Get Customizable Annotations From PDB Or PFAM Databases
Get customizable annotations for query results from PDB or PFAM.
pdb.annotate(ids, anno.terms = NULL, unique = FALSE, verbose = FALSE,
extra.terms = NULL)
pdb.pfam(ids, best.only = TRUE, compact = TRUE)ids |
A charater vector of one or more 4-letter PDB codes/identifiers of the files for query, or a ‘blast’ object containing ‘pdb.id’. |
anno.terms |
Terms can be used for query. The "anno.terms" can be "structureId", "chainId", "macromoleculeType", "chainLength", "experimentalTechnique", "resolution", "scopDomain", "pfam", "ligandId", "ligandName", "source", "structureTitle", "citation", "rObserved", "rFree", "rWork", and "spaceGroup". If anno.terms=NULL, all information would be returned. |
unique |
logical, if TRUE only unique PDB entries are returned. Alternatively data for each chain ID is provided. |
verbose |
logical, if TRUE more details are printed. |
extra.terms |
Additional annotation terms to retrieve from PDB. Currently not supported. |
best.only |
logical, if TRUE only the lowest eValue match for a given input id will be reported. Otherwise all significant matches will be returned. |
compact |
logical, if TRUE only a subset of annotation terms are returned. Otherwise full match details are reported (see examples). |
Given a list of PDB IDs (and query terms for the pdb.annotate function), these functions will download annotation information from the RCSB PDB and PFAM databases.
Returns a data frame of query results with a row for each PDB record, and annotation terms column-wise.
Hongyang Li, Barry Grant, Lars Skjaerven, Xin-Qiu Yao
# PDB server connection required - testing excluded
# Fetch all annotation terms
ids <- c("6Q21_B", "1NVW", "1P2U_A")
anno <- pdb.annotate(ids)
# Access terms, e.g. ligand names:
anno$ligandName
## only unique PDB IDs
anno <- pdb.annotate(ids, unique=TRUE)
# Fetch only specific terms
pdb.annotate(ids, anno.terms = c("pfam", "ligandId", "citation"))
## Not run:
# PFAM server connection required - testing excluded
# Find PFAM annotations of PDB entries
pdb.pfam(c("6Q21_A", "1NVW", "1P2U_A"))
# More details and a not fond entry warning
pdb.pfam(c("1P2U_A", "6Q21_B"), compact=FALSE)
## End(Not run)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.