inspect.connectivity(pdbs, cut=4.)
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. Investigate protein coordinates to determine if the structure has missing residues.
Utility function for checking if the PDB structures in a ‘pdbs’ object contains missing residues inside the structure.
Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696.
## 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")|======================================================================| 100%## Sequence Alignement, and connectivity check pdbs <- pdbaln(files)Reading PDB files: raw_pdbs/split_chain/1a70_A.pdb raw_pdbs/split_chain/1czp_A.pdb raw_pdbs/split_chain/1frd_A.pdb raw_pdbs/split_chain/1fxi_A.pdb raw_pdbs/split_chain/1iue_A.pdb raw_pdbs/split_chain/1pfd_A.pdb . PDB has ALT records, taking A only, rm.alt=TRUE ..... Extracting sequences pdb/seq: 1 name: raw_pdbs/split_chain/1a70_A.pdb pdb/seq: 2 name: raw_pdbs/split_chain/1czp_A.pdb PDB has ALT records, taking A only, rm.alt=TRUE pdb/seq: 3 name: raw_pdbs/split_chain/1frd_A.pdb pdb/seq: 4 name: raw_pdbs/split_chain/1fxi_A.pdb pdb/seq: 5 name: raw_pdbs/split_chain/1iue_A.pdb pdb/seq: 6 name: raw_pdbs/split_chain/1pfd_A.pdbcons <- inspect.connectivity(pdbs) ## omit files with missing residues files = files[cons]