Formula element errors for local CSV files ...

[schymane]

An anecdote for debugging the formula element errors for local CSV files... @sneumann

This seems to throw element errors for less-well-known elements seemingly only when MonoisotopicMass is not correctly defined, i.e. with a column Monoisotopic_Mass, the import calculates a new column MonoisotopicMass happily (but we end up with a numeric scoring term Monoisotopic_Mass) and throws no formula errors. If the column header is adjusted to the correct MonoisotopicMass, the less-well-known elements throw these errors:

de.ipbhalle.metfraglib.exceptions.AtomTypeNotKnownFromInputListException: Os not found (C6H10O8Os1)
at de.ipbhalle.metfraglib.molecularformula.ByteMolecularFormula.parseMolecularFormula(ByteMolecularFormula.java:289)
at de.ipbhalle.metfraglib.molecularformula.ByteMolecularFormula.initialise(ByteMolecularFormula.java:126)
at de.ipbhalle.metfraglib.molecularformula.ByteMolecularFormula.(ByteMolecularFormula.java:47)
at de.ipbhalle.metfraglib.database.AbstractFileDatabase.checkFilter(AbstractFileDatabase.java:95)
at de.ipbhalle.metfraglib.database.LocalCSVDatabase.readCandidatesFromFile(LocalCSVDatabase.java:141)
at de.ipbhalle.metfraglib.database.AbstractFileDatabase.getCandidateIdentifiers(AbstractFileDatabase.java:146)
at de.ipbhalle.metfraglib.database.AbstractFileDatabase.getCandidateIdentifiers(AbstractFileDatabase.java:67)
at de.ipbhalle.metfraglib.process.CombinedMetFragProcess.retrieveCompounds(CombinedMetFragProcess.java:77)
at de.ipbhalle.metfrag.commandline.CommandLineTool.main(CommandLineTool.java:104)
java.lang.NullPointerException
at de.ipbhalle.metfraglib.molecularformula.ByteMolecularFormula.compareTo(ByteMolecularFormula.java:174)
at de.ipbhalle.metfraglib.database.AbstractFileDatabase.checkFilter(AbstractFileDatabase.java:99)
at de.ipbhalle.metfraglib.database.LocalCSVDatabase.readCandidatesFromFile(LocalCSVDatabase.java:141)
at de.ipbhalle.metfraglib.database.AbstractFileDatabase.getCandidateIdentifiers(AbstractFileDatabase.java:146)
at de.ipbhalle.metfraglib.database.AbstractFileDatabase.getCandidateIdentifiers(AbstractFileDatabase.java:67)
at de.ipbhalle.metfraglib.process.CombinedMetFragProcess.retrieveCompounds(CombinedMetFragProcess.java:77)
at de.ipbhalle.metfrag.commandline.CommandLineTool.main(CommandLineTool.java:104)
ERROR de.ipbhalle.metfrag.commandline.CommandLineTool - Error when retrieving compounds.

Full badlist so far for PCLite:

/Kr|Dy|Ir|La|Lu|Nd|Nb|Os|Pd|Pt|Pu|Pr|Re|Rh|Ru|Sm|Sc|Ag|Ta|Tc|Tb|Th|Tm|Ti|W|Ac|Am|Er|Eu|Gd|Hf|Ho|Xe|Yb|Rn|Sr|Be|Cm|Cf|Cs|Md|Pm|Fr|Pa|Np|Bk|Es|Fm|No|Lr|Rf|Db|Sg|Bh|Hs|Mt|Ds|Rg|Cn|Nh|Fl|Mc|Lv|Ts|Og/