R: Read PQR output from pdcBD File

read.pdcBD {bio3d} | R Documentation

## Read PQR output from pdcBD File

### Description

Read a pdcBD PQR coordinate file.

### Usage

    read.pdcBD(file, maxlines = 50000, multi = FALSE, rm.insert = FALSE,
             rm.alt = TRUE, verbose = TRUE)

### Arguments

`file` | the name of the pdcBD PQR file to be read.
`maxlines` | the maximum number of lines to read before giving up with large files. Default is 50,000 lines.
`multi` | logical, if TRUE multiple ATOM records are read for all models in multi-model files.
`rm.insert` | logical, if TRUE PDB insert records are ignored.
`rm.alt` | logical, if TRUE PDB alternate records are ignored.
`verbose` | print details of the reading process.

### Details

`maxlines` may require increasing for some large multi-model files. The preferred means of reading such data is via binary DCD format trajectory files (see the `read.dcd` function).

### Value

Returns a list of class `"pdb"` with the following components:

`atom` | a character matrix containing all atomic coordinate ATOM data, with a row per ATOM and a column per record type. See below for details of the record type naming convention (useful for accessing columns).
`het` | a character matrix containing atomic coordinate records for atoms within “non-standard” HET groups (see `atom`).
`helix` | ‘start’, ‘end’ and ‘length’ of H type sse, where start and end are residue numbers “resno”.
`sheet` | ‘start’, ‘end’ and ‘length’ of E type sse, where start and end are residue numbers “resno”.
`seqres` | sequence from SEQRES field.
`xyz` | a numeric vector of ATOM coordinate data.
`calpha` | logical vector with length equal to `nrow(atom)` with TRUE values indicating a C-alpha “elety”.

### Note

For both `atom` and `het` list components the column names can be used as a convenient means of data access, namely: Atom serial number “eleno” , Atom type “elety”, Alternate location indicator “alt”, Residue name “resid”, Chain identifier “chain”, Residue sequence number “resno”, Code for insertion of residues “insert”, Orthogonal coordinates “x”, Orthogonal coordinates “y”, Orthogonal coordinates “z”, Occupancy “o”, and Temperature factor “b”. See examples for further details.

### Author(s)

Barry Grant

### References

Grant, B.J. et al. (2006) Bioinformatics 22, 2695–2696.

For a description of PDB format (version3.3) see:
http://www.wwpdb.org/documentation/format33/v3.3.html.

### See Also

`atom.select`, `write.pdb`, `read.dcd`, `read.fasta.pdb`, `read.fasta`

### Examples

    # PDB server connection required - testing excluded

    # Read a PDB file
    pdb <- read.pdb( "1bg2" )

    # Print data for the first atom
    pdb$atom[1,]
    # Look at the first het atom
    pdb$het[1,]
    # Print some coordinate data
    pdb$atom[1:20, c("x","y","z")]

    # Print C-alpha coordinates (can also use 'atom.select')
    ##pdb$xyz[pdb$calpha, c("resid","x","y","z")]

    # Print SSE data (for helix and sheet)
    pdb$helix
    pdb$sheet$start

    # Print SEQRES data
    pdb$seqres

    # Renumber residues
    nums <- as.numeric(pdb$atom[,"resno"])
    pdb$atom[,"resno"] <- nums - (nums[1] - 1)

    # Write out renumbered PDB file
    #write.pdb(pdb=pdb,file="eg.pdb")

[Package bio3d version 2.3-3 Index]