vanddraabe (version 1.1.1)

BoundWaterEnvPlots: Bound Water Environment Barplots

Description

Normalized B-value Barplots for Cluster with at least 50% Conservation

Usage

BoundWaterEnvPlots(data, passed.waters = TRUE, pct.conserved.gte = 50,
  num.clusters = 50)

Arguments

data

The h2o.clusters.summary data.frame from the ClusterWaters function containing the nBvalue.mu information.

passed.waters

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

pct.conserved.gte

minimum percent conservation within a water cluster; default: 50.0If the number of clusters is less than the number of clusters defined by num.clusters, then the number of clusters defined by pct.conserved.gte is displayed.

num.clusters

number (integer) of clusters to display. If the number of clusters is less than the number of clusters defined by pct.conserved.gte, then the number of clusters defined by num.clusters is displayed. A value of NULL results in the provided value for pct.conserved.gte being used.

Details

Constructs a barplot with corresponding density plot for the mean normalized B-value value for all water within each cluster with at least 50% water conservation. 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.

The normalized B-value values are calculated by the NormalizedBvalue function.

This plot was inspired by Figure 1 of Sanschagrin and Kuhn (1998).

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

See Also

Other plots: BoundWaterEnvSummaryPlot, BvalueBarplot.summ, BvalueBarplot, ClusterSummaryPlots, MobNormBvalEvalPlots, MobilityBarplot.summ, MobilityBarplot, OccupancyBarplot.summ, OccupancyBarplot, nBvalueBarplot, normBvalueBarplot.summ

Examples

# NOT RUN {
  
# }
# NOT RUN {
  bwe.plots <- BoundWaterEnvPlots(data=thrombin10.conservedWaters,
                                  passed.waters=TRUE,
                                  pct.conserved.gte = 50.0,
                                  num.clusters = 50)
  
# }
# NOT RUN {
# }