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C++ implementation of the kmeans algorithm (http://en.wikipedia.org/wiki/K-means_clustering) for finding clusters of stable microstates when studying ligand migration in proteins
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MMunibas/kmeans_proteins_clusters
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kmeans clustering for studying migrations in proteins ===================================================== C++ implementation of the kmeans algorithm (http://en.wikipedia.org/wiki/K-means_clustering) for finding clusters of stable microstates when studying ligand migration in proteins Molecular systems are realigned using the Kabsch algorithm (http://en.wikipedia.org/wiki/Kabsch_algorithm) Copyright (c) 2015, Florent Hédin, Pierre-André Cazade, and the University of Basel. All rights reserved. The 3-clause BSD license is applied to this software. See LICENSE.txt ----------- Compiling : ----------- The Kabsch algorithm implementation for realigning the dcd frames requires the BLAS and LAPACK development packages to be installed on your system : On rpm based systems: sudo yum install blas-devel lapack-devel On deb based systems: sudo apt-get install libblas-dev liblapack-dev ------------------ Print help/usage : ------------------ ./kmeans Error, not enough arguments, usage is : kmeans -idx {index of atom to study (taken from a PSF for example)} -dcd {number of dcd files} {paths to DCDs} -out {path to outputFile} -xyz {path to outputXYZ} inputDCDs and outputFile and outputXYZ are necessary fileNames optional arguments : -align {first} {last} if present, align all frames from all dcds relative to first frame of first dcd before starting clustering -interactive if present the user will have to provide parameters interactively -cycles provide number of cycles -cutoff provide cutoff value for cluster determination -mult provide the Multiplicator factor of the cutoff for exclusion of lonely microstates -thresh provide the Threshold to consider a microstate is in water -tolerance provide the Tolerance for convergence ---------------------------------------------------- Run with all parameters provided from command line : ---------------------------------------------------- If we want to use all coordinates of atom 2534 from 2 dcds as starting points for the list of mictro states, aligning all dcd frames to atoms 1 to 2532 ./kmeans -idx 2536 -dcd 2 ../1111/run_0.dcd ../rst1/1111/rst1_0.dcd -out test1111.out -xyz test1111.xyz -cutoff 1.8 -mult 4.5 -align 1 2532
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C++ implementation of the kmeans algorithm (http://en.wikipedia.org/wiki/K-means_clustering) for finding clusters of stable microstates when studying ligand migration in proteins
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