get_remarks465_pdb: Get "REMARK 465" data from PDB file

Description Usage Arguments Value Author(s) See Also Examples

Description

This function extracts the data concerning missing amino acids in PDB protein structure from the PDB file

Usage

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get_remarks465_pdb(pdb_path, chain_identifier)

Arguments

pdb_path

A string specifying the path tp the PDB file

chain_identifier

A character specifying the chain to be considered

Value

aa_numbers

A numeric vector of indices of missing amino acids

chain

A character specifying the chain which was considered in remark 465 data extraction

Author(s)

Michal Stolarczyk & Alicja Pluciennik

See Also

read.pdb

Examples

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require(Rpdb)
chain_identifier = "A"
pdb_path = system.file("extdata", "4jnc.pdb", package = "BALCONY")
print(pdb_path)
#pdb_file_path = "path_to_file"
remark465_data = get_remarks465_pdb(pdb_path,chain_identifier)

Example output

Loading required package: seqinr
Loading required package: Rpdb
Loading required package: rgl

Attaching package: 'Rpdb'

The following objects are masked from 'package:base':

    norm, replicate, unsplit

Loading required package: scales

Attaching package: 'BALCONY'

The following object is masked from 'package:seqinr':

    consensus

Warning messages:
1: In rgl.init(initValue, onlyNULL) : RGL: unable to open X11 display
2: 'rgl_init' failed, running with rgl.useNULL = TRUE 
3: .onUnload failed in unloadNamespace() for 'rgl', details:
  call: fun(...)
  error: object 'rgl_quit' not found 
[1] "/usr/local/lib/R/site-library/BALCONY/extdata/4jnc.pdb"

BALCONY documentation built on May 1, 2019, 10:31 p.m.