Check the Connectivity of Protein Structures

Investigate protein coordinates to determine if the structure has missing residues.

inspect.connectivity(pdbs, cut=4.)

Arguments

pdbs	an object of class 3daling as obtained from function pdbaln or read.fasta.pdb; a xyz matrix containing the cartesian coordinates of C-alpha atoms; or a ‘pdb’ object as obtained from function read.pdb.
cut	cutoff value to determine residue connectvitiy.

Details

Utility function for checking if the PDB structures in a ‘pdbs’ object contains missing residues inside the structure.

Value

Returns a vector.

References

Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696.

Author

Lars Skjaerven

See also

dm, gap.inspect

Examples

if (FALSE) {
## Fetch PDB files and split to chain A only PDB files
ids <- c("1a70_A", "1czp_A", "1frd_A", "1fxi_A", "1iue_A", "1pfd_A")
raw.files <- get.pdb(ids, path = "raw_pdbs")
files <- pdbsplit(raw.files, ids, path = "raw_pdbs/split_chain")

## Sequence Alignement, and connectivity check
pdbs <- pdbaln(files)

cons <- inspect.connectivity(pdbs)

## omit files with missing residues
files = files[cons]
}