Filter or Trim a PDBs Object

Usage

"trim"(pdbs, row.inds=NULL, col.inds=NULL, ...)

Arguments

pdbs

an object of class pdbs as obtained from function pdbaln or read.fasta.pdb; a xyz matrix containing the cartesian coordinates of C-alpha atoms.

row.inds

a numeric vector of indices pointing to the PDB structures to keep (rows in the pdbs$ali matrix).

col.inds

a numeric vector of indices pointing to the alignment columns to keep (columns in the pdbs$ali matrix).

...

additional arguments passed to and from functions.

Examples

## 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")

Warning message:
raw_pdbs/1a70.pdb  exists. Skipping download
Warning message:
raw_pdbs/1czp.pdb  exists. Skipping download
Warning message:
raw_pdbs/1frd.pdb  exists. Skipping download
Warning message:
raw_pdbs/1fxi.pdb  exists. Skipping download
Warning message:
raw_pdbs/1iue.pdb  exists. Skipping download
Warning message:
raw_pdbs/1pfd.pdb  exists. Skipping download
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.pdb 


cons <- inspect.connectivity(pdbs)

## omit files with missing residues
trim.pdbs(pdbs, row.inds=which(cons))

                               1        .         .         .         .         50 
[Truncated_Name:1]1a70_A.pdb   AAYKVTL--VTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCA
[Truncated_Name:2]1czp_A.pdb   ATFKVTLINEAEGTKHEIEVPDDEYILDAAEEQGYDLPFSCRAGACSTCA
[Truncated_Name:3]1frd_A.pdb   ASYQVRLINKKQDIDTTIEIDEETTILDGAEENGIELPFSCHSGSCSSCV
[Truncated_Name:4]1fxi_A.pdb   ASYKVTL--KTPDGDNVITVPDDEYILDVAEEEGLDLPYSCRAGACSTCA
[Truncated_Name:5]1iue_A.pdb   AFYNITL--RTNDGEKKIECNEDEYILDASERQNVELPYSCRGGSCSTCA
[Truncated_Name:6]1pfd_A.pdb   ATYNVKL--ITPDGEVEFKCDDDVYVLDQAEEEGIDIPYSCRAGSCSSCA
                               * ^ ^ *              ^^  ^**  *    ^^*^**^ * **^*  
                               1        .         .         .         .         50 

                              51        .         .         .         .         100 
[Truncated_Name:1]1a70_A.pdb   GKLKTGSLNQDDQSFLDDDQIDEGWVLTCAAYPVSDVTIETHKKEELTA-
[Truncated_Name:2]1czp_A.pdb   GKLVSGTVDQSDQSFLDDDQIEAGYVLTCVAYPTSDVVIQTHKEEDLY--
[Truncated_Name:3]1frd_A.pdb   GKVVEGEVDQSDQIFLDDEQMGKGFALLCVTYPRSNCTIKTHQEPYLA--
[Truncated_Name:4]1fxi_A.pdb   GKLVSGPAPDEDQSFLDDDQIQAGYILTCVAYPTGDCVIETHKEEALY--
[Truncated_Name:5]1iue_A.pdb   AKLVEGEVDNDDQSYLDEEQIKKKYILLCTCYPKSDCVIETHKEDELHDM
[Truncated_Name:6]1pfd_A.pdb   GKVVSGSIDQSDQSFLDDEQMDAGYVLTCHAYPTSDVVIETHKEEEIV--
                               ^*^  *     ** ^**^^*^   ^ * *  **     * **    ^    
                              51        .         .         .         .         100 

Call:
  trim.pdbs(pdbs = pdbs, row.inds = which(cons))

Class:
  pdbs, fasta

Alignment dimensions:
  6 sequence rows; 100 position columns (96 non-gap, 4 gap) 

+ attr: id, xyz, resno, b, chain, ali, resid, sse, call

See also

Author