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PACHA: Pairwise Chemical Aligner

Overview

PACHA - a chemical graph alignment software.

Description

PACHA is a chemical graph alignment software. Given two chemical compounds represented as small graphs, PACHA outputs an alignment, a.k.a atom-atom mapping, between two compounds. Graph alignements are useful for building from a compound-compound pair a feature vector that can be used for an input of machine learning, e.g., support vector machine. Main applications are reconstructions of metabolic pathway, virtual screening and so forth. See [1] for detail.

Demo

cd pacha/src
make
./pacha --input_file=../dat/target_compounds/ --output_file=output.txt
output.txt includes alignment results between all pairs of cheical graphs in ../dat/target_compounds/

Requirement

GNU C++ compiler
Higher version is preferable if you use multiple threads.

Usage

usage: ./pacha --input_file=string --output_file=string [options] ...
options:
-i, --input_file input file name (string)
-o, --output_file output file name (string)
-d, --dist maximum distance for computing vertex features (unsigned long long [=5])
-k, --topk number of alignments starting from vertex pairs of topk matching scores (unsigned long long [=10])
-n, --num_threads # of threads (unsigned long long [=1])
-t, --threshold theshold (float [=0])
-c, --inter_cuts maximum number of intermolecular cuts (unsigned long long [=100000000])
-a, --intra_cuts maximum number of intramolecular cuts (unsigned long long [=100000000])
-?, --help print this message

Install

cd pacha/src
make

Licence

New BSD Licence

Author

Yasuo Tabei (yasuo.tabei@gmail.com)
Homepage
tb-yasu

Reference

[1] Yoshihiro Yamanishi*, Yasuo Tabei*, Masaaki Kotera: Metabolome-scale de novo pathway reconstruction using regioisomer-sensitive graph alignments, In Proceedings of ISMB/ECCB, 2015. (*joint first author)

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