write.conservedWaters.pdb: Write Conserved Waters to PDB File

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

Description

Writes conserved water information to a PDB file.

Usage

write.conservedWaters.pdb(file, h2o.clusters.summary)

Arguments

file	Filename with ".pdb" extension.
h2o.clusters.summary	The conserved water clusters summary.

Details

Using the bio3d::write.pdb() function this function writes a PDB file for the conserved water oxygen atoms with the percentage of structures with a water participting in the cluster (written to the occupancy column) and the calculated B-value – using the rmsf of the waters in the cluster – for the waters participating in the cluster (written to the B-value column). This function is called from the ConservedWaters() function.

All water molecules will include the water's oxygen atom (elety), be assigned the residue name (resid) HOH, and the chain (chain) A while the atom number (eleno) and residue number (resno) both start at 1.

NOTE: This is a non-public function.

Value

Writes a PDB file with the X, Y, and Z coordinates, percent conserved within the analyzed structures, and the calculated B-value for the oxygen atoms of the clustered waters.

Author(s)

Emilio Xavier Esposito [e-mail]

See Also

Other utilities: ConservationSet, DetermineChainsOfInterest, ExtractFileTimeStamp, ExtractPDBids, FileTimeStamp, HasXWaters, Nearby, ProtHetWatIndices, RescaleValues, RetainChainsOfInterest, ReturnPDBfullPath, StandardizeAsparticAcidNames, StandardizeCysteineNames, StandardizeGlutamicAcidNames, StandardizeHistidineNames, StandardizeLysineNames, TimeSpan, UniqueAtomHashes, aaStandardizeNames, getAtomTypeCounts, getResTypeCounts, res2xyz, resAtomType2AtomClass, write.basic.pdb

Examples

  ## Not run: 
    write.conservedWaters.pdb(file = "system_conservedWaters.pdb",
                              h2o.clusters.summary)
  
## End(Not run)

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