make a jtable

Hello


I have a problem regarding the java and marvin view.





Actually marvin sketch is used to view the strucutral view of molecule - and it reads the various file formats,such as .mol , .csmol and .sdf files . I dont know how it reads the information from this files,like i am using eclipse -and marvin beans to open the marvin sketch ,and then after opening the .mol file from marvin view(which was opened by the java program) - i see a picture of the molecular structure .





Then when we go into the Edit menu of marvin sketch and cllick the source ,i can see the source of the strucutral molecule ,i can change the format of that source to different types by clicking into formats menu of the source panel.








Now coming to my problem -i have a sdf file in my computer ,which contains some 1000 molecules in a single file, i am opening the marvin sketch in eclipse, and then when i open the sdf file throught this marvin sketch ,it asks for the molecule to sketch between those 1000 molecules,for example if i say 10 ,then it sketchs the 10th molecule of that sdf file, and when i edit source for that file, it reads in the format of MDL SD file.


The task is now to make a jtable ,containing different columns ,one column should give the name of the strucutre from that MDL SD file, second column should give its properties, and third column should display the image of the strcture, like as in marvin sketch.





So could any one help me regarding this,i would really thank ful.





i am giving 2 molecules as attachment from that sdf file.





1,1,1,2-Tetrachloroethane


MZcorina 05110412443D 1 1.00000 0.00000 0


CORINA 3.05 0043 15.12.2003


8 7 0 0 0 0 999 V2000


0.0021 -0.0041 0.0020 Cl 0 0 0 0 0 0 0 0 0 0 0 0


-0.0224 1.7987 0.0119 C 0 0 0 0 0 0 0 0 0 0 0 0


1.4130 2.3283 0.0011 C 0 0 0 0 0 0 0 0 0 0 0 0


2.2569 1.7469 -1.4823 Cl 0 0 0 0 0 0 0 0 0 0 0 0


1.3886 4.1311 0.0110 Cl 0 0 0 0 0 0 0 0 0 0 0 0


2.2850 1.7310 1.4618 Cl 0 0 0 0 0 0 0 0 0 0 0 0


-0.5496 2.1598 -0.8711 H 0 0 0 0 0 0 0 0 0 0 0 0


-0.5326 2.1503 0.9087 H 0 0 0 0 0 0 0 0 0 0 0 0


1 2 1 0 0 0 0


2 3 1 0 0 0 0


2 7 1 0 0 0 0


2 8 1 0 0 0 0


3 4 1 0 0 0 0


3 5 1 0 0 0 0


3 6 1 0 0 0 0


M END


> <SCAFFOLD>


unknown





> <CLASS>


-99999





> <SMILES>


ClCC(Cl)(Cl)Cl





> <FTREE>


@ftree "1,1,1,2-Tetrachloroethane" 2 6 5 0 1 ClC(.)_C(.)(Cl)(Cl)Cl_


0 2.00000 | 4 41.18965 -0.01015 0.89730 0.00695 2.14240 0 | 0 0 0 0 0 1


1 4.00000 | 4 65.58173 1.83588 2.48432 -0.00210 2.50168 0 | 0 0 0 0 0 0


0 1 0 0 0 2.43445





> <MOL2>


[1]





> <MOLECULE_NAME>


1,1,1,2-Tetrachloroethane





> <SYNONYMS>


unknown





> <IUPAC>


unknown





> <CAS_RN>


unknown





> <CAS_NAME>


unknown





> <SCAI_BIO_RN>


SCAI.BIO-000001caea





> <MESH>


unknown





> <NLM_CLASS>


unknown





> <CHEM_ONTOLOGY>


unknown





> <PATENT>


unknown





> <TARGET>


unknown





> <PDB_ID>


unknown





> <EC_NR>


unknown





> <BIO_ONTOLOGY>


unknown





> <MECHANISM_OF_ACTION>


unknown





> <PRIMARY_SCREEN>


-2.180000





> <SECONDARY_SCREEN>


-2.794000





> <ACTIVITY_LABEL>


unknown





> <ASSAY_TYPE>


unknown





> <ASSAY_INFO>


measured log(solubility:mol/L)





> <SOURCEPOOL>


-999999





> <DATA_SET_NAME>


Delaney set





> <LOCAL_PATH>


/home/bio/groupshare/databases/compounds/esol





> <AUTHOR>


Marc Zimmermann





> <TIME_STAMP>


2004-03-25





> <SOURCE>


DOI: 10.1021/ci034243x





> <LIT_REFERENCE>


J. Chem. Inf. Comput. Sci.; 2004; ASAP





> <PMID>


-99999





> <NOTES>


ESOL: Estimating Aqueous Solubility Directly from Molecular Structure





$$$$


1,1,1-Trichloroethane


MZcorina 05110412443D 1 1.00000 0.00000 0


CORINA 3.05 0043 15.12.2003


8 7 0 0 0 0 999 V2000


-0.0187 1.5258 0.0104 C 0 0 0 0 0 0 0 0 0 0 0 0


0.0021 -0.0041 0.0020 C 0 0 0 0 0 0 0 0 0 0 0 0


0.8741 -0.6013 1.4627 Cl 0 0 0 0 0 0 0 0 0 0 0 0


-1.6894 -0.6281 0.0148 Cl 0 0 0 0 0 0 0 0 0 0 0 0


0.8460 -0.5855 -1.4814 Cl 0 0 0 0 0 0 0 0 0 0 0 0


1.0039 1.9031 0.0027 H 0 0 0 0 0 0 0 0 0 0 0 0


-0.5459 1.8868 -0.8726 H 0 0 0 0 0 0 0 0 0 0 0 0


-0.5289 1.8773 0.9072 H 0 0 0 0 0 0 0 0 0 0 0 0


1 2 1 0 0 0 0


1 6 1 0 0 0 0


1 7 1 0 0 0 0


1 8 1 0 0 0 0


2 3 1 0 0 0 0


2 4 1 0 0 0 0


2 5 1 0 0 0 0


M END


> <SCAFFOLD>


unknown





> <CLASS>


-99999





> <SMILES>


CC(Cl)(Cl)Cl





> <FTREE>


@ftree "1,1,1-Trichloroethane" 2 6 5 0 2 C(.)_C(.)(Cl)(Cl)Cl_


0 1.00000 | 4 29.69732 -0.01870 1.52580 0.01040 1.92107 0 | 0 0 0 0 0 1


1 4.00000 | 4 65.58173 0.00820 -0.45475 -0.00048 2.50168 0 | 0 0 0 0 0 0


0 1 0 0 0 1.98076





> <MOL2>


[2]





> <MOLECULE_NAME>


1,1,1-Trichloroethane





> <SYNONYMS>


unknown





> <IUPAC>


unknown





> <CAS_RN>


unknown





> <CAS_NAME>


unknown





> <SCAI_BIO_RN>


SCAI.BIO-000001ca42





> <MESH>


unknown





> <NLM_CLASS>


unknown





> <CHEM_ONTOLOGY>


unknown





> <PATENT>


unknown





> <TARGET>


unknown





> <PDB_ID>


unknown





> <EC_NR>


unknown





> <BIO_ONTOLOGY>


unknown





> <MECHANISM_OF_ACTION>


unknown





> <PRIMARY_SCREEN>


-2.000000





> <SECONDARY_SCREEN>


-2.232000





> <ACTIVITY_LABEL>


unknown





> <ASSAY_TYPE>


unknown





> <ASSAY_INFO>


measured log(solubility:mol/L)





> <SOURCEPOOL>


-999999





> <DATA_SET_NAME>


Delaney set





> <LOCAL_PATH>


/home/bio/groupshare/databases/compounds/esol





> <AUTHOR>


Marc Zimmermann





> <TIME_STAMP>


2004-03-25





> <SOURCE>


DOI: 10.1021/ci034243x





> <LIT_REFERENCE>


J. Chem. Inf. Comput. Sci.; 2004; ASAP





> <PMID>


-99999





> <NOTES>


ESOL: Estimating Aqueous Solubility Directly from Molecular Structure





$$$$

Why don't you use viewer for displaying structures?





MarvinView can display SD file in a molecule table. MarvinView can show also molecule properties - not only the structure.


In MarvinView application you can use "Table" menu (on the menubar) to show properties.





If you use the Marvin Beans API, you can customize the layout of the molecule table.


http://www.chemaxon.com/marvin/doc/dev/viewman.html#advanced.layout





In the following Marvin Beans example you can see howto customize the layout of the molecule table:


http://www.chemaxon.com/marvin/examples/view-checkbox/MViewExampleWithCheckbox.java.txt


http://www.chemaxon.com/marvin/examples/view-popup/MViewPopupExample.java.txt





You can find more examples for molecule tables in Marvin Applets examples.


http://www.chemaxon.com/marvin/doc/dev/index.html#examples





You can find a JTable example in the Marvin Beans package.


http://www.chemaxon.com/marvin/examples/jtable/JTableExample.java.txt





To tell the truth I do not suggest you the JTable with several viewer because it requires huge memory if you have a lot of molecules.


Please see the linking topic: http://www.chemaxon.hu/forum/ftopic69.html





Instead of JTable with several viewer, I suggest you a scrollable viewer with customized layout to display multiple molecules and molecule properties.


Is it a suitable solution for you? Which one do you prefer?