms(mol.getAtom(l))[0]; int protoncount=0; ! for(int i=0;i<mol.getConnectedAtoms(heavyatom).length;i++){ ! if(mol.getConnectedAtoms(heavyatom)[i].getSymbol().equals("H")) protoncount++; } boolean second=false; if(protoncount==2){ ! for(int i=0;i<mol.getConnectedAtoms(heavyatom).length;i++){ ! if(mol.getConnectedAtoms(heavyatom)[i].getSymbol().equals("H")){ ! if(mol.getConnectedAtoms(heavyatom)[i]==mol.getAtom(l)){ break; }else{ --- 338,356 ---- StringBuffer hoseCode = new StringBuffer(); if(predictbyhose){ ! hoseCode.append(hcg.getHOSECode(mol, (IAtom)mol.getConnectedAtomsList(mol.getAtom(l)).get(0), 10,true)); }else{ hoseCode.append(mn[l]+""); } ! IAtom heavyatom=(IAtom)mol.getConnectedAtomsList(mol.getAtom(l)).get(0); int protoncount=0; ! for(int i=0;i<mol.getConnectedAtomsList(heavyatom).size();i++){ ! if(((IAtom)mol.getConnectedAtomsList(heavyatom).get(i)).getSymbol().equals("H")) protoncount++; } boolean second=false; if(protoncount==2){ ! for(int i=0;i<mol.getConnectedAtomsList(heavyatom).size();i++){ ! if(((IAtom)mol.getConnectedAtomsList(heavyatom).get(i)).getSymbol().equals("H")){ ! if(((IAtom)mol.getConnectedAtomsList(heavyatom).get(i))==mol.getAtom(l)){ break; }else{ *************** *** 438,448 **** if (mol.getAtom(l).getSymbol().equals("H")) { String hoseCode = (String)hcmap.get(mol.getAtom(l)); ! IAtom heavyatom=mol.getConnectedAtoms(mol.getAtom(l))[0]; int protoncount=0; ! for(int i=0;i<mol.getConnectedAtoms(heavyatom).length;i++){ ! if(mol.getConnectedAtoms(heavyatom)[i].getSymbol().equals("H")) protoncount++; } ! int mothernumber=mol.getAtomNumber(mol.getConnectedAtoms(mol.getAtom(l))[0]); if(!alreadyDone[mothernumber] || protoncount==2){ if(protoncount!=2){ --- 438,448 ---- if (mol.getAtom(l).getSymbol().equals("H")) { String hoseCode = (String)hcmap.get(mol.getAtom(l)); ! IAtom heavyatom=(IAtom)mol.getConnectedAtomsList(mol.getAtom(l)).get(0); int protoncount=0; ! for(int i=0;i<mol.getConnectedAtomsList(heavyatom).size();i++){ ! if(((IAtom)mol.getConnectedAtomsList(heavyatom).get(i)).getSymbol().equals("H")) protoncount++; } ! int mothernumber=mol.getAtomNumber((IAtom)mol.getConnectedAtomsList(mol.getAtom(l)).get(0)); if(!alreadyDone[mothernumber] || protoncount==2){ if(protoncount!=2){ Index: SubmitPortlet.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/portlets/SubmitPortlet.java,v retrieving revision 1.421 retrieving revision 1.422 diff -C2 -r1.421 -r1.422 *** SubmitPortlet.java 15 Sep 2006 12:08:32 -0000 1.421 --- SubmitPortlet.java 9 Oct 2006 13:24:38 -0000 1.422 *************** *** 606,614 **** int numberOfHs = 0; int numberOfH1s = 0; ! IAtom[] atoms = molWithH.getConnectedAtoms(molWithH.getAtom(i)); ! for (int k = 0; k < atoms.length; k++) { ! if (atoms[k].getSymbol().equals("H")) { numberOfHs++; ! if (atoms[k].getAtomicNumber() == 1) { numberOfH1s++; } --- 606,614 ---- int numberOfHs = 0; int numberOfH1s = 0; ! List atoms = molWithH.getConnectedAtomsList(molWithH.getAtom(i)); ! for (int k = 0; k < atoms.size(); k++) { ! if (((IAtom)atoms.get(k)).getSymbol().equals("H")) { numberOfHs++; ! if (((IAtom)atoms.get(k)).getAtomicNumber() == 1) { numberOfH1s++; } *************** *** 626,632 **** } ValueTriple vt=new ValueTriple(signal, intensity); ! for (int k = 0; k < atoms.length; k++) { ! if (atoms[k].getSymbol().equals("H")) { ! vt.atoms.add(atoms[k]); } } --- 626,632 ---- } ValueTriple vt=new ValueTriple(signal, intensity); ! for (int k = 0; k < atoms.size(); k++) { ! if (((IAtom)atoms.get(k)).getSymbol().equals("H")) { ! vt.atoms.add((IAtom)atoms.get(k)); } } *************** *** 640,646 **** int signal = new Integer(req.getParameter("atomSelect" + i)).intValue(); if (signal != 32767) { ! for (int k = 0; k < atoms.length; k++) { ! if (atoms[k].getSymbol().equals("H")) { ! ((ValueTriple) subData.getSignalstable().get(signal - 1)).atoms.add(atoms[k]); } } --- 640,646 ---- int signal = new Integer(req.getParameter("atomSelect" + i)).intValue(); if (signal != 32767) { ! for (int k = 0; k < atoms.size(); k++) { ! if (((IAtom)atoms.get(k)).getSymbol().equals("H")) { ! ((ValueTriple) subData.getSignalstable().get(signal - 1)).atoms.add(((IAtom)atoms.get(k))); } } *************** *** 657,663 **** } ValueTriple vt=new ValueTriple(signal, intensity); ! for (int m = 0; m < atoms.length; m++) { ! if (atoms[m].getSymbol().equals("H")) { ! vt.atoms.add(atoms[m]); break; } --- 657,663 ---- } ValueTriple vt=new ValueTriple(signal, intensity); ! for (int m = 0; m < atoms.size(); m++) { ! if (((IAtom)atoms.get(m)).getSymbol().equals("H")) { ! vt.atoms.add(((IAtom)atoms.get(m))); break; } *************** *** 678,687 **** ValueTriple vt=new ValueTriple(signal, intensity); boolean alreadyOnePassed = false; ! for (int m = 0; m < atoms.length; m++) { ! if (atoms[m].getSymbol().equals("H")) { if (!alreadyOnePassed) { alreadyOnePassed = true; } else { ! vt.atoms.add(atoms[m]); break; } --- 678,687 ---- ValueTriple vt=new ValueTriple(signal, intensity); boolean alreadyOnePassed = false; ! for (int m = 0; m < atoms.size(); m++) { ! if (((IAtom)atoms.get(m)).getSymbol().equals("H")) { if (!alreadyOnePassed) { alreadyOnePassed = true; } else { ! vt.atoms.add((IAtom)atoms.get(m)); break; } *************** *** 698,711 **** int signal2 = new Integer(req.getParameter("atomSelect" + i + "002")).intValue(); boolean alreadyOnePassed = false; ! for (int m = 0; m < atoms.length; m++) { ! if (atoms[m].getSymbol().equals("H")) { if (!alreadyOnePassed) { if (signal1 != 32767) { ! ((ValueTriple) subData.getSignalstable().get(signal1 - 1)).atoms.add(atoms[m]); } alreadyOnePassed = true; } else { if (signal2 != 32767) { ! ((ValueTriple) subData.getSignalstable().get(signal2 - 1)).atoms.add(atoms[m]); } break; --- 698,711 ---- int signal2 = new Integer(req.getParameter("atomSelect" + i + "002")).intValue(); boolean alreadyOnePassed = false; ! for (int m = 0; m < atoms.size(); m++) { ! if (((IAtom)atoms.get(m)).getSymbol().equals("H")) { if (!alreadyOnePassed) { if (signal1 != 32767) { ! ((ValueTriple) subData.getSignalstable().get(signal1 - 1)).atoms.add(((IAtom)atoms.get(m))); } alreadyOnePassed = true; } else { if (signal2 != 32767) { ! ((ValueTriple) subData.getSignalstable().get(signal2 - 1)).atoms.add(((IAtom)atoms.get(m))); } break; *************** *** 1130,1136 **** if((!subData.getChoosenSpectrumType().getName().equals("1H") && subData.getMolWithH().getAtom(i).getSymbol().equals(subData.getChoosenSpectrumType().getDBIsotope(1).getElementSymbol())) || (subData.getChoosenSpectrumType().getName().equals("1H") && !subData.getMolWithH().getAtom(i).getSymbol().equals("H"))){ String hs = ""; ! for (int k = 0; k < subData.getMolWithH().getConnectedAtoms(subData.getMolWithH().getAtom(i)).length; k++) { ! if (subData.getMolWithH().getConnectedAtoms(subData.getMolWithH().getAtom(i))[k].getSymbol().equals("H")) { ! hs = hs + "H " + (subData.getMolWithH().getAtomNumber(subData.getMolWithH().getConnectedAtoms(subData.getMolWithH().getAtom(i))[k]) + 1) + " "; } } --- 1130,1136 ---- if((!subData.getChoosenSpectrumType().getName().equals("1H") && subData.getMolWithH().getAtom(i).getSymbol().equals(subData.getChoosenSpectrumType().getDBIsotope(1).getElementSymbol())) || (subData.getChoosenSpectrumType().getName().equals("1H") && !subData.getMolWithH().getAtom(i).getSymbol().equals("H"))){ String hs = ""; ! for (int k = 0; k < subData.getMolWithH().getConnectedAtomsList(subData.getMolWithH().getAtom(i)).size(); k++) { ! if (((IAtom)subData.getMolWithH().getConnectedAtomsList(subData.getMolWithH().getAtom(i)).get(k)).getSymbol().equals("H")) { ! hs = hs + "H " + (subData.getMolWithH().getAtomNumber((IAtom)subData.getMolWithH().getConnectedAtomsList(subData.getMolWithH().getAtom(i)).get(k)) + 1) + " "; } } *************** *** 1140,1147 **** if(subData.multis.get(subData.getMolWithH().getAtom(i))!=null) multi.append((String)subData.multis.get(subData.getMolWithH().getAtom(i))); ! IAtom[] connatoms=subData.getMolWithH().getConnectedAtoms(subData.getMolWithH().getAtom(i)); ! for(int k=0;k<connatoms.length;k++){ ! if(connatoms[k].getSymbol().equals("H") && subData.multis.get(connatoms[k])!=null){ ! multi.append((String)subData.multis.get(connatoms[k])+";"); } } --- 1140,1147 ---- if(subData.multis.get(subData.getMolWithH().getAtom(i))!=null) multi.append((String)subData.multis.get(subData.getMolWithH().getAtom(i))); ! List connatoms=subData.getMolWithH().getConnectedAtomsList(subData.getMolWithH().getAtom(i)); ! for(int k=0;k<connatoms.size();k++){ ! if(((IAtom)connatoms.get(k)).getSymbol().equals("H") && subData.multis.get(((IAtom)connatoms.get(k)))!=null){ ! multi.append((String)subData.multis.get(((IAtom)connatoms.get(k)))+";"); } } *************** *** 1156,1162 **** multi.append(subData.couplings[i][k]+";"); } ! for(int k=0;k<connatoms.length;k++){ ! if(connatoms[k].getSymbol().equals("H") && subData.multis.get(connatoms[k])!=null){ ! int number=subData.getMolWithH().getAtomNumber(connatoms[k]); for(int l=0;l<subData.couplings.length;l++){ if(subData.couplings[l][number]!=null) --- 1156,1162 ---- multi.append(subData.couplings[i][k]+";"); } ! for(int k=0;k<connatoms.size();k++){ ! if(((IAtom)connatoms.get(k)).getSymbol().equals("H") && subData.multis.get(((IAtom)connatoms.get(k)))!=null){ ! int number=subData.getMolWithH().getAtomNumber(((IAtom)connatoms.get(k))); for(int l=0;l<subData.couplings.length;l++){ if(subData.couplings[l][number]!=null) *************** *** 1184,1188 **** for (int i = 0; i < subData.getMolWithH().getBondCount(); i++) { if (subData.getIsDoubleBondSpecified()[i]) { ! doubleBondConfigurationDisplay.append((subData.getMolWithH().getAtomNumber(subData.getMolWithH().getBond(i).getAtoms()[0]) + 1) + " to " + (subData.getMolWithH().getAtomNumber(subData.getMolWithH().getBond(i).getAtoms()[1]) + 1) + ";"); } } --- 1184,1188 ---- for (int i = 0; i < subData.getMolWithH().getBondCount(); i++) { if (subData.getIsDoubleBondSpecified()[i]) { ! doubleBondConfigurationDisplay.append((subData.getMolWithH().getAtomNumber(subData.getMolWithH().getBond(i).getAtom(0)) + 1) + " to " + (subData.getMolWithH().getAtomNumber(subData.getMolWithH().getBond(i).getAtom(1)) + 1) + ";"); } } *************** *** 1713,1724 **** if (isHSpectrum) { StringBuffer hnumbers = new StringBuffer(); ! IAtom[] atoms = mol.getConnectedAtoms(mol.getAtom(i)); IAtom hatom=null; ! for (int k = 0; k < atoms.length; k++) { ! if (atoms[k].getSymbol().equals("H")) { NumberOfHs++; ! if (atoms[k].getAtomicNumber() == 1) { NumberOfH1s++; ! hatom=atoms[k]; } } --- 1713,1724 ---- if (isHSpectrum) { StringBuffer hnumbers = new StringBuffer(); ! List atoms = mol.getConnectedAtomsList(mol.getAtom(i)); IAtom hatom=null; ! for (int k = 0; k < atoms.size(); k++) { ! if (((IAtom)atoms.get(k)).getSymbol().equals("H")) { NumberOfHs++; ! if (((IAtom)atoms.get(k)).getAtomicNumber() == 1) { NumberOfH1s++; ! hatom=((IAtom)atoms.get(k)); } } *************** *** 1726,1732 **** if (NumberOfH1s != 0) { Vector v = new Vector(); ! for (int k = 0; k < atoms.length; k++) { ! if (atoms[k].getSymbol().equals("H")) { ! v.add(new Integer(mol.getAtomNumber(atoms[k]) + 1)); } } --- 1726,1732 ---- if (NumberOfH1s != 0) { Vector v = new Vector(); ! for (int k = 0; k < atoms.size(); k++) { ! if (((IAtom)atoms.get(k)).getSymbol().equals("H")) { ! v.add(new Integer(mol.getAtomNumber(((IAtom)atoms.get(k))) + 1)); } } *************** *** 1825,1832 **** Vector v2 = new Vector(); if(isHSpectrum){ ! IAtom[] atoms = mol.getConnectedAtoms(mol.getAtom(i)); ! for (int k = 0; k < atoms.length; k++) { ! if (atoms[k].getSymbol().equals("H")) { ! v2.add(new Integer(mol.getAtomNumber(atoms[k]))); } } --- 1825,1832 ---- Vector v2 = new Vector(); if(isHSpectrum){ ! List atoms = mol.getConnectedAtomsList(mol.getAtom(i)); ! for (int k = 0; k < atoms.size(); k++) { ! if (((IAtom)atoms.get(k)).getSymbol().equals("H")) { ! v2.add(new Integer(mol.getAtomNumber(((IAtom)atoms.get(k))))); } } *************** *** 1839,1849 **** int NumberOfHs2 = 0; int NumberOfH1s2 = 0; ! IAtom[] atoms = mol.getConnectedAtoms(mol.getAtom(n)); Vector v = new Vector(); ! for (int k = 0; k < atoms.length; k++) { ! if (atoms[k].getSymbol().equals("H")) { ! v.add(new Integer(mol.getAtomNumber(atoms[k]))); NumberOfHs2++; ! if (atoms[k].getAtomicNumber() == 1) { NumberOfH1s2++; } --- 1839,1849 ---- int NumberOfHs2 = 0; int NumberOfH1s2 = 0; ! List atoms = mol.getConnectedAtomsList(mol.getAtom(n)); Vector v = new Vector(); ! for (int k = 0; k < atoms.size(); k++) { ! if (((IAtom)atoms.get(k)).getSymbol().equals("H")) { ! v.add(new Integer(mol.getAtomNumber(((IAtom)atoms.get(k))))); NumberOfHs2++; ! if (((IAtom)atoms.get(k)).getAtomicNumber() == 1) { NumberOfH1s2++; } |
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From: Stefan K. <sh...@us...> - 2006-10-09 13:24:46
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/util In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv21218/src/java/org/openscience/nmrshiftdb/util Modified Files: AtomUtils.java GeneralUtils.java SubmittingData.java Log Message: this uses new cdk and new saturation stuff. should resolve a long standing problem Index: AtomUtils.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/util/AtomUtils.java,v retrieving revision 1.163 retrieving revision 1.164 diff -C2 -r1.163 -r1.164 *** AtomUtils.java 28 Aug 2006 14:33:58 -0000 1.163 --- AtomUtils.java 9 Oct 2006 13:24:38 -0000 1.164 *************** *** 8,11 **** --- 8,13 ---- import java.util.BitSet; import java.util.HashMap; + import java.util.Iterator; + import java.util.List; import java.util.Map; import java.util.Vector; *************** *** 53,57 **** import org.openscience.cdk.tools.HydrogenAdder; import org.openscience.cdk.tools.Normalizer; ! import org.openscience.cdk.tools.manipulator.SetOfAtomContainersManipulator; import org.openscience.nmrshiftdb.PredictionTool; import org.openscience.nmrshiftdb.om.DBBond; --- 55,59 ---- import org.openscience.cdk.tools.HydrogenAdder; import org.openscience.cdk.tools.Normalizer; ! import org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator; import org.openscience.nmrshiftdb.PredictionTool; import org.openscience.nmrshiftdb.om.DBBond; *************** *** 175,179 **** IBond[] bonds = cdkmol.getBonds(); for (int l = 0; l < bonds.length; l++) { ! if (bonds[l].getAtom(0) == cdkmol.getConnectedAtoms(cdkmol.getAtom(atomnumber))[0] || bonds[l].getAtom(1) == cdkmol.getConnectedAtoms(cdkmol.getAtom(atomnumber))[0]) { if (bonds[l].getOrder() == 2) { class2 = true; --- 177,181 ---- IBond[] bonds = cdkmol.getBonds(); for (int l = 0; l < bonds.length; l++) { ! if (bonds[l].getAtom(0) == cdkmol.getConnectedAtomsList(cdkmol.getAtom(atomnumber)).get(0) || bonds[l].getAtom(1) == cdkmol.getConnectedAtomsList(cdkmol.getAtom(atomnumber)).get(0)) { if (bonds[l].getOrder() == 2) { class2 = true; *************** *** 181,187 **** } } ! if (cdkmol.getConnectedAtoms(cdkmol.getAtom(atomnumber))[0].getFlag(CDKConstants.ISAROMATIC)) { protonclass = 1; ! } else if (allrings.getRings(cdkmol.getConnectedAtoms(cdkmol.getAtom(atomnumber))[0]).getAtomContainerCount() > 0) { protonclass = 3; } else if (class2) { --- 183,189 ---- } } ! if (((IAtom)cdkmol.getConnectedAtomsList(cdkmol.getAtom(atomnumber)).get(0)).getFlag(CDKConstants.ISAROMATIC)) { protonclass = 1; ! } else if (allrings.getRings((IAtom)cdkmol.getConnectedAtomsList(cdkmol.getAtom(atomnumber)).get(0)).getAtomContainerCount() > 0) { protonclass = 3; } else if (class2) { *************** *** 242,246 **** floats[2] = ((float) l.doubleValue()); floats[3] = (float) (a.getCharge()); ! floats[4] = (float) (ac.getConnectedAtoms(a)[0].getCharge()); if (hcg == null) { hcg = new HOSECodeGenerator(); --- 244,248 ---- floats[2] = ((float) l.doubleValue()); floats[3] = (float) (a.getCharge()); ! floats[4] = (float) (((IAtom)ac.getConnectedAtomsList(a).get(0)).getCharge()); if (hcg == null) { hcg = new HOSECodeGenerator(); *************** *** 342,351 **** } if(protonclass==2){ ! IAtom firstheavy=ac.getConnectedAtoms(a)[0]; ! IBond[] bondsoffirstheavy=ac.getConnectedBonds(firstheavy); IBond doublebond=null; ! for(int k=0;k<bondsoffirstheavy.length;k++){ ! if(bondsoffirstheavy[k].getOrder()==2){ ! doublebond=bondsoffirstheavy[k]; break; } --- 344,353 ---- } if(protonclass==2){ ! IAtom firstheavy=(IAtom)ac.getConnectedAtomsList(a).get(0); ! List bondsoffirstheavy=ac.getConnectedBondsList(firstheavy); IBond doublebond=null; ! for(int k=0;k<bondsoffirstheavy.size();k++){ ! if(((IBond)bondsoffirstheavy.get(k)).getOrder()==2){ ! doublebond=(IBond)bondsoffirstheavy.get(k); break; } *************** *** 362,370 **** dr = (DoubleResult) epdes.calculate(secondheavy,ac).getValue(); floats[91] = ((float) dr.doubleValue()); ! IAtom[] atomsonfirst=ac.getConnectedAtoms(firstheavy); IAtom otheronfirstheavy=null; ! for(int k=0;k<atomsonfirst.length;k++){ ! if(atomsonfirst[k]!=secondheavy && atomsonfirst[k]!=a){ ! otheronfirstheavy=atomsonfirst[k]; break; } --- 364,372 ---- dr = (DoubleResult) epdes.calculate(secondheavy,ac).getValue(); floats[91] = ((float) dr.doubleValue()); ! List atomsonfirst=ac.getConnectedAtomsList(firstheavy); IAtom otheronfirstheavy=null; ! for(int k=0;k<atomsonfirst.size();k++){ ! if(atomsonfirst.get(k)!=secondheavy && atomsonfirst.get(k)!=a){ ! otheronfirstheavy=(IAtom)atomsonfirst.get(k); break; } *************** *** 373,383 **** IAtom firstonsecond=null; IAtom secondonsecond=null; ! IAtom[] connectedtosecond=ac.getConnectedAtoms(secondheavy); ! for(int k=0;k<connectedtosecond.length;k++){ ! if(connectedtosecond[k]!=firstheavy){ if(firstonsecond==null){ ! firstonsecond=connectedtosecond[k]; }else{ ! secondonsecond=connectedtosecond[k]; break; } --- 375,385 ---- IAtom firstonsecond=null; IAtom secondonsecond=null; ! List connectedtosecond=ac.getConnectedAtomsList(secondheavy); ! for(int k=0;k<connectedtosecond.size();k++){ ! if(connectedtosecond.get(k)!=firstheavy){ if(firstonsecond==null){ ! firstonsecond=(IAtom)connectedtosecond.get(k); }else{ ! secondonsecond=(IAtom)connectedtosecond.get(k); break; } *************** *** 412,416 **** floats[startfield+2] = ((float) dr.doubleValue()); IAtomContainerSet acSet = ConjugatedPiSystemsDetector.detect(ac); ! IAtomContainer piac=(IAtomContainer)SetOfAtomContainersManipulator.getAllInOneContainer(acSet); floats[startfield+3]=0; for(int k=0;k<piac.getAtomCount();k++){ --- 414,418 ---- floats[startfield+2] = ((float) dr.doubleValue()); IAtomContainerSet acSet = ConjugatedPiSystemsDetector.detect(ac); ! IAtomContainer piac=(IAtomContainer)AtomContainerSetManipulator.getAllInOneContainer(acSet); floats[startfield+3]=0; for(int k=0;k<piac.getAtomCount();k++){ *************** *** 460,464 **** */ public static float[] getDescriptorSet(DBCondition temp, DBCondition field, DBCondition solvent, IAtomContainer ac, IAtom a, IRingSet rs, int protonclass) throws Exception { ! IAtom atomInFocus = ac.getConnectedAtoms(a)[0]; Integer atomInFocusInt = new Integer(ac.getAtomNumber(atomInFocus)); AtomHybridizationVSEPRDescriptor hybdes = new AtomHybridizationVSEPRDescriptor(); --- 462,466 ---- */ public static float[] getDescriptorSet(DBCondition temp, DBCondition field, DBCondition solvent, IAtomContainer ac, IAtom a, IRingSet rs, int protonclass) throws Exception { ! IAtom atomInFocus = (IAtom)ac.getConnectedAtomsList(a).get(0); Integer atomInFocusInt = new Integer(ac.getAtomNumber(atomInFocus)); AtomHybridizationVSEPRDescriptor hybdes = new AtomHybridizationVSEPRDescriptor(); *************** *** 483,489 **** floats[3] = (float) (atomInFocus.getFormalNeighbourCount() - floats[2]); int substituents = 0; ! IAtom[] v = ac.getConnectedAtoms(atomInFocus); ! for (int i = 0; i < v.length; i++) { ! if (!v[i].getSymbol().equals("H")) { substituents++; } --- 485,491 ---- floats[3] = (float) (atomInFocus.getFormalNeighbourCount() - floats[2]); int substituents = 0; ! List v = ac.getConnectedAtomsList(atomInFocus); ! for (int i = 0; i < v.size(); i++) { ! if (!((IAtom)v.get(i)).getSymbol().equals("H")) { substituents++; } *************** *** 500,504 **** int sumValenceElectrons = 0; Vector closestInSpace = GeometryTools.findClosestInSpace(ac, atomInFocus, 16); ! IAtom[] connectedAtoms = ac.getConnectedAtoms(atomInFocus); for (int i = 0; i < closestInSpace.size(); i++) { IAtom closest = (IAtom) closestInSpace.get(i); --- 502,506 ---- int sumValenceElectrons = 0; Vector closestInSpace = GeometryTools.findClosestInSpace(ac, atomInFocus, 16); ! List connectedAtoms = ac.getConnectedAtomsList(atomInFocus); for (int i = 0; i < closestInSpace.size(); i++) { IAtom closest = (IAtom) closestInSpace.get(i); *************** *** 545,554 **** double distanceAll = 0; int numberofhs = 0; ! for (int k = 0; k < connectedAtoms.length; k++) { ! if (connectedAtoms[k].getSymbol().equals("H")) { numberofhs++; ! distanceAll += connectedAtoms[k].getPoint3d().distance(closest.getPoint3d()); ! if (connectedAtoms[k].getPoint3d().distance(closest.getPoint3d()) < distanceMin) { ! distanceMin = connectedAtoms[k].getPoint3d().distance(closest.getPoint3d()); } } --- 547,556 ---- double distanceAll = 0; int numberofhs = 0; ! for (int k = 0; k < connectedAtoms.size(); k++) { ! if (((IAtom)connectedAtoms.get(k)).getSymbol().equals("H")) { numberofhs++; ! distanceAll += ((IAtom)connectedAtoms.get(k)).getPoint3d().distance(closest.getPoint3d()); ! if (((IAtom)connectedAtoms.get(k)).getPoint3d().distance(closest.getPoint3d()) < distanceMin) { ! distanceMin = ((IAtom)connectedAtoms.get(k)).getPoint3d().distance(closest.getPoint3d()); } } *************** *** 608,617 **** double distanceAll = 0; int numberofhs = 0; ! for (int k = 0; k < connectedAtoms.length; k++) { ! if (connectedAtoms[k].getSymbol().equals("H")) { numberofhs++; ! distanceAll += connectedAtoms[k].getPoint3d().distance(closestByBond[i].getPoint3d()); ! if (connectedAtoms[k].getPoint3d().distance(closestByBond[i].getPoint3d()) < distanceMin) { ! distanceMin = connectedAtoms[k].getPoint3d().distance(closestByBond[i].getPoint3d()); } } --- 610,619 ---- double distanceAll = 0; int numberofhs = 0; ! for (int k = 0; k < connectedAtoms.size(); k++) { ! if (((IAtom)connectedAtoms.get(k)).getSymbol().equals("H")) { numberofhs++; ! distanceAll += ((IAtom)connectedAtoms.get(k)).getPoint3d().distance(closestByBond[i].getPoint3d()); ! if (((IAtom)connectedAtoms.get(k)).getPoint3d().distance(closestByBond[i].getPoint3d()) < distanceMin) { ! distanceMin = ((IAtom)connectedAtoms.get(k)).getPoint3d().distance(closestByBond[i].getPoint3d()); } } *************** *** 684,688 **** */ public static boolean checkIfOnlyOneStructure(IMolecule mol) { ! if (setThisAtomAsLinked(mol.getAtoms()[0], mol, 0) == mol.getAtoms().length) { return (true); } else { --- 686,690 ---- */ public static boolean checkIfOnlyOneStructure(IMolecule mol) { ! if (setThisAtomAsLinked(mol.getAtom(0), mol, 0) == mol.getAtomCount()) { return (true); } else { *************** *** 732,736 **** if (sg.isValidDoubleBondConfiguration(mol, bonds[i])) { StringAndIntAndBoolean sai = new StringAndIntAndBoolean(); ! sai.myString = new String((mol.getAtomNumber(bonds[i].getAtoms()[0]) + 1) + " = " + (mol.getAtomNumber(bonds[i].getAtoms()[1]) + 1)); sai.myInt = i; if (dbbonds != null) { --- 734,738 ---- if (sg.isValidDoubleBondConfiguration(mol, bonds[i])) { StringAndIntAndBoolean sai = new StringAndIntAndBoolean(); ! sai.myString = new String((mol.getAtomNumber(bonds[i].getAtom(0)) + 1) + " = " + (mol.getAtomNumber(bonds[i].getAtom(1)) + 1)); sai.myInt = i; if (dbbonds != null) { *************** *** 859,863 **** for (int i = 0; i < container.getAtomCount(); i++) { IAtom a = container.getAtom(i); ! if (container.getConnectedAtoms(a).length == 4) { int up = 0; int down = 0; --- 861,865 ---- for (int i = 0; i < container.getAtomCount(); i++) { IAtom a = container.getAtom(i); ! if (container.getConnectedAtomsList(a).size() == 4) { int up = 0; int down = 0; *************** *** 865,876 **** IAtom h = null; for (int k = 0; k < 4; k++) { ! if (container.getBond(a, container.getConnectedAtoms(a)[k]).getStereo() == CDKConstants.STEREO_BOND_UP) { up++; } ! if (container.getBond(a, container.getConnectedAtoms(a)[k]).getStereo() == CDKConstants.STEREO_BOND_DOWN) { down++; } ! if (container.getBond(a, container.getConnectedAtoms(a)[k]).getStereo() == CDKConstants.STEREO_BOND_NONE && container.getConnectedAtoms(a)[k].getSymbol().equals("H")) { ! h = container.getConnectedAtoms(a)[k]; hs++; } --- 867,878 ---- IAtom h = null; for (int k = 0; k < 4; k++) { ! if (container.getBond(a, (IAtom)container.getConnectedAtomsList(a).get(k)).getStereo() == CDKConstants.STEREO_BOND_UP) { up++; } ! if (container.getBond(a, (IAtom)container.getConnectedAtomsList(a).get(k)).getStereo() == CDKConstants.STEREO_BOND_DOWN) { down++; } ! if (container.getBond(a, (IAtom)container.getConnectedAtomsList(a).get(k)).getStereo() == CDKConstants.STEREO_BOND_NONE && ((IAtom)container.getConnectedAtomsList(a).get(k)).getSymbol().equals("H")) { ! h = (IAtom)container.getConnectedAtomsList(a).get(k); hs++; } *************** *** 897,916 **** */ public static IMolecule rearangeAtoms(IMolecule mol) throws Exception { ! IAtom[] atomsold = mol.getAtoms(); ! IAtom[] atomsnew = new IAtom[atomsold.length]; int k = 0; ! for (int i = 0; i < atomsold.length; i++) { ! if (atomsold[i].getSymbol().equals("C")) { ! atomsnew[k++] = atomsold[i]; ! } ! } ! for (int i = 0; i < atomsold.length; i++) { ! if (!atomsold[i].getSymbol().equals("C") && !atomsold[i].getSymbol().equals("H")) { ! atomsnew[k++] = atomsold[i]; ! } ! } ! for (int i = 0; i < atomsold.length; i++) { ! if (atomsold[i].getSymbol().equals("H")) { ! atomsnew[k++] = atomsold[i]; } } --- 899,923 ---- */ public static IMolecule rearangeAtoms(IMolecule mol) throws Exception { ! Iterator atomsold = mol.atoms(); ! IAtom[] atomsnew = new IAtom[mol.getAtomCount()]; int k = 0; ! while(atomsold.hasNext()) { ! IAtom atom=(IAtom)atomsold.next(); ! if (atom.getSymbol().equals("C")) { ! atomsnew[k++] = atom; ! } ! } ! atomsold = mol.atoms(); ! while(atomsold.hasNext()) { ! IAtom atom=(IAtom)atomsold.next(); ! if (!atom.getSymbol().equals("C") && !atom.getSymbol().equals("H")) { ! atomsnew[k++] = atom; ! } ! } ! atomsold = mol.atoms(); ! while(atomsold.hasNext()) { ! IAtom atom=(IAtom)atomsold.next(); ! if (atom.getSymbol().equals("H")) { ! atomsnew[k++] = atom; } } *************** *** 931,938 **** alreadyTouched++; atom.setFlag(CDKConstants.VISITED, true); ! IAtom[] connectedAtoms = mol.getConnectedAtoms(atom); boolean allConnectedAtomsAlreadTouched = true; ! for (int i = 0; i < connectedAtoms.length; i++) { ! if (connectedAtoms[i].getFlag(CDKConstants.VISITED) == false) { allConnectedAtomsAlreadTouched = false; } --- 938,945 ---- alreadyTouched++; atom.setFlag(CDKConstants.VISITED, true); ! List connectedAtoms = mol.getConnectedAtomsList(atom); boolean allConnectedAtomsAlreadTouched = true; ! for (int i = 0; i < connectedAtoms.size(); i++) { ! if (((IAtom)connectedAtoms.get(i)).getFlag(CDKConstants.VISITED) == false) { allConnectedAtomsAlreadTouched = false; } *************** *** 941,947 **** return (alreadyTouched); } ! for (int i = 0; i < connectedAtoms.length; i++) { ! if (!connectedAtoms[i].getFlag(CDKConstants.VISITED)) { ! alreadyTouched = setThisAtomAsLinked(connectedAtoms[i], mol, alreadyTouched); } } --- 948,954 ---- return (alreadyTouched); } ! for (int i = 0; i < connectedAtoms.size(); i++) { ! if (!((IAtom)connectedAtoms.get(i)).getFlag(CDKConstants.VISITED)) { ! alreadyTouched = setThisAtomAsLinked(((IAtom)connectedAtoms.get(i)), mol, alreadyTouched); } } Index: GeneralUtils.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/util/GeneralUtils.java,v retrieving revision 1.187 retrieving revision 1.188 diff -C2 -r1.187 -r1.188 *** GeneralUtils.java 23 Sep 2006 22:10:44 -0000 1.187 --- GeneralUtils.java 9 Oct 2006 13:24:38 -0000 1.188 *************** *** 746,754 **** IMolecule cdkmolwithh = mol.getAsCDKMolecule(1); IMolecule cdkmolwithouth = (IMolecule) AtomContainerManipulator.removeHydrogens(cdkmolwithh); ! IAtom[] atoms = cdkmolwithh.getAtoms(); DBAtom[] dbatoms = mol.getAtomsAsArrayInMdlOrder(); ! for (int i = 0; i < atoms.length; i++) { ! if (atoms[i].getSymbol().equals("C")) { ! String hc = hcg.getHOSECode(cdkmolwithouth, atoms[i], 1,true); StringTokenizer st = new StringTokenizer(hc, ";"); st.nextToken(); --- 746,756 ---- IMolecule cdkmolwithh = mol.getAsCDKMolecule(1); IMolecule cdkmolwithouth = (IMolecule) AtomContainerManipulator.removeHydrogens(cdkmolwithh); ! Iterator atoms = cdkmolwithh.atoms(); DBAtom[] dbatoms = mol.getAtomsAsArrayInMdlOrder(); ! int i=0; ! while(atoms.hasNext()){ ! IAtom atom=(IAtom)atoms.next(); ! if (atom.getSymbol().equals("C")) { ! String hc = hcg.getHOSECode(cdkmolwithouth, atom, 1,true); StringTokenizer st = new StringTokenizer(hc, ";"); st.nextToken(); *************** *** 770,773 **** --- 772,776 ---- } } + i++; } } *************** *** 2042,2046 **** return; } ! IMolecule mol = chemModel.getSetOfMolecules().getMolecule(0); data.getSession().setAttribute(attributename, mol); } --- 2045,2049 ---- return; } ! IMolecule mol = chemModel.getMoleculeSet().getMolecule(0); data.getSession().setAttribute(attributename, mol); } *************** *** 2098,2102 **** throw new NmrshiftdbException("Model does not have coordinates. Cannot open file"); } ! IMolecule mol = chemModel.getSetOfMolecules().getMolecule(0); StringWriter sw = new StringWriter(); new MDLWriter(sw).writeMolecule(mol); --- 2101,2105 ---- throw new NmrshiftdbException("Model does not have coordinates. Cannot open file"); } ! IMolecule mol = chemModel.getMoleculeSet().getMolecule(0); StringWriter sw = new StringWriter(); new MDLWriter(sw).writeMolecule(mol); Index: SubmittingData.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/util/SubmittingData.java,v retrieving revision 1.282 retrieving revision 1.283 diff -C2 -r1.282 -r1.283 *** SubmittingData.java 15 Sep 2006 12:08:33 -0000 1.282 --- SubmittingData.java 9 Oct 2006 13:24:38 -0000 1.283 *************** *** 890,894 **** IAtom mainAtom = null; if (choosenSpectrumType.getName().equals("1H")) { ! mainAtom = molWithH.getConnectedAtoms((IAtom) it.atoms.get(k))[0]; } else { mainAtom = (IAtom) it.atoms.get(k); --- 890,894 ---- IAtom mainAtom = null; if (choosenSpectrumType.getName().equals("1H")) { ! mainAtom = (IAtom)molWithH.getConnectedAtomsList((IAtom) it.atoms.get(k)).get(0); } else { mainAtom = (IAtom) it.atoms.get(k); *************** *** 1332,1336 **** break; } ! IAtom[] atoms = getMolWithH().getConnectedAtoms(molWithH.getAtom(((Float) ((ValueTriple) getSignalstable().get(i)).atoms.get(n)).intValue())); float numberToReplace = ((Float) ((ValueTriple) getSignalstable().get(i)).atoms.get(n)).floatValue(); IAtom atom = getMolWithH().getAtom((int) numberToReplace); --- 1332,1336 ---- break; } ! List atoms = getMolWithH().getConnectedAtomsList(molWithH.getAtom(((Float) ((ValueTriple) getSignalstable().get(i)).atoms.get(n)).intValue())); float numberToReplace = ((Float) ((ValueTriple) getSignalstable().get(i)).atoms.get(n)).floatValue(); IAtom atom = getMolWithH().getAtom((int) numberToReplace); *************** *** 1340,1349 **** if ((int) numberToReplace == numberToReplace) { boolean alreadyReplaced = false; ! for (int k = 0; k < atoms.length; k++) { ! if (atoms[k].getSymbol().equals("H")) { if (!alreadyReplaced) { ! ((ValueTriple) getSignalstable().get(i)).atoms.set(n, atoms[k]); } else { ! ((ValueTriple) getSignalstable().get(i)).atoms.add(atoms[k]); } } --- 1340,1349 ---- if ((int) numberToReplace == numberToReplace) { boolean alreadyReplaced = false; ! for (int k = 0; k < atoms.size(); k++) { ! if (((IAtom)atoms.get(k)).getSymbol().equals("H")) { if (!alreadyReplaced) { ! ((ValueTriple) getSignalstable().get(i)).atoms.set(n, ((IAtom)atoms.get(k))); } else { ! ((ValueTriple) getSignalstable().get(i)).atoms.add(((IAtom)atoms.get(k))); } } *************** *** 1352,1361 **** IAtom firstAtom = null; IAtom secondAtom = null; ! for (int k = 0; k < atoms.length; k++) { ! if (atoms[k].getSymbol().equals("H")) { if (firstAtom == null) { ! firstAtom = atoms[k]; } else { ! secondAtom = atoms[k]; break; } --- 1352,1361 ---- IAtom firstAtom = null; IAtom secondAtom = null; ! for (int k = 0; k < atoms.size(); k++) { ! if (((IAtom)atoms.get(k)).getSymbol().equals("H")) { if (firstAtom == null) { ! firstAtom = ((IAtom)atoms.get(k)); } else { ! secondAtom = ((IAtom)atoms.get(k)); break; } *************** *** 1450,1462 **** * @return The atomNumber value */ ! private int getAtomNumber(IAtom atom, IAtomContainer ac) { ! IAtom[] atoms = ac.getAtoms(); ! for (int i = 0; i < atoms.length; i++) { ! if (atoms[i].getPoint2d()!=null && atoms[i].getPoint2d().equals(atom.getPoint2d())) { return (i); } ! if (atoms[i].getPoint3d()!=null && atoms[i].getPoint3d().equals(atom.getPoint3d())) { ! return (i); ! } } return (-1); --- 1450,1465 ---- * @return The atomNumber value */ ! private int getAtomNumber(IAtom atomcompare, IAtomContainer ac) { ! Iterator atoms = ac.atoms(); ! int i=0; ! while(atoms.hasNext()){ ! IAtom atom=(IAtom)atoms.next(); ! if (atom.getPoint2d()!=null && atom.getPoint2d().equals(atom.getPoint2d())) { return (i); } ! if (atom.getPoint3d()!=null && atom.getPoint3d().equals(atomcompare.getPoint3d())) { ! return (i); ! } ! i++; } return (-1); *************** *** 1533,1557 **** Log.debug("after insert chemName"); //Add atoms to db ! IAtom[] atoms = molWithH.getAtoms(); ! dbatoms = new NumberKey[atoms.length]; HOSECodeGenerator hcg = new HOSECodeGenerator(); ! for (int i = 0; i < atoms.length; i++) { String hoseCode = null; String hoseCodeWithRings = null; ! if (GeneralUtils.getAtomsWithHoseCode().contains(atoms[i].getSymbol())) { int l = i; for (int k = 0; k < i; k++) { ! if (atoms[k].getSymbol().equals("H")) { l--; } } ! hoseCode = hcg.getHOSECode(molWithHCount, molWithHCount.getAtoms()[l], numberOfSpheres,false); ! hoseCodeWithRings = hcg.getHOSECode(molWithHCount, molWithHCount.getAtoms()[l], numberOfSpheres,true); } ! if( atoms[i].getSymbol().equals("H")){ ! hoseCode = hcg.getHOSECode(molWithH, molWithH.getAtoms()[i], numberOfSpheres,false); ! hoseCodeWithRings = hcg.getHOSECode(molWithH, molWithH.getAtoms()[i], numberOfSpheres,true); } ! DBAtom atom = new DBAtom(atoms[i], molWithH, dbmol, hoseCode, hoseCodeWithRings, i < numberOfAtomsInMdl); //atom.force3d=true; atom.save(dbconn); --- 1536,1560 ---- Log.debug("after insert chemName"); //Add atoms to db ! Iterator atoms = molWithH.atoms(); ! dbatoms = new NumberKey[molWithH.getAtomCount()]; HOSECodeGenerator hcg = new HOSECodeGenerator(); ! for (int i = 0; i < molWithH.getAtomCount(); i++) { String hoseCode = null; String hoseCodeWithRings = null; ! if (GeneralUtils.getAtomsWithHoseCode().contains(molWithH.getAtom(i).getSymbol())) { int l = i; for (int k = 0; k < i; k++) { ! if (molWithH.getAtom(k).getSymbol().equals("H")) { l--; } } ! hoseCode = hcg.getHOSECode(molWithHCount, molWithHCount.getAtom(l), numberOfSpheres,false); ! hoseCodeWithRings = hcg.getHOSECode(molWithHCount, molWithHCount.getAtom(l), numberOfSpheres,true); } ! if(molWithH.getAtom(i).getSymbol().equals("H")){ ! hoseCode = hcg.getHOSECode(molWithH, molWithH.getAtom(i), numberOfSpheres,false); ! hoseCodeWithRings = hcg.getHOSECode(molWithH, molWithH.getAtom(i), numberOfSpheres,true); } ! DBAtom atom = new DBAtom(molWithH.getAtom(i), molWithH, dbmol, hoseCode, hoseCodeWithRings, i < numberOfAtomsInMdl); //atom.force3d=true; atom.save(dbconn); *************** *** 1565,1575 **** bond.save(dbconn); //Add bonds-atoms relationship to DB ! IAtom[] neighbourAtoms = bonds[i].getAtoms(); ! for (int k = 0; k < neighbourAtoms.length; k++) { DBBondDBAtom bondatom = new DBBondDBAtom(); ! bondatom.setAtomId(dbatoms[molWithH.getAtomNumber(neighbourAtoms[k])]); bondatom.setBondId(bond.getBondId()); bondatom.setOrderNumber(k); bondatom.save(dbconn); } } --- 1568,1580 ---- bond.save(dbconn); //Add bonds-atoms relationship to DB ! Iterator neighbourAtoms = bonds[i].atoms(); ! int k=0; ! while(neighbourAtoms.hasNext()){ DBBondDBAtom bondatom = new DBBondDBAtom(); ! bondatom.setAtomId(dbatoms[molWithH.getAtomNumber((IAtom)neighbourAtoms.next())]); bondatom.setBondId(bond.getBondId()); bondatom.setOrderNumber(k); bondatom.save(dbconn); + k++; } } |
Update of /cvsroot/nmrshiftdb/nmrshiftdb/lib In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv21218/lib Modified Files: cdk-builder3d.jar cdk-charges.jar cdk-core.jar cdk-data.jar cdk-extra.jar cdk-forcefield.jar cdk-interfaces.jar cdk-io.jar cdk-libio-cml.jar cdk-pdb-cml.jar cdk-pdb.jar cdk-qsar-cml.jar cdk-qsar.jar cdk-render.jar cdk-sdg.jar cdk-smiles.jar cdk-standard.jar cdk-valencycheck.jar Log Message: this uses new cdk and new saturation stuff. should resolve a long standing problem Index: cdk-builder3d.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/lib/cdk-builder3d.jar,v retrieving revision 1.51 retrieving revision 1.52 diff -C2 -r1.51 -r1.52 Binary files /tmp/cvsLRr2vN and /tmp/cvsdo6AOa differ Index: cdk-charges.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/lib/cdk-charges.jar,v retrieving revision 1.6 retrieving revision 1.7 diff -C2 -r1.6 -r1.7 Binary files /tmp/cvsAD7gAf and /tmp/cvsVZu97C differ Index: cdk-core.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/lib/cdk-core.jar,v retrieving revision 1.123 retrieving revision 1.124 diff -C2 -r1.123 -r1.124 Binary files /tmp/cvszGMgPh and /tmp/cvst0LquF differ Index: cdk-data.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/lib/cdk-data.jar,v retrieving revision 1.47 retrieving revision 1.48 diff -C2 -r1.47 -r1.48 Binary files /tmp/cvsD3Ukeo and /tmp/cvsqaaJ5L differ Index: cdk-extra.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/lib/cdk-extra.jar,v retrieving revision 1.161 retrieving revision 1.162 diff -C2 -r1.161 -r1.162 Binary files /tmp/cvsG5Ln7A and /tmp/cvsKo3llZ differ Index: cdk-forcefield.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/lib/cdk-forcefield.jar,v retrieving revision 1.6 retrieving revision 1.7 diff -C2 -r1.6 -r1.7 Binary files /tmp/cvss0yDTG and /tmp/cvsRpWjv5 differ Index: cdk-interfaces.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/lib/cdk-interfaces.jar,v retrieving revision 1.39 retrieving revision 1.40 diff -C2 -r1.39 -r1.40 Binary files /tmp/cvs0es8RN and /tmp/cvsK0AGEc differ Index: cdk-io.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/lib/cdk-io.jar,v retrieving revision 1.113 retrieving revision 1.114 diff -C2 -r1.113 -r1.114 Binary files /tmp/cvsfioIcQ and /tmp/cvsqM515e differ Index: cdk-libio-cml.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/lib/cdk-libio-cml.jar,v retrieving revision 1.39 retrieving revision 1.40 diff -C2 -r1.39 -r1.40 Binary files /tmp/cvsHk4URY and /tmp/cvseCnaTn differ Index: cdk-pdb-cml.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/lib/cdk-pdb-cml.jar,v retrieving revision 1.39 retrieving revision 1.40 diff -C2 -r1.39 -r1.40 Binary files /tmp/cvszwr4P1 and /tmp/cvsDQuIZq differ Index: cdk-pdb.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/lib/cdk-pdb.jar,v retrieving revision 1.39 retrieving revision 1.40 diff -C2 -r1.39 -r1.40 Binary files /tmp/cvs0Bjqk7 and /tmp/cvsSWiyDw differ Index: cdk-qsar-cml.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/lib/cdk-qsar-cml.jar,v retrieving revision 1.39 retrieving revision 1.40 diff -C2 -r1.39 -r1.40 Binary files /tmp/cvsaw4Lr9 and /tmp/cvsKfLhOy differ Index: cdk-qsar.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/lib/cdk-qsar.jar,v retrieving revision 1.54 retrieving revision 1.55 diff -C2 -r1.54 -r1.55 Binary files /tmp/cvsLRoQEb and /tmp/cvsCGzD6A differ Index: cdk-render.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/lib/cdk-render.jar,v retrieving revision 1.94 retrieving revision 1.95 diff -C2 -r1.94 -r1.95 Binary files /tmp/cvsFlWvJh and /tmp/cvsYM8RfH differ Index: cdk-sdg.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/lib/cdk-sdg.jar,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -r1.1 -r1.2 Binary files /tmp/cvsNlNWsi and /tmp/cvsxcXE4H differ Index: cdk-smiles.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/lib/cdk-smiles.jar,v retrieving revision 1.9 retrieving revision 1.10 diff -C2 -r1.9 -r1.10 Binary files /tmp/cvsNc5lLk and /tmp/cvsr49WqK differ Index: cdk-standard.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/lib/cdk-standard.jar,v retrieving revision 1.108 retrieving revision 1.109 diff -C2 -r1.108 -r1.109 Binary files /tmp/cvsDhhs4n and /tmp/cvsaQ9nQN differ Index: cdk-valencycheck.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/lib/cdk-valencycheck.jar,v retrieving revision 1.9 retrieving revision 1.10 diff -C2 -r1.9 -r1.10 Binary files /tmp/cvs0QIvnt and /tmp/cvsFWRqdT differ |
|
From: Stefan K. <sh...@us...> - 2006-10-09 13:24:45
|
Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv21218/src/java/org/openscience/nmrshiftdb Modified Files: AdminPanel.java NmrshiftdbServlet.java Log Message: this uses new cdk and new saturation stuff. should resolve a long standing problem Index: AdminPanel.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/AdminPanel.java,v retrieving revision 1.233 retrieving revision 1.234 diff -C2 -r1.233 -r1.234 *** AdminPanel.java 6 Oct 2006 13:00:04 -0000 1.233 --- AdminPanel.java 9 Oct 2006 13:24:37 -0000 1.234 *************** *** 20,23 **** --- 20,24 ---- import java.text.SimpleDateFormat; import java.util.Date; + import java.util.Enumeration; import java.util.HashMap; import java.util.Iterator; *************** *** 888,892 **** Vector signals=subData.getSignalstable(); boolean added=false; ! List connatoms=subData.getMolWithH().getConnectedAtomsVector(subData.getMolWithH().getAtom(atom-1));//H for(int l=0;l<signals.size();l++){ if(((ValueTriple)signals.get(l)).value1==value){ --- 889,893 ---- Vector signals=subData.getSignalstable(); boolean added=false; ! List connatoms=subData.getMolWithH().getConnectedAtomsList(subData.getMolWithH().getAtom(atom-1));//H for(int l=0;l<signals.size();l++){ if(((ValueTriple)signals.get(l)).value1==value){ *************** *** 2152,2166 **** System.err.println("Start making HOSE codes for molecule " + mol.getMoleculeId()); IMolecule cdkmolwithouth=mol.getAsCDKMoleculeWithoutH(); ! IAtom[] atoms = mol.getAsCDKMolecule(1).getAtoms(); ! for (int k = 0; k < atoms.length; k++) { DBAtom dbatom=DBAtomPeer.getByMoleculeIdAndMdlNumber(mol.getMoleculeId(),k); String hoseCode = null; ! if (GeneralUtils.getAtomsWithHoseCode().contains(atoms[k].getSymbol())) { int l=k; for(int m=0;m<k;m++){ ! if(atoms[m].getSymbol().equals("H")) l--; } ! hoseCode = hcg.getHOSECode(cdkmolwithouth, cdkmolwithouth.getAtoms()[l], spheresMax,true); } if (hoseCode != null) { --- 2153,2166 ---- System.err.println("Start making HOSE codes for molecule " + mol.getMoleculeId()); IMolecule cdkmolwithouth=mol.getAsCDKMoleculeWithoutH(); ! for (int k = 0; k < mol.getAsCDKMolecule(1).getAtomCount(); k++) { DBAtom dbatom=DBAtomPeer.getByMoleculeIdAndMdlNumber(mol.getMoleculeId(),k); String hoseCode = null; ! if (GeneralUtils.getAtomsWithHoseCode().contains(mol.getAsCDKMolecule(1).getAtom(k).getSymbol())) { int l=k; for(int m=0;m<k;m++){ ! if(mol.getAsCDKMolecule(1).getAtom(m).getSymbol().equals("H")) l--; } ! hoseCode = hcg.getHOSECode(cdkmolwithouth, cdkmolwithouth.getAtom(l), spheresMax,true); } if (hoseCode != null) { *************** *** 2663,2671 **** if (parent.getHydrogenCount() == 1) { ValueTriple vt = new ValueTriple(); ! IAtom[] children = molWithH.getConnectedAtoms(molWithH.getAtom(i)); ! for (int k = 0; k < children.length; k++) { ! if (children[k].getSymbol().equals("H")) { ! vt.value1 = (float)((java.lang.Math.floor(((Double) children[k].getProperty(CDKConstants.NMRSHIFT_HYDROGEN)).floatValue() * 100)) / 100); ! vt.atoms.add(children[k]); } } --- 2663,2671 ---- if (parent.getHydrogenCount() == 1) { ValueTriple vt = new ValueTriple(); ! List children = molWithH.getConnectedAtomsList(molWithH.getAtom(i)); ! for (int k = 0; k < children.size(); k++) { ! if (((IAtom)children.get(k)).getSymbol().equals("H")) { ! vt.value1 = (float)((java.lang.Math.floor(((Double) ((IAtom)children.get(k)).getProperty(CDKConstants.NMRSHIFT_HYDROGEN)).floatValue() * 100)) / 100); ! vt.atoms.add((IAtom)children.get(k)); } } *************** *** 2673,2683 **** } if (parent.getHydrogenCount() == 2) { ! IAtom[] children = molWithH.getConnectedAtoms(molWithH.getAtom(i)); String appendix = ".1"; ! for (int k = 0; k < children.length; k++) { ! if (children[k].getSymbol().equals("H")) { ValueTriple vt = new ValueTriple(); ! vt.value1 = (float)((java.lang.Math.floor(((Double) children[k].getProperty(CDKConstants.NMRSHIFT_HYDROGEN)).floatValue() * 100)) / 100); ! vt.atoms.add(children[k]); signalstable.add(vt); if (appendix.equals(".1")) { --- 2673,2683 ---- } if (parent.getHydrogenCount() == 2) { ! List children = molWithH.getConnectedAtomsList(molWithH.getAtom(i)); String appendix = ".1"; ! for (int k = 0; k < children.size(); k++) { ! if (((IAtom)children.get(k)).getSymbol().equals("H")) { ValueTriple vt = new ValueTriple(); ! vt.value1 = (float)((java.lang.Math.floor(((Double) ((IAtom)children.get(k)).getProperty(CDKConstants.NMRSHIFT_HYDROGEN)).floatValue() * 100)) / 100); ! vt.atoms.add((IAtom)children.get(k)); signalstable.add(vt); if (appendix.equals(".1")) { *************** *** 2688,2698 **** } if (parent.getHydrogenCount() > 2) { ! IAtom[] children = molWithH.getConnectedAtoms(molWithH.getAtom(i)); double altogether = 0; ValueTriple vt = new ValueTriple(); ! for (int k = 0; k < children.length; k++) { ! if (children[k].getSymbol().equals("H")) { ! altogether += ((Double) children[k].getProperty(CDKConstants.NMRSHIFT_HYDROGEN)).doubleValue(); ! vt.atoms.add(children[k]); } } --- 2688,2698 ---- } if (parent.getHydrogenCount() > 2) { ! List children = molWithH.getConnectedAtomsList(molWithH.getAtom(i)); double altogether = 0; ValueTriple vt = new ValueTriple(); ! for (int k = 0; k < children.size(); k++) { ! if (((IAtom)children.get(k)).getSymbol().equals("H")) { ! altogether += ((Double) ((IAtom)children.get(k)).getProperty(CDKConstants.NMRSHIFT_HYDROGEN)).doubleValue(); ! vt.atoms.add((IAtom)children.get(k)); } } *************** *** 2877,2881 **** IMolecule cdkmol=mol.getAsCDKMolecule(1); for(int l=0;l<cdkmol.getAtomCount();l++){ ! if(cdkmol.getAtom(l).getSymbol().equals("H") && mol.getAtomsAsArrayInMdlOrder()[l].getDBSignalsBySpectrumType("1H").size()>0 && cdkmol.getConnectedAtoms(cdkmol.getAtom(l))[0].getSymbol().equals("C")){ try{ double predicted=PredictionTool.generalPredict(cdkmol, cdkmol.getAtom(l), true, true, startmol, endmol, new StringBuffer(""), false, false, null, new HashMap(), -1, false, new StringBuffer(), 6, true, true)[1]; --- 2877,2881 ---- IMolecule cdkmol=mol.getAsCDKMolecule(1); for(int l=0;l<cdkmol.getAtomCount();l++){ ! if(cdkmol.getAtom(l).getSymbol().equals("H") && mol.getAtomsAsArrayInMdlOrder()[l].getDBSignalsBySpectrumType("1H").size()>0 && ((IAtom)cdkmol.getConnectedAtomsList(cdkmol.getAtom(l)).get(0)).getSymbol().equals("C")){ try{ double predicted=PredictionTool.generalPredict(cdkmol, cdkmol.getAtom(l), true, true, startmol, endmol, new StringBuffer(""), false, false, null, new HashMap(), -1, false, new StringBuffer(), 6, true, true)[1]; *************** *** 2991,2995 **** IMolecule mol4ringc= (IMolecule) new MDLReader(new StringReader(mol4)).read(new org.openscience.cdk.Molecule()); IMolecule mol3ringc= (IMolecule) new MDLReader(new StringReader(mol3)).read(new org.openscience.cdk.Molecule()); ! QueryAtomContainer mol4ring=QueryAtomContainerCreator.createBasicQueryContainer(mol4ringc); for(int k=0;k<mol4ring.getAtomCount();k++){ AnyOrderQueryBond q=new AnyOrderQueryBond(); --- 2991,2995 ---- IMolecule mol4ringc= (IMolecule) new MDLReader(new StringReader(mol4)).read(new org.openscience.cdk.Molecule()); IMolecule mol3ringc= (IMolecule) new MDLReader(new StringReader(mol3)).read(new org.openscience.cdk.Molecule()); ! /*QueryAtomContainer mol4ring=QueryAtomContainerCreator.createBasicQueryContainer(mol4ringc); for(int k=0;k<mol4ring.getAtomCount();k++){ AnyOrderQueryBond q=new AnyOrderQueryBond(); *************** *** 3002,3011 **** q.setAtoms(mol3ring.getBond(k).getAtoms()); mol3ring.setElectronContainer(k,q); ! } int rightmapping=1; ! List l=UniversalIsomorphismTester.getSubgraphAtomsMaps(sd.getMolWithH(),mol4ring); if(l.size()==0){ ! l=UniversalIsomorphismTester.getSubgraphAtomsMaps(sd.getMolWithH(),mol3ring); System.err.println("dreier "+l); }else{ --- 3002,3011 ---- q.setAtoms(mol3ring.getBond(k).getAtoms()); mol3ring.setElectronContainer(k,q); ! }*/ int rightmapping=1; ! List l=null;//UniversalIsomorphismTester.getSubgraphAtomsMaps(sd.getMolWithH(),mol4ring); if(l.size()==0){ ! //l=UniversalIsomorphismTester.getSubgraphAtomsMaps(sd.getMolWithH(),mol3ring); System.err.println("dreier "+l); }else{ Index: NmrshiftdbServlet.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/NmrshiftdbServlet.java,v retrieving revision 1.92 retrieving revision 1.93 diff -C2 -r1.92 -r1.93 *** NmrshiftdbServlet.java 28 Aug 2006 14:33:58 -0000 1.92 --- NmrshiftdbServlet.java 9 Oct 2006 13:24:37 -0000 1.93 *************** *** 57,61 **** import org.apache.velocity.VelocityContext; import org.apache.velocity.app.Velocity; ! import org.openscience.cdk.SetOfAtomContainers; import org.openscience.cdk.interfaces.IMolecule; import org.openscience.cdk.io.RssWriter; --- 57,61 ---- import org.apache.velocity.VelocityContext; import org.apache.velocity.app.Velocity; ! import org.openscience.cdk.AtomContainerSet; import org.openscience.cdk.interfaces.IMolecule; import org.openscience.cdk.io.RssWriter; *************** *** 140,144 **** RssWriter rssWriter=new RssWriter(); rssWriter.setWriter(res.getWriter()); ! SetOfAtomContainers soac=new SetOfAtomContainers(); String query="select distinct MOLECULE.MOLECULE_ID from MOLECULE, SPECTRUM where SPECTRUM.MOLECULE_ID = MOLECULE.MOLECULE_ID and SPECTRUM.REVIEW_FLAG =\"true\" order by MOLECULE.DATE desc;"; List l=NmrshiftdbUserPeer.executeQuery(query); --- 140,144 ---- RssWriter rssWriter=new RssWriter(); rssWriter.setWriter(res.getWriter()); ! AtomContainerSet soac=new AtomContainerSet(); String query="select distinct MOLECULE.MOLECULE_ID from MOLECULE, SPECTRUM where SPECTRUM.MOLECULE_ID = MOLECULE.MOLECULE_ID and SPECTRUM.REVIEW_FLAG =\"true\" order by MOLECULE.DATE desc;"; List l=NmrshiftdbUserPeer.executeQuery(query); |
|
From: Stefan K. <sh...@us...> - 2006-10-09 13:24:45
|
Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/webservices In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv21218/src/java/org/openscience/nmrshiftdb/webservices Modified Files: NMRShiftDBServiceBindingImpl.java Log Message: this uses new cdk and new saturation stuff. should resolve a long standing problem Index: NMRShiftDBServiceBindingImpl.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/webservices/NMRShiftDBServiceBindingImpl.java,v retrieving revision 1.21 retrieving revision 1.22 diff -C2 -r1.21 -r1.22 *** NMRShiftDBServiceBindingImpl.java 12 Sep 2006 14:30:42 -0000 1.21 --- NMRShiftDBServiceBindingImpl.java 9 Oct 2006 13:24:38 -0000 1.22 *************** *** 75,79 **** CMLReader cmlreader=new CMLReader(new ByteArrayInputStream(elmol.toXML().getBytes())); cfile=(IChemFile)cmlreader.read(cfile); ! IMolecule mol=cfile.getChemSequence(0).getChemModel(0).getSetOfMolecules().getMolecule(0); TurbineConfig tc = new TurbineConfig("", webinfdir+"conf/TurbineResources.properties"); File nmrpropsFile = new File(webinfdir+"conf/NMRShiftDB.properties"); --- 75,79 ---- CMLReader cmlreader=new CMLReader(new ByteArrayInputStream(elmol.toXML().getBytes())); cfile=(IChemFile)cmlreader.read(cfile); ! IMolecule mol=cfile.getChemSequence(0).getChemModel(0).getMoleculeSet().getMolecule(0); TurbineConfig tc = new TurbineConfig("", webinfdir+"conf/TurbineResources.properties"); File nmrpropsFile = new File(webinfdir+"conf/NMRShiftDB.properties"); *************** *** 190,194 **** subData.setChoosenSpectrumType(type); CMLReader cmlreader=new CMLReader(new ByteArrayInputStream(cmlmol.toXML().getBytes())); ! IMolecule cdkmol=((ChemFileCDO)cmlreader.read(new ChemFile())).getChemSequence(0).getChemModel(0).getSetOfMolecules().getMolecule(0); //we remove all explicit Hs not around stereo centers/double bond configurations boolean[] doublebondconfigurationsprov=new boolean[cdkmol.getBondCount()]; --- 190,194 ---- subData.setChoosenSpectrumType(type); CMLReader cmlreader=new CMLReader(new ByteArrayInputStream(cmlmol.toXML().getBytes())); ! IMolecule cdkmol=((ChemFileCDO)cmlreader.read(new ChemFile())).getChemSequence(0).getChemModel(0).getMoleculeSet().getMolecule(0); //we remove all explicit Hs not around stereo centers/double bond configurations boolean[] doublebondconfigurationsprov=new boolean[cdkmol.getBondCount()]; *************** *** 201,209 **** Vector toremove=new Vector(); for(int k=0;k<cdkmol.getBondCount();k++){ ! IAtom atom1=cdkmol.getBond(k).getAtoms()[0]; if(!doublebondconfigurationsprov[k] && !BondTools.isStereo(cdkmol, atom1)){ toremove.add(atom1); } ! IAtom atom2=cdkmol.getBond(k).getAtoms()[1]; if(!doublebondconfigurationsprov[k] && !BondTools.isStereo(cdkmol, atom2)){ toremove.add(atom2); --- 201,209 ---- Vector toremove=new Vector(); for(int k=0;k<cdkmol.getBondCount();k++){ ! IAtom atom1=cdkmol.getBond(k).getAtom(0); if(!doublebondconfigurationsprov[k] && !BondTools.isStereo(cdkmol, atom1)){ toremove.add(atom1); } ! IAtom atom2=cdkmol.getBond(k).getAtom(1); if(!doublebondconfigurationsprov[k] && !BondTools.isStereo(cdkmol, atom2)){ toremove.add(atom2); *************** *** 211,218 **** } for(int k=0;k<toremove.size();k++){ ! IAtom[] conn=cdkmol.getConnectedAtoms((IAtom)toremove.get(k)); ! for(int l=0;l<conn.length;l++){ ! if(conn[l].getSymbol().equals("H")) ! cdkmol.removeAtomAndConnectedElectronContainers(conn[l]); } } --- 211,218 ---- } for(int k=0;k<toremove.size();k++){ ! List conn=cdkmol.getConnectedAtomsList((IAtom)toremove.get(k)); ! for(int l=0;l<conn.size();l++){ ! if(((IAtom)conn.get(l)).getSymbol().equals("H")) ! cdkmol.removeAtomAndConnectedElectronContainers((IAtom)conn.get(l)); } } |
