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)
pdb.pfam(ids, best.only = TRUE, compact = TRUE)

Arguments

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", "experimentalTechnique", "resolution", "chainId", "ligandId", "ligandName", "source", "scopDomain", "classification", "compound","title", "citation", "citationAuthor", "journalName", "publicationYear", "rObserved", "rFree" or "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 details of the RCurl postForm routine is printed.
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).

Details

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.

Value

Returns a data frame of query results with a row for each PDB record, and annotation terms column-wise.

Author

Hongyang Li, Barry Grant, Lars Skjaerven

Examples

# \donttest{
# PDB server connection required - testing excluded

# Fetch all annotation terms
ids <- c("6Q21_B", "1NVW", "1P2U_A")
anno <- pdb.annotate(ids)
#> Warning: ids should be standard 4 character PDB-IDs: trying first 4 characters...

# Access terms, e.g. ligand names:
anno$ligandName
#> NULL

## only unique PDB IDs
anno <- pdb.annotate(ids, unique=TRUE)
#> Warning: ids should be standard 4 character PDB-IDs: trying first 4 characters...

# Fetch only specific terms
pdb.annotate(ids, anno.terms = c("ligandId", "citation"))
#> Warning: ids should be standard 4 character PDB-IDs: trying first 4 characters...
#>          ligandId                        citation
#> 6Q21_B     GCP,MG   Milburn et al. Science (1990)
#> 1NVW_Q GNP,MG,PO4     Margarit et al. Cell (2003)
#> 1NVW_R        PO4     Margarit et al. Cell (2003)
#> 1NVW_S        PO4     Margarit et al. Cell (2003)
#> 1P2U_A GNP,IPA,MG Buhrman et al. Structure (2003)

# }

if (FALSE) {
# 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)
}