pdb.annotate {bio3d} | R Documentation |
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)
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 |
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
# 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)