stride                 package:bio3d                 R Documentation

_S_e_c_o_n_d_a_r_y _S_t_r_u_c_t_u_r_e _A_n_a_l_y_s_i_s _w_i_t_h _S_T_R_I_D_E

_D_e_s_c_r_i_p_t_i_o_n:

     Secondary structure assignment according to the method of Frishman
     and Argos.

_U_s_a_g_e:

     stride(pdb, exepath = "")

_A_r_g_u_m_e_n_t_s:

     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). 

_D_e_t_a_i_l_s:

     This function calls the 'STRIDE' program to define secondary
     structure and psi and phi torsion angles.

_V_a_l_u_e:

     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. 

_N_o_t_e:

     A system call is made to the 'STRIDE' program which must be
     installed on your system and in the search path for executables.

_A_u_t_h_o_r(_s):

     Barry Grant

_R_e_f_e_r_e_n_c_e_s:

     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:
      <URL: http://www.embl-heidelberg.de/stride/stride_info.html>, or
     copy it from an installation of VMD.

_S_e_e _A_l_s_o:

     'read.pdb', 'dssp', 'torsion.pdb', 'torsion.xyz'

_E_x_a_m_p_l_e_s:

     ## 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)

