Man pages for vanddraabe
Identification and Statistical Analysis of Conserved Waters Near 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 |
| FreeSASAcheck | FreeSASA Check |
| FreeSASA.diff | Atomic SASA difference of hydrated PDB via FreeSASA |
| getAtomTypeCounts | Get AtomType Counts |
| getProtAtomsNearWater | Number of Solvent Accessible/Exposed Protein Atoms Near a... |
| 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 |
| thrombin10.PDBs.align | Thrombin10 Vignette's Primary Sequence Alignment |
| thrombin.1hai | PDB Structure of Thrombin |
| TimeSpan | Time Span |
| UniqueAtomHashes | Create Unique Atom Hashes |
| vanddraabe | vanddraabe: Identification and Statistical Analysis of... |
| write.basic.pdb | Write Basic PDB File |
| write.conservedWaters.pdb | Write Conserved Waters to PDB File |
