Check the Connectivity of Protein Structures
Investigate protein coordinates to determine if the structure has missing residues.
inspect.connectivity(pdbs, cut=4.)
pdbs |
an object of class |
cut |
cutoff value to determine residue connectvitiy. |
Utility function for checking if the PDB structures in a ‘pdbs’ object contains missing residues inside the structure.
Returns a vector.
Lars Skjaerven
Grant, B.J. et al. (2006) Bioinformatics 22, 2695–2696.
## Not run:
## 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]
## End(Not run)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.