vanddraabe (version 1.1.1)

ConservationPlot: Conservation Plot (Number of Waters Per Cluster Histogram)

Description

Histogram and density plots for number of cluster with number of atoms

Usage

ConservationPlot(data, passed.waters = TRUE)

Arguments

data

The h2o.clusters.summary data.frame from the ClusterWaters() function containing the num.waters information. The num.waters values are integers.

passed.waters

Logical indicator to plot results for waters passing Mobility() and NormalizedBvalue() OR using all waters within the PDB files.

Details

Constructs a histogram for the number of waters per cluster. Clusters with less than 50% conservation are light grey, clusters with 50 to 69% water conseration are dark red, clusters with 70 to 79% conservation are red, 80 to 89% conservation are light blue, 90 to 99% conservation are blue, and 100% conservation (waters from all structures) are dark blue.

References

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. DOI: 10.1002/pro.5560071002 PMID: 9792092 WatCH webpage

Examples

# NOT RUN {
  
# }
# NOT RUN {
  Conservation.plot <- ConservationPlot(data=thrombin10.conservedWaters,
                                        passed.waters=TRUE)
  
# }
# NOT RUN {
# }