binaries/src/tcoffee/t_coffee_source/dp_lib/evaluate_for_struc.h

   1 /******************************COPYRIGHT NOTICE*******************************/
   2 /*  (c) Centro de Regulacio Genomica                                                        */
   3 /*  and                                                                                     */
   4 /*  Cedric Notredame                                                                        */
   5 /*  12 Aug 2014 - 22:07.                                                                    */
   6 /*All rights reserved.                                                                      */
   7 /*This file is part of T-COFFEE.                                                            */
   8 /*                                                                                          */
   9 /*    T-COFFEE is free software; you can redistribute it and/or modify                      */
  10 /*    it under the terms of the GNU General Public License as published by                  */
  11 /*    the Free Software Foundation; either version 2 of the License, or                     */
  12 /*    (at your option) any later version.                                                   */
  13 /*                                                                                          */
  14 /*    T-COFFEE is distributed in the hope that it will be useful,                           */
  15 /*    but WITHOUT ANY WARRANTY; without even the implied warranty of                        */
  16 /*    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the                         */
  17 /*    GNU General Public License for more details.                                          */
  18 /*                                                                                          */
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  20 /*    along with Foobar; if not, write to the Free Software                                 */
  21 /*    Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA             */
  22 /*...............................................                                           */
  23 /*  If you need some more information                                                       */
  24 /*  cedric.notredame@europe.com                                                             */
  25 /*...............................................                                           */
  26 /******************************COPYRIGHT NOTICE*******************************/
  27 char * pdb2lib (Sequence *S, char *mode,float max, char *name);
  28
  29 int apdb (int argc, char *argv[]);
  30
  31 Constraint_list * set_constraint_list4align_pdb (Constraint_list *inCL,int seq, char *dp_mode, char *hasch_mode, char *param_file);
  32 int evaluate_ca_trace_sap2_bubble (Constraint_list *CL, int s1, int r1, int s2, int r2);
  33 int evaluate_ca_trace_nb (Constraint_list *CL, int s1, int s2, int r1, int r2);
  34 int evaluate_ca_trace_bubble (Constraint_list *CL, int s1, int s2, int r1, int r2);
  35 int evaluate_ca_trace_sap1_bubble (Constraint_list *CL, int s1, int s2, int r1, int r2);
  36 int evaluate_ca_trace_3D_bubble (Constraint_list *CL, int s1, int s2, int r1, int r2);
  37 int evaluate_ca_trace_transversal (Constraint_list *CL, int s1, int s2, int r1, int r2);
  38 int evaluate_ca_trace_bubble_2 (Constraint_list *CL, int s1, int s2, int r1, int r2);
  39 int evaluate_ca_trace_bubble_3 (Constraint_list *CL, int s1, int s2, int r1, int r2);
  40
  41
  42 /*********************************************************************************************/
  43 /*                                                                                           */
  44 /*         FUNCTIONS FOR COMPARING TWO NEIGHBORHOODS:START                                   */
  45 /*                                                                                           */
  46 /*********************************************************************************************/
  47 float matrix_match (Constraint_list *CL, int s1, int s2, int r1, int r2, Struct_nb *nbs1, Struct_nb *nbs2);
  48 float transversal_match (Constraint_list *CL, int s1, int s2, int r1, int r2, Struct_nb *nbs1, Struct_nb *nbs2);
  49 float neighborhood_match (Constraint_list *CL, int s1, int s2, int r1, int r2,Struct_nb *nbs1, Struct_nb *nbs2);
  50 float sap1_neighborhood_match (Constraint_list *CL, int s1, int s2, int r1, int r2, Struct_nb *nbs1, Struct_nb *nbs2);
  51 float sap2_neighborhood_match (Constraint_list *CL, int s1, int s2, int r1, int r2, Struct_nb *nbs1, Struct_nb *nbs2);
  52
  53
  54 /*********************************************************************************************/
  55 /*                                                                                           */
  56 /*         FUNCTIONS FOR COMPARING TWO NEIGHBORHOODS:END                                     */
  57 /*                                                                                           */
  58 /*********************************************************************************************/
  59 Alignment * analyse_pdb ( Alignment *A, Alignment *ST, char *filename);
  60 Alignment * msa2struc_dist ( Alignment *A, Alignment *ST, char *filename, int gapped, int min_ncol);
  61 float **** analyse_pdb_residues ( Alignment *A, Constraint_list *CL, Pdb_param *pdb_param);
  62
  63 float square_atom ( Atom *X);
  64 Atom* reframe_atom ( Atom *X, Atom*Y, Atom *Z, Atom *IN, Atom *R);
  65 Atom* add_atom ( Atom *A, Atom*B, Atom *R);
  66 Atom* diff_atom ( Atom *A, Atom*B, Atom *R);
  67 Atom * copy_atom ( Atom *A, Atom*R);
  68 /************************************************************************/
  69 /*                                                                      */
  70 /*                            NUSSINOV                                  */
  71 /*                                                                      */
  72 /************************************************************************/
  73 char *nussinov (char *S, int min_dist);
  74 char * rna_struc2rna_lib ( char *seq_name, char *seq, char *name);
  75 int display_rna_ss ( int pos, char *seq, char *struc, FILE *fp);