Calculate the number of solvent exposed protein atoms near a water.
getProtAtomsNearWater(h2o.oi, h2o.idc, atoms.oi, h2o.prot.dists, h2o.prot.dists.tf)
The index of the water of interest
The indices of the waters within the protein structure
This function is called within
determine protein atoms near each water oxygen.
This function is designed to work with the
base::lapply() function and
h2o.oi is independently evaluated
This function returns a
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
dist.is.min: ; see
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.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
Emilio Xavier Esposito emilio@exeResearch.com
1 2 3 4 5 6 7 8
## 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)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.