Add assigning SSE from file?

[Kyle Stiers]

Hello again,

I was wondering if it would be (or already is somehow I'm not thinking of) possible to add a function that reads a .dssp file into the sse class of a pdb object. Perhaps just simply adding in a new method possibility so if a path to a .dssp is given instead of .exe, it reads in the .dssp file without calling the executable?

Reasoning being for those on a station that has R and can get bio3D but doesn't have admin access to get dssp into the PATH but being able to run it as an .exe and get the .dssp file.

Thanks! Kyle

[Xinqiu Yao]

Hi Kyle,

Sorry for late response. I think it is a good idea and could be useful when local dssp executable is unavailable. We will add it to ToDo and thanks for your proposal!

[Xinqiu Yao]

This request has been resolved with the latest commit here. The new function read.dssp() is to read existing DSSP output file. For example

sse <- read.dssp('1tag.dssp')
sse
Call:
  read.dssp(file = "1tag.dssp")

Class:
  sse

Helices:  17 
        42-53 (A)      59-86 (A)     96-109 (A)    117-128 (A)    130-136 (A)
      148-152 (A)    155-158 (A)    167-172 (A)    238-250 (A)    267-273 (A)
      292-304 (A)    325-339 (A)    139-142 (A)    201-208 (A)    223-227 (A)
      253-255 (A)    279-281 (A)

Sheets:   6 
        28-35 (A)    182-187 (A)    190-197 (A)    216-222 (A)    259-265 (A)
      316-319 (A)

Turns:   21 
        38-39 (A)      87-88 (A)      94-95 (A)    112-113 (A)    137-138 (A)
      143-143 (A)    146-147 (A)    153-154 (A)    159-159 (A)    161-162 (A)
      188-189 (A)    209-213 (A)    234-235 (A)    251-251 (A)    256-257 (A)
      274-276 (A)    282-282 (A)    284-285 (A)    305-306 (A)    308-312 (A)
      322-323 (A)

Output is provided in residue numbers

[Barry Grant]

I see that this is now available as 'new_funs/read.dssp.R' and should be downloaded and sourced by the user if required.

Note however that any user that can run dssp outside of bio3d should be able to run it within bio3d by following the instructions here (in the "additional utilities" section): http://thegrantlab.org/bio3d/tutorials/installing-bio3d and detailed further in the responses to this previous question: https://bitbucket.org/Grantlab/bio3d/issue/145/where-should-be-muscle-or-dssp-placed