pyRMSD: a Python package for efficient pairwise RMSD matrix calculation and handling

pyRMSD: a Python package for efficient pairwise RMSD matrix calculation and handling

SUMMARY We introduce pyRMSD, an open source standalone Python package that aims at offering an integrative and efficient way of performing Root Mean Square Deviation (RMSD)-related calculations of large sets of structures. It is specially tuned to do fast collective RMSD calculations, as pairwise RMSD matrices, implementing up to three well-known superposition algorithms. pyRMSD provides its ow...

A Fast 3×N Matrix Multiply Routine for Calculation of Protein RMSD

The bottleneck for the rapid calculation of the root-mean-square deviation in atomic coordinates (RMSD) between pairs of protein structures for large numbers of conformations is the evaluation of a 3×N x N × 3 matrix product over conformation pairs. Here we describe two matrix multiply routines specialized for the 3×N case that are able to significantly outperform (by up to 3X) offthe-shelf hig...

On inconsistency of a pairwise comparison matrix

PYCHEM: a multivariate analysis package for python

UNLABELLED We have implemented a multivariate statistical analysis toolbox, with an optional standalone graphical user interface (GUI), using the Python scripting language. This is a free and open source project that addresses the need for a multivariate analysis toolbox in Python. Although the functionality provided does not cover the full range of multivariate tools that are available, it has...

DREAMTools: a Python package for scoring collaborative

DREAM challenges are community competitions designed to advance computational methods and address fundamental questions in system biology and translational medicine. Each challenge asks participants to develop and apply computational methods to either predict unobserved outcomes or to identify unknown model parameters given a set of training data. Computational methods are evaluated using an au...