error occured in IJC 5.6 - ChemAxon Forum Archive

User 1887159699

28-10-2011 20:58:42

Hi,

while searching in a database produced by IJC5.6, i got an error:

chemaxon.formats.MolFormatException: ;: unknown ChemAxon Extended SMILES feature
   at chemaxon.marvin.io.formats.smiles.CxsmilesImport.readExtendedFeatures(CxsmilesImport.java:916)
   at chemaxon.marvin.io.formats.smiles.SmilesImport.readMol(SmilesImport.java:569)
   at chemaxon.marvin.io.formats.smiles.CxsmilesImport.readMol(CxsmilesImport.java:63)
[catch] at chemaxon.jchem.db.JChemSearch$ABASThread.run(JChemSearch.java:619)

The log file is empty and the query is:

C(C1CCCC1)C1CCCC1 |LN:0:1.100,2:1.20,10:1.20|

What is wrong with the query?

Best, Hinnerk

The environment is:

Instant JChem Version: 5.6.0.2 (build: 201110041526-149372)
JChem Version: 5.6.0.2
JChem Table Version: 5060000
Marvin Version: 5.6.0.2 (build date: 2011-09-30)
Java: 1.6.0_26; Java HotSpot(TM) 64-Bit Server VM 20.1-b02
System: Windows 7 version 6.1 running on amd64; Cp1252; de_DE (instantjchem)
NetBeans build: 110214-aec102d89c78
Userdir: C:\Users\...\AppData\Roaming\.instantjchem\ijc_5_6
Java Web Start: No
Plugins:
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ChemAxon fb166edcbd

31-10-2011 13:44:05

It seems that the query is OK and it is the target which causes the problem: there is a ';' character in its CXSMILES representation and this character cannot be interpreted by CXSMILES import.

User 1887159699

31-10-2011 13:48:38

Many thx for the quick answwer. How do I figure out, which entry in my Table (100k compounds, based on MOL input) causes the problem and how can i fix it? I canceled the query, as it seems to run some hours.

ChemAxon fa971619eb

03-11-2011 12:43:54

Hi Hinnerk

I think you need to search the database to find these. The data is stored in the CD_SMILES column. I'm not sure what you need to search for as its not eactly clear what he offending characters are, but it seems that a seach for

;:

(that's semi-colon followed by colon) migth find it.

If you have direct access to the database then you can query this using SQL. You would likley need SQL like this:

select CD_ID from <your_table> where CD_SMILES like '%;:%'

In IJC you can promote the CD_SMILES column so that it is a normal IJC field (text field) and then run searches on it in IJC.e.g seeach using the contains operator and search for ;:

Not sure if this will find just the offending record, but hopefully you should be able to find it with an approach like this.

Once you do find it please send us the offending mol file (from the CD_STRUCTURE column).

Thanks

Tim

User 1887159699

04-11-2011 15:36:27

Hi Tim,

I am new to IJC, therefore i need some assistance, where / how to find the needed information.

My workflow was:

Creating a localdb from a sdfile (100k compounds, organic, oranometallics, inorganic, markush).

I used the default values and always clicked OK if needed.

The I created my query, which produced the crash. Other (simpler queries) are OK. Maybe the screening did not select the problematic compound for further abas. I know, that the complex query uses abas at an quite early stage in the query (or do you have screens for linknode?).

Since i use a localDB, i do not know, how to access the structures from "external" (like in an external database via sql). Where are the structures stored and how could I access them (is it for example a mysql DB, or is it a proprietary db-engine / file)?

Best, Hinnerk

ChemAxon fa971619eb

04-11-2011 15:49:10

The local DB is a Derby DB. It can be acccessed as a normal database. Instructions can be found here:
http://www.chemaxon.com/instantjchem/ijc_latest/docs/user/help/htmlfiles/tips_and_tricks/db_explorer.html

But most likley you wll find it easier to do this directly in IJC. Try this:

1. open the schema editor by double clicking on the 'localdb' node in the projects window

2. find the appropriate entity under the Entities section and expand the Fields node.

3. right click on the fields node and choose 'Promote field' and choose CD_SMILES. This column should be added as a field.

4. Go to the grid view for that entity. Show the Smiles column (if not already shown)

5. Run the query mentioned earlier on this field.

Tim

User 1887159699

04-11-2011 19:58:28

Hi Tim,

after some iterative testing, I found this structure, which causes the errors (above query as substructure).

It is not the only one, which has ";" in cxsmiles. I hve dozens, which also have ";" and are OK with the query.

Best, Hinnerk

-----------

Mrv0541 11041117482D

9 8 0 0 0 0            999 V2000
    3.2711   -1.7964    0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0
    2.8492   -1.0862    0.0000 C   0 0 0 0 0 0 0 0 0 0 0 0
    2.4440   -1.8048    0.0000 C   0 0 0 0 0 0 0 0 0 0 0 0
    3.5719   -0.6600    0.0000 N   0 0 0 0 0 0 0 0 0 0 0 0
    4.2988   -1.0736    0.0000 C   0 0 0 0 0 0 0 0 0 0 0 0
    3.5636    0.1671    0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0
    2.1306   -0.6810    0.0000 C   0 0 0 0 0 0 0 0 0 0 0 0
    1.4162   -1.1029    0.0000 O   0 0 0 0 0 0 0 0 0 0 0 0
    2.1181    0.1546    0.0000 O   0 0 0 0 0 0 0 0 0 0 0 0
2 7 1 0 0 0 0
2 4 1 0 0 0 0
7 8 1 0 0 0 0
2 1 1 0 0 0 0
7 9 2 0 0 0 0
4 5 1 0 0 0 0
3 2 1 0 0 0 0
4 6 1 0 0 0 0
A    3
^$R1
A    5
^$R4
M RGP 2   1   1   6   4
M END

----------------------

ChemAxon 25dcd765a3

07-11-2011 10:58:20

Hi Hinnerk,

Thank you for the report. We start to fix this issue ASAP.

Andras

ChemAxon 25dcd765a3

09-11-2011 13:03:09

Hi Hinnerk,

We have fixed this issue.

The 5.7 release commit deadline is over but the 5.8 release will contain the fix.

Andras