bio3d (version 2.2-4)

pdb.annotate: Get Customizable Annotations From PDB

Description

Get customizable annotations for query results from PDB.

Usage

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

Arguments

ids

A charater vector of one or more 4-letter PDB codes/identifiers of the files for query.

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". 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.

Value

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

Details

Given a list of PDB IDs and query terms, this function will download the required information from PDB, and return a data frame of query results.

Examples

# 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("ligandId", "citation"))