.codecov.yml
.gitignore
.travis.yml
LICENSE
README.rst
setup.py
todo
barnaba/__init__.py
barnaba/calc_mats.py
barnaba/cluster.py
barnaba/definitions.py
barnaba/enm.py
barnaba/escore.py
barnaba/functions.py
barnaba/kde.py
barnaba/model.py
barnaba/nucleic.py
barnaba/reader.py
barnaba/residue.py
barnaba/smm.py
barnaba/smm_old.py
barnaba.egg-info/PKG-INFO
barnaba.egg-info/SOURCES.txt
barnaba.egg-info/dependency_links.txt
barnaba.egg-info/not-zip-safe
barnaba.egg-info/requires.txt
barnaba.egg-info/top_level.txt
bin/barnaba
doc/Makefile
doc/source/conf.py
doc/source/index.rst
examples/.gitignore
examples/README.rst
examples/example1_ermsd.ipynb
examples/example2_torsion.ipynb
examples/example3_single_strand_motif.ipynb
examples/example4_double_strand.ipynb
examples/example5_annotate.ipynb
examples/example6_cluster.ipynb
examples/example7_scalar_couplings.ipynb
examples/example8_snippet.ipynb
examples/example9_elastic_network_model.ipynb
examples/uucg2.pdb
test/README.md
test/comp_mine.py
test/compare.py
test/compare1.py
test/compare_annotation.py
test/plot_karplus.py
test/test_angles.py
test/test_annotate.py
test/test_cluster.py
test/test_couplings.py
test/test_dsmotif.py
test/test_dump.py
test/test_enm.py
test/test_ermsd.py
test/test_escore.py
test/test_rmsd.py
test/test_smm.py
test/test_snippet.py
test/test_ssmotif.py
test/test_sugar.py
test/data/1S72.pdb
test/data/1y26.pdb
test/data/2n82.pdb
test/data/430d.pdb
test/data/4v7t-pdb-bundle3_G521_00006.align.pdb
test/data/GNRA.pdb
test/data/SARCIN.pdb
test/data/UUCG.native.pdb
test/data/UUCG.pdb
test/data/UUCG.xtc
test/data/centroid_01.pdb
test/data/centroid_06.pdb
test/data/centroid_10.pdb
test/data/sample1.pdb
test/data/sample2.pdb
test/data/sampleh.pdb
test/data/samples.pdb
test/data/samples.xtc
test/reference/#aligned_1.pdb#
test/reference/1S72_1005_A_0_0_00001.pdb
test/reference/1S72_1012_A_0_0_00002.pdb
test/reference/1S72_1230_A_0_0_00003.pdb
test/reference/1S72_1329_A_0_0_00004.pdb
test/reference/1S72_1355_A_0_0_00005.pdb
test/reference/1S72_1526_A_0_0_00006.pdb
test/reference/1S72_484_A_0_0_00000.pdb
test/reference/aligned_1.pdb
test/reference/aligned_2.pdb
test/reference/aligned_3.xtc
test/reference/angles_01.test.dat
test/reference/angles_02.test.dat
test/reference/angles_03.test.dat
test/reference/angles_04.test.dat
test/reference/cluster_000.test.pdb
test/reference/cluster_001.test.pdb
test/reference/cluster_002.test.pdb
test/reference/cluster_003.test.pdb
test/reference/cluster_004.test.pdb
test/reference/cluster_005.test.pdb
test/reference/cluster_006.test.pdb
test/reference/cluster_007.test.pdb
test/reference/cluster_008.test.pdb
test/reference/cluster_009.test.pdb
test/reference/cluster_010.test.pdb
test/reference/cluster_011.test.pdb
test/reference/cluster_012.test.pdb
test/reference/cluster_013.test.pdb
test/reference/couplings_01.test.dat
test/reference/couplings_02.test.dat
test/reference/dotbracket_01.test.dat
test/reference/dotbracket_02.test.dat
test/reference/ds_motif_00001_C_0.pdb
test/reference/ds_motif_00002_U_0.pdb
test/reference/ds_motif_00003_A_0.pdb
test/reference/ds_motif_00004_G_0.pdb
test/reference/ds_motif_00005_A_0.pdb
test/reference/ds_motif_00006_C_0.pdb
test/reference/ds_motif_00007_G_0.pdb
test/reference/dsmotif_01.test.dat
test/reference/dump_01.test.dat
test/reference/dump_02.test.dat
test/reference/enm_01.test.dat
test/reference/enm_02.test.dat
test/reference/enm_03.test.dat
test/reference/enm_03b.test.dat
test/reference/enm_04.test.dat
test/reference/enm_05.test.dat
test/reference/enm_06.test.dat
test/reference/enm_07.test.dat
test/reference/enm_08.test.dat
test/reference/enm_09.test.dat
test/reference/enm_10.test.dat
test/reference/enm_11.test.dat
test/reference/enm_12.test.dat
test/reference/enm_13.test.dat
test/reference/enm_14.test.pdb
test/reference/ermsd_01.test.dat
test/reference/ermsd_02.test.dat
test/reference/ermsd_03.test.dat
test/reference/ermsd_04.test.dat
test/reference/pairings_01.test.dat
test/reference/pairings_02.test.dat
test/reference/rmsd_01.test.dat
test/reference/rmsd_02.test.dat
test/reference/rmsd_03.test.dat
test/reference/score_01.test.dat
test/reference/ss_motif_00001_C_252_0_0.pdb
test/reference/ss_motif_00002_U_468_0_0.pdb
test/reference/ss_motif_00003_C_576_0_0.pdb
test/reference/ss_motif_00004_G_690_0_0.pdb
test/reference/ss_motif_00005_C_804_0_0.pdb
test/reference/ss_motif_00006_U_1326_0_0.pdb
test/reference/ss_motif_00007_G_1628_0_0.pdb
test/reference/ss_motif_00008_C_1862_0_0.pdb
test/reference/ss_motif_00009_C_2248_0_0.pdb
test/reference/ss_motif_00010_C_2411_0_0.pdb
test/reference/ss_motif_00011_C_2629_0_0.pdb
test/reference/ss_motif_00012_C_2695_0_0.pdb
test/reference/ss_motif_00013_G_2876_0_0.pdb
test/reference/ss_motif_00014_C_89_1_0.pdb
test/reference/ss_motif_00015_C_1594_0_0.pdb
test/reference/ss_motif_00016_U_493_0_0.pdb
test/reference/ss_motif_00017_G_1054_0_0.pdb
test/reference/ss_motif_00018_C_1793_0_0.pdb
test/reference/ssmotif_01.test.dat
test/reference/stackings_01.test.dat
test/reference/stackings_02.test.dat
test/reference/sugar_01.test.dat
test/reference/sugar_02.test.dat
test/reference/sugar_03.test.dat
test/reference/sugar_04.test.dat