Removes hydrogen and modeled atoms from a RCSB/PDB structure along with waters beyond a user defined distance from protein atoms.
CleanProteinStructures(prefix = "./alignTesting",
CleanHydrogenAtoms = TRUE, CleanModeledAtoms = TRUE,
cutoff.prot.h2o.dist = 6, min.num.h2o = 20,
cleanDir = "ProteinSystem", filename = "ProteinSystem")The directory with the PDB files to be cleaned
A logical indication if hydrogen atoms should be
removed; default: TRUE
A logical indication if modeled atoms should be
removed; default: TRUE
A numerical value setting the maximum distance
between a protein atom (heteroatoms are ignored) and water oxygen atoms.
The oxygen atoms equal to or less than this distance are retained;
default: 6.0 Angstroms
Minimum number of water oxygen atoms within a protein structure for it to be included in the conserved water analysis; default: 20
A character string for the "cleaned" PDB structures to be
written. The provided character string are appended with "_CLEANED";
default: "ProteinSystem"
The filename prefix for the returned results. Default is "ProteinSystem"
The following data is returned:
cleaning.summary: summary indicating
if hydrogen atoms were removed TRUE/FALSE
number of out of range atoms for B-values and occupancy values
number of modeled (and thus removed)
number of atoms NOT modeled (and thus retained)
number of water oxygen atoms beyond the user defined cutoff
the number of water oxygen atoms within the user defined cutoff.
Bvalue.counts: binned B-value values with binwidths = 5 (0 to 100)
normBvalue.counts: binned normalized B-value values with binwidths = 0.1 (-4 to 6)
occupancy.counts: binned occupancy values with binwidths = 0.1 (0 to 1)
mobility.counts: binned mobility values with binwidths = 0.1 (0 to 6)
Excel workbook: containing the cleaning.summary, Bvalue.counts, normBvalue.counts, occupancy.counts, and mobility.counts data as individual tabs
PDBids.retained: a vector of PDBids
call: parameters provided by the user
PDB files obtained from the PDB conform to a specific set of formatting standards but this does not mean the data within the PDB files is always correct. This function cleans the PDB file and summaries the atom evaluations.
This function does the following (in this order):
Reads in the PDB file
Adds/updates the element symbol (elesy) using the atom type (elety)
via the bio3d::atom2ele() function
Removes hydrogen atoms via RemoveHydrogenAtoms() (user option)
Removes atoms with occupancy values determined to be out of range (OoR)
via RemoveOoR.o()
Removes atoms with B-values determined to be out of range (OoR)
via RemoveOoR.b()
Bins (counts) the occupancy values
Bins (counts) the B-values
Bins (counts) the normalized B-values
Bins (counts) the mobility values
Removes modeled atoms via RemoveModeledAtoms() (user option)
Removes water oxygen atoms greater than user defined value
cutoff.prot.h2o.dist from the protein via RetainWatersWithinX()
(user option)
Writes cleaned protein structure to a PDB file
Other "Clean Protein Structure": RemoveHydrogenAtoms,
RemoveModeledAtoms,
RemoveOoR.b, RemoveOoR.o,
RetainWatersWithinX