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

In ptm: Analyses of Protein Post-Translational Modifications

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).

Details

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

Value

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

Author(s)

Juan Carlos Aledo

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')

ptm documentation built on Aug. 7, 2022, 5:05 p.m.