From d291aa8546d12be2611313bf02d71da024fa5200 Mon Sep 17 00:00:00 2001
From: Chris Maffeo <cmaffeo2@illinois.edu>
Date: Wed, 5 Sep 2018 14:54:19 -0500
Subject: [PATCH] Renamed project to 'mrdna'
---
MANIFEST.in | 2 +-
README.md | 2 +-
bin/{dnarbd => mrdna} | 10 +++++-----
{dnarbd => mrdna}/__init__.py | 0
{dnarbd => mrdna}/coords.py | 0
{dnarbd => mrdna}/examples/from_cadnano.py | 4 ++--
{dnarbd => mrdna}/examples/from_code.py | 4 ++--
{dnarbd => mrdna}/model/CanonicalNucleotideAtoms.py | 0
{dnarbd => mrdna}/model/__init__.py | 0
{dnarbd => mrdna}/model/arbdmodel.py | 0
{dnarbd => mrdna}/model/dna_sequence.py | 0
{dnarbd => mrdna}/model/nbPot.py | 0
{dnarbd => mrdna}/model/nonbonded.py | 0
{dnarbd => mrdna}/readers/__init__.py | 0
{dnarbd => mrdna}/readers/cadnano_segments.py | 0
{dnarbd => mrdna}/readers/polygon_mesh.py | 0
{dnarbd => mrdna}/readers/segmentmodel_from_lists.py | 0
{dnarbd => mrdna}/readers/segmentmodel_from_pdb.py | 0
{dnarbd => mrdna}/resources/A-fwd-3prime.angles.txt | 0
{dnarbd => mrdna}/resources/A-fwd-3prime.bonds.txt | 0
{dnarbd => mrdna}/resources/A-fwd-3prime.dat | 0
{dnarbd => mrdna}/resources/A-fwd-3prime.dihedrals.txt | 0
{dnarbd => mrdna}/resources/A-fwd-3prime.impropers.txt | 0
{dnarbd => mrdna}/resources/A-fwd-5prime.angles.txt | 0
{dnarbd => mrdna}/resources/A-fwd-5prime.bonds.txt | 0
{dnarbd => mrdna}/resources/A-fwd-5prime.dat | 0
{dnarbd => mrdna}/resources/A-fwd-5prime.dihedrals.txt | 0
{dnarbd => mrdna}/resources/A-fwd-5prime.impropers.txt | 0
{dnarbd => mrdna}/resources/A-fwd-singlet.angles.txt | 0
{dnarbd => mrdna}/resources/A-fwd-singlet.bonds.txt | 0
{dnarbd => mrdna}/resources/A-fwd-singlet.dat | 0
.../resources/A-fwd-singlet.dihedrals.txt | 0
.../resources/A-fwd-singlet.impropers.txt | 0
{dnarbd => mrdna}/resources/A-fwd.angles.txt | 0
{dnarbd => mrdna}/resources/A-fwd.bonds.txt | 0
{dnarbd => mrdna}/resources/A-fwd.dat | 0
{dnarbd => mrdna}/resources/A-fwd.dihedrals.txt | 0
{dnarbd => mrdna}/resources/A-fwd.impropers.txt | 0
{dnarbd => mrdna}/resources/A-rev-3prime.angles.txt | 0
{dnarbd => mrdna}/resources/A-rev-3prime.bonds.txt | 0
{dnarbd => mrdna}/resources/A-rev-3prime.dat | 0
{dnarbd => mrdna}/resources/A-rev-3prime.dihedrals.txt | 0
{dnarbd => mrdna}/resources/A-rev-3prime.impropers.txt | 0
{dnarbd => mrdna}/resources/A-rev-5prime.angles.txt | 0
{dnarbd => mrdna}/resources/A-rev-5prime.bonds.txt | 0
{dnarbd => mrdna}/resources/A-rev-5prime.dat | 0
{dnarbd => mrdna}/resources/A-rev-5prime.dihedrals.txt | 0
{dnarbd => mrdna}/resources/A-rev-5prime.impropers.txt | 0
{dnarbd => mrdna}/resources/A-rev-singlet.angles.txt | 0
{dnarbd => mrdna}/resources/A-rev-singlet.bonds.txt | 0
{dnarbd => mrdna}/resources/A-rev-singlet.dat | 0
.../resources/A-rev-singlet.dihedrals.txt | 0
.../resources/A-rev-singlet.impropers.txt | 0
{dnarbd => mrdna}/resources/A-rev.angles.txt | 0
{dnarbd => mrdna}/resources/A-rev.bonds.txt | 0
{dnarbd => mrdna}/resources/A-rev.dat | 0
{dnarbd => mrdna}/resources/A-rev.dihedrals.txt | 0
{dnarbd => mrdna}/resources/A-rev.impropers.txt | 0
{dnarbd => mrdna}/resources/C-fwd-3prime.angles.txt | 0
{dnarbd => mrdna}/resources/C-fwd-3prime.bonds.txt | 0
{dnarbd => mrdna}/resources/C-fwd-3prime.dat | 0
{dnarbd => mrdna}/resources/C-fwd-3prime.dihedrals.txt | 0
{dnarbd => mrdna}/resources/C-fwd-3prime.impropers.txt | 0
{dnarbd => mrdna}/resources/C-fwd-5prime.angles.txt | 0
{dnarbd => mrdna}/resources/C-fwd-5prime.bonds.txt | 0
{dnarbd => mrdna}/resources/C-fwd-5prime.dat | 0
{dnarbd => mrdna}/resources/C-fwd-5prime.dihedrals.txt | 0
{dnarbd => mrdna}/resources/C-fwd-5prime.impropers.txt | 0
{dnarbd => mrdna}/resources/C-fwd-singlet.angles.txt | 0
{dnarbd => mrdna}/resources/C-fwd-singlet.bonds.txt | 0
{dnarbd => mrdna}/resources/C-fwd-singlet.dat | 0
.../resources/C-fwd-singlet.dihedrals.txt | 0
.../resources/C-fwd-singlet.impropers.txt | 0
{dnarbd => mrdna}/resources/C-fwd.angles.txt | 0
{dnarbd => mrdna}/resources/C-fwd.bonds.txt | 0
{dnarbd => mrdna}/resources/C-fwd.dat | 0
{dnarbd => mrdna}/resources/C-fwd.dihedrals.txt | 0
{dnarbd => mrdna}/resources/C-fwd.impropers.txt | 0
{dnarbd => mrdna}/resources/C-rev-3prime.angles.txt | 0
{dnarbd => mrdna}/resources/C-rev-3prime.bonds.txt | 0
{dnarbd => mrdna}/resources/C-rev-3prime.dat | 0
{dnarbd => mrdna}/resources/C-rev-3prime.dihedrals.txt | 0
{dnarbd => mrdna}/resources/C-rev-3prime.impropers.txt | 0
{dnarbd => mrdna}/resources/C-rev-5prime.angles.txt | 0
{dnarbd => mrdna}/resources/C-rev-5prime.bonds.txt | 0
{dnarbd => mrdna}/resources/C-rev-5prime.dat | 0
{dnarbd => mrdna}/resources/C-rev-5prime.dihedrals.txt | 0
{dnarbd => mrdna}/resources/C-rev-5prime.impropers.txt | 0
{dnarbd => mrdna}/resources/C-rev-singlet.angles.txt | 0
{dnarbd => mrdna}/resources/C-rev-singlet.bonds.txt | 0
{dnarbd => mrdna}/resources/C-rev-singlet.dat | 0
.../resources/C-rev-singlet.dihedrals.txt | 0
.../resources/C-rev-singlet.impropers.txt | 0
{dnarbd => mrdna}/resources/C-rev.angles.txt | 0
{dnarbd => mrdna}/resources/C-rev.bonds.txt | 0
{dnarbd => mrdna}/resources/C-rev.dat | 0
{dnarbd => mrdna}/resources/C-rev.dihedrals.txt | 0
{dnarbd => mrdna}/resources/C-rev.impropers.txt | 0
{dnarbd => mrdna}/resources/G-fwd-3prime.angles.txt | 0
{dnarbd => mrdna}/resources/G-fwd-3prime.bonds.txt | 0
{dnarbd => mrdna}/resources/G-fwd-3prime.dat | 0
{dnarbd => mrdna}/resources/G-fwd-3prime.dihedrals.txt | 0
{dnarbd => mrdna}/resources/G-fwd-3prime.impropers.txt | 0
{dnarbd => mrdna}/resources/G-fwd-5prime.angles.txt | 0
{dnarbd => mrdna}/resources/G-fwd-5prime.bonds.txt | 0
{dnarbd => mrdna}/resources/G-fwd-5prime.dat | 0
{dnarbd => mrdna}/resources/G-fwd-5prime.dihedrals.txt | 0
{dnarbd => mrdna}/resources/G-fwd-5prime.impropers.txt | 0
{dnarbd => mrdna}/resources/G-fwd-singlet.angles.txt | 0
{dnarbd => mrdna}/resources/G-fwd-singlet.bonds.txt | 0
{dnarbd => mrdna}/resources/G-fwd-singlet.dat | 0
.../resources/G-fwd-singlet.dihedrals.txt | 0
.../resources/G-fwd-singlet.impropers.txt | 0
{dnarbd => mrdna}/resources/G-fwd.angles.txt | 0
{dnarbd => mrdna}/resources/G-fwd.bonds.txt | 0
{dnarbd => mrdna}/resources/G-fwd.dat | 0
{dnarbd => mrdna}/resources/G-fwd.dihedrals.txt | 0
{dnarbd => mrdna}/resources/G-fwd.impropers.txt | 0
{dnarbd => mrdna}/resources/G-rev-3prime.angles.txt | 0
{dnarbd => mrdna}/resources/G-rev-3prime.bonds.txt | 0
{dnarbd => mrdna}/resources/G-rev-3prime.dat | 0
{dnarbd => mrdna}/resources/G-rev-3prime.dihedrals.txt | 0
{dnarbd => mrdna}/resources/G-rev-3prime.impropers.txt | 0
{dnarbd => mrdna}/resources/G-rev-5prime.angles.txt | 0
{dnarbd => mrdna}/resources/G-rev-5prime.bonds.txt | 0
{dnarbd => mrdna}/resources/G-rev-5prime.dat | 0
{dnarbd => mrdna}/resources/G-rev-5prime.dihedrals.txt | 0
{dnarbd => mrdna}/resources/G-rev-5prime.impropers.txt | 0
{dnarbd => mrdna}/resources/G-rev-singlet.angles.txt | 0
{dnarbd => mrdna}/resources/G-rev-singlet.bonds.txt | 0
{dnarbd => mrdna}/resources/G-rev-singlet.dat | 0
.../resources/G-rev-singlet.dihedrals.txt | 0
.../resources/G-rev-singlet.impropers.txt | 0
{dnarbd => mrdna}/resources/G-rev.angles.txt | 0
{dnarbd => mrdna}/resources/G-rev.bonds.txt | 0
{dnarbd => mrdna}/resources/G-rev.dat | 0
{dnarbd => mrdna}/resources/G-rev.dihedrals.txt | 0
{dnarbd => mrdna}/resources/G-rev.impropers.txt | 0
{dnarbd => mrdna}/resources/T-fwd-3prime.angles.txt | 0
{dnarbd => mrdna}/resources/T-fwd-3prime.bonds.txt | 0
{dnarbd => mrdna}/resources/T-fwd-3prime.dat | 0
{dnarbd => mrdna}/resources/T-fwd-3prime.dihedrals.txt | 0
{dnarbd => mrdna}/resources/T-fwd-3prime.impropers.txt | 0
{dnarbd => mrdna}/resources/T-fwd-5prime.angles.txt | 0
{dnarbd => mrdna}/resources/T-fwd-5prime.bonds.txt | 0
{dnarbd => mrdna}/resources/T-fwd-5prime.dat | 0
{dnarbd => mrdna}/resources/T-fwd-5prime.dihedrals.txt | 0
{dnarbd => mrdna}/resources/T-fwd-5prime.impropers.txt | 0
{dnarbd => mrdna}/resources/T-fwd-singlet.angles.txt | 0
{dnarbd => mrdna}/resources/T-fwd-singlet.bonds.txt | 0
{dnarbd => mrdna}/resources/T-fwd-singlet.dat | 0
.../resources/T-fwd-singlet.dihedrals.txt | 0
.../resources/T-fwd-singlet.impropers.txt | 0
{dnarbd => mrdna}/resources/T-fwd.angles.txt | 0
{dnarbd => mrdna}/resources/T-fwd.bonds.txt | 0
{dnarbd => mrdna}/resources/T-fwd.dat | 0
{dnarbd => mrdna}/resources/T-fwd.dihedrals.txt | 0
{dnarbd => mrdna}/resources/T-fwd.impropers.txt | 0
{dnarbd => mrdna}/resources/T-rev-3prime.angles.txt | 0
{dnarbd => mrdna}/resources/T-rev-3prime.bonds.txt | 0
{dnarbd => mrdna}/resources/T-rev-3prime.dat | 0
{dnarbd => mrdna}/resources/T-rev-3prime.dihedrals.txt | 0
{dnarbd => mrdna}/resources/T-rev-3prime.impropers.txt | 0
{dnarbd => mrdna}/resources/T-rev-5prime.angles.txt | 0
{dnarbd => mrdna}/resources/T-rev-5prime.bonds.txt | 0
{dnarbd => mrdna}/resources/T-rev-5prime.dat | 0
{dnarbd => mrdna}/resources/T-rev-5prime.dihedrals.txt | 0
{dnarbd => mrdna}/resources/T-rev-5prime.impropers.txt | 0
{dnarbd => mrdna}/resources/T-rev-singlet.angles.txt | 0
{dnarbd => mrdna}/resources/T-rev-singlet.bonds.txt | 0
{dnarbd => mrdna}/resources/T-rev-singlet.dat | 0
.../resources/T-rev-singlet.dihedrals.txt | 0
.../resources/T-rev-singlet.impropers.txt | 0
{dnarbd => mrdna}/resources/T-rev.angles.txt | 0
{dnarbd => mrdna}/resources/T-rev.bonds.txt | 0
{dnarbd => mrdna}/resources/T-rev.dat | 0
{dnarbd => mrdna}/resources/T-rev.dihedrals.txt | 0
{dnarbd => mrdna}/resources/T-rev.impropers.txt | 0
.../resources/cadnano2pdb.seq.m13mp18.dat | 0
.../resources/charmm36.nbfix/par_all36_na.prm | 0
.../resources/charmm36.nbfix/par_water_ions_na.prm | 0
.../resources/charmm36.nbfix/top_all36_na.rtf | 0
.../resources/enm-corrections-honecomb.json | 0
.../resources/enm-template-honeycomb.json | 0
{dnarbd => mrdna}/resources/enm-template-square.json | 0
.../enm-templates/.backup/convert-tcl-to-dict.py~ | 0
.../resources/enm-templates/convert-tcl-to-dict.py | 0
.../resources/enm-templates/corrections.tcl | 0
.../resources/enm-templates/template-exb-square.tcl | 0
.../resources/enm-templates/template-exb.tcl | 0
.../resources/generate-nts/.backup/build.tcl~ | 0
.../resources/generate-nts/1-w3dna/AT.pdb | 0
.../resources/generate-nts/1-w3dna/CG.pdb | 0
.../resources/generate-nts/1-w3dna/GC.pdb | 0
.../resources/generate-nts/1-w3dna/TA.pdb | 0
{dnarbd => mrdna}/resources/generate-nts/build.tcl | 0
.../resources/generate-nts/charmm36/top_all36_na.rtf | 0
{dnarbd => mrdna}/resources/jj-nar-dna-pmf-100Mg.dat | 0
.../resources/jj-nar-dna-pmf-20Mg-200Na.dat | 0
{dnarbd => mrdna}/resources/json/bend-000.json | 0
{dnarbd => mrdna}/resources/json/bend-030.json | 0
{dnarbd => mrdna}/resources/json/bend-060.json | 0
{dnarbd => mrdna}/resources/json/bend-090.json | 0
{dnarbd => mrdna}/resources/json/bend-120.json | 0
{dnarbd => mrdna}/resources/json/bend-150.json | 0
{dnarbd => mrdna}/resources/json/bend-180.json | 0
{dnarbd => mrdna}/resources/json/gear180-mod.json | 0
{dnarbd => mrdna}/resources/json/left-twist-mod2.json | 0
.../resources/json/pointer_v1_12_from_dietz.json | 0
{dnarbd => mrdna}/resources/json/right-twist-mod2.json | 0
{dnarbd => mrdna}/resources/json/robot_v1.9_bent.json | 0
{dnarbd => mrdna}/segmentmodel.py | 0
{dnarbd => mrdna}/simulate.py | 0
setup.py | 8 ++++----
214 files changed, 15 insertions(+), 15 deletions(-)
rename bin/{dnarbd => mrdna} (89%)
rename {dnarbd => mrdna}/__init__.py (100%)
rename {dnarbd => mrdna}/coords.py (100%)
rename {dnarbd => mrdna}/examples/from_cadnano.py (87%)
rename {dnarbd => mrdna}/examples/from_code.py (91%)
rename {dnarbd => mrdna}/model/CanonicalNucleotideAtoms.py (100%)
rename {dnarbd => mrdna}/model/__init__.py (100%)
rename {dnarbd => mrdna}/model/arbdmodel.py (100%)
rename {dnarbd => mrdna}/model/dna_sequence.py (100%)
rename {dnarbd => mrdna}/model/nbPot.py (100%)
rename {dnarbd => mrdna}/model/nonbonded.py (100%)
rename {dnarbd => mrdna}/readers/__init__.py (100%)
rename {dnarbd => mrdna}/readers/cadnano_segments.py (100%)
rename {dnarbd => mrdna}/readers/polygon_mesh.py (100%)
rename {dnarbd => mrdna}/readers/segmentmodel_from_lists.py (100%)
rename {dnarbd => mrdna}/readers/segmentmodel_from_pdb.py (100%)
rename {dnarbd => mrdna}/resources/A-fwd-3prime.angles.txt (100%)
rename {dnarbd => mrdna}/resources/A-fwd-3prime.bonds.txt (100%)
rename {dnarbd => mrdna}/resources/A-fwd-3prime.dat (100%)
rename {dnarbd => mrdna}/resources/A-fwd-3prime.dihedrals.txt (100%)
rename {dnarbd => mrdna}/resources/A-fwd-3prime.impropers.txt (100%)
rename {dnarbd => mrdna}/resources/A-fwd-5prime.angles.txt (100%)
rename {dnarbd => mrdna}/resources/A-fwd-5prime.bonds.txt (100%)
rename {dnarbd => mrdna}/resources/A-fwd-5prime.dat (100%)
rename {dnarbd => mrdna}/resources/A-fwd-5prime.dihedrals.txt (100%)
rename {dnarbd => mrdna}/resources/A-fwd-5prime.impropers.txt (100%)
rename {dnarbd => mrdna}/resources/A-fwd-singlet.angles.txt (100%)
rename {dnarbd => mrdna}/resources/A-fwd-singlet.bonds.txt (100%)
rename {dnarbd => mrdna}/resources/A-fwd-singlet.dat (100%)
rename {dnarbd => mrdna}/resources/A-fwd-singlet.dihedrals.txt (100%)
rename {dnarbd => mrdna}/resources/A-fwd-singlet.impropers.txt (100%)
rename {dnarbd => mrdna}/resources/A-fwd.angles.txt (100%)
rename {dnarbd => mrdna}/resources/A-fwd.bonds.txt (100%)
rename {dnarbd => mrdna}/resources/A-fwd.dat (100%)
rename {dnarbd => mrdna}/resources/A-fwd.dihedrals.txt (100%)
rename {dnarbd => mrdna}/resources/A-fwd.impropers.txt (100%)
rename {dnarbd => mrdna}/resources/A-rev-3prime.angles.txt (100%)
rename {dnarbd => mrdna}/resources/A-rev-3prime.bonds.txt (100%)
rename {dnarbd => mrdna}/resources/A-rev-3prime.dat (100%)
rename {dnarbd => mrdna}/resources/A-rev-3prime.dihedrals.txt (100%)
rename {dnarbd => mrdna}/resources/A-rev-3prime.impropers.txt (100%)
rename {dnarbd => mrdna}/resources/A-rev-5prime.angles.txt (100%)
rename {dnarbd => mrdna}/resources/A-rev-5prime.bonds.txt (100%)
rename {dnarbd => mrdna}/resources/A-rev-5prime.dat (100%)
rename {dnarbd => mrdna}/resources/A-rev-5prime.dihedrals.txt (100%)
rename {dnarbd => mrdna}/resources/A-rev-5prime.impropers.txt (100%)
rename {dnarbd => mrdna}/resources/A-rev-singlet.angles.txt (100%)
rename {dnarbd => mrdna}/resources/A-rev-singlet.bonds.txt (100%)
rename {dnarbd => mrdna}/resources/A-rev-singlet.dat (100%)
rename {dnarbd => mrdna}/resources/A-rev-singlet.dihedrals.txt (100%)
rename {dnarbd => mrdna}/resources/A-rev-singlet.impropers.txt (100%)
rename {dnarbd => mrdna}/resources/A-rev.angles.txt (100%)
rename {dnarbd => mrdna}/resources/A-rev.bonds.txt (100%)
rename {dnarbd => mrdna}/resources/A-rev.dat (100%)
rename {dnarbd => mrdna}/resources/A-rev.dihedrals.txt (100%)
rename {dnarbd => mrdna}/resources/A-rev.impropers.txt (100%)
rename {dnarbd => mrdna}/resources/C-fwd-3prime.angles.txt (100%)
rename {dnarbd => mrdna}/resources/C-fwd-3prime.bonds.txt (100%)
rename {dnarbd => mrdna}/resources/C-fwd-3prime.dat (100%)
rename {dnarbd => mrdna}/resources/C-fwd-3prime.dihedrals.txt (100%)
rename {dnarbd => mrdna}/resources/C-fwd-3prime.impropers.txt (100%)
rename {dnarbd => mrdna}/resources/C-fwd-5prime.angles.txt (100%)
rename {dnarbd => mrdna}/resources/C-fwd-5prime.bonds.txt (100%)
rename {dnarbd => mrdna}/resources/C-fwd-5prime.dat (100%)
rename {dnarbd => mrdna}/resources/C-fwd-5prime.dihedrals.txt (100%)
rename {dnarbd => mrdna}/resources/C-fwd-5prime.impropers.txt (100%)
rename {dnarbd => mrdna}/resources/C-fwd-singlet.angles.txt (100%)
rename {dnarbd => mrdna}/resources/C-fwd-singlet.bonds.txt (100%)
rename {dnarbd => mrdna}/resources/C-fwd-singlet.dat (100%)
rename {dnarbd => mrdna}/resources/C-fwd-singlet.dihedrals.txt (100%)
rename {dnarbd => mrdna}/resources/C-fwd-singlet.impropers.txt (100%)
rename {dnarbd => mrdna}/resources/C-fwd.angles.txt (100%)
rename {dnarbd => mrdna}/resources/C-fwd.bonds.txt (100%)
rename {dnarbd => mrdna}/resources/C-fwd.dat (100%)
rename {dnarbd => mrdna}/resources/C-fwd.dihedrals.txt (100%)
rename {dnarbd => mrdna}/resources/C-fwd.impropers.txt (100%)
rename {dnarbd => mrdna}/resources/C-rev-3prime.angles.txt (100%)
rename {dnarbd => mrdna}/resources/C-rev-3prime.bonds.txt (100%)
rename {dnarbd => mrdna}/resources/C-rev-3prime.dat (100%)
rename {dnarbd => mrdna}/resources/C-rev-3prime.dihedrals.txt (100%)
rename {dnarbd => mrdna}/resources/C-rev-3prime.impropers.txt (100%)
rename {dnarbd => mrdna}/resources/C-rev-5prime.angles.txt (100%)
rename {dnarbd => mrdna}/resources/C-rev-5prime.bonds.txt (100%)
rename {dnarbd => mrdna}/resources/C-rev-5prime.dat (100%)
rename {dnarbd => mrdna}/resources/C-rev-5prime.dihedrals.txt (100%)
rename {dnarbd => mrdna}/resources/C-rev-5prime.impropers.txt (100%)
rename {dnarbd => mrdna}/resources/C-rev-singlet.angles.txt (100%)
rename {dnarbd => mrdna}/resources/C-rev-singlet.bonds.txt (100%)
rename {dnarbd => mrdna}/resources/C-rev-singlet.dat (100%)
rename {dnarbd => mrdna}/resources/C-rev-singlet.dihedrals.txt (100%)
rename {dnarbd => mrdna}/resources/C-rev-singlet.impropers.txt (100%)
rename {dnarbd => mrdna}/resources/C-rev.angles.txt (100%)
rename {dnarbd => mrdna}/resources/C-rev.bonds.txt (100%)
rename {dnarbd => mrdna}/resources/C-rev.dat (100%)
rename {dnarbd => mrdna}/resources/C-rev.dihedrals.txt (100%)
rename {dnarbd => mrdna}/resources/C-rev.impropers.txt (100%)
rename {dnarbd => mrdna}/resources/G-fwd-3prime.angles.txt (100%)
rename {dnarbd => mrdna}/resources/G-fwd-3prime.bonds.txt (100%)
rename {dnarbd => mrdna}/resources/G-fwd-3prime.dat (100%)
rename {dnarbd => mrdna}/resources/G-fwd-3prime.dihedrals.txt (100%)
rename {dnarbd => mrdna}/resources/G-fwd-3prime.impropers.txt (100%)
rename {dnarbd => mrdna}/resources/G-fwd-5prime.angles.txt (100%)
rename {dnarbd => mrdna}/resources/G-fwd-5prime.bonds.txt (100%)
rename {dnarbd => mrdna}/resources/G-fwd-5prime.dat (100%)
rename {dnarbd => mrdna}/resources/G-fwd-5prime.dihedrals.txt (100%)
rename {dnarbd => mrdna}/resources/G-fwd-5prime.impropers.txt (100%)
rename {dnarbd => mrdna}/resources/G-fwd-singlet.angles.txt (100%)
rename {dnarbd => mrdna}/resources/G-fwd-singlet.bonds.txt (100%)
rename {dnarbd => mrdna}/resources/G-fwd-singlet.dat (100%)
rename {dnarbd => mrdna}/resources/G-fwd-singlet.dihedrals.txt (100%)
rename {dnarbd => mrdna}/resources/G-fwd-singlet.impropers.txt (100%)
rename {dnarbd => mrdna}/resources/G-fwd.angles.txt (100%)
rename {dnarbd => mrdna}/resources/G-fwd.bonds.txt (100%)
rename {dnarbd => mrdna}/resources/G-fwd.dat (100%)
rename {dnarbd => mrdna}/resources/G-fwd.dihedrals.txt (100%)
rename {dnarbd => mrdna}/resources/G-fwd.impropers.txt (100%)
rename {dnarbd => mrdna}/resources/G-rev-3prime.angles.txt (100%)
rename {dnarbd => mrdna}/resources/G-rev-3prime.bonds.txt (100%)
rename {dnarbd => mrdna}/resources/G-rev-3prime.dat (100%)
rename {dnarbd => mrdna}/resources/G-rev-3prime.dihedrals.txt (100%)
rename {dnarbd => mrdna}/resources/G-rev-3prime.impropers.txt (100%)
rename {dnarbd => mrdna}/resources/G-rev-5prime.angles.txt (100%)
rename {dnarbd => mrdna}/resources/G-rev-5prime.bonds.txt (100%)
rename {dnarbd => mrdna}/resources/G-rev-5prime.dat (100%)
rename {dnarbd => mrdna}/resources/G-rev-5prime.dihedrals.txt (100%)
rename {dnarbd => mrdna}/resources/G-rev-5prime.impropers.txt (100%)
rename {dnarbd => mrdna}/resources/G-rev-singlet.angles.txt (100%)
rename {dnarbd => mrdna}/resources/G-rev-singlet.bonds.txt (100%)
rename {dnarbd => mrdna}/resources/G-rev-singlet.dat (100%)
rename {dnarbd => mrdna}/resources/G-rev-singlet.dihedrals.txt (100%)
rename {dnarbd => mrdna}/resources/G-rev-singlet.impropers.txt (100%)
rename {dnarbd => mrdna}/resources/G-rev.angles.txt (100%)
rename {dnarbd => mrdna}/resources/G-rev.bonds.txt (100%)
rename {dnarbd => mrdna}/resources/G-rev.dat (100%)
rename {dnarbd => mrdna}/resources/G-rev.dihedrals.txt (100%)
rename {dnarbd => mrdna}/resources/G-rev.impropers.txt (100%)
rename {dnarbd => mrdna}/resources/T-fwd-3prime.angles.txt (100%)
rename {dnarbd => mrdna}/resources/T-fwd-3prime.bonds.txt (100%)
rename {dnarbd => mrdna}/resources/T-fwd-3prime.dat (100%)
rename {dnarbd => mrdna}/resources/T-fwd-3prime.dihedrals.txt (100%)
rename {dnarbd => mrdna}/resources/T-fwd-3prime.impropers.txt (100%)
rename {dnarbd => mrdna}/resources/T-fwd-5prime.angles.txt (100%)
rename {dnarbd => mrdna}/resources/T-fwd-5prime.bonds.txt (100%)
rename {dnarbd => mrdna}/resources/T-fwd-5prime.dat (100%)
rename {dnarbd => mrdna}/resources/T-fwd-5prime.dihedrals.txt (100%)
rename {dnarbd => mrdna}/resources/T-fwd-5prime.impropers.txt (100%)
rename {dnarbd => mrdna}/resources/T-fwd-singlet.angles.txt (100%)
rename {dnarbd => mrdna}/resources/T-fwd-singlet.bonds.txt (100%)
rename {dnarbd => mrdna}/resources/T-fwd-singlet.dat (100%)
rename {dnarbd => mrdna}/resources/T-fwd-singlet.dihedrals.txt (100%)
rename {dnarbd => mrdna}/resources/T-fwd-singlet.impropers.txt (100%)
rename {dnarbd => mrdna}/resources/T-fwd.angles.txt (100%)
rename {dnarbd => mrdna}/resources/T-fwd.bonds.txt (100%)
rename {dnarbd => mrdna}/resources/T-fwd.dat (100%)
rename {dnarbd => mrdna}/resources/T-fwd.dihedrals.txt (100%)
rename {dnarbd => mrdna}/resources/T-fwd.impropers.txt (100%)
rename {dnarbd => mrdna}/resources/T-rev-3prime.angles.txt (100%)
rename {dnarbd => mrdna}/resources/T-rev-3prime.bonds.txt (100%)
rename {dnarbd => mrdna}/resources/T-rev-3prime.dat (100%)
rename {dnarbd => mrdna}/resources/T-rev-3prime.dihedrals.txt (100%)
rename {dnarbd => mrdna}/resources/T-rev-3prime.impropers.txt (100%)
rename {dnarbd => mrdna}/resources/T-rev-5prime.angles.txt (100%)
rename {dnarbd => mrdna}/resources/T-rev-5prime.bonds.txt (100%)
rename {dnarbd => mrdna}/resources/T-rev-5prime.dat (100%)
rename {dnarbd => mrdna}/resources/T-rev-5prime.dihedrals.txt (100%)
rename {dnarbd => mrdna}/resources/T-rev-5prime.impropers.txt (100%)
rename {dnarbd => mrdna}/resources/T-rev-singlet.angles.txt (100%)
rename {dnarbd => mrdna}/resources/T-rev-singlet.bonds.txt (100%)
rename {dnarbd => mrdna}/resources/T-rev-singlet.dat (100%)
rename {dnarbd => mrdna}/resources/T-rev-singlet.dihedrals.txt (100%)
rename {dnarbd => mrdna}/resources/T-rev-singlet.impropers.txt (100%)
rename {dnarbd => mrdna}/resources/T-rev.angles.txt (100%)
rename {dnarbd => mrdna}/resources/T-rev.bonds.txt (100%)
rename {dnarbd => mrdna}/resources/T-rev.dat (100%)
rename {dnarbd => mrdna}/resources/T-rev.dihedrals.txt (100%)
rename {dnarbd => mrdna}/resources/T-rev.impropers.txt (100%)
rename {dnarbd => mrdna}/resources/cadnano2pdb.seq.m13mp18.dat (100%)
rename {dnarbd => mrdna}/resources/charmm36.nbfix/par_all36_na.prm (100%)
rename {dnarbd => mrdna}/resources/charmm36.nbfix/par_water_ions_na.prm (100%)
rename {dnarbd => mrdna}/resources/charmm36.nbfix/top_all36_na.rtf (100%)
rename {dnarbd => mrdna}/resources/enm-corrections-honecomb.json (100%)
rename {dnarbd => mrdna}/resources/enm-template-honeycomb.json (100%)
rename {dnarbd => mrdna}/resources/enm-template-square.json (100%)
rename {dnarbd => mrdna}/resources/enm-templates/.backup/convert-tcl-to-dict.py~ (100%)
rename {dnarbd => mrdna}/resources/enm-templates/convert-tcl-to-dict.py (100%)
rename {dnarbd => mrdna}/resources/enm-templates/corrections.tcl (100%)
rename {dnarbd => mrdna}/resources/enm-templates/template-exb-square.tcl (100%)
rename {dnarbd => mrdna}/resources/enm-templates/template-exb.tcl (100%)
rename {dnarbd => mrdna}/resources/generate-nts/.backup/build.tcl~ (100%)
rename {dnarbd => mrdna}/resources/generate-nts/1-w3dna/AT.pdb (100%)
rename {dnarbd => mrdna}/resources/generate-nts/1-w3dna/CG.pdb (100%)
rename {dnarbd => mrdna}/resources/generate-nts/1-w3dna/GC.pdb (100%)
rename {dnarbd => mrdna}/resources/generate-nts/1-w3dna/TA.pdb (100%)
rename {dnarbd => mrdna}/resources/generate-nts/build.tcl (100%)
rename {dnarbd => mrdna}/resources/generate-nts/charmm36/top_all36_na.rtf (100%)
rename {dnarbd => mrdna}/resources/jj-nar-dna-pmf-100Mg.dat (100%)
rename {dnarbd => mrdna}/resources/jj-nar-dna-pmf-20Mg-200Na.dat (100%)
rename {dnarbd => mrdna}/resources/json/bend-000.json (100%)
rename {dnarbd => mrdna}/resources/json/bend-030.json (100%)
rename {dnarbd => mrdna}/resources/json/bend-060.json (100%)
rename {dnarbd => mrdna}/resources/json/bend-090.json (100%)
rename {dnarbd => mrdna}/resources/json/bend-120.json (100%)
rename {dnarbd => mrdna}/resources/json/bend-150.json (100%)
rename {dnarbd => mrdna}/resources/json/bend-180.json (100%)
rename {dnarbd => mrdna}/resources/json/gear180-mod.json (100%)
rename {dnarbd => mrdna}/resources/json/left-twist-mod2.json (100%)
rename {dnarbd => mrdna}/resources/json/pointer_v1_12_from_dietz.json (100%)
rename {dnarbd => mrdna}/resources/json/right-twist-mod2.json (100%)
rename {dnarbd => mrdna}/resources/json/robot_v1.9_bent.json (100%)
rename {dnarbd => mrdna}/segmentmodel.py (100%)
rename {dnarbd => mrdna}/simulate.py (100%)
diff --git a/MANIFEST.in b/MANIFEST.in
index 37f9a31..cb825ec 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -1 +1 @@
-recursive-include dnarbd/resources *
\ No newline at end of file
+recursive-include mrdna/resources *
\ No newline at end of file
diff --git a/README.md b/README.md
index c325ac4..e918603 100644
--- a/README.md
+++ b/README.md
@@ -1,3 +1,3 @@
-# DNArbd: multiresolution coarse-grained simulations of DNA nanotechnology
+# Multi-Resolution DNA simulations
...
diff --git a/bin/dnarbd b/bin/mrdna
similarity index 89%
rename from bin/dnarbd
rename to bin/mrdna
index f03ba6c..ed63432 100755
--- a/bin/dnarbd
+++ b/bin/mrdna
@@ -4,9 +4,9 @@
import argparse
import re
import pathlib
-from dnarbd.simulate import multiresolution_simulation as simulate
+from mrdna.simulate import multiresolution_simulation as simulate
-parser = argparse.ArgumentParser(prog="dnarbd",
+parser = argparse.ArgumentParser(prog="mrdna",
description="""Easy multiresolution simulations of DNA nanotechnology objects using ARBD""")
parser.add_argument('-o','--output-prefix', type=str, default=None,
@@ -42,11 +42,11 @@ if __name__ == '__main__':
raise Exception("Unrecognized input file '{}'".format(infile))
if extension == '.json':
- from dnarbd.readers import read_cadnano as read_model
+ from mrdna.readers import read_cadnano as read_model
elif extension == '.ma':
- from dnarbd.readers import read_vhelix as read_model
+ from mrdna.readers import read_vhelix as read_model
elif extension == '.pdb':
- from dnarbd.readers import read_atomic_pdb as read_model
+ from mrdna.readers import read_atomic_pdb as read_model
else:
raise Exception("Unrecognized input file '{}'".format(infile))
diff --git a/dnarbd/__init__.py b/mrdna/__init__.py
similarity index 100%
rename from dnarbd/__init__.py
rename to mrdna/__init__.py
diff --git a/dnarbd/coords.py b/mrdna/coords.py
similarity index 100%
rename from dnarbd/coords.py
rename to mrdna/coords.py
diff --git a/dnarbd/examples/from_cadnano.py b/mrdna/examples/from_cadnano.py
similarity index 87%
rename from dnarbd/examples/from_cadnano.py
rename to mrdna/examples/from_cadnano.py
index 8e03586..982a9c5 100644
--- a/dnarbd/examples/from_cadnano.py
+++ b/mrdna/examples/from_cadnano.py
@@ -3,8 +3,8 @@ import sys
from glob import glob
import re
-from dnarbd.readers import cadnano_reader()
-from dnarbd.simulate import run_multiresolution_simulation as simulate
+from mrdna.readers import cadnano_reader()
+from mrdna.simulate import run_multiresolution_simulation as simulate
if __name__ == '__main__':
if len(sys.argv) > 1:
diff --git a/dnarbd/examples/from_code.py b/mrdna/examples/from_code.py
similarity index 91%
rename from dnarbd/examples/from_code.py
rename to mrdna/examples/from_code.py
index 557f4ab..54e5e80 100644
--- a/dnarbd/examples/from_code.py
+++ b/mrdna/examples/from_code.py
@@ -1,6 +1,6 @@
import numpy as np
-from dnarbd import SegmentModel, SingleStrandedSegment, DoubleStrandedSegment
-from dnarbd.simulate import run_multiresolution_simulation as simulate
+from mrdna import SegmentModel, SingleStrandedSegment, DoubleStrandedSegment
+from mrdna.simulate import run_multiresolution_simulation as simulate
"""
Example using segmentmodel API to construct a model
diff --git a/dnarbd/model/CanonicalNucleotideAtoms.py b/mrdna/model/CanonicalNucleotideAtoms.py
similarity index 100%
rename from dnarbd/model/CanonicalNucleotideAtoms.py
rename to mrdna/model/CanonicalNucleotideAtoms.py
diff --git a/dnarbd/model/__init__.py b/mrdna/model/__init__.py
similarity index 100%
rename from dnarbd/model/__init__.py
rename to mrdna/model/__init__.py
diff --git a/dnarbd/model/arbdmodel.py b/mrdna/model/arbdmodel.py
similarity index 100%
rename from dnarbd/model/arbdmodel.py
rename to mrdna/model/arbdmodel.py
diff --git a/dnarbd/model/dna_sequence.py b/mrdna/model/dna_sequence.py
similarity index 100%
rename from dnarbd/model/dna_sequence.py
rename to mrdna/model/dna_sequence.py
diff --git a/dnarbd/model/nbPot.py b/mrdna/model/nbPot.py
similarity index 100%
rename from dnarbd/model/nbPot.py
rename to mrdna/model/nbPot.py
diff --git a/dnarbd/model/nonbonded.py b/mrdna/model/nonbonded.py
similarity index 100%
rename from dnarbd/model/nonbonded.py
rename to mrdna/model/nonbonded.py
diff --git a/dnarbd/readers/__init__.py b/mrdna/readers/__init__.py
similarity index 100%
rename from dnarbd/readers/__init__.py
rename to mrdna/readers/__init__.py
diff --git a/dnarbd/readers/cadnano_segments.py b/mrdna/readers/cadnano_segments.py
similarity index 100%
rename from dnarbd/readers/cadnano_segments.py
rename to mrdna/readers/cadnano_segments.py
diff --git a/dnarbd/readers/polygon_mesh.py b/mrdna/readers/polygon_mesh.py
similarity index 100%
rename from dnarbd/readers/polygon_mesh.py
rename to mrdna/readers/polygon_mesh.py
diff --git a/dnarbd/readers/segmentmodel_from_lists.py b/mrdna/readers/segmentmodel_from_lists.py
similarity index 100%
rename from dnarbd/readers/segmentmodel_from_lists.py
rename to mrdna/readers/segmentmodel_from_lists.py
diff --git a/dnarbd/readers/segmentmodel_from_pdb.py b/mrdna/readers/segmentmodel_from_pdb.py
similarity index 100%
rename from dnarbd/readers/segmentmodel_from_pdb.py
rename to mrdna/readers/segmentmodel_from_pdb.py
diff --git a/dnarbd/resources/A-fwd-3prime.angles.txt b/mrdna/resources/A-fwd-3prime.angles.txt
similarity index 100%
rename from dnarbd/resources/A-fwd-3prime.angles.txt
rename to mrdna/resources/A-fwd-3prime.angles.txt
diff --git a/dnarbd/resources/A-fwd-3prime.bonds.txt b/mrdna/resources/A-fwd-3prime.bonds.txt
similarity index 100%
rename from dnarbd/resources/A-fwd-3prime.bonds.txt
rename to mrdna/resources/A-fwd-3prime.bonds.txt
diff --git a/dnarbd/resources/A-fwd-3prime.dat b/mrdna/resources/A-fwd-3prime.dat
similarity index 100%
rename from dnarbd/resources/A-fwd-3prime.dat
rename to mrdna/resources/A-fwd-3prime.dat
diff --git a/dnarbd/resources/A-fwd-3prime.dihedrals.txt b/mrdna/resources/A-fwd-3prime.dihedrals.txt
similarity index 100%
rename from dnarbd/resources/A-fwd-3prime.dihedrals.txt
rename to mrdna/resources/A-fwd-3prime.dihedrals.txt
diff --git a/dnarbd/resources/A-fwd-3prime.impropers.txt b/mrdna/resources/A-fwd-3prime.impropers.txt
similarity index 100%
rename from dnarbd/resources/A-fwd-3prime.impropers.txt
rename to mrdna/resources/A-fwd-3prime.impropers.txt
diff --git a/dnarbd/resources/A-fwd-5prime.angles.txt b/mrdna/resources/A-fwd-5prime.angles.txt
similarity index 100%
rename from dnarbd/resources/A-fwd-5prime.angles.txt
rename to mrdna/resources/A-fwd-5prime.angles.txt
diff --git a/dnarbd/resources/A-fwd-5prime.bonds.txt b/mrdna/resources/A-fwd-5prime.bonds.txt
similarity index 100%
rename from dnarbd/resources/A-fwd-5prime.bonds.txt
rename to mrdna/resources/A-fwd-5prime.bonds.txt
diff --git a/dnarbd/resources/A-fwd-5prime.dat b/mrdna/resources/A-fwd-5prime.dat
similarity index 100%
rename from dnarbd/resources/A-fwd-5prime.dat
rename to mrdna/resources/A-fwd-5prime.dat
diff --git a/dnarbd/resources/A-fwd-5prime.dihedrals.txt b/mrdna/resources/A-fwd-5prime.dihedrals.txt
similarity index 100%
rename from dnarbd/resources/A-fwd-5prime.dihedrals.txt
rename to mrdna/resources/A-fwd-5prime.dihedrals.txt
diff --git a/dnarbd/resources/A-fwd-5prime.impropers.txt b/mrdna/resources/A-fwd-5prime.impropers.txt
similarity index 100%
rename from dnarbd/resources/A-fwd-5prime.impropers.txt
rename to mrdna/resources/A-fwd-5prime.impropers.txt
diff --git a/dnarbd/resources/A-fwd-singlet.angles.txt b/mrdna/resources/A-fwd-singlet.angles.txt
similarity index 100%
rename from dnarbd/resources/A-fwd-singlet.angles.txt
rename to mrdna/resources/A-fwd-singlet.angles.txt
diff --git a/dnarbd/resources/A-fwd-singlet.bonds.txt b/mrdna/resources/A-fwd-singlet.bonds.txt
similarity index 100%
rename from dnarbd/resources/A-fwd-singlet.bonds.txt
rename to mrdna/resources/A-fwd-singlet.bonds.txt
diff --git a/dnarbd/resources/A-fwd-singlet.dat b/mrdna/resources/A-fwd-singlet.dat
similarity index 100%
rename from dnarbd/resources/A-fwd-singlet.dat
rename to mrdna/resources/A-fwd-singlet.dat
diff --git a/dnarbd/resources/A-fwd-singlet.dihedrals.txt b/mrdna/resources/A-fwd-singlet.dihedrals.txt
similarity index 100%
rename from dnarbd/resources/A-fwd-singlet.dihedrals.txt
rename to mrdna/resources/A-fwd-singlet.dihedrals.txt
diff --git a/dnarbd/resources/A-fwd-singlet.impropers.txt b/mrdna/resources/A-fwd-singlet.impropers.txt
similarity index 100%
rename from dnarbd/resources/A-fwd-singlet.impropers.txt
rename to mrdna/resources/A-fwd-singlet.impropers.txt
diff --git a/dnarbd/resources/A-fwd.angles.txt b/mrdna/resources/A-fwd.angles.txt
similarity index 100%
rename from dnarbd/resources/A-fwd.angles.txt
rename to mrdna/resources/A-fwd.angles.txt
diff --git a/dnarbd/resources/A-fwd.bonds.txt b/mrdna/resources/A-fwd.bonds.txt
similarity index 100%
rename from dnarbd/resources/A-fwd.bonds.txt
rename to mrdna/resources/A-fwd.bonds.txt
diff --git a/dnarbd/resources/A-fwd.dat b/mrdna/resources/A-fwd.dat
similarity index 100%
rename from dnarbd/resources/A-fwd.dat
rename to mrdna/resources/A-fwd.dat
diff --git a/dnarbd/resources/A-fwd.dihedrals.txt b/mrdna/resources/A-fwd.dihedrals.txt
similarity index 100%
rename from dnarbd/resources/A-fwd.dihedrals.txt
rename to mrdna/resources/A-fwd.dihedrals.txt
diff --git a/dnarbd/resources/A-fwd.impropers.txt b/mrdna/resources/A-fwd.impropers.txt
similarity index 100%
rename from dnarbd/resources/A-fwd.impropers.txt
rename to mrdna/resources/A-fwd.impropers.txt
diff --git a/dnarbd/resources/A-rev-3prime.angles.txt b/mrdna/resources/A-rev-3prime.angles.txt
similarity index 100%
rename from dnarbd/resources/A-rev-3prime.angles.txt
rename to mrdna/resources/A-rev-3prime.angles.txt
diff --git a/dnarbd/resources/A-rev-3prime.bonds.txt b/mrdna/resources/A-rev-3prime.bonds.txt
similarity index 100%
rename from dnarbd/resources/A-rev-3prime.bonds.txt
rename to mrdna/resources/A-rev-3prime.bonds.txt
diff --git a/dnarbd/resources/A-rev-3prime.dat b/mrdna/resources/A-rev-3prime.dat
similarity index 100%
rename from dnarbd/resources/A-rev-3prime.dat
rename to mrdna/resources/A-rev-3prime.dat
diff --git a/dnarbd/resources/A-rev-3prime.dihedrals.txt b/mrdna/resources/A-rev-3prime.dihedrals.txt
similarity index 100%
rename from dnarbd/resources/A-rev-3prime.dihedrals.txt
rename to mrdna/resources/A-rev-3prime.dihedrals.txt
diff --git a/dnarbd/resources/A-rev-3prime.impropers.txt b/mrdna/resources/A-rev-3prime.impropers.txt
similarity index 100%
rename from dnarbd/resources/A-rev-3prime.impropers.txt
rename to mrdna/resources/A-rev-3prime.impropers.txt
diff --git a/dnarbd/resources/A-rev-5prime.angles.txt b/mrdna/resources/A-rev-5prime.angles.txt
similarity index 100%
rename from dnarbd/resources/A-rev-5prime.angles.txt
rename to mrdna/resources/A-rev-5prime.angles.txt
diff --git a/dnarbd/resources/A-rev-5prime.bonds.txt b/mrdna/resources/A-rev-5prime.bonds.txt
similarity index 100%
rename from dnarbd/resources/A-rev-5prime.bonds.txt
rename to mrdna/resources/A-rev-5prime.bonds.txt
diff --git a/dnarbd/resources/A-rev-5prime.dat b/mrdna/resources/A-rev-5prime.dat
similarity index 100%
rename from dnarbd/resources/A-rev-5prime.dat
rename to mrdna/resources/A-rev-5prime.dat
diff --git a/dnarbd/resources/A-rev-5prime.dihedrals.txt b/mrdna/resources/A-rev-5prime.dihedrals.txt
similarity index 100%
rename from dnarbd/resources/A-rev-5prime.dihedrals.txt
rename to mrdna/resources/A-rev-5prime.dihedrals.txt
diff --git a/dnarbd/resources/A-rev-5prime.impropers.txt b/mrdna/resources/A-rev-5prime.impropers.txt
similarity index 100%
rename from dnarbd/resources/A-rev-5prime.impropers.txt
rename to mrdna/resources/A-rev-5prime.impropers.txt
diff --git a/dnarbd/resources/A-rev-singlet.angles.txt b/mrdna/resources/A-rev-singlet.angles.txt
similarity index 100%
rename from dnarbd/resources/A-rev-singlet.angles.txt
rename to mrdna/resources/A-rev-singlet.angles.txt
diff --git a/dnarbd/resources/A-rev-singlet.bonds.txt b/mrdna/resources/A-rev-singlet.bonds.txt
similarity index 100%
rename from dnarbd/resources/A-rev-singlet.bonds.txt
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diff --git a/dnarbd/resources/A-rev-singlet.dat b/mrdna/resources/A-rev-singlet.dat
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similarity index 100%
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similarity index 100%
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rename to mrdna/resources/T-fwd-3prime.angles.txt
diff --git a/dnarbd/resources/T-fwd-3prime.bonds.txt b/mrdna/resources/T-fwd-3prime.bonds.txt
similarity index 100%
rename from dnarbd/resources/T-fwd-3prime.bonds.txt
rename to mrdna/resources/T-fwd-3prime.bonds.txt
diff --git a/dnarbd/resources/T-fwd-3prime.dat b/mrdna/resources/T-fwd-3prime.dat
similarity index 100%
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diff --git a/dnarbd/resources/T-fwd-3prime.dihedrals.txt b/mrdna/resources/T-fwd-3prime.dihedrals.txt
similarity index 100%
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diff --git a/dnarbd/resources/T-fwd-3prime.impropers.txt b/mrdna/resources/T-fwd-3prime.impropers.txt
similarity index 100%
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diff --git a/dnarbd/resources/T-fwd-5prime.angles.txt b/mrdna/resources/T-fwd-5prime.angles.txt
similarity index 100%
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similarity index 100%
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similarity index 100%
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similarity index 100%
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similarity index 100%
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similarity index 100%
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similarity index 100%
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similarity index 100%
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rename to mrdna/resources/T-fwd-singlet.dat
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similarity index 100%
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similarity index 100%
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similarity index 100%
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similarity index 100%
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similarity index 100%
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similarity index 100%
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similarity index 100%
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diff --git a/dnarbd/resources/T-rev-3prime.angles.txt b/mrdna/resources/T-rev-3prime.angles.txt
similarity index 100%
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rename to mrdna/resources/T-rev-3prime.angles.txt
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similarity index 100%
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similarity index 100%
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similarity index 100%
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similarity index 100%
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similarity index 100%
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similarity index 100%
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similarity index 100%
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diff --git a/dnarbd/resources/T-rev-singlet.angles.txt b/mrdna/resources/T-rev-singlet.angles.txt
similarity index 100%
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similarity index 100%
rename from dnarbd/resources/T-rev-singlet.bonds.txt
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diff --git a/dnarbd/resources/T-rev-singlet.dat b/mrdna/resources/T-rev-singlet.dat
similarity index 100%
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diff --git a/dnarbd/resources/T-rev-singlet.dihedrals.txt b/mrdna/resources/T-rev-singlet.dihedrals.txt
similarity index 100%
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similarity index 100%
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similarity index 100%
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diff --git a/dnarbd/resources/T-rev.bonds.txt b/mrdna/resources/T-rev.bonds.txt
similarity index 100%
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diff --git a/dnarbd/resources/T-rev.dat b/mrdna/resources/T-rev.dat
similarity index 100%
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rename to mrdna/resources/T-rev.dat
diff --git a/dnarbd/resources/T-rev.dihedrals.txt b/mrdna/resources/T-rev.dihedrals.txt
similarity index 100%
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diff --git a/dnarbd/resources/T-rev.impropers.txt b/mrdna/resources/T-rev.impropers.txt
similarity index 100%
rename from dnarbd/resources/T-rev.impropers.txt
rename to mrdna/resources/T-rev.impropers.txt
diff --git a/dnarbd/resources/cadnano2pdb.seq.m13mp18.dat b/mrdna/resources/cadnano2pdb.seq.m13mp18.dat
similarity index 100%
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rename to mrdna/resources/cadnano2pdb.seq.m13mp18.dat
diff --git a/dnarbd/resources/charmm36.nbfix/par_all36_na.prm b/mrdna/resources/charmm36.nbfix/par_all36_na.prm
similarity index 100%
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rename to mrdna/resources/charmm36.nbfix/par_all36_na.prm
diff --git a/dnarbd/resources/charmm36.nbfix/par_water_ions_na.prm b/mrdna/resources/charmm36.nbfix/par_water_ions_na.prm
similarity index 100%
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rename to mrdna/resources/charmm36.nbfix/par_water_ions_na.prm
diff --git a/dnarbd/resources/charmm36.nbfix/top_all36_na.rtf b/mrdna/resources/charmm36.nbfix/top_all36_na.rtf
similarity index 100%
rename from dnarbd/resources/charmm36.nbfix/top_all36_na.rtf
rename to mrdna/resources/charmm36.nbfix/top_all36_na.rtf
diff --git a/dnarbd/resources/enm-corrections-honecomb.json b/mrdna/resources/enm-corrections-honecomb.json
similarity index 100%
rename from dnarbd/resources/enm-corrections-honecomb.json
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diff --git a/dnarbd/resources/enm-template-honeycomb.json b/mrdna/resources/enm-template-honeycomb.json
similarity index 100%
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diff --git a/dnarbd/resources/enm-template-square.json b/mrdna/resources/enm-template-square.json
similarity index 100%
rename from dnarbd/resources/enm-template-square.json
rename to mrdna/resources/enm-template-square.json
diff --git a/dnarbd/resources/enm-templates/.backup/convert-tcl-to-dict.py~ b/mrdna/resources/enm-templates/.backup/convert-tcl-to-dict.py~
similarity index 100%
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diff --git a/dnarbd/resources/enm-templates/convert-tcl-to-dict.py b/mrdna/resources/enm-templates/convert-tcl-to-dict.py
similarity index 100%
rename from dnarbd/resources/enm-templates/convert-tcl-to-dict.py
rename to mrdna/resources/enm-templates/convert-tcl-to-dict.py
diff --git a/dnarbd/resources/enm-templates/corrections.tcl b/mrdna/resources/enm-templates/corrections.tcl
similarity index 100%
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rename to mrdna/resources/enm-templates/corrections.tcl
diff --git a/dnarbd/resources/enm-templates/template-exb-square.tcl b/mrdna/resources/enm-templates/template-exb-square.tcl
similarity index 100%
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diff --git a/dnarbd/resources/enm-templates/template-exb.tcl b/mrdna/resources/enm-templates/template-exb.tcl
similarity index 100%
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diff --git a/dnarbd/resources/generate-nts/.backup/build.tcl~ b/mrdna/resources/generate-nts/.backup/build.tcl~
similarity index 100%
rename from dnarbd/resources/generate-nts/.backup/build.tcl~
rename to mrdna/resources/generate-nts/.backup/build.tcl~
diff --git a/dnarbd/resources/generate-nts/1-w3dna/AT.pdb b/mrdna/resources/generate-nts/1-w3dna/AT.pdb
similarity index 100%
rename from dnarbd/resources/generate-nts/1-w3dna/AT.pdb
rename to mrdna/resources/generate-nts/1-w3dna/AT.pdb
diff --git a/dnarbd/resources/generate-nts/1-w3dna/CG.pdb b/mrdna/resources/generate-nts/1-w3dna/CG.pdb
similarity index 100%
rename from dnarbd/resources/generate-nts/1-w3dna/CG.pdb
rename to mrdna/resources/generate-nts/1-w3dna/CG.pdb
diff --git a/dnarbd/resources/generate-nts/1-w3dna/GC.pdb b/mrdna/resources/generate-nts/1-w3dna/GC.pdb
similarity index 100%
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rename to mrdna/resources/generate-nts/1-w3dna/GC.pdb
diff --git a/dnarbd/resources/generate-nts/1-w3dna/TA.pdb b/mrdna/resources/generate-nts/1-w3dna/TA.pdb
similarity index 100%
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rename to mrdna/resources/generate-nts/1-w3dna/TA.pdb
diff --git a/dnarbd/resources/generate-nts/build.tcl b/mrdna/resources/generate-nts/build.tcl
similarity index 100%
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diff --git a/dnarbd/resources/generate-nts/charmm36/top_all36_na.rtf b/mrdna/resources/generate-nts/charmm36/top_all36_na.rtf
similarity index 100%
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rename to mrdna/resources/generate-nts/charmm36/top_all36_na.rtf
diff --git a/dnarbd/resources/jj-nar-dna-pmf-100Mg.dat b/mrdna/resources/jj-nar-dna-pmf-100Mg.dat
similarity index 100%
rename from dnarbd/resources/jj-nar-dna-pmf-100Mg.dat
rename to mrdna/resources/jj-nar-dna-pmf-100Mg.dat
diff --git a/dnarbd/resources/jj-nar-dna-pmf-20Mg-200Na.dat b/mrdna/resources/jj-nar-dna-pmf-20Mg-200Na.dat
similarity index 100%
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rename to mrdna/resources/jj-nar-dna-pmf-20Mg-200Na.dat
diff --git a/dnarbd/resources/json/bend-000.json b/mrdna/resources/json/bend-000.json
similarity index 100%
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rename to mrdna/resources/json/bend-000.json
diff --git a/dnarbd/resources/json/bend-030.json b/mrdna/resources/json/bend-030.json
similarity index 100%
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diff --git a/dnarbd/resources/json/bend-060.json b/mrdna/resources/json/bend-060.json
similarity index 100%
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diff --git a/dnarbd/resources/json/bend-090.json b/mrdna/resources/json/bend-090.json
similarity index 100%
rename from dnarbd/resources/json/bend-090.json
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diff --git a/dnarbd/resources/json/bend-120.json b/mrdna/resources/json/bend-120.json
similarity index 100%
rename from dnarbd/resources/json/bend-120.json
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diff --git a/dnarbd/resources/json/bend-150.json b/mrdna/resources/json/bend-150.json
similarity index 100%
rename from dnarbd/resources/json/bend-150.json
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diff --git a/dnarbd/resources/json/bend-180.json b/mrdna/resources/json/bend-180.json
similarity index 100%
rename from dnarbd/resources/json/bend-180.json
rename to mrdna/resources/json/bend-180.json
diff --git a/dnarbd/resources/json/gear180-mod.json b/mrdna/resources/json/gear180-mod.json
similarity index 100%
rename from dnarbd/resources/json/gear180-mod.json
rename to mrdna/resources/json/gear180-mod.json
diff --git a/dnarbd/resources/json/left-twist-mod2.json b/mrdna/resources/json/left-twist-mod2.json
similarity index 100%
rename from dnarbd/resources/json/left-twist-mod2.json
rename to mrdna/resources/json/left-twist-mod2.json
diff --git a/dnarbd/resources/json/pointer_v1_12_from_dietz.json b/mrdna/resources/json/pointer_v1_12_from_dietz.json
similarity index 100%
rename from dnarbd/resources/json/pointer_v1_12_from_dietz.json
rename to mrdna/resources/json/pointer_v1_12_from_dietz.json
diff --git a/dnarbd/resources/json/right-twist-mod2.json b/mrdna/resources/json/right-twist-mod2.json
similarity index 100%
rename from dnarbd/resources/json/right-twist-mod2.json
rename to mrdna/resources/json/right-twist-mod2.json
diff --git a/dnarbd/resources/json/robot_v1.9_bent.json b/mrdna/resources/json/robot_v1.9_bent.json
similarity index 100%
rename from dnarbd/resources/json/robot_v1.9_bent.json
rename to mrdna/resources/json/robot_v1.9_bent.json
diff --git a/dnarbd/segmentmodel.py b/mrdna/segmentmodel.py
similarity index 100%
rename from dnarbd/segmentmodel.py
rename to mrdna/segmentmodel.py
diff --git a/dnarbd/simulate.py b/mrdna/simulate.py
similarity index 100%
rename from dnarbd/simulate.py
rename to mrdna/simulate.py
diff --git a/setup.py b/setup.py
index 9cf1532..4a43ce4 100644
--- a/setup.py
+++ b/setup.py
@@ -8,18 +8,18 @@ with open("LICENSE", "r") as fh:
setuptools.setup(
- name="dnarbd",
+ name="mrdna",
version="0.1.dev0",
author="Christopher Maffeo",
author_email="cmaffeo2@illinois.edu",
- description="Tools for simulating DNA nanotechnology with ARBD",
+ description="Multi-resolution DNA simulations",
license=license,
long_description=long_description,
long_description_content_type="text/markdown",
- url="https://gitlab.engr.illinois.edu/tbgl/tools/dnarbd",
+ url="https://gitlab.engr.illinois.edu/tbgl/tools/mrdna",
packages=setuptools.find_packages(),
include_package_data=True,
- scripts=['bin/dnarbd'],
+ scripts=['bin/mrdna'],
install_requires=(
'numpy>=1.14',
'scipy>=1.1',
--
GitLab