R: Get Customizable Annotations From PDB Or PFAM Databases

pdb.annotate {bio3d} | R Documentation

## 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)
    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.
`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(s)

Hongyang Li, Barry Grant, Lars Skjaerven

### 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"))

    ## 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)

[Package bio3d version 2.4-0 Index]