Pfam single and multiple sequences mapping

Description Usage Arguments Value Examples

View source: R/PFAM2PDB.R

Download and annotate the PDB files associated with the PFAM domain sequences in the sth file

choose_PDBs_for_a_pfamid(
  pfamid = "PF00075",
  pfamSthFile = NA,
  max2take = 12,
  resolution.th = 3,
  experimentalTech = "X-RAY DIFFRACTION",
  pfamseqResource = "rp75",
  pdb.local.db,
  sth.local.db
)

`pfamid`	A Pfam id string.
`pfamSthFile`	A pfam sth file for pfamid.
`max2take`	The maximal number of PDB files to download with the given resolution (default = 3.0).
`resolution.th`	Minimal resoultion required for a solved structure to be considered.
`experimentalTech`	Experimental method required for the structre (default is X-RAY).
`pfamseqResource`	A sequence redundancy level as inidcated in Pfam - relevant when downloading the sth file.
`pdb.local.db`	A directory path to a local pdb database or temporary directory to save downloaded sth files. Can be used to accomulate files and avoid repeated downloads.
`sth.local.db`	A directory path to a local pfam database or temporary directory to save downloaded sth files. Can be used to accomulate files and avoid repeated downloads.

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

#In this example we download all relevant relevant PDB files pfam domain PF00075.
#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.
tmp <- choose_PDBs_for_a_pfamid(pfamid = "PF00075", pfamSthFile = "/tmp/PF00075_rp75.sth",
                                pdb.local.db = "/tmp/", sth.local.db = "/tmp/", max2take = 3)