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mrannotator will not parse 2i7z #271

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
I reprocessed this for the cing project and realized that very little of the 
data had been parsed. I don't know, but it might have to do with the '\par' 
tags at the end of the lines. That doesn't make a lot of sense though, since 
the restraints that did get parsed had those tags also. This is the mrannotator 
output:

Moving the MR file to the database.
Trying to convert block: 0 of type: MR format, comment, n/a, n/a
Trying to convert block: 1 of type: XPLOR/CNS, distance, NOE, simple
input5710253257177235761.tmp    0    1    0

Trying to convert block: 2 of type: XPLOR/CNS, distance, general distance, 
simple
input8012689324534304016.tmp  178   25  179

ERROR: please check the input. An error was recorded.
Trying to convert block: 3 of type: XPLOR/CNS, distance, hydrogen bond, simple
input6529881724977799178.tmp  198   11  199

ERROR: please check the input. An error was recorded.
Trying to convert block: 4 of type: XPLOR/CNS, dihedral angle, n/a, n/a
input8781226951609676387.tmp    0  401  559

ERROR: please check the input. An error was recorded.
Trying to convert block: 5 of type: XPLOR/CNS, planarity, n/a, n/a
Skipping block: 5
Trying to convert block: 6 of type: XPLOR/CNS, dipolar coupling, n/a, n/a
ERROR: 
Wattos.Converters.Xplor.TokenMgrError: Lexical error at line 175, column 1.  
Encountered: "}" (125), after : ""
    at Wattos.Converters.Xplor.XplorParserAllTokenManager.getNextToken(XplorParserAllTokenManager.java:1179)
    at Wattos.Converters.Xplor.XplorParserAll.getToken(XplorParserAll.java:1067)
    at Wattos.Converters.Xplor.Utils.error_skipto(Utils.java:124)
    at Wattos.Converters.Xplor.XplorParserAll.error_skipto(XplorParserAll.java:945)
    at Wattos.Converters.Xplor.XplorParserAll.AssiStateDipolarCoupling(XplorParserAll.java:338)
    at Wattos.Converters.Xplor.XplorParserAll.AssiListDipolarCoupling(XplorParserAll.java:193)
    at Wattos.Converters.Xplor.XplorParserAll.AssiListDipolarCoupling(XplorParserAll.java:194)
    at Wattos.Converters.Xplor.XplorParserAll.AssiListDipolarCoupling(XplorParserAll.java:194)
    at Wattos.Converters.Xplor.XplorParserAll.AssiListDipolarCoupling(XplorParserAll.java:194)
    at Wattos.Converters.Xplor.XplorParserAll.AssiListDipolarCoupling(XplorParserAll.java:194)
    at Wattos.Converters.Xplor.XplorParserAll.AssiListDipolarCoupling(XplorParserAll.java:194)
    at Wattos.Converters.Xplor.XplorParserAll.AssiListDipolarCoupling(XplorParserAll.java:194)
    at Wattos.Converters.Xplor.XplorParserAll.AssiListDipolarCoupling(XplorParserAll.java:194)
    at Wattos.Converters.Xplor.XplorParserAll.AssiListDipolarCoupling(XplorParserAll.java:194)
    at Wattos.Converters.Xplor.XplorParserAll.AssiListDipolarCoupling(XplorParserAll.java:194)
    at Wattos.Converters.Xplor.XplorParserAll.AssiListDipolarCoupling(XplorParserAll.java:194)
    at Wattos.Converters.Xplor.XplorParserAll.AssiListDipolarCoupling(XplorParserAll.java:194)
    at Wattos.Converters.Xplor.XplorParserAll.AssiListDipolarCoupling(XplorParserAll.java:194)
    at Wattos.Converters.Xplor.XplorParserAll.AssiListDipolarCoupling(XplorParserAll.java:194)
    at Wattos.Converters.Xplor.XplorParserAll.AssiListDipolarCoupling(XplorParserAll.java:194)
    at Wattos.Converters.Xplor.XplorParserAll.AssiListDipolarCoupling(XplorParserAll.java:194)
    at Wattos.Converters.Xplor.XplorParserAll.AssiListDipolarCoupling(XplorParserAll.java:194)
    at Wattos.Converters.Xplor.XplorParserAll.AssiListDipolarCoupling(XplorParserAll.java:194)
    at Wattos.Converters.Xplor.XplorParserAll.AssiListDipolarCoupling(XplorParserAll.java:194)
    at Wattos.Converters.Xplor.XplorParserAll.AssiListDipolarCoupling(XplorParserAll.java:194)
    at Wattos.Converters.Xplor.XplorParserAll.AssiListDipolarCoupling(XplorParserAll.java:194)
    at Wattos.Converters.Xplor.XplorParserAll.AssiListDipolarCoupling(XplorParserAll.java:194)
    at Wattos.Converters.Xplor.XplorParserAll.AssiListDipolarCoupling(XplorParserAll.java:194)
    at Wattos.Converters.Xplor.XplorParserAll.AssiListDipolarCoupling(XplorParserAll.java:194)
    at Wattos.Converters.Xplor.XplorParserAll.AssiListDipolarCoupling(XplorParserAll.java:194)
    at Wattos.Converters.Xplor.XplorParserAll.getInputDipolarCoupling(XplorParserAll.java:169)
    at Wattos.Converters.Xplor.XplorParserAll.getInput(XplorParserAll.java:104)
    at Wattos.Converters.Xplor.XplorParserAll.parse(XplorParserAll.java:75)
    at Wattos.Converters.Xplor.StarOutAll.convertToStarFileNode(StarOutAll.java:134)
    at Wattos.Episode_II.DBMRBlock.convertCNSDipolarNaNa(DBMRBlock.java:636)
    at Wattos.Episode_II.DBMRBlock.convert(DBMRBlock.java:498)
    at Wattos.Episode_II.MRSTARFile.addData(MRSTARFile.java:291)
    at Wattos.Episode_II.MRSTARFile.init(MRSTARFile.java:141)
    at Wattos.Episode_II.DBMRFile.doConversion(DBMRFile.java:936)
    at Wattos.Episode_II.DBMRFile.doConversions(DBMRFile.java:993)
    at Wattos.Episode_II.MRAnnotate.annotateEntry(MRAnnotate.java:410)
    at Wattos.Episode_II.MRAnnotate.annotateLoop(MRAnnotate.java:244)
    at Wattos.Episode_II.MRAnnotate.main(MRAnnotate.java:795)

ERROR: Found throwable error above
ERROR: 
java.lang.NullPointerException
    at Wattos.Episode_II.DBMRBlock.getItemCount(DBMRBlock.java:988)
    at Wattos.Episode_II.DBMRBlock.convert(DBMRBlock.java:555)
    at Wattos.Episode_II.MRSTARFile.addData(MRSTARFile.java:291)
    at Wattos.Episode_II.MRSTARFile.init(MRSTARFile.java:141)
    at Wattos.Episode_II.DBMRFile.doConversion(DBMRFile.java:936)
    at Wattos.Episode_II.DBMRFile.doConversions(DBMRFile.java:993)
    at Wattos.Episode_II.MRAnnotate.annotateEntry(MRAnnotate.java:410)
    at Wattos.Episode_II.MRAnnotate.annotateLoop(MRAnnotate.java:244)
    at Wattos.Episode_II.MRAnnotate.main(MRAnnotate.java:795)

ERROR: Found throwable error above
Skipping block: 6
Trying to convert block: 7 of type: MR format, nomenclature mapping, n/a, n/a
Skipping block: 7
input5344095296057599091.tmp    0    1    0

input6446891978137028346.tmp  178   25  179

ERROR: please check the input. An error was recorded.
input4971122972956657902.tmp  198   11  199

ERROR: please check the input. An error was recorded.
input6839087484360844760.tmp    0  401  559

ERROR: please check the input. An error was recorded.
Skipping block: 5
ERROR: 
Wattos.Converters.Xplor.TokenMgrError: Lexical error at line 175, column 1.  
Encountered: "}" (125), after : ""
    at Wattos.Converters.Xplor.XplorParserAllTokenManager.getNextToken(XplorParserAllTokenManager.java:1179)
    at Wattos.Converters.Xplor.XplorParserAll.getToken(XplorParserAll.java:1067)
    at Wattos.Converters.Xplor.Utils.error_skipto(Utils.java:124)
    at Wattos.Converters.Xplor.XplorParserAll.error_skipto(XplorParserAll.java:945)
    at Wattos.Converters.Xplor.XplorParserAll.AssiStateDipolarCoupling(XplorParserAll.java:338)
    at Wattos.Converters.Xplor.XplorParserAll.AssiListDipolarCoupling(XplorParserAll.java:193)
    at Wattos.Converters.Xplor.XplorParserAll.AssiListDipolarCoupling(XplorParserAll.java:194)
    at Wattos.Converters.Xplor.XplorParserAll.AssiListDipolarCoupling(XplorParserAll.java:194)
    at Wattos.Converters.Xplor.XplorParserAll.AssiListDipolarCoupling(XplorParserAll.java:194)
    at Wattos.Converters.Xplor.XplorParserAll.AssiListDipolarCoupling(XplorParserAll.java:194)
    at Wattos.Converters.Xplor.XplorParserAll.AssiListDipolarCoupling(XplorParserAll.java:194)
    at Wattos.Converters.Xplor.XplorParserAll.AssiListDipolarCoupling(XplorParserAll.java:194)
    at Wattos.Converters.Xplor.XplorParserAll.AssiListDipolarCoupling(XplorParserAll.java:194)
    at Wattos.Converters.Xplor.XplorParserAll.AssiListDipolarCoupling(XplorParserAll.java:194)
    at Wattos.Converters.Xplor.XplorParserAll.AssiListDipolarCoupling(XplorParserAll.java:194)
    at Wattos.Converters.Xplor.XplorParserAll.AssiListDipolarCoupling(XplorParserAll.java:194)
    at Wattos.Converters.Xplor.XplorParserAll.AssiListDipolarCoupling(XplorParserAll.java:194)
    at Wattos.Converters.Xplor.XplorParserAll.AssiListDipolarCoupling(XplorParserAll.java:194)
    at Wattos.Converters.Xplor.XplorParserAll.AssiListDipolarCoupling(XplorParserAll.java:194)
    at Wattos.Converters.Xplor.XplorParserAll.AssiListDipolarCoupling(XplorParserAll.java:194)
    at Wattos.Converters.Xplor.XplorParserAll.AssiListDipolarCoupling(XplorParserAll.java:194)
    at Wattos.Converters.Xplor.XplorParserAll.AssiListDipolarCoupling(XplorParserAll.java:194)
    at Wattos.Converters.Xplor.XplorParserAll.AssiListDipolarCoupling(XplorParserAll.java:194)
    at Wattos.Converters.Xplor.XplorParserAll.AssiListDipolarCoupling(XplorParserAll.java:194)
    at Wattos.Converters.Xplor.XplorParserAll.AssiListDipolarCoupling(XplorParserAll.java:194)
    at Wattos.Converters.Xplor.XplorParserAll.AssiListDipolarCoupling(XplorParserAll.java:194)
    at Wattos.Converters.Xplor.XplorParserAll.AssiListDipolarCoupling(XplorParserAll.java:194)
    at Wattos.Converters.Xplor.XplorParserAll.AssiListDipolarCoupling(XplorParserAll.java:194)
    at Wattos.Converters.Xplor.XplorParserAll.AssiListDipolarCoupling(XplorParserAll.java:194)
    at Wattos.Converters.Xplor.XplorParserAll.AssiListDipolarCoupling(XplorParserAll.java:194)
    at Wattos.Converters.Xplor.XplorParserAll.getInputDipolarCoupling(XplorParserAll.java:169)
    at Wattos.Converters.Xplor.XplorParserAll.getInput(XplorParserAll.java:104)
    at Wattos.Converters.Xplor.XplorParserAll.parse(XplorParserAll.java:75)
    at Wattos.Converters.Xplor.StarOutAll.convertToStarFileNode(StarOutAll.java:134)
    at Wattos.Episode_II.DBMRBlock.convertCNSDipolarNaNa(DBMRBlock.java:636)
    at Wattos.Episode_II.DBMRBlock.convert(DBMRBlock.java:498)
    at Wattos.Episode_II.MRSTARFile.addData(MRSTARFile.java:291)
    at Wattos.Episode_II.MRSTARFile.init(MRSTARFile.java:141)
    at Wattos.Episode_II.DBMRFile.doConversion(DBMRFile.java:936)
    at Wattos.Episode_II.DBMRFile.doConversions(DBMRFile.java:1004)
    at Wattos.Episode_II.MRAnnotate.annotateEntry(MRAnnotate.java:410)
    at Wattos.Episode_II.MRAnnotate.annotateLoop(MRAnnotate.java:244)
    at Wattos.Episode_II.MRAnnotate.main(MRAnnotate.java:795)

ERROR: Found throwable error above
ERROR: 
java.lang.NullPointerException
    at Wattos.Episode_II.DBMRBlock.getItemCount(DBMRBlock.java:988)
    at Wattos.Episode_II.DBMRBlock.convert(DBMRBlock.java:555)
    at Wattos.Episode_II.MRSTARFile.addData(MRSTARFile.java:291)
    at Wattos.Episode_II.MRSTARFile.init(MRSTARFile.java:141)
    at Wattos.Episode_II.DBMRFile.doConversion(DBMRFile.java:936)
    at Wattos.Episode_II.DBMRFile.doConversions(DBMRFile.java:1004)
    at Wattos.Episode_II.MRAnnotate.annotateEntry(MRAnnotate.java:410)
    at Wattos.Episode_II.MRAnnotate.annotateLoop(MRAnnotate.java:244)
    at Wattos.Episode_II.MRAnnotate.main(MRAnnotate.java:795)

ERROR: Found throwable error above

Original issue reported on code.google.com by schulte....@gmail.com on 31 Mar 2011 at 2:54

GoogleCodeExporter commented 9 years ago 
This is an NRG issue because the input is a latex format. Chris can you ask the 
authors for straight up X-PLOR or alternates?

Original comment by jurge...@gmail.com on 1 Apr 2011 at 8:25

GoogleCodeExporter commented 9 years ago 
Sure.

Original comment by schulte....@gmail.com on 1 Apr 2011 at 1:59

GoogleCodeExporter commented 9 years ago 
I'm not too hopeful about this. This is from 4 years ago. But it is from Sam's 
group and he's usually quite helpful.

Original comment by schulte....@gmail.com on 1 Apr 2011 at 2:52