tzok / mcq4structures

A parent project for a set of subprojects related to Mean of Circular Quantities (MCQ).

Mean of Circular Quantities (MCQ)

Mean of Circular Quantities (MCQ) is a dissimilarity measure useful in comparison of 3D protein and/or RNA structures. It calculates an average difference between corresponding torsion angle values (rotations around bonds). More information can be found in:

Zok, T., Popenda, M., & Szachniuk, M. (2014). MCQ4Structures to compute similarity of molecule structures. Central European Journal of Operations Research, 22(3), 457–473. https://doi.org/10.1007/s10100-013-0296-5

Installation

git clone https://github.com/tzok/mcq4structures.git
cd mcq4structures
mvn install

Contents

This project consists of a few subprojets:

• mcq-common: base functionality
• mcq-clustering: partitional and hierarchical clustering
• mcq-cli: command-line interface
• mcq-gui: graphical interface

Main Ideas

• Use pl.poznan.put.comparison.MCQ#compareGlobally to compare two 3D structures and obtain a global value of dissimilarity. You can use pl.poznan.put.comparison.global.ParallelGlobalComparator to process multiple inputs in parallel
• Use pl.poznan.put.comparison.MCQ#comparePair to obtain detailed information about dissimilarity of two 3D structures
• Use pl.poznan.put.comparison.MCQ#compareModels in a situation where a distinguished reference 3D structure is known and you want to know how 3D models compare to it

Clustering

• Use pl.poznan.put.clustering.hierarchical.Clusterer to construct dendrograms from a distance matrix (with COMPLETE, SINGLE or AVERAGE linkage option)
• Use pl.poznan.put.clustering.partitional.KMedoids to perform partitional clustering based on distance matrix
• Use pl.poznan.put.clustering.partitional.KScanner#parallelScan to find optimum number of clusters with respect to silhouette score

mcq4structures's Issues

MCQ4structures installation dependency issue

Dear Tomasz,

I am trying to install MCQ4structures by cloning mcq-parent, however, I am facing the following error:

Failed to execute goal on project circular: Could not resolve dependencies for project pl.poznan.put:circular:jar:1.3.2: Failure to find pl.poznan.put:TzokCommons:jar:1.5.1 in https://repo.maven.apache.org/maven2 was cached in the local repository, resolution will not be reattempted until the update interval of central has elapsed or updates are forced -> [Help 1]

I am not sure about the origin of this error. My Java version is 1.8.0_311. Could this be a problem?

Looking forward to your reply.

Best Regards,
Mandar Kulkarni