pdb.annotate: Get Customizable Annotations From PDB Or PFAM Databases

In bio3d: Biological Structure Analysis

Get Customizable Annotations From PDB Or PFAM Databases

Description

Get customizable annotations for query results from PDB or PFAM.

Usage

pdb.annotate(ids, anno.terms = NULL, unique = FALSE, verbose = FALSE,
             extra.terms = NULL)
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", "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).

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(s)

Hongyang Li, Barry Grant, Lars Skjaerven, Xin-Qiu Yao

Examples

# PDB server connection required - testing excluded
try({

# 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"))

}, silent=TRUE)
if(inherits(.Last.value, "try-error")) {
   message("Need internet to run the example")
}


## 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)

bio3d documentation built on Oct. 30, 2024, 1:08 a.m.