automatic inchi generation

Can jchem manager automaticaly generate inchi strings from an sdf file during a database import via the jchem manager as it does with smile strings?





Also does the jchem api support the conversion of a mol file into an inchi string which can be implemented on the web. E.g. I have a html form to accept a mol file. when the user submits the form the mol file needs to be converted into an inchi string which can be displayed on the corresponding page. Does the jchem or marvin api provide a script to implement the above task?

Hi,

Quote:

Can jchem manager automatically generate inchi strings from an sdf file during a database import via the jchem manager as it does with smile strings?

From the next major release (JChem 3.2) one will be able to assign Chemical Terms ( http://www.chemaxon.com/jchem/doc/user/EvaluatorLanguage.html ) expressions to database columns.


We will also introduce a new Chemical Terms function called molString(), which will return the string representation of the structure in any supported format, including InChi.

Quote:

Also does the jchem api support the conversion of a mol file into an inchi string which can be implemented on the web. E.g. I have a html form to accept a mol file. when the user submits the form the mol file needs to be converted into an inchi string which can be displayed on the corresponding page. Does the jchem or marvin api provide a script to implement the above task?

In case of web applications we recommend using JSP (which is essentially Java), because that is the most efficient way to access our complete Java API.


The conversion would look something like:

Code:

Molecule mol=MolImporter.importMol(molString); String inchi=mol.toFormat("inchi");

We also have a command-line tool called MolConverter ( http://www.chemaxon.com/marvin/doc/user/molconvert.html ) , but due to the high cost of starting a new Java Virtual Machine for each molecule I do not recommend calling it from a web application.





Best regards,





Szilard

Hi





Any idea when the new jchem 3.2 with chemical terms expressions to database columns will be released?





I am currently using ASP - can Active Server Pages be used to generate inchi strings in web applications using your JAVA API?





Do you have some sample to code to achieve the above task of converting a mol file provided via a web form into an inchi string using ASP code?





Your help would be greatly appreciated

Hi,

Quote:

Any idea when the new jchem 3.2 with chemical terms expressions to database columns will be released?

In about two months.


However I have built a fresh developer version containing this feature, it can be downloaded from here (TEST_2006_07_14):





http://www.chemaxon.com/download.php?d=/data/download/jchem/test





(Please note that this is an untested, developer version)





You can add extra columns to your table and specify the following Chemical Terms expression:

Code:

molString("inchi")

You may also use Evaluator to add InChi strings to SDFiles, for example:

Code:

evaluate -e "molString('inchi')" -S -t INCHI -o output.sdf input.sdf

The advantage of using the Evaluator is that you can continue using the stable version in the live system.

Quote:

I am currently using ASP - can Active Server Pages be used to generate inchi strings in web applications using your JAVA API?

Yes, but it's much more complicated than the solutions I have presented.





Best regards,





Szilard

hi





I have tried using the following code to generate inchi strings:

Code:

evaluate -e "molString('inchi')" -S -t INCHI -o output.sdf input.sdf

However i keep getting the following error message:

Code:

chemaxon.nfunk.jep.parseException:SyntaxError(Implicit multiplication not enabled) at chemaxon.nfunk.jep.Parser.MultiplicativeExpression(Parse.java:557)

Any idea why this is? Is the molString() function only available in the test release because I am using the current version of jchem to run the above code?I am not sure I quite understood you but do I need to use the test release to run the above function?





Also can the same function be used to generate smiles in the same format/notation that marvinSketch generates them instead of the ChemAxon Extended SMILES notation which are generated using jchem manager during a sdf file import into a database?





On the other hand can marvinSketch generate smilestrings in the chemaxon extended smiles notation aswell as the present notation?





Also is there any intention to develop marvinsketch so that it can generate inchi strings using an unsigned applet?

Hi,

Quote:

I am not sure I quite understood you but do I need to use the test release to run the above function?

Yes it only works in the latest test version.

Quote:

Also can the same function be used to generate smiles in the same format/notation that marvinSketch generates them instead of the ChemAxon Extended SMILES notation which are generated using jchem manager during a sdf file import into a database?

Yes, just specify "smiles" as the format.





Please see this page for the supported formats:





http://www.chemaxon.com/marvin/doc/dev/formats.html





Each format description begins with a code name (e.g. "smiles"), this is what you should specify.


It can be extended by some options.

Quote:

On the other hand can marvinSketch generate smilestrings in the chemaxon extended smiles notation aswell as the present notation?

Yes, of course.

Quote:

Also is there any intention to develop marvinsketch so that it can generate inchi strings using an unsigned applet?

Usually the signed applet is fine for everybody, so we provide only a signed version.


Here is a description how you can unsign jar files in marvin:


http://www.chemaxon.com/forum/ftopic65.html





Regards,





Szilard

Quote:

Also is there any intention to develop marvinsketch so that it can generate inchi strings using an unsigned applet?

Presently we use non-Java code provided by IUPAC to generate InChi through JNI. This solution requires signed applet. We don't plan to develop a Java version. However, if a freely available Java implementation will be available, then we will integrate it.