PDBs2Pfam: Map all known PDB residues' coordinates to an Pfam STH file.

In etaijacob/MAPDB: PDB/Uniprot/Pfam single and multiple sequences mapping

Description

Map all known PDB residues' coordinates to an Pfam STH file.

Usage

PDBs2Pfam(
  pfamid,
  pfamSthFile = NA,
  max2take = 12,
  resolution.th = 3,
  sth.local.db = "/tmp/",
  pdb.local.db = "/tmp/",
  pfamseqResource = "rp75"
)

Arguments

pfamid	A Pfam id string
pfamSthFile	A pfam sth file for pfamid - if not given will be downloaded to sth.local.db.
max2take	maximal number of pdb entries to associate with the sth sequences with the given resolution threshold.
resolution.th	minimal resolution to include in analysis
sth.local.db	A path to a local pfam database or temporary directory to save downloaded sth files.
pdb.local.db	A path to a local pdb database or temporary directory to save downloaded pdb files.
pfamseqResource	A sequence redundancy level as inidcated in Pfam - relevant when downloading the sth file.

Value

A map of all known PDB residues to the msa file by PDB chain. TODO: add description

Examples

#In this example we download all relevant files for PF00075,
#including PDB files and sth alignment for the pfam domain.
#We limit the download to a total of 12 pdb instances with a resolution below 3.0 Ang.
#If any of the pdb files was already downloaded and located in the pdb.local.db,
#then it will be used to avoid
#unnecessary download.
myPfamMap <- PDBs2Pfam(pfamid = "PF00075", sth.local.db = "/tmp/",
                       max2take = 2, resolution.th = 3.0)

#In this example we have already downloaded the sth file
#therefore including it in the call for the function in order
#to avoid unnecessary download

myPfamMap <- PDBs2Pfam(pfamid = "PF00075", pfamSthFile = "/tmp/PF00075_rp75.sth",
                       sth.local.db = "/tmp/", max2take = 2, resolution.th = 3.0)

etaijacob/MAPDB documentation built on Dec. 10, 2019, 1:01 p.m.