Calculate molecular weight of non-labeled compounds

Hi,

we have a database of radioactive materials. The formulas include isotopes like ¹⁴C or T. IJC Calculates their molecular weight automatically including these isotopes. Is there a function to calculate the mw of the substance without the radioactive label (for example, using ¹²C instead of ¹⁴C) ?

Thanks

Anna

Hi Anna,

please use this formula to achieve mass calculation ignoring isotopes:

elementalAnalysis(dotDisconnectedFormula,'mass')

This term takes standard atomic weight for atoms - "the ones written in periodic table of elements" - regardless of thier actual mass number.

Filip

I forgot to mention that the expression should be used in the Chemical Terms Field.

Hi Filip,

thanks. When I try to create a chemical terms fields I get an error message -see below.

Any idea where this is coming from?

Thanks

Anna

org.springframework.jdbc.UncategorizedSQLException: StatementCallback; uncategorized SQLException for SQL [ALTER INDEX RACIMS.KEMCOMPOUND_IDX PARAMETERS('sep=! addAutoCalcCtWcn=MOL_WEIGHT_NON_LABELED;FLOAT(32);elementalAnalysis(dotDisconnectedFormula,''mass'')

')]; SQL state [99999]; error code [29869]; ORA-29869: cannot issue ALTER without REBUILD on a domain index marked FAILED
; nested exception is java.sql.SQLException: ORA-29869: cannot issue ALTER without REBUILD on a domain index marked FAILED

 at org.springframework.jdbc.support.AbstractFallbackSQLExceptionTranslator.translate(AbstractFallbackSQLExceptionTranslator.java:83)
 at org.springframework.jdbc.support.AbstractFallbackSQLExceptionTranslator.translate(AbstractFallbackSQLExceptionTranslator.java:80)
 at org.springframework.jdbc.support.AbstractFallbackSQLExceptionTranslator.translate(AbstractFallbackSQLExceptionTranslator.java:80)
 at org.springframework.jdbc.core.JdbcTemplate.execute(JdbcTemplate.java:406)
 at org.springframework.jdbc.core.JdbcTemplate.execute(JdbcTemplate.java:427)
 at com.im.ijcs.impl.ddl.JChemTableManagerImpl$CartTableVersionHandler.fixChemTermsDefinitionForJChemIndex(JChemTableManagerImpl.java:2647)
 at com.im.ijcs.impl.ddl.JChemTableManagerImpl$CartVersionLatest.addChemicalTermsColumnDefinitionForJChemIndex(JChemTableManagerImpl.java:2674)
 at com.im.ijcs.impl.ddl.JChemCartridgeStandardTableModification.addChemicalTermsColumn(JChemCartridgeStandardTableModification.java:64)
 at com.im.ijcs.impl.ddl.JChemTableManagerImpl.addChemicalTermsColumn(JChemTableManagerImpl.java:2030)
 at com.im.ijcs.impl.ddl.operations.column.AddChemicalTermsColumnOperation.executeImpl(AddChemicalTermsColumnOperation.java:137)
 at com.im.ijcs.impl.ddl.operations.AbstractOperation.execute(AbstractOperation.java:116)
 at com.im.ijcs.impl.ddl.DefaultDDLService.performOperations(DefaultDDLService.java:774)
 at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
 at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
 at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
 at java.lang.reflect.Method.invoke(Unknown Source)
 at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:309)
 at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
 at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
 at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:110)
 at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
 at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
 at $Proxy17.performOperations(Unknown Source)
 at com.im.df.impl.db.DBSchemaImpl.applyOperations(DBSchemaImpl.java:1121)
 at com.im.df.impl.db.field.DBNewFieldAbstractNT.create(DBNewFieldAbstractNT.java:59)
 at com.im.df.impl.db.field.DBNewCTFieldNT.create(DBNewCTFieldNT.java:165)
 at com.im.ijc.core.wizards.newdfitem.NewDFItemWizardPanel1$2.phase1InRequestProcessor(NewDFItemWizardPanel1.java:135)
 at com.im.commons.progress.BackgroundRunner.processTheTask(BackgroundRunner.java:128)
 at com.im.commons.progress.BackgroundRunner$1.run(BackgroundRunner.java:91)
 at org.openide.util.RequestProcessor$Task.run(RequestProcessor.java:1418)
 at org.openide.util.RequestProcessor$Processor.run(RequestProcessor.java:1957)
Caused by: java.sql.SQLException: ORA-29869: cannot issue ALTER without REBUILD on a domain index marked FAILED

 at oracle.jdbc.driver.SQLStateMapping.newSQLException(SQLStateMapping.java:70)
 at oracle.jdbc.driver.DatabaseError.newSQLException(DatabaseError.java:133)
 at oracle.jdbc.driver.DatabaseError.throwSqlException(DatabaseError.java:206)
 at oracle.jdbc.driver.T4CTTIoer.processError(T4CTTIoer.java:455)
 at oracle.jdbc.driver.T4CTTIoer.processError(T4CTTIoer.java:413)
 at oracle.jdbc.driver.T4C8Oall.receive(T4C8Oall.java:1034)
 at oracle.jdbc.driver.T4CStatement.doOall8(T4CStatement.java:183)
 at oracle.jdbc.driver.T4CStatement.executeForRows(T4CStatement.java:942)
 at oracle.jdbc.driver.OracleStatement.doExecuteWithTimeout(OracleStatement.java:1222)
 at oracle.jdbc.driver.OracleStatement.executeInternal(OracleStatement.java:1770)
 at oracle.jdbc.driver.OracleStatement.execute(OracleStatement.java:1739)
 at oracle.jdbc.driver.OracleStatementWrapper.execute(OracleStatementWrapper.java:299)
 at org.apache.commons.dbcp.DelegatingStatement.execute(DelegatingStatement.java:264)
 at org.apache.commons.dbcp.DelegatingStatement.execute(DelegatingStatement.java:264)
 at org.apache.commons.dbcp.DelegatingStatement.execute(DelegatingStatement.java:264)
 at org.springframework.jdbc.core.JdbcTemplate$1ExecuteStatementCallback.doInStatement(JdbcTemplate.java:420)
 at org.springframework.jdbc.core.JdbcTemplate.execute(JdbcTemplate.java:395)
 ... 27 more

Hi Anna,

this should be resolved by rebuilding the cartridge index on affected tables. Did you upgrade JChem cartridge without rebuilding index? Or did you use newer IJC with older JChem cartridge? I can imagine that one of this scenario could cause the error. Anyway... rebuilding index should help.

Filip

Hi Filip,

I rebuilt the index and the calculation works now.

Thanks!
Anna