.coveragerc
.gitignore
.readthedocs.yaml
CONTRIBUTING.md
LICENSE
README.md
codecov.yml
logo.svg
pyproject.toml
tox.ini
.github/dependabot.yml
.github/workflows/ci.yml
.github/workflows/dist.yml
.github/workflows/security.yml
data/cgdna-params/Di_hmethyl_methylated-hemi_combine.mat
data/cgdna-params/Prmset_cgDNA+_CGF_10mus_int_12mus_ends.mat
data/cgdna-params/Prmset_cgDNA+_CGF_10mus_int_12mus_ends.txt
data/cgdna-params/Prmset_cgRNA+_OL3_CGF_10mus_int_12mus_ends.mat
data/cgdna-params/README
data/cgdna-params/cgDNA+_Curves_BSTJ_10mus_FS.mat
data/cgdna-params/cgDNA+_Curves_BSTJ_10mus_FS.txt
data/cgdna-params/cgDNA+_MLE_ends12mus_ends_CGF_BSC1.mat
data/cgdna-params/cgDNA+ps1.mat
data/cgdna-params/cgHYB+_CGF_OL3_BSC1_10mus_FS_GC_ends.mat
data/cgdna-params/cgHYB+_CGF_OL3_BSC1_10mus_FS_GC_ends.txt
data/full_reparam_oxdna1/mechanical/60bp_duplex/input
data/full_reparam_oxdna1/mechanical/60bp_duplex/sys.conf
data/full_reparam_oxdna1/mechanical/60bp_duplex/sys.top
data/full_reparam_oxdna1/mechanical/lammps/40bp_duplex/data
data/full_reparam_oxdna1/mechanical/lammps/40bp_duplex/data.oxdna
data/full_reparam_oxdna1/mechanical/lammps/40bp_duplex/data.top
data/full_reparam_oxdna1/mechanical/lammps/40bp_duplex/in
data/full_reparam_oxdna1/structural/20bp_duplex/input
data/full_reparam_oxdna1/structural/20bp_duplex/sys.conf
data/full_reparam_oxdna1/structural/20bp_duplex/sys.top
data/full_reparam_oxdna1/structural/20bp_duplex_nicked/input
data/full_reparam_oxdna1/structural/20bp_duplex_nicked/sys.conf
data/full_reparam_oxdna1/structural/20bp_duplex_nicked/sys.top
data/full_reparam_oxdna1/thermodynamic/5bp_duplex/5bp_duplex.conf
data/full_reparam_oxdna1/thermodynamic/5bp_duplex/5bp_duplex.top
data/full_reparam_oxdna1/thermodynamic/5bp_duplex/input
data/full_reparam_oxdna1/thermodynamic/5bp_duplex/op.txt
data/full_reparam_oxdna1/thermodynamic/5bp_duplex/wfile.txt
data/full_reparam_oxdna1/thermodynamic/5bp_duplex_dangling_end/5bp_duplex_dangling_end.conf
data/full_reparam_oxdna1/thermodynamic/5bp_duplex_dangling_end/5bp_duplex_dangling_end.top
data/full_reparam_oxdna1/thermodynamic/5bp_duplex_dangling_end/energy.dat
data/full_reparam_oxdna1/thermodynamic/5bp_duplex_dangling_end/input
data/full_reparam_oxdna1/thermodynamic/5bp_duplex_dangling_end/last_conf.dat
data/full_reparam_oxdna1/thermodynamic/5bp_duplex_dangling_end/last_hist.dat
data/full_reparam_oxdna1/thermodynamic/5bp_duplex_dangling_end/op.txt
data/full_reparam_oxdna1/thermodynamic/5bp_duplex_dangling_end/traj_hist.dat
data/full_reparam_oxdna1/thermodynamic/5bp_duplex_dangling_end/trajectory.dat
data/full_reparam_oxdna1/thermodynamic/5bp_duplex_dangling_end/wfile.txt
data/full_reparam_oxdna1/thermodynamic/5bp_duplex_terminal_mismatch/5bp_duplex_terminal_mismatch.conf
data/full_reparam_oxdna1/thermodynamic/5bp_duplex_terminal_mismatch/5bp_duplex_terminal_mismatch.top
data/full_reparam_oxdna1/thermodynamic/5bp_duplex_terminal_mismatch/energy.dat
data/full_reparam_oxdna1/thermodynamic/5bp_duplex_terminal_mismatch/input
data/full_reparam_oxdna1/thermodynamic/5bp_duplex_terminal_mismatch/input_MD
data/full_reparam_oxdna1/thermodynamic/5bp_duplex_terminal_mismatch/last_conf.dat
data/full_reparam_oxdna1/thermodynamic/5bp_duplex_terminal_mismatch/last_hist.dat
data/full_reparam_oxdna1/thermodynamic/5bp_duplex_terminal_mismatch/op.txt
data/full_reparam_oxdna1/thermodynamic/5bp_duplex_terminal_mismatch/output.dat
data/full_reparam_oxdna1/thermodynamic/5bp_duplex_terminal_mismatch/split_energy.dat
data/full_reparam_oxdna1/thermodynamic/5bp_duplex_terminal_mismatch/traj_hist.dat
data/full_reparam_oxdna1/thermodynamic/5bp_duplex_terminal_mismatch/trajectory.dat
data/full_reparam_oxdna1/thermodynamic/5bp_duplex_terminal_mismatch/wfile.txt
data/full_reparam_oxdna1/thermodynamic/5bp_stem_5bp_loop_hairpin/5bp_stem_5bp_loop_hairpin.conf
data/full_reparam_oxdna1/thermodynamic/5bp_stem_5bp_loop_hairpin/5bp_stem_5bp_loop_hairpin.dat
data/full_reparam_oxdna1/thermodynamic/5bp_stem_5bp_loop_hairpin/5bp_stem_5bp_loop_hairpin.top
data/full_reparam_oxdna1/thermodynamic/5bp_stem_5bp_loop_hairpin/input
data/full_reparam_oxdna1/thermodynamic/5bp_stem_5bp_loop_hairpin/op.txt
data/full_reparam_oxdna1/thermodynamic/5bp_stem_5bp_loop_hairpin/wfile.txt
data/full_reparam_oxdna1/thermodynamic/8bp_duplex/8bp_duplex.conf
data/full_reparam_oxdna1/thermodynamic/8bp_duplex/8bp_duplex.top
data/full_reparam_oxdna1/thermodynamic/8bp_duplex/input
data/full_reparam_oxdna1/thermodynamic/8bp_duplex/op.txt
data/full_reparam_oxdna1/thermodynamic/8bp_duplex/sys.top
data/full_reparam_oxdna1/thermodynamic/8bp_duplex/wfile.txt
data/full_reparam_oxdna1/thermodynamic/8bp_duplex_1bp_bulge/8bp_duplex_1bp_bulge.conf
data/full_reparam_oxdna1/thermodynamic/8bp_duplex_1bp_bulge/8bp_duplex_1bp_bulge.top
data/full_reparam_oxdna1/thermodynamic/8bp_duplex_1bp_bulge/energy.dat
data/full_reparam_oxdna1/thermodynamic/8bp_duplex_1bp_bulge/input
data/full_reparam_oxdna1/thermodynamic/8bp_duplex_1bp_bulge/last_conf.dat
data/full_reparam_oxdna1/thermodynamic/8bp_duplex_1bp_bulge/last_hist.dat
data/full_reparam_oxdna1/thermodynamic/8bp_duplex_1bp_bulge/op.txt
data/full_reparam_oxdna1/thermodynamic/8bp_duplex_1bp_bulge/traj_hist.dat
data/full_reparam_oxdna1/thermodynamic/8bp_duplex_1bp_bulge/trajectory.dat
data/full_reparam_oxdna1/thermodynamic/8bp_duplex_1bp_bulge/wfile.txt
data/full_reparam_oxdna1/thermodynamic/8bp_duplex_2bp_bubble/8bp_duplex_2bp_bubble.conf
data/full_reparam_oxdna1/thermodynamic/8bp_duplex_2bp_bubble/8bp_duplex_2bp_bubble.top
data/full_reparam_oxdna1/thermodynamic/8bp_duplex_2bp_bubble/energy.dat
data/full_reparam_oxdna1/thermodynamic/8bp_duplex_2bp_bubble/input
data/full_reparam_oxdna1/thermodynamic/8bp_duplex_2bp_bubble/last_conf.dat
data/full_reparam_oxdna1/thermodynamic/8bp_duplex_2bp_bubble/last_hist.dat
data/full_reparam_oxdna1/thermodynamic/8bp_duplex_2bp_bubble/op.txt
data/full_reparam_oxdna1/thermodynamic/8bp_duplex_2bp_bubble/traj_hist.dat
data/full_reparam_oxdna1/thermodynamic/8bp_duplex_2bp_bubble/trajectory.dat
data/full_reparam_oxdna1/thermodynamic/8bp_duplex_2bp_bubble/wfile.txt
data/seq-specific/seq_oxdna1.txt
data/seq-specific/seq_oxdna2.txt
data/seq-specific/seq_rna.txt
data/sys-defs/hairpins/4bp_stem_8nt_loop/init.conf
data/sys-defs/hairpins/4bp_stem_8nt_loop/input
data/sys-defs/hairpins/4bp_stem_8nt_loop/op.txt
data/sys-defs/hairpins/4bp_stem_8nt_loop/sys.top
data/sys-defs/hairpins/4bp_stem_8nt_loop/wfile.txt
data/sys-defs/hairpins/6bp_stem_6nt_loop/init_bound.conf
data/sys-defs/hairpins/6bp_stem_6nt_loop/init_unbound.conf
data/sys-defs/hairpins/6bp_stem_6nt_loop/input
data/sys-defs/hairpins/6bp_stem_6nt_loop/op.txt
data/sys-defs/hairpins/6bp_stem_6nt_loop/sys.top
data/sys-defs/hairpins/6bp_stem_6nt_loop/wfile.txt
data/sys-defs/lb-seqs/seq1/seq.conf
data/sys-defs/lb-seqs/seq1/seq.top
data/sys-defs/persistence-length/init.conf
data/sys-defs/persistence-length/init.top
data/sys-defs/persistence-length/notes.txt
data/sys-defs/persistence-length/relaxed.dat
data/sys-defs/persistence-length-500bp/init.top
data/sys-defs/persistence-length-500bp/relaxed.dat
data/sys-defs/simple-helix/bound.conf
data/sys-defs/simple-helix/bound_relaxed.conf
data/sys-defs/simple-helix/sys.top
data/sys-defs/simple-helix/unbound.conf
data/sys-defs/tm-1op/6bp/init_bound.conf
data/sys-defs/tm-1op/6bp/init_unbound.conf
data/sys-defs/tm-1op/6bp/input
data/sys-defs/tm-1op/6bp/op.txt
data/sys-defs/tm-1op/6bp/sys.top
data/sys-defs/tm-1op/6bp/wfile.txt
data/sys-defs/tm-1op/8bp/init_bound.conf
data/sys-defs/tm-1op/8bp/init_unbound.conf
data/sys-defs/tm-1op/8bp/input
data/sys-defs/tm-1op/8bp/op.txt
data/sys-defs/tm-1op/8bp/sys.top
data/sys-defs/tm-1op/8bp/wfile.txt
data/sys-defs/tm-2op/5bp/init_bound.conf
data/sys-defs/tm-2op/5bp/init_unbound.conf
data/sys-defs/tm-2op/5bp/input
data/sys-defs/tm-2op/5bp/op.txt
data/sys-defs/tm-2op/5bp/seq.txt
data/sys-defs/tm-2op/5bp/sys.top
data/sys-defs/tm-2op/5bp/wfile.txt
data/sys-defs/tm-2op/8bp/init_bound.conf
data/sys-defs/tm-2op/8bp/init_unbound.conf
data/sys-defs/tm-2op/8bp/input
data/sys-defs/tm-2op/8bp/op.txt
data/sys-defs/tm-2op/8bp/sys.top
data/sys-defs/tm-2op/8bp/wfile.txt
data/sys-defs/tm-mismatch11-1op/8bp/init_bound.conf
data/sys-defs/tm-mismatch11-1op/8bp/init_unbound.conf
data/sys-defs/tm-mismatch11-1op/8bp/input
data/sys-defs/tm-mismatch11-1op/8bp/op.txt
data/sys-defs/tm-mismatch11-1op/8bp/sys.top
data/sys-defs/tm-mismatch11-1op/8bp/wfile.txt
data/sys-defs/wlc-fit/generated.dat
data/sys-defs/wlc-fit/generated.top
data/templates/model_template.h
data/templates/1A1L/1a1l.pdb
data/templates/1A1L/complex.conf
data/templates/1A1L/complex.top
data/templates/1A1L/dna.pdb
data/templates/1A1L/input_relaxMC
data/templates/1A1L/protein.conf
data/templates/1A1L/protein.par
data/templates/1A1L/protein.pdb
data/templates/1A1L/protein.top
data/templates/1A1L/relax_sim.log
data/templates/1A1L/relaxed.dat
data/templates/1AAY/1aay.pdb
data/templates/1AAY/complex.conf
data/templates/1AAY/complex.top
data/templates/1AAY/dna.pdb
data/templates/1AAY/input_relaxMC
data/templates/1AAY/protein.conf
data/templates/1AAY/protein.par
data/templates/1AAY/protein.pdb
data/templates/1AAY/protein.top
data/templates/1AAY/relaxed.dat
data/templates/1ZAA/1zaa.pdb
data/templates/1ZAA/complex.conf
data/templates/1ZAA/complex.top
data/templates/1ZAA/dna.pdb
data/templates/1ZAA/input_relaxMC
data/templates/1ZAA/protein.conf
data/templates/1ZAA/protein.par
data/templates/1ZAA/protein.pdb
data/templates/1ZAA/protein.top
data/templates/1ZAA/relax_sim.log
data/templates/1ZAA/relaxed.dat
data/templates/2ht-tc-rmse-rna/external_model.txt
data/templates/2ht-tc-rmse-rna/init.conf
data/templates/2ht-tc-rmse-rna/input
data/templates/2ht-tc-rmse-rna/rna_sequence_dependent_parameters.txt
data/templates/2ht-tc-rmse-rna/sys.top
data/templates/2ht-tc-rmse-rna/target.conf
data/templates/5ht-tc-rmse-rna/external_model.txt
data/templates/5ht-tc-rmse-rna/init.conf
data/templates/5ht-tc-rmse-rna/input
data/templates/5ht-tc-rmse-rna/rna_sequence_dependent_parameters.txt
data/templates/5ht-tc-rmse-rna/sys.top
data/templates/5ht-tc-rmse-rna/target.conf
data/templates/bak/tors-mod-20bp/init.conf
data/templates/bak/tors-mod-20bp/sys.top
data/templates/bak/torsional-modulus-20bp/init.conf
data/templates/bak/torsional-modulus-20bp/input
data/templates/bak/torsional-modulus-20bp/sys.top
data/templates/bak/torsional-modulus-20bp-vmmc/init.conf
data/templates/bak/torsional-modulus-20bp-vmmc/input
data/templates/bak/torsional-modulus-20bp-vmmc/sys.top
data/templates/bak/torsional-modulus-30bp/init.conf
data/templates/bak/torsional-modulus-30bp/input
data/templates/bak/torsional-modulus-30bp/sys.top
data/templates/bak/torsional-modulus-30bp-constrained/init.conf
data/templates/bak/torsional-modulus-30bp-constrained/input
data/templates/bak/torsional-modulus-30bp-constrained/sys.top
data/templates/bak/torsional-modulus-30bp-vmmc/init.conf
data/templates/bak/torsional-modulus-30bp-vmmc/input
data/templates/bak/torsional-modulus-30bp-vmmc/sys.top
data/templates/burns_natnano_2015/input
data/templates/burns_natnano_2015/notes.txt
data/templates/burns_natnano_2015/relaxed.conf
data/templates/burns_natnano_2015/sys.top
data/templates/burns_natnano_2015/unrelaxed.conf
data/templates/ds-142bp-rna/init.conf
data/templates/ds-142bp-rna/input
data/templates/ds-142bp-rna/sys.top
data/templates/force-ext/init.conf
data/templates/force-ext/input
data/templates/force-ext/sys.top
data/templates/force-ext/externals/external_0.025.conf
data/templates/force-ext/externals/external_0.05.conf
data/templates/force-ext/externals/external_0.1.conf
data/templates/force-ext/externals/external_0.15.conf
data/templates/force-ext/externals/external_0.2.conf
data/templates/force-ext/externals/external_0.25.conf
data/templates/force-ext/externals/external_0.3.conf
data/templates/force-ext/externals/external_0.375.conf
data/templates/hairpins/4bp_stem_8nt_loop/init.conf
data/templates/hairpins/4bp_stem_8nt_loop/input
data/templates/hairpins/4bp_stem_8nt_loop/op.txt
data/templates/hairpins/4bp_stem_8nt_loop/sys.top
data/templates/hairpins/4bp_stem_8nt_loop/wfile.txt
data/templates/hairpins/6bp_stem_6nt_loop/init_bound.conf
data/templates/hairpins/6bp_stem_6nt_loop/init_unbound.conf
data/templates/hairpins/6bp_stem_6nt_loop/input
data/templates/hairpins/6bp_stem_6nt_loop/op.txt
data/templates/hairpins/6bp_stem_6nt_loop/sys.top
data/templates/hairpins/6bp_stem_6nt_loop/wfile-oxdna2.txt
data/templates/hairpins/6bp_stem_6nt_loop/wfile.txt
data/templates/lammps-stretch-tors/data
data/templates/lammps-stretch-tors/input
data/templates/martini/m2/DMPC/273K/index.ndx
data/templates/martini/m2/DMPC/273K/md.mdp
data/templates/martini/m2/DMPC/273K/membrane.gro
data/templates/martini/m2/DMPC/273K/representative.tpr
data/templates/martini/m2/DMPC/273K/topol.top
data/templates/persistence-length/init.conf
data/templates/persistence-length/input
data/templates/persistence-length/sys.top
data/templates/rna-13bp/init.conf
data/templates/rna-13bp/input
data/templates/rna-13bp/sys.top
data/templates/rna-overhang/6bp-3p/init_bound.conf
data/templates/rna-overhang/6bp-3p/init_unbound.conf
data/templates/rna-overhang/6bp-3p/input
data/templates/rna-overhang/6bp-3p/op.txt
data/templates/rna-overhang/6bp-3p/sys.top
data/templates/rna-overhang/6bp-3p/wfile.txt
data/templates/rna-overhang/6bp-3p-unique/init_bound.conf
data/templates/rna-overhang/6bp-3p-unique/init_unbound.conf
data/templates/rna-overhang/6bp-3p-unique/input
data/templates/rna-overhang/6bp-3p-unique/op.txt
data/templates/rna-overhang/6bp-3p-unique/sys.top
data/templates/rna-overhang/6bp-3p-unique/wfile.txt
data/templates/rna-overhang/6bp-5p/init_bound.conf
data/templates/rna-overhang/6bp-5p/init_unbound.conf
data/templates/rna-overhang/6bp-5p/input
data/templates/rna-overhang/6bp-5p/op.txt
data/templates/rna-overhang/6bp-5p/sys.top
data/templates/rna-overhang/6bp-5p/wfile.txt
data/templates/rna-overhang/6bp-5p-unique/init_bound.conf
data/templates/rna-overhang/6bp-5p-unique/init_unbound.conf
data/templates/rna-overhang/6bp-5p-unique/input
data/templates/rna-overhang/6bp-5p-unique/op.txt
data/templates/rna-overhang/6bp-5p-unique/sys.top
data/templates/rna-overhang/6bp-5p-unique/wfile.txt
data/templates/rna2-13bp-md/init.conf
data/templates/rna2-13bp-md/input
data/templates/rna2-13bp-md/sys.top
data/templates/simple-helix/init.conf
data/templates/simple-helix/input
data/templates/simple-helix/sys.top
data/templates/simple-helix-12bp/init.conf
data/templates/simple-helix-12bp/input
data/templates/simple-helix-12bp/sys.top
data/templates/simple-helix-60bp/init.conf
data/templates/simple-helix-60bp/input
data/templates/simple-helix-60bp/sys.top
data/templates/simple-helix-60bp-oxdna1/init.conf
data/templates/simple-helix-60bp-oxdna1/input
data/templates/simple-helix-60bp-oxdna1/sys.top
data/templates/simple-helix-60bp-oxdna1-lammps/init.conf.lammps
data/templates/simple-helix-60bp-oxdna1-lammps/input
data/templates/simple-helix-60bp-oxdna1-lammps/log.lammps
data/templates/simple-helix-60bp-oxdna1-lammps/sys.top
data/templates/simple-helix-60bp-oxdna1-lammps/trajectory.dat
data/templates/simple-helix-60bp-oxdna2-lammps/init.conf.lammps
data/templates/simple-helix-60bp-oxdna2-lammps/input
data/templates/simple-helix-60bp-oxdna2-lammps/log.lammps
data/templates/simple-helix-60bp-oxdna2-lammps/sys.top
data/templates/simple-helix-60bp-oxdna2-lammps/trajectory.dat
data/templates/simple-helix-60bp-ss/init.conf
data/templates/simple-helix-60bp-ss/input
data/templates/simple-helix-60bp-ss/seq_oxdna2.txt
data/templates/simple-helix-60bp-ss/sys.top
data/templates/ss100/init.conf
data/templates/ss100/sys.top
data/templates/ss20/init.conf
data/templates/ss20/sys.top
data/templates/tm-10bp-1mm-rna/init_bound.conf
data/templates/tm-10bp-1mm-rna/init_unbound.conf
data/templates/tm-10bp-1mm-rna/input
data/templates/tm-10bp-1mm-rna/op.txt
data/templates/tm-10bp-1mm-rna/sys.top
data/templates/tm-10bp-1mm-rna/wfile.txt
data/templates/tm-10bp-1mm-rna-2op/init_bound.conf
data/templates/tm-10bp-1mm-rna-2op/init_unbound.conf
data/templates/tm-10bp-1mm-rna-2op/input
data/templates/tm-10bp-1mm-rna-2op/op.txt
data/templates/tm-10bp-1mm-rna-2op/sys.top
data/templates/tm-10bp-1mm-rna-2op/wfile.txt
data/templates/tm-10bp-1mm-rna-unique/init_bound.conf
data/templates/tm-10bp-1mm-rna-unique/init_unbound.conf
data/templates/tm-10bp-1mm-rna-unique/input
data/templates/tm-10bp-1mm-rna-unique/op.txt
data/templates/tm-10bp-1mm-rna-unique/op_full.txt
data/templates/tm-10bp-1mm-rna-unique/sys.top
data/templates/tm-10bp-1mm-rna-unique/wfile.txt
data/templates/tm-10bp-1mm-rna-unique/wfile_ones.txt
data/templates/tm-10bp-1mm-rna-unique/wfile_petr.txt
data/templates/tm-6bp/init_bound.conf
data/templates/tm-6bp/init_unbound.conf
data/templates/tm-6bp/input
data/templates/tm-6bp/op.txt
data/templates/tm-6bp/sys.top
data/templates/tm-6bp/wfile-oxdna2.txt
data/templates/tm-6bp/wfile.txt
data/templates/tm-6bp-2op/init_bound.conf
data/templates/tm-6bp-2op/input
data/templates/tm-6bp-2op/op.txt
data/templates/tm-6bp-2op/sys.top
data/templates/tm-6bp-2op/test_init.conf
data/templates/tm-6bp-2op/wfile.txt
data/templates/tm-8bp/init_bound.conf
data/templates/tm-8bp/init_unbound.conf
data/templates/tm-8bp/input
data/templates/tm-8bp/op.txt
data/templates/tm-8bp/sys.top
data/templates/tm-8bp/wfile-oxdna2.txt
data/templates/tm-8bp/wfile.txt
data/templates/tm-8bp-1mm-rna-unique/init_bound.conf
data/templates/tm-8bp-1mm-rna-unique/init_unbound.conf
data/templates/tm-8bp-1mm-rna-unique/input
data/templates/tm-8bp-1mm-rna-unique/op.txt
data/templates/tm-8bp-1mm-rna-unique/sys.top
data/templates/tm-8bp-1mm-rna-unique/wfile.txt
data/templates/tm-8bp-1mm-rna-unique-full/init_bound.conf
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