Cluster the conserved waters.
The water oxygens' X, Y, and Z coordinates, B-values, and occupancy values.
Numerical value provided by the user for the distance between water oxygen atoms to form a cluster; default: 2.4 Angstroms.
Method of clustering the waters; default is
Calculate the conserved waters using a collection of crystallographic protein structures.
This function returns:
h2o.clusters.raw: Initial waters with assigned cluster ID
h2o.clusters.summary: Each cluster's:
number of waters
X, Y, and Z cooridinates
bound water environment measurements
mean distance between waters comprising the cluster
mean distance between waters comprising the cluster and the cluster's centroid
h2o.occurrence: A table indicating the structures (PDBs) contributing to each cluster. This summary table includes the PDB structure's:
occupancy (mean and standard deviation)
mobility (mean and standard deviation)
B-value (mean and standard deviation)
number of waters in each cluster
number of waters passing the mobility cutoff
number of waters passing the normalized B-value
number of waters passing both cutoff values
percentage of waters passing both cutoffs
number of clusters the structure contributes to
True/False table indicating if the protein structure contributed to the water cluster
clustering.info: size and timing information
Emilio Xavier Esposito emilio@exeResearch.com
Paul C Sanschagrin and Leslie A Kuhn. Cluster analysis of
consensus water sites in thrombin and trypsin shows conservation between
serine proteases and contributions to ligand specificity. Protein
Science, 1998, 7 (10), pp 2054-2064.
Fionn Murtagh and Pierre Legendre. Ward's Hierarchical Agglomerative
Clustering Method: Which Algorithms Implement Ward's Criterion?
Journal of Classification, 2014, 31, (3), pp
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