How to use logP,pKa with SMILES strings

To whom it concerns,


I have just received the Academic Package. My research involves generating SMILES strings which I would like to be able to determine the logP, pKa etc. of. Could somebody please advise me as to how I should proceed with the various ChemAxon software components? At the moment, I would like to write a JAVA based application which will use methods from the logP class. It appears to me that the logP.class which is in the package chemaxon.calculations is different to the Class LogP which is described in the JChem API documentation www.chemaxon.com/jchem/doc/api/chemaxon/descriptors/scalarLogP.





Any advise would be greatly appreciated.





Regards,


Miriam

You need the logP class in the chemaxon.marvin.calculations package. All calculator plugins (pKa, logP, logD, ...) are in this package. The molceular descriptor logP that you have found in JChem is different: it uses logP to build a molecular desriptor used for fingerprint generation / molecule similarity calculation.





API usage examples can be found in the API class headers, for logP see


http://www.chemaxon.com/jchem/doc/api/chemaxon/marvin/calculations/logPPlugin.html





You can also access the plugin calculations in batch mode (cxcalc) and through our chemical terms evaluator, here is a forum topic on these:


http://www.chemaxon.com/forum/ftopic271.html

Hi,





Is it possible to output either the molecules names/SMILES representation when you use cxcalc?





For example, lets say I have a file called Test.smiles which contains the following :





c1ccccc1.





When I type the following at the command line,





cxcalc logp Test.smiles





I would like to see either Benzene or c1ccccc1 displayed with the logP results.





Is this possible to achieve?





Regards,


Miriam

Currently this is not possible directly, but the molecule ID (which is either the molecule index in the input file or the molecule name stored in an SDF tag) is displayed:

Code:

cxcalc logp test1.smiles id      logP 1       2.05 2       2.56

Code:

cxcalc -i ID logp test2.sdf id      logP ID1       2.05 ID2       2.56

I can easily add the SMILES output possibility in the ID column or in other way for the next minor release.





Please let me know if you would like this option in the ID column or you prefer some other output format.

There is a tricky way to output both the SMILES and the logP value:

Code:

cxcalc -S logp "C1CCCCNCCC1" | molconvert smiles:TlogP C1CCCCNCCC1 1.71

This line first writes the logP value in an SDF tag and outputs the SDF - then converts this SDF to SMILES together with the logP SDF tag (separated by a space).

Hi Nora,





It would be great if you could include the SMILES output in the ID column.





Thanks for all of your help. It is greatly appreciated.





Regards,


Miriam

I have just added the option to specify "-i smiles" which will output the SMILES in the ID column. This will be available in the next Marvin release (4.0.2).


Example:

Code:

cxcalc -i smiles logp pka "OC1CCCCN=CCC1" "OC1CCCCNCCC1" id      logP    apKa1   apKa2   bpKa1   bpKa2   atoms OC1CCCCN=CCC1   0.51    15.24           8.34            1,7 OC1CCCCNCCC1    0.65    15.25           10.75           1,7

Hi Nora,





Thanks for adding the SMILES info. Have you a release date for Marvin 4.0.2?





Regards,


Miriam

A pre-released Marvin 4.0.2 (test version) can be downloaded from:


http://www.chemaxon.com/test/marvin/

Hi Nora,





Which of the classes have you added the 'SMILES' capability? For example,





cxcalc -i smiles logp c1ccccc1





Where is the 'smiles' class?








Thanks,


Miriam

There is no SMILES class added, this is only a parameter of cxcalc - it uses the already existing





mol.toFormat("smiles");





method that invokes our usual SMILES export module to write the molecule into SMILES format.