import problem

I'm using jcman with Postgres.


I created a structure table by adding one more column using the following command.





> jcman c strtest --coldefs ", cid int4" ....





Then I would like to add data into the table.


For example, all my data is in a file (importdata.txt ) with the following format (First column = structure, second column = cid ).





cc3C(=O)N2C(c4ccc(cc4)Cl)C(=O)O)I)Cl 656933








Then using the following command, I tried to upload data into the structure table.





> jcman a strtest importdata.txt





It seems successful, but when I look at the content of the strtest table,


there is no data loaded into cid column, which I created.





Is there any problem in my import file format? Or should I specify some other options?





Please help me.

Hi You jung,





If you want to import data to your custom fields in database, you have to bind that fields with fields in the import file.


See the --connect option in jcman help. (jcman --help)


If your import file contains smiles formatted compounds with tab separated fields, that custom fields have no explicit name, however they have implicit name: field_x where "x" is meaning number of the field.


You can add custom name your fields, if you edit the input file, and insert a new line above first compound definition:


#SMILES fieldName1 fieldName2 ...


Important! This line must be tab separated.





Regards:


Edvard

I tried as you suggested, but it didn't work.





My file format is as below.





#SMILES CID


(cc3C(=O)N2C(c4ccc(cc4)Cl)C(=O)O)I)Cl 656933





And when I tried importing the file, it generates the following exceptions.





Collecting file information ...


Done.


Importing structures from importfile ...


java.io.IOException: file format not recognized


at chemaxon.formats.MolInputStream.init(MolInputStream.java:424)


at chemaxon.formats.MolInputStream.<init>(MolInputStream.java:123)


at chemaxon.formats.MolInputStream.<init>(MolInputStream.java:86)


at chemaxon.util.MolHandler.importMol(MolHandler.java:678)


at chemaxon.util.MolHandler.setMolecule(MolHandler.java:159)


at chemaxon.util.MolHandler.<init>(MolHandler.java:94)


at chemaxon.jchem.db.FileToSQLHandler.importFile(FileToSQLHandler.java:252)


at chemaxon.jchem.db.Importer.importMols(Importer.java:444)


at chemaxon.jchem.Command.importFromFile(Command.java:940)


at chemaxon.jchem.Command.main(Command.java:432)


Error in molecule 1


chemaxon.formats.MolFormatException: java.io.IOException: file format not recognized


at chemaxon.util.MolHandler.toMolFormatException(MolHandler.java:699)


at chemaxon.util.MolHandler.importMol(MolHandler.java:687)


at chemaxon.util.MolHandler.setMolecule(MolHandler.java:159)


at chemaxon.util.MolHandler.<init>(MolHandler.java:94)


at chemaxon.jchem.db.FileToSQLHandler.importFile(FileToSQLHandler.java:252)


at chemaxon.jchem.db.Importer.importMols(Importer.java:444)


at chemaxon.jchem.Command.importFromFile(Command.java:940)


at chemaxon.jchem.Command.main(Command.java:432)


Imported 1 structures


Done.

Sorry, the second method works only in developer version, but the first manner (field_0 is the name of your custom field) is working in the released version.