jCompoundMapper Fingerprinting algorithms for your use
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jCompoundMapper Description

jCompoundMapper was created in order to provide popular fingerprinting algorithms for chemical graphs. Among this graphs we can find the depth-first search fingerprints, shortest-path fingerprints, extended connectivity fingerprints, autocorrelation fingerprints (e.g. CATS2D), radial fingerprints (e.g. Molprint2D), geometrical Molprint, atom pairs, and pharmacophore fingerprints. jCompoundMapper provides exporters for several formats for machine learning tools such as LIBSVM, LIBLINEAR, and WEKA. The application allows for a parameterization like search depth, distance cut-offs, or atom typing. In case of hashed fingerprints you may configure the size of the hash space. jCompoundMapper for the computation of similarity matrices for clustering approaches or as input format for LIBSVM The software can be used as a lightweight jar library or a stand-alone executable jCompoundMapper is solely based on open source software with a liberal license. It uses the chemical expert system of the Chemistry Development Kit. The program's main goal is to: · Provide standard fingerprint implementations for data mining experiments · Open source implementations with an exact definition · Easy-to-use command-line tool for the described tasks · Provide a basis for the development of new fingerprint encodings which can be compared, for example, to algorithms with exactly the same labeling algorithm.

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