JWS-112 Bumping version of T-Coffee to version 11.00.8cbe486.

[jabaws.git] / binaries / src / tcoffee / t_coffee_source / dp_lib / evaluate_for_struc.h

diff --git a/binaries/src/tcoffee/t_coffee_source/dp_lib/evaluate_for_struc.h b/binaries/src/tcoffee/t_coffee_source/dp_lib/evaluate_for_struc.h
new file mode 100644 (file)
index 0000000..14e76b8
--- /dev/null
+++ b/binaries/src/tcoffee/t_coffee_source/dp_lib/evaluate_for_struc.h
@@ -0,0 +1,75 @@
+/******************************COPYRIGHT NOTICE*******************************/
+/*  (c) Centro de Regulacio Genomica                                                        */
+/*  and                                                                                     */
+/*  Cedric Notredame                                                                        */
+/*  12 Aug 2014 - 22:07.                                                                    */
+/*All rights reserved.                                                                      */
+/*This file is part of T-COFFEE.                                                            */
+/*                                                                                          */
+/*    T-COFFEE is free software; you can redistribute it and/or modify                      */
+/*    it under the terms of the GNU General Public License as published by                  */
+/*    the Free Software Foundation; either version 2 of the License, or                     */
+/*    (at your option) any later version.                                                   */
+/*                                                                                          */
+/*    T-COFFEE is distributed in the hope that it will be useful,                           */
+/*    but WITHOUT ANY WARRANTY; without even the implied warranty of                        */
+/*    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the                         */
+/*    GNU General Public License for more details.                                          */
+/*                                                                                          */
+/*    You should have received a copy of the GNU General Public License                     */
+/*    along with Foobar; if not, write to the Free Software                                 */
+/*    Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA             */
+/*...............................................                                           */
+/*  If you need some more information                                                       */
+/*  cedric.notredame@europe.com                                                             */
+/*...............................................                                           */
+/******************************COPYRIGHT NOTICE*******************************/
+char * pdb2lib (Sequence *S, char *mode,float max, char *name);
+
+int apdb (int argc, char *argv[]);
+
+Constraint_list * set_constraint_list4align_pdb (Constraint_list *inCL,int seq, char *dp_mode, char *hasch_mode, char *param_file);
+int evaluate_ca_trace_sap2_bubble (Constraint_list *CL, int s1, int r1, int s2, int r2);
+int evaluate_ca_trace_nb (Constraint_list *CL, int s1, int s2, int r1, int r2);
+int evaluate_ca_trace_bubble (Constraint_list *CL, int s1, int s2, int r1, int r2);
+int evaluate_ca_trace_sap1_bubble (Constraint_list *CL, int s1, int s2, int r1, int r2);
+int evaluate_ca_trace_3D_bubble (Constraint_list *CL, int s1, int s2, int r1, int r2);
+int evaluate_ca_trace_transversal (Constraint_list *CL, int s1, int s2, int r1, int r2);
+int evaluate_ca_trace_bubble_2 (Constraint_list *CL, int s1, int s2, int r1, int r2);
+int evaluate_ca_trace_bubble_3 (Constraint_list *CL, int s1, int s2, int r1, int r2);
+
+
+/*********************************************************************************************/
+/*                                                                                           */
+/*         FUNCTIONS FOR COMPARING TWO NEIGHBORHOODS:START                                   */
+/*                                                                                           */
+/*********************************************************************************************/
+float matrix_match (Constraint_list *CL, int s1, int s2, int r1, int r2, Struct_nb *nbs1, Struct_nb *nbs2);
+float transversal_match (Constraint_list *CL, int s1, int s2, int r1, int r2, Struct_nb *nbs1, Struct_nb *nbs2);
+float neighborhood_match (Constraint_list *CL, int s1, int s2, int r1, int r2,Struct_nb *nbs1, Struct_nb *nbs2);
+float sap1_neighborhood_match (Constraint_list *CL, int s1, int s2, int r1, int r2, Struct_nb *nbs1, Struct_nb *nbs2);
+float sap2_neighborhood_match (Constraint_list *CL, int s1, int s2, int r1, int r2, Struct_nb *nbs1, Struct_nb *nbs2);
+
+
+/*********************************************************************************************/
+/*                                                                                           */
+/*         FUNCTIONS FOR COMPARING TWO NEIGHBORHOODS:END                                     */
+/*                                                                                           */
+/*********************************************************************************************/
+Alignment * analyse_pdb ( Alignment *A, Alignment *ST, char *filename);
+Alignment * msa2struc_dist ( Alignment *A, Alignment *ST, char *filename, int gapped, int min_ncol);
+float **** analyse_pdb_residues ( Alignment *A, Constraint_list *CL, Pdb_param *pdb_param);
+
+float square_atom ( Atom *X);
+Atom* reframe_atom ( Atom *X, Atom*Y, Atom *Z, Atom *IN, Atom *R);
+Atom* add_atom ( Atom *A, Atom*B, Atom *R);
+Atom* diff_atom ( Atom *A, Atom*B, Atom *R);
+Atom * copy_atom ( Atom *A, Atom*R);
+/************************************************************************/
+/*                                                                      */
+/*                            NUSSINOV                                  */
+/*                                                                      */
+/************************************************************************/
+char *nussinov (char *S, int min_dist);
+char * rna_struc2rna_lib ( char *seq_name, char *seq, char *name);
+int display_rna_ss ( int pos, char *seq, char *struc, FILE *fp);