ptm (version 0.2.2)

mkdssp: Compute DSSP File Using an In-House Version of the DSSP Software

Description

Computes the DSSP file using an in-house version of the DSSP software.

Usage

mkdssp(pdb, method = 'ptm', exefile = "dssp")

Arguments

pdb

is either a 4-character identifier of the PDB structure, or the path to a pdb file.

method

a character string specifying the desired method to get the dssp dataframe; it should be one of 'ptm' or 'bio3d'.

exefile

file path to the DSSP executable on your system (i.e. how is DSSP invoked).

Value

Returns either a dataframe containing the information extracted from the dssp file (method ptm), or a list with that information (method bio3d).

Details

The structure of the output data depends on the method chosen, but it will always contain the DSSP-related data.

References

Touw et al (2015) Nucl. Ac. Res. 43(Database issue): D364-D368 (PMID: 25352545).

See Also

download.dssp(), parse.dssp(), compute.dssp() and acc.dssp()

Examples

# NOT RUN {
mkdssp('3cwm', method = 'ptm')
# }