Description Usage Arguments Value Examples
Map all known PDB residues' coordinates to an Pfam STH file.
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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. |
A map of all known PDB residues to the msa file by PDB chain. TODO: add description
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | #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)
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