RNAmotiFold 1.0.0__py3-none-any.whl

RNAmotiFold/RNALoops/Algebras/DotBracket/Parts/algpart_cofold_dotBracket.gap

@@ -0,0 +1,57 @@
+  string sadd_cut_noduplex(Subsequence lb,string e) {
+    string res;
+    append(res, '+');
+    append(res, e);
+    return res;
+  }
+  string sadd_cut(Subsequence lb,string e) {
+    string res;
+    append(res, '+');
+    append(res, e);
+    return res;
+  }
+  string hl_cut(Subsequence lb,Subsequence region,Subsequence rb) {
+    string res;
+    append(res, '(');
+    appendSeperatorRegion(res, region);
+    append(res, ')');
+    return res;
+  }
+  string bl_cut(Subsequence lb,Subsequence lregion,string e,Subsequence rb) {
+    string res;
+    append(res, '(');
+    appendSeperatorRegion(res, lregion);
+    append(res, e);
+    append(res, ')');
+    return res;
+  }
+  string br_cut(Subsequence lb,string e,Subsequence rregion,Subsequence rb) {
+    string res;
+    append(res, '(');
+    append(res, e);
+    appendSeperatorRegion(res, rregion);
+    append(res, ')');
+    return res;
+  }
+  string il_cut(Subsequence lb,Subsequence lregion,string e,Subsequence rregion,Subsequence rb) {
+    string res;
+    append(res, '(');
+    appendSeperatorRegion(res, lregion);
+    append(res, e);
+    appendSeperatorRegion(res, rregion);
+    append(res, ')');
+    return res;
+  }
+  string addss_cut(string e,Subsequence rb) {
+    string res;
+    append(res, e);
+    appendSeperatorRegion(res, rb);
+    return res;
+  }
+  string ml_cut(Subsequence lb,string e,Subsequence rb) {
+    string res;
+    append(res, '(');
+    append(res, e);
+    append(res, ')');
+    return res;
+  }

RNAmotiFold/RNALoops/Algebras/DotBracket/Parts/algpart_dotBracket_basic.gap

@@ -0,0 +1,153 @@
+  string sadd(Subsequence lb,string e) {
+    string res;
+    append(res, '.');
+    append(res, e);
+    return res;
+  }
+
+  string cadd(string le,string re) {
+    string res;
+    append(res, le);
+    append(res, re);
+    return res;
+  }
+
+  string nil(Subsequence loc) {
+    string r;
+    return r;
+  }
+
+  string edl(Subsequence lb,string e, Subsequence loc) {
+    string res;
+    append(res, '.');
+    append(res, e);
+    return res;
+  }
+
+  string edr(Subsequence loc, string e,Subsequence rb) {
+    string res;
+    append(res, e);
+    append(res, '.');
+    return res;
+  }
+
+  string edlr(Subsequence lb,string e,Subsequence rb) {
+    string res;
+    append(res, '.');
+    append(res, e);
+    append(res, '.');
+    return res;
+  }
+
+  string drem(Subsequence lloc, string e, Subsequence rloc) {
+    return e;
+  }
+
+  string dall(Subsequence lloc, string e, Subsequence rloc) {
+    return e;
+  }
+
+  string sr(Subsequence lb,string e,Subsequence rb) {
+    string res;
+    append(res, '(');
+    append(res, e);
+    append(res, ')');
+    return res;
+  }
+
+  string hl(Subsequence lb,Subsequence region,Subsequence rb) {
+    string res;
+    append(res, '(');
+    append(res, '.', size(region));
+    append(res, ')');
+    return res;
+  }
+
+
+  string bl(Subsequence lb,Subsequence lregion,string e,Subsequence rb) {
+    string res;
+    append(res, '(');
+    append(res, '.', size(lregion));
+    append(res, e);
+    append(res, ')');
+    return res;
+  }
+
+  string br(Subsequence lb,string e,Subsequence rregion,Subsequence rb) {
+    string res;
+    append(res, '(');
+    append(res, e);
+    append(res, '.', size(rregion));
+    append(res, ')');
+    return res;
+  }
+
+  string il(Subsequence lb,Subsequence lregion,string e,Subsequence rregion,Subsequence rb) {
+    string res;
+    append(res, '(');
+    append(res, '.', size(lregion));
+    append(res, e);
+    append(res, '.', size(rregion));
+    append(res, ')');
+    return res;
+  }
+
+  string ml(Subsequence lb,string e,Subsequence rb) {
+    string res;
+    append(res, '(');
+    append(res, e);
+    append(res, ')');
+    return res;
+  }
+
+  string mlall(Subsequence lb,string e,Subsequence rb) {
+    string res;
+    append(res, '(');
+    append(res, e);
+    append(res, ')');
+    return res;
+  }
+
+  string mldr(Subsequence lb,string e,Subsequence dr,Subsequence rb) {
+    string res;
+    append(res, '(');
+    append(res, e);
+    append(res, '.');
+    append(res, ')');
+    return res;
+  }
+
+  string mldlr(Subsequence lb,Subsequence dl,string e,Subsequence dr,Subsequence rb) {
+    string res;
+    append(res, '(');
+    append(res, '.');
+    append(res, e);
+    append(res, '.');
+    append(res, ')');
+    return res;
+  }
+
+  string mldl(Subsequence lb,Subsequence dl,string e,Subsequence rb) {
+    string res;
+    append(res, '(');
+    append(res, '.');
+    append(res, e);
+    append(res, ')');
+    return res;
+  }
+
+  string addss(string e,Subsequence rb) {
+    string res;
+    append(res, e);
+    append(res, '.', size(rb));
+    return res;
+  }
+
+  string incl(string e) {
+    return e;
+  }
+
+  choice [string] h([string] i) {
+    //~ return list(minimum(i));
+    return i;
+  }

RNAmotiFold/RNALoops/Algebras/DotBracket/Parts/algpart_dotBracket_macrostate.gap

@@ -0,0 +1,111 @@
+  string cadd_Pr(string le,string re) {
+    string res;
+    append(res, le);
+    append(res, re);
+    return res;
+  }
+
+  string cadd_Pr_Pr(string le,string re) {
+    string res;
+    append(res, le);
+    append(res, re);
+    return res;
+  }
+
+  string cadd_Pr_Pr_Pr(string le,string re) {
+    string res;
+    append(res, le);
+    append(res, re);
+    return res;
+  }
+
+  string ambd(string le,Subsequence b,string re) {
+    string res;
+    append(res, le);
+    append(res, '.');
+    append(res, re);
+    return res;
+  }
+
+  string ambd_Pr(string le,Subsequence b,string re) {
+    string res;
+    append(res, le);
+    append(res, '.');
+    append(res, re);
+    return res;
+  }
+
+  string mladr(Subsequence lb,string e,Subsequence dr,Subsequence rb) {
+    string res;
+    append(res, '(');
+    append(res, e);
+    append(res, '.');
+    append(res, ')');
+    return res;
+  }
+
+  string mladlr(Subsequence lb,Subsequence dl,string e,Subsequence dr,Subsequence rb) {
+    string res;
+    append(res, '(');
+    append(res, '.');
+    append(res, e);
+    append(res, '.');
+    append(res, ')');
+    return res;
+  }
+
+  string mldladr(Subsequence lb,Subsequence dl,string e,Subsequence dr,Subsequence rb) {
+    string res;
+    append(res, '(');
+    append(res, '.');
+    append(res, e);
+    append(res, '.');
+    append(res, ')');
+    return res;
+  }
+
+  string mladldr(Subsequence lb,Subsequence dl,string e,Subsequence dr,Subsequence rb) {
+    string res;
+    append(res, '(');
+    append(res, '.');
+    append(res, e);
+    append(res, '.');
+    append(res, ')');
+    return res;
+  }
+
+  string mladl(Subsequence lb,Subsequence dl,string e,Subsequence rb) {
+    string res;
+    append(res, '(');
+    append(res, '.');
+    append(res, e);
+    append(res, ')');
+    return res;
+  }
+
+  string ssadd(Subsequence lb,string e) {
+    string res;
+    append(res, '.', size(lb));
+    append(res, e);
+    return res;
+  }
+
+  string trafo(string e) {
+    return e;
+  }
+
+  string combine(string le,string re) {
+    string res;
+    append(res, le);
+    append(res, re);
+    return res;
+  }
+
+  string acomb(string le,Subsequence b,string re) {
+    string res;
+    append(res, le);
+    append(res, '.');
+    append(res, re);
+    return res;
+  }
+

RNAmotiFold/RNALoops/Algebras/DotBracket/Parts/algpart_outside_dotBracket.gap

@@ -0,0 +1,112 @@
+	string sep(string innerRight, Subsequence sepChar, string innerLeft) {
+		string res;
+		append(res, innerRight);
+		append(res, '#');
+		append(res, innerLeft);
+		return res;
+	}
+	string outer_drem(Subsequence locr, string x, Subsequence locl) {
+		return x;
+	}
+	string outer_dall(Subsequence locr, string x, Subsequence locl) {
+		return x;
+	}
+	string outer_edl(Subsequence locr, string x, Subsequence lb) {
+		string res;
+		append(res, x);
+		append(res, '.');
+		return res;
+	}
+	string outer_edr(Subsequence rb, string x, Subsequence locl) {
+		string res;
+		append(res, '.');
+		append(res, x);
+		return res;
+	}
+	string outer_edlr(Subsequence rb, string x, Subsequence lb) {
+		string res;
+		append(res, '.');
+		append(res, x);
+		append(res, '.');
+		return res;
+	}
+	string outer_sr(Subsequence rb, string x, Subsequence lb) {
+		string res;
+		append(res, ')');
+		append(res, x);
+		append(res, '(');
+		return res;
+	}
+	string outer_bl(Subsequence loc, string x, Subsequence leftRegion) {
+		string res;
+		append(res, x);
+		append(res, '.', size(leftRegion));
+		return res;
+	}
+	string outer_br(Subsequence rightRegion, string x, Subsequence loc) {
+		string res;
+		append(res, '.', size(rightRegion));
+		append(res, x);
+		return res;
+	}
+	string outer_il(Subsequence rightRegion, string x, Subsequence leftRegion) {
+		string res;
+		append(res, '.', size(rightRegion));
+		append(res, x);
+		append(res, '.', size(leftRegion));
+		return res;
+	}
+	string outer_ml(Subsequence rb, string x, Subsequence lb) {
+		string res;
+		append(res, ')');
+		append(res, x);
+		append(res, '(');
+		return res;
+	}
+	string outer_mlall(Subsequence rb, string x, Subsequence lb) {
+		string res;
+		append(res, ')');
+		append(res, x);
+		append(res, '(');
+		return res;
+	}
+	string outer_mldl(Subsequence rb, string x, Subsequence ul, Subsequence lb) {
+		string res;
+		append(res, ')');
+		append(res, x);
+		append(res, '.');
+		append(res, '(');
+		return res;
+	}
+	string outer_mldr(Subsequence rb, Subsequence ur, string x, Subsequence lb) {
+		string res;
+		append(res, ')');
+		append(res, '.');
+		append(res, x);
+		append(res, '(');
+		return res;
+	}
+	string outer_mldlr(Subsequence rb, Subsequence ur, string x, Subsequence ul, Subsequence lb) {
+		string res;
+		append(res, ')');
+		append(res, '.');
+		append(res, x);
+		append(res, '.');
+		append(res, '(');
+		return res;
+	}
+	string outer_bp(Subsequence rb, string x, Subsequence lb) {
+		string res;
+		append(res, ')');
+		append(res, x);
+		append(res, '(');
+		return res;
+	}
+	string window(Subsequence l, string x, Subsequence r) {
+		string res;
+		append(res, ' ', size(l));
+		append(res, x);
+		append(res, ' ', size(r));
+		return res;
+	}
+	string makeplot(Subsequence pos) { string res; return res; }