Current SMARTCyp version is 2.4.2
Executable Java jar file for use on command line.
Usage: java -jar smartcyp.jar [-nocsv] [-nohtml] [-printall] [-outputdir dirname] input-file-names
-nocsv results in only html output.
-nohtml results in only csv output and increased speed since no images are generated.
-printall will print all non-hydrogen atoms to the csv file for easier import into other software.
-outputdir dirname will save output files in dirname, if dirname does not exist it will be created.
-outputfile filename will save output files with basename "filename", i.e. filename.csv and filename.html
-png will create the old type of html output with png images, which was default until version 2.0. This is compatible with older web browsers, but makes SMARTCyp run slower, and will make the html pages load slower.
-smiles smilesstring will use the smiles string as input molecule.
-noempcorr will not use the new empirical N-oxidation correction implemented by default in version 2.3 and forward.
-filter XX will in addition to standard functionality also filter the input structures. All molecules containing a site with a score less than XX will be removed, and a new structure file will be saved as output without such molecules.
- HTML and CSV file output is generated in the working directory.
- Tested on Windows XP, Linux, and MacOSX.
Java source code
Requires CDK and JChemPaint jar files or source code for compilation.
SMARTCyp is released under the Lesser GPL license.
If you use this program for publications, please cite P. Rydberg, D. E. Gloriam, J. Zaretzki, C. Breneman and L. Olsen, ACS Med. Chem. Lett., 2010, 1, 96-100 , P. Rydberg, D. E. Gloriam and L. Olsen, Bioinformatics, 2010, 26, 2988-2989, P. Rydberg and L. Olsen, ACS Med. Chem. Lett., 2012, 3, 69-73, P. Rydberg and L. Olsen, ChemMedChem, 2012, 7, 1202-1209, P. Rydberg et al., Angew. Chem, Int. Ed. 2013, 52, 993-997 and P. Rydberg et al., Mol. Pharmaceutics 2013, 10, 1216-1223.