Identification and Statistical Analysis of Conserved Waters Near Proteins


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Documentation for package ‘vanddraabe’ version 1.1.1

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vanddraabe-package vanddraabe: Identification and Statistical Analysis of Conserved Waters in Proteins
aaStandardizeNames Standardize Amino Acid Names
AlignOverlap Alignment Overlap Check
BoundWaterEnvironment Bound Water Environment
BoundWaterEnvironment.interact Bound Water Environment (interactions)
BoundWaterEnvironment.quality Bound Water Environment (atomic quality)
BoundWaterEnvPlots Bound Water Environment Barplots
BoundWaterEnvSummaryPlot Bound Water Environment Summary Plot
BvalueBarplot B-value Barplots
BvalueBarplot.summ B-value Summary Barplots
CalcAlignOverlap Calculate Alignment Overlap
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
CleanProteinStructures Clean Protein Structures
ClusterSummaryPlots Cluster Summary Plots
ClusterWaters Cluster Conserved Waters
ClusterWaters.MDS Cluster Conserved Waters (MDS)
colorPalettes Color Values for Plots
ConservationPlot Conservation Plot (Number of Waters Per Cluster Histogram)
ConservationSet Conservation Set
ConservedWaters Conserved Crystallographic Waters
ConservedWaters.MDS Conserved Molecular Dynamics Simulation Waters
ConservedWaterStats Conserved Water Statistics
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
getAtomTypeCounts Get AtomType Counts
getProtAtomsNearWater Number of Solvent Accessible/Exposed Protein Atoms Near a Water
getRCSBdata Clean RCSB Dataset
getResidueData Number of Residues and Solvent Accessible/Exposed Residues
getResTypeCounts Get ResType Counts
HasXWaters Has "X" Waters
HydrophilicityEvaluation Hydrophilicity Evaluation
HydrophilicityTable Residue Atom Type Hydrophilicity Values
Mobility Water Molecule Mobility
MobilityBarplot Mobility Barplots
MobilityBarplot.summ Mobility Summary Barplots
MobNormBvalEvalPlots Mobility and Normalized B-values Evaluation Plots
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
nBvalueBarplot Normalized B-value Barplots
Nearby Nearby
NormalizedBvalue B-value Normalization
normBvalueBarplot.summ Normalized B-value Summary Barplots
OccupancyBarplot Occupancy Barplots
OccupancyBarplot.summ Occupancy 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
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
res2xyz Residue Indices to Coordinate Indices
resAtomType2AtomClass Convert Residue-AtomType to AtomType Class
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
thrombin.1hai PDB Structure of Thrombin
thrombin10.PDBs.align Thrombin10 Vignette's Primary Sequence Alignment
TimeSpan Time Span
UniqueAtomHashes Create Unique Atom Hashes
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