Louis BECQUEY / biorseo

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Louis BECQUEY
ad7fc4ee 2 parents c8d751c8 d832791e

Merge branch 'master' of https://github.com/persalteas/biominserter

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Showing 1 changed file with 14 additions and 34 deletions
......@@ -318,40 +318,6 @@ void MOIP::define_problem_constraints(void)
}
// forbid lonely basepairs
if (verbose_) cout << "\t>forbidding lonely basepairs..." << endl;
// for (u = 0; u < n; u++) {
// IloExpr c2(env_); // for the case where s[u] is paired to s[v], v>u
// count = 0;
// for (v = u; v < n; v++)
// if (allowed_basepair(u - 1, v)) c2 += y(u - 1, v);
// for (v = u + 1; v < n; v++)
// if (allowed_basepair(u, v)) {
// c2 -= y(u, v);
// count++;
// }
// for (v = u + 2; v < n; v++)
// if (allowed_basepair(u + 1, v)) c2 += y(u + 1, v);
// if (count) {
// model_.add(c2 >= 0);
// if (verbose_) cout << "\t\t" << (c2 >= 0) << endl;
// }
// }
// for (v = 2; v < n; v++) {
// IloExpr c2p(env_); // for the case where s[u] is paired to s[v], v<u
// count = 0;
// for (u = 0; u <= v - 2; u++)
// if (allowed_basepair(u, v - 1)) c2p += y(u, v - 1);
// for (u = 0; u <= v - 1; u++)
// if (allowed_basepair(u, v)) {
// c2p -= y(u, v);
// count++;
// }
// for (u = 0; u <= v; u++)
// if (allowed_basepair(u, v + 1)) c2p += y(u, v + 1);
// if (count) {
// model_.add(c2p >= 0);
// if (verbose_) cout << "\t\t" << (c2p >= 0) << endl;
// }
// }
for (u = 0; u < n - 5; u++)
for (v = u + 4; v < n; v++) {
if (allowed_basepair(u, v)) {
......@@ -423,6 +389,20 @@ void MOIP::define_problem_constraints(void)
model_.add(c5 == jm1 * C(i, 0));
if (verbose_) cout << "\t\t>motif " << i << " : " << (c5 == jm1 * C(i, 0)) << endl;
}
// Forbid pseudoknots
if (verbose_) cout << "\t>forbidding pseudoknots..." << endl;
for (size_t u = 0; u < n - 6; u++)
for (size_t v = u + 4; v < n - 1; v++)
if (allowed_basepair(u, v))
for (size_t k = u + 1; k < v; ++k)
for (size_t l = v + 1; l < n; ++l)
if (allowed_basepair(k, l)) {
IloExpr c(env_);
c += y(u, v);
c += y(k, l);
model_.add(c <= 1);
if (verbose_) cout << "\t\t" << (c <= 1) << endl;
}
}
void MOIP::search_between(double lambdaMin, double lambdaMax)
......