Upgrade / InChi support

I currently use MarvinSketch 3.5.1 and would like to upgrade for the recent version that (as I understand) supports the InChi. Is there any way how to do it without uninstall old / install new release ? Another question: could the molconverter be capable of generating the InChi names in batch mode using e.g. smiles as an input ?

Quote:

I currently use MarvinSketch 3.5.1 and would like to upgrade for the recent version that (as I understand) supports the InChi. Is there any way how to do it without uninstall old / install new release ?

If you really want to overwrite your Marvin Beans with the new one, I suggest you the following way:


1. Download the zip version of the Marvin Beans package: marvinbeans-4.0.3.zip


2. Uncompress it somewhere to your machine. You will get a "marvinbeans" directory.


3. Copy all files from the new directory into the old one (where the Marvin Beans installed).


Actually, overwriting the lib sub-directory inside the Marvin Beans package is enough to be able to use the new Marvin Beans. Thus, if you do not want to waste your time with upgrading the documentation, overwrite only the lib directory.

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Another question: could the molconverter be capable of generating the InChi names in batch mode using e.g. smiles as an input ?

Yes, you can do it:

Code:

molconvert inchi mysmol.smiles > mymol.inchi

Thanks, will do.

Quote:

Another question: could the molconverter be capable of generating the InChi names in batch mode using e.g. smiles as an input ?

Yes, you can do it:

Code:

molconvert inchi mysmol.smiles > mymol.inchi

Shouldn't I for this feature overwrite also the bin folder with the new molconvert.bat ?

molconvert is a unix script. You do not need this if you have got Windows. Use the molconvert.bat which is a batch file.


Actually, overwriting the bin folder is not too lucky. But if you have done it, it is not a tragedy. The installed version of molconvert.bat included the absolute path of the Marvin Beans folder. The advantage of the installed version of molconvert.bat is that it can be launched from anywhere from your machine (since the installer wrote the Marvin Beans location into the file). There may be problem at using of the other molconvert.bat if you launch it outside the Marvin Beans' home directory.

Tamas wrote:

Actually, overwriting the bin folder is not too lucky.

I permitted (fortunately) to overwrite ONLY the lib folder and all seems to work perfectly :-). Also molconvert performs the InChi conversion in batch mode well, any way how to retain a molID (present in smiles tab separated) in the inchi output in similar fashion ?

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Also molconvert performs the InChi conversion in batch mode well, any way how to retain a molID (present in smiles tab separated) in the inchi output in similar fashion ?

Inchi doesn't allow comments or molecule names to be inserted.

Tamas wrote:

Quote: Also molconvert performs the InChi conversion in batch mode well, any way how to retain a molID (present in smiles tab separated) in the inchi output in similar fashion ? Inchi doesn't allow comments or molecule names to be inserted.

I did not express myself correctly: when generating batch of InChi names from batch of smiles it would be useful to use smiles file containing in separate field (e.g. tab separated) also molecule ID and in the target InChi files retain those IDs not as a part of InChi name but again tab or similarly separated from the InChi string. It would prevent mess in correspondence smiles-InChi in larger batches.

I don't think that the batch file is the best choice for you to manipulate the output of the converter. I suggest you to use the Marvin Beans API to append your text to the inchi export output.


I have created a simple example where the molecules are exported in both inchi and SMILES format into the output file.


You can run the attached example like this:

Code:

java test/InchiAndSmiles inchi mols.smiles mols.inchi