Restore multi-loop functionality

- remove _debug, move to tests
- start explictly testing parts of the RNA structure in https://academic.oup.com/nar/article/45/14/8541/3861610

Makefile

@@ -1,6 +1,7 @@
+.PHONY: examples
+
 install:
 	python3 setup.py install
-	pip3 install . --user
 
 test:
 	python3 -m unittest discover tests -p '*_test.py'
@@ -19,5 +20,8 @@ minor: test
 	python3 setup.py sdist bdist_wheel
 	python3 -m twine upload dist/* --skip-existing
 
+examples:
+	python3 ./tests/fold_examples.py
+
 profile: install
 	python3 ./tests/fold_profile.py

data/rna.py.template

@@ -6,5 +6,5 @@ from .types import Comp, MultiBranch, BpEnergy, LoopEnergy, Energies
 
 RNA_COMPLEMENT: Comp = {"A": "U", "U": "A", "G": "C", "C": "G", "N": "N"}
 
-RNA_MULTIBRANCH: MultiBranch = (9.3, -0.6, 0)
+RNA_MULTIBRANCH: MultiBranch = (2.5, 0.1, 0.4, 2.0)
 

examples/dna.csv

@@ -1,7 +1,9 @@
 seqfold,UNAFold,seq
--10.82,-10.94,GGGAGGTCGTTACATCTGGGTAACACCGGTACTGATCCGGTGACCTCCC
+-1.87,-10.94,GGGAGGTCGTTACATCTGGGTAACACCGGTACTGATCCGGTGACCTCCC
+-12.94,-23.4,GGGAGGTCGCTCCAGCTGGGAGGAGCGTTGGGGGTATATACCCCCAACACCGGTACTGATCCGGTGACCTCCC
 -7.5,-3.8,CGCAGGGAUACCCGCG
--9.3,-6.85,TAGCTCAGCTGGGAGAGCGCCTGCTTTGCACGCAGGAGGT
--17.22,-15.5,GGGGGCATAGCTCAGCTGGGAGAGCGCCTGCTTTGCACGCAGGAGGTCTGCGGTTCGATCCCGCGCGCTCCCACCA
+inf,-6.85,TAGCTCAGCTGGGAGAGCGCCTGCTTTGCACGCAGGAGGT
+-4.07,-15.5,GGGGGCATAGCTCAGCTGGGAGAGCGCCTGCTTTGCACGCAGGAGGTCTGCGGTTCGATCCCGCGCGCTCCCACCA
 -18.9,-18.1,TGAGACGGAAGGGGATGATTGTCCCCTTCCGTCTCA
 -3.89,-3.65,ACCCCCTCCTTCCTTGGATCAAGGGGCTCAA
+1600.0,-9.35,TGTCAGAAGTTTCCAAATGGCCAGCAATCAACCCATTCCATTGGGGATACAATGGTACAGTTTCGCATATTGTCGGTGAAAATGGTTCCATTAAACTCC

seqfold/__init__.py

@@ -10,4 +10,4 @@
 finally:
     del get_distribution, DistributionNotFound
 
-from .fold import calc_dg, Cache, Struct
+from .fold import calc_dg, fold, Cache, Struct

seqfold/dna.py

@@ -7,8 +7,15 @@
 
 DNA_COMPLEMENT: Comp = {"A": "T", "T": "A", "G": "C", "C": "G", "N": "N"}
 
-DNA_MULTIBRANCH: MultiBranch = (4.5, 0.2, 0.2)
-"""a, b and c in a linear multi-branch energy change function."""
+DNA_MULTIBRANCH: MultiBranch = (2.6, 0.2, 0.2, 2.0)
+"""a, b, c, d in a linear multi-branch energy change function.
+
+Inferred from:
+Supplemental Material: Annu.Rev.Biophs.Biomol.Struct.33:415-40
+doi: 10.1146/annurev.biophys.32.110601.141800
+The Termodynamicso f DNA Structural Motifs
+SantaLucia and Hicks, 2004
+"""
 
 DNA_NN: BpEnergy = {
     "init": (0.2, -5.7),