stride {bio3d} | R Documentation |
Secondary structure assignment according to the method of Frishman and Argos.
stride(pdb, exepath = "")
pdb |
a structure object of class '"pdb"', obtained from
read.pdb . |
exepath |
path to the ‘STRIDE’ program on your system (i.e. the directory where ‘STRIDE’ is stored). |
This function calls the ‘STRIDE’ program to define secondary structure and psi and phi torsion angles.
Returns a list with the following components:
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”. |
turn |
‘start’, ‘end’ and ‘length’ of T type sse, where start and end are residue numbers “resno”. |
phi |
a numeric vector of phi angles. |
psi |
a numeric vector of psi angles. |
A system call is made to the ‘STRIDE’ program which must be installed on your system and in the search path for executables.
Barry Grant
Grant, B.J. et al. (2006) Bioinformatics 22, 2695–2696.
‘STRIDE’ is the work of Frishman and Argos: Frishman and Argos (1995) Proteins. 3, 566–579.
For information on obtaining the ‘STRIDE’ program, see:
http://www.embl-heidelberg.de/stride/stride_info.html,
or copy it from an installation of VMD.
read.pdb
, dssp
,
torsion.pdb
, torsion.xyz
## Not run: # Read a PDB file pdb <- read.pdb(system.file("examples/d1bg2__.ent", package="bio3d")) sse <- stride(pdb) # Helix data sse$helix # Precent SSE content sum(sse$helix$length)/sum(pdb$calpha) * 100 sum(sse$sheet$length)/sum(pdb$calpha) * 100 ## End(Not run)