AlignOverlap            Alignment Overlap Check
BoundWaterEnvPlots      Bound Water Environment Barplots
BoundWaterEnvSummaryPlot
                        Bound Water Environment Summary Plot
BoundWaterEnvironment   Bound Water Environment
BoundWaterEnvironment.interact
                        Bound Water Environment (interactions)
BoundWaterEnvironment.quality
                        Bound Water Environment (atomic quality)
BvalueBarplot           B-value Barplots
BvalueBarplot.summ      B-value Summary Barplots
CalcAlignOverlap        Calculate Alignment Overlap
CleanProteinStructures
                        Clean Protein Structures
ClusterSummaryPlots     Cluster Summary Plots
ClusterWaters           Cluster Conserved Waters
ClusterWaters.MDS       Cluster Conserved Waters (MDS)
ConservationPlot        Conservation Plot (Number of Waters Per Cluster
                        Histogram)
ConservationSet         Conservation Set
ConservedWaterStats     Conserved Water Statistics
ConservedWaters         Conserved Crystallographic Waters
ConservedWaters.MDS     Conserved Molecular Dynamics Simulation Waters
CreatePyMOLscript       Create PyMOL Script File
DetermineChainsOfInterest
                        Determine Chains Of Interest
ExtractFileTimeStamp    Extract Filename Time Stamp
ExtractPDBids           Extract PDB IDs
FileTimeStamp           Filename Time Stamp
FreeSASA.diff           Atomic SASA difference of hydrated PDB via
                        FreeSASA
FreeSASAcheck           FreeSASA Check
HasXWaters              Has "X" Waters
HydrophilicityEvaluation
                        Hydrophilicity Evaluation
HydrophilicityTable     Residue Atom Type Hydrophilicity Values
MobNormBvalEvalPlots    Mobility and Normalized B-values Evaluation
                        Plots
Mobility                Water Molecule Mobility
MobilityBarplot         Mobility Barplots
MobilityBarplot.summ    Mobility Summary Barplots
Nearby                  Nearby
NormalizedBvalue        B-value Normalization
OccupancyBarplot        Occupancy Barplots
OccupancyBarplot.summ   Occupancy Summary Barplots
PDB.1ecd                PDB Structure of Erythrocruorin
PDB.5rxn                PDB Structure of Rubredoxin
ProtHetWatIndices       Protein, HET, and Water Atom Indices
RemoveHydrogenAtoms     Remove Hydrogen and Deuterium Atoms
RemoveModeledAtoms      Remove Modeled Atoms
RemoveOoR.b             Remove B-value Out of Range Atoms
RemoveOoR.o             Remove Occupancy Out of Range Atoms
RescaleValues           Rescale Values
RetainChainsOfInterest
                        Retain Chains Of Interest
RetainWatersWithinX     Retain Waters Within X Angstroms of Protein
ReturnPDBfullPath       Return PDB Full Path
StandardizeAsparticAcidNames
                        Standardize Aspartic Acid Names
StandardizeCysteineNames
                        Standardize Cysteine Names
StandardizeGlutamicAcidNames
                        Standardize Glutamic Acid Names
StandardizeHistidineNames
                        Standardize Histidine Names
StandardizeLysineNames
                        Standardize Lysine Names
TimeSpan                Time Span
UniqueAtomHashes        Create Unique Atom Hashes
aaStandardizeNames      Standardize Amino Acid Names
calcAtomClassHydrophilicity
                        Atom Class Hydration Fraction
calcAtomHydrationEstimate
                        Estimated Atomic Hydration Fraction
calcBvalue              Calculate B-value
calcNearbyHydrationFraction
                        Calculate Nearby Atom Hydration Fraction
calcNumHydrogenBonds    Calculate Number of Hydrogen Bonds
check.cluster.method    Check Clustering Method
colorPalettes           Color Values for Plots
getAtomTypeCounts       Get AtomType Counts
getProtAtomsNearWater   Number of Solvent Accessible/Exposed Protein
                        Atoms Near a Water
getRCSBdata             Clean RCSB Dataset
getResTypeCounts        Get ResType Counts
getResidueData          Number of Residues and Solvent
                        Accessible/Exposed Residues
nBvalueBarplot          Normalized B-value Barplots
names.backbone.atoms    Backbone Atom Names
names.polar.atoms       Polar Atom Names
names.res.AtomTypes     Residue and AtomType Names
names.resATs.carb.sulf
                        Carbon and Sulfur Residue-AtomType Names
names.resATs.nitro.neut
                        Neutral Nitrogen Residue-AtomType Names
names.resATs.nitro.pos
                        Positive Nitrogen Residue-AtomType Names
names.resATs.oxy.neg    Negative Oxygen Residue-AtomType Names
names.resATs.oxy.neut   Neutral Oxygen Residue-AtomType Names
names.residues          Residue Names
names.sidechain.atoms   Sidechain Atom Names
names.waters            Water Residue Names
normBvalueBarplot.summ
                        Normalized B-value Summary Barplots
openxlsxCellStyles      openxlsx Cell Style
oxAlignOverlapSheet     Align Overlap Data Sheet
oxClusterStatsSheet     openxlsx Water Cluster Statistics
oxClusterSummarySheet   openxlsx Cluster Summary Sheet
oxInitWaterDataSheet    Initial Water Data Sheet
oxPDBcleanedSummarySheet
                        Cleaned PDB Structures Data Sheet
oxPlainDataSheet        Plain Data Sheet
oxRCSBinfoSheet         openxlsx PDB/RCSB Summary Sheet
oxWaterOccurrenceSheet
                        openxlsx Water Occurrence Summary
res2xyz                 Residue Indices to Coordinate Indices
resAtomType2AtomClass   Convert Residue-AtomType to AtomType Class
thrombin.1hai           PDB Structure of Thrombin
thrombin10.PDBs.align   Thrombin10 Vignette's Primary Sequence
                        Alignment
vanddraabe              vanddraabe: Identification and Statistical
                        Analysis of Conserved Waters in Proteins
write.basic.pdb         Write Basic PDB File
write.conservedWaters.pdb
                        Write Conserved Waters to PDB File
