Welcome to BitQT’s documentation!

BitQT is a Python command-line interface (CLI) conceived to speed up the Heyer’s Quality Threshold (QT) 1 clustering of long Molecular Dynamics. The package implements a heuristic approach to this exact variant of QT.

The construction of a binary-encoded RMSD matrix, instead of the classical (half/single/double)-precision float matrix, led to considerable RAM savings compared to the few existing QT implementations. This binary matrix also allows implementing the significant steps as bitwise operations, which are faster than the corresponding set operations when dealing with considerable amounts of data.

1

Heyer, L. J.; Kruglyak, S.; Yooseph, S. Exploring Expression Data Identification and Analysis of Coexpressed Genes. Genome Res. 1999, 9 (11), 1106–1115.