getProtAtomsNearWater: Number of Solvent Accessible/Exposed Protein Atoms Near a...

In vanddraabe: Identification and Statistical Analysis of Conserved Waters Near Proteins

Description

Calculate the number of solvent exposed protein atoms near a water.

Usage

getProtAtomsNearWater(h2o.oi, h2o.idc, atoms.oi, h2o.prot.dists,
  h2o.prot.dists.tf)

Arguments

h2o.oi	The index of the water of interest
h2o.idc	The indices of the waters within the protein structure
atoms.oi	The protein data.frame with the SASA and SASA lost values for each atom within the protein.
h2o.prot.dists	Distance matrix for all water-protein through space distances
h2o.prot.dists.tf	The TRUE/FALSE matrix indicating if the protein- water distances are less than or equal to the user defined cutoff value denoted by the h2o.prot.dist.max parameter for HydrophilicityEvaluation(). From HydrophilicityEvaluation(): the maximum distance between the water oxygen atoms and the protein for consideration in the determination for hydrophilicity values; default: 6.0

Details

This function is called within HydrophilicityEvaluation() to determine protein atoms near each water oxygen.

This function is designed to work with the base::lapply() function and thus each h2o.oi is independently evaluated

Value

This function returns a data.frame with:

• nearby.prot.atoms: protein atoms within the user specified distance of a water's oxygen atom

• distances: The distance – in Angstroms – from the water to the closest solvent accessible protein atom so long as the distance is equal to or less than the user provided value; see h2o.prot.dists.tf above

• dist.is.min: ; see h2o.prot.dists.tf above

• SASA.and.minDist: TRUE/FALSE indicating if the protein atom is BOTH solvent accessible and at least the user defined number of Angstroms from a water's oxygen atom; see h2o.prot.dists.tf above

• h2o.atom.ids: Unique water atom ID

• h2o.x: Atom coordinate X for the water's oxygen atom

• h2o.y: Atom coordinate Y for the water's oxygen atom

• h2o.z: Atom coordinate Z for the water's oxygen atom

These values are returned in df.nearby.prot.atoms of the results of HydrophilicityEvaluation()

Author(s)

Emilio Xavier Esposito [e-mail]

See Also

Other "Hydrophilicity Evaluation" "Bound Water Environment": HydrophilicityEvaluation, calcAtomClassHydrophilicity, calcAtomHydrationEstimate, getResidueData

Examples

  ## Not run: 
  getProtAtomsNearWater(h2o.oi = PDB.1hai.h2o.oi,
                        h2o.idc = PDB.1hai.clean.h2o.idc,
                        atoms.oi = PDB.1hai.aoi.clean.SASA,
                        h2o.prot.dists = PDB.1hai.h2o.prot.dists,
                        h2o.prot.dists.tf = PDB.1hai.h2o.prot.dists.tf)
  
## End(Not run)

vanddraabe documentation built on June 8, 2019, 1:03 a.m.