bio3d (version 2.2-4)

inspect.connectivity: Check the Connectivity of Protein Structures

Description

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

Usage

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.

Value

Returns a vector.

Details

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

References

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

See Also

dm, gap.inspect

Examples

## 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)