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Searched refs:loop_degree (Results 1 – 18 of 18) sorted by relevance

/dports/biology/viennarna/ViennaRNA-2.4.18/src/ViennaRNA/
H A DRNAstruct.c166 loop_degree[0] = 0; /* open structure has degree 0 */ in b2C()
185 loop_degree[++loops] = 1; in b2C()
199 switch (loop_degree[loop[lp]]) { in b2C()
216 loop_degree[loop[--lp]]++; in b2C()
250 loop_degree[0] = 0; /* open structure has degree 0 */ in b2Shapiro()
271 loop_degree[++loops] = 1; in b2Shapiro()
285 switch (loop_degree[loop[lp]]) { in b2Shapiro()
310 loop_degree[loop[--lp]]++; in b2Shapiro()
370 loop[0] = loop_degree[0] = 0; /* open structure has degree 0 */ in parse_structure()
388 loop_degree[++loops] = 1; in parse_structure()
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H A DRNAstruct.h182 DEPRECATED(extern int loop_degree[STRUC],
/dports/biology/viennarna/ViennaRNA-2.4.18/src/ViennaRNA/utils/
H A Dstructure_tree.c364 *loop_degree, *helix_size; in db2Shapiro() local
379 loop_degree = (unsigned int *)vrna_alloc(sizeof(unsigned int) * (n / 2 + 1)); in db2Shapiro()
400 loop_degree[++loops] = 1; in db2Shapiro()
416 switch (loop_degree[loop[lp]]) { in db2Shapiro()
454 loop_degree[loop[--lp]]++; in db2Shapiro()
474 free(loop_degree); in db2Shapiro()
/dports/biology/viennarna/ViennaRNA-2.4.18/interfaces/
H A Dcompare.i28 int loop_degree[1000]; // loop degrees of a structure variable
/dports/biology/viennarna/ViennaRNA-2.4.18/tests/python/
H A Dtest-RNA.py123 self.assertEqual(RNA.intP_getitem(RNA.cvar.loop_degree,1),2)
/dports/biology/viennarna/ViennaRNA-2.4.18/tests/perl5/
H A Dtest-RNA.pl132 is($RNA::loop_degree->[1],2);
/dports/biology/viennarna/ViennaRNA-2.4.18/interfaces/Perl/
H A DRNA.pod444 $loop_degree[int *] holds all loop degrees
716 RNA::parse_structure($structure); # fills the $RNA::loop_degree array
717 @ldegrees = unpack "I*", RNA::cdata($RNA::loop_degree, ($RNA::loops+1)*4);
H A DRNA.pm3202 *loop_degree = *RNAc::loop_degree;
H A DRNA_wrap.cpp10001 for (; ii < (size_t)1000; ++ii) *(int *)&loop_degree[ii] = *((int *)inp + ii); in _wrap_loop_degree_set()
10019 SV *v = newSViv(loop_degree[i]); in _wrap_loop_degree_get()
/dports/biology/viennarna/ViennaRNA-2.4.18/tests/python3/
H A Dtest-RNA.py3117 self.assertEqual(RNA.intP_getitem(RNA.cvar.loop_degree,1),2)
/dports/biology/viennarna/ViennaRNA-2.4.18/interfaces/Perl/RNA/
H A DParams.pm1715 $string .= "/* F = cu*n_unpaired + cc + ci*loop_degree (+TermAU) */\n";
/dports/biology/viennarna/ViennaRNA-2.4.18/man/
H A DRNAlib.texi903 @code{E = cu*n_unpaired + ci*loop_degree + cc}
905 loop_degree is the number of helices forming the loop. In addition a
1082 @deftypevar int loop_degree[]
/dports/biology/viennarna/ViennaRNA-2.4.18/misc/
H A Ddna_mathews1999.par9864 /* F = cu*n_unpaired + cc + ci*loop_degree (+TermAU) */
H A Drna_turner1999.par9853 /* F = cu*n_unpaired + cc + ci*loop_degree (+TermAU) */
H A Drna_andronescu2007.par9853 /* F = cu*n_unpaired + cc + ci*loop_degree (+TermAU) */
H A Drna_langdon2018.par9850 /* F = cu*n_unpaired + cc + ci*loop_degree (+TermAU) */
/dports/biology/viennarna/ViennaRNA-2.4.18/interfaces/Python/
H A DRNA_wrap.cpp60183 for (; ii < (size_t)1000; ++ii) *(int *)&loop_degree[ii] = *((int *)inp + ii); in Swig_var_loop_degree_set()
60197 pyobj = SWIG_NewPointerObj(SWIG_as_voidptr(loop_degree), SWIGTYPE_p_int, 0 ); in Swig_var_loop_degree_get()
/dports/biology/viennarna/ViennaRNA-2.4.18/interfaces/Python3/
H A DRNA_wrap.cpp60642 for (; ii < (size_t)1000; ++ii) *(int *)&loop_degree[ii] = *((int *)inp + ii); in Swig_var_loop_degree_set()
60656 pyobj = SWIG_NewPointerObj(SWIG_as_voidptr(loop_degree), SWIGTYPE_p_int, 0 ); in Swig_var_loop_degree_get()