WSTester updated to work plus hopefully all the other changes that need to go into...

[jabaws.git] / binaries / src / ViennaRNA / H / inverse.h

diff --git a/binaries/src/ViennaRNA/H/inverse.h b/binaries/src/ViennaRNA/H/inverse.h
new file mode 100644 (file)
index 0000000..2f1e000
--- /dev/null
+++ b/binaries/src/ViennaRNA/H/inverse.h
@@ -0,0 +1,67 @@
+#ifndef __VIENNA_RNA_PACKAGE_INVERSE_H__
+#define __VIENNA_RNA_PACKAGE_INVERSE_H__
+
+/**
+ */
+
+/**
+ *  \addtogroup inverse_fold
+ *  We provide two functions that search for sequences with a given
+ *  structure, thereby inverting the folding routines.
+ *  
+ *  @{
+ *    \file inverse.h
+ *    \brief Inverse folding routines
+ */
+
+/**
+ *  \brief This global variable points to the allowed bases, initially "AUGC".
+ *  It can be used to design sequences from reduced alphabets.
+ */
+extern char *symbolset;
+/** when to stop inverse_pf_fold() */
+extern  float final_cost;
+/** default 0: try to minimize structure distance even if no exact solution can be found */
+extern  int   give_up;
+/** print out substructure on which inverse_fold() fails */
+extern  int   inv_verbose;
+
+/**
+ *  \brief Find sequences with predefined structure
+ * 
+ *  This function searches for a sequence with minimum free energy structure
+ *  provided in the parameter 'target', starting with sequence 'start'.
+ *  It returns 0 if the search was successful, otherwise a structure distance
+ *  in terms of the energy difference between the search result and the actual
+ *  target 'target' is returned. The found sequence is returned in 'start'.
+ *  If #give_up is set to 1, the function will return as soon as it is
+ *  clear that the search will be unsuccessful, this speeds up the algorithm
+ *  if you are only interested in exact solutions.
+ * 
+ *  \param  start   The start sequence
+ *  \param  target  The target secondary structure in dot-bracket notation
+ *  \return         The distance to the target in case a search was unsuccessful, 0 otherwise
+ */
+float inverse_fold( char *start,
+                    const char *target);
+
+/**
+ *  \brief Find sequence that maximizes probability of a predefined structure
+ * 
+ *  This function searches for a sequence with maximum probability to fold into
+ *  the provided structure 'target' using the partition function algorithm.
+ *  It returns \f$-kT \cdot \log(p)\f$ where \f$p\f$ is the frequency of 'target' in
+ *  the ensemble of possible structures. This is usually much slower than
+ *  inverse_fold().
+ * 
+ *  \param  start   The start sequence
+ *  \param  target  The target secondary structure in dot-bracket notation
+ *  \return         The distance to the target in case a search was unsuccessful, 0 otherwise
+ */
+float inverse_pf_fold(char *start,
+                      const char *target);
+
+/**
+ *  @}
+ */
+#endif