R: Renumber and Convert Between Various PDB formats

convert.pdb {bio3d} | R Documentation

## Renumber and Convert Between Various PDB formats

### Description

Renumber and convert between CHARMM, Amber, Gromacs and Brookhaven PDB formats.

### Usage

    convert.pdb(pdb, type=c("original", "pdb", "charmm", "amber", "gromacs"),
                    renumber = FALSE, first.resno = 1, first.eleno = 1,
                    consecutive=TRUE, rm.h = TRUE, rm.wat = FALSE,
                    verbose=TRUE)

### Arguments

`pdb` | a structure object of class `"pdb"`, obtained from `read.pdb`.
`type` | output format, one of ‘original’, ‘pdb’, ‘charmm’, ‘amber’, or ‘gromacs’. The default option of ‘original’ results in no conversion.
`renumber` | logical, if TRUE atom and residue records are renumbered using ‘first.resno’ and ‘first.eleno’.
`first.resno` | first residue number to be used if ‘renumber’ is TRUE.
`first.eleno` | first element number to be used if ‘renumber’ is TRUE.
`consecutive` | logical, if TRUE renumbering will result in consecutive residue numbers spanning all chains. Otherwise new residue numbers will begin at ‘first.resno’ for each chain.
`rm.h` | logical, if TRUE hydrogen atoms are removed.
`rm.wat` | logical, if TRUE water atoms are removed.
`verbose` | logical, if TRUE details of the conversion process are printed.

### Details

Convert atom names and residue names, renumber atom and residue records, strip water and hydrogen atoms from `pdb` objects.

Format `type` can be one of “ori”, “pdb”, “charmm”, “amber” or “gromacs”.

### 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

    ## Not run:

    # Read a PDB file
    pdb <- read.pdb("4q21")
    pdb
    head( pdb$atom[pdb$calpha,"resno"] )

    # Convert to CHARMM format
    new <- convert.pdb(pdb, type="amber", renumber=TRUE, first.resno=22 )
    head( new$atom[new$calpha,"resno"] )

    # Write a PDB file
    #write.pdb(new, file="tmp4amber.pdb")

    ## End(Not run)

[Package bio3d version 2.4-2 Index]