JOELib Tutorial: A Java based cheminformatics/computational chemistry package | ||
---|---|---|
Prev | Chapter 10. Example applications | Next |
Example application for comparing molecules. Molecules can be compared using fingerprints (tanimoto) or descriptor values (euklidian distance).
sh comparison.sh typeTarget targetFile typeToCompare toCompareFile descriptorFile outputFile identifier
typeTarget
Input/Output type of the target file.targetFile
Target file (size T). This file will be loaded into the memory.typeToCompare
Input/Output type of the file to which the target file will be compared.toCompareFile
Comparison file (size C). This file will be loaded from file and can be huge.descriptorFile
These descriptors will be used for comparing molecules. If this is a fingerprint descriptor the tanimoto coefficient will be calculated. If a list of native value descriptors is available, the euklidian distance value will be calculated for these descriptor values.outputFile
The output file for the similarity/distance values. This will be a matrix of size T*C.identifier
The molecule identifier of the molecules in the comparison file which will be the first entry in every line.