diff --git a/MANIFEST.in b/MANIFEST.in index 37f9a31562a902138a8b24f98c959be6f9d506b5..cb825ec5d567c29322bda452e835172bd298b2ab 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 c325ac4440ce7524ff4ee13c12455cf00c7e776c..e9186036dfb468680d6215886b4017ad7328b820 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 f03ba6ce6af9bca159fb79a11fc09acd26273de0..ed63432009bccfbc580eab3d2c2fe4bbb0d4ae4c 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 8e0358671c228b42c16ccd92e5aafdcb78ecb042..982a9c5662c4071993e0637168dceb29ae31a7d3 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 557f4abb4ba9571848bba737bfd4dcbee2637ac9..54e5e805edd48fa493b6a86431599c31f1f2f0c6 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 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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 rename to mrdna/resources/enm-corrections-honecomb.json diff --git a/dnarbd/resources/enm-template-honeycomb.json b/mrdna/resources/enm-template-honeycomb.json similarity index 100% rename from dnarbd/resources/enm-template-honeycomb.json rename to mrdna/resources/enm-template-honeycomb.json 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% rename from dnarbd/resources/enm-templates/.backup/convert-tcl-to-dict.py~ rename to mrdna/resources/enm-templates/.backup/convert-tcl-to-dict.py~ 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% rename from dnarbd/resources/enm-templates/corrections.tcl 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% rename from dnarbd/resources/enm-templates/template-exb-square.tcl rename to mrdna/resources/enm-templates/template-exb-square.tcl diff --git a/dnarbd/resources/enm-templates/template-exb.tcl b/mrdna/resources/enm-templates/template-exb.tcl similarity index 100% rename from dnarbd/resources/enm-templates/template-exb.tcl rename to mrdna/resources/enm-templates/template-exb.tcl 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% rename from dnarbd/resources/generate-nts/1-w3dna/GC.pdb 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% rename from dnarbd/resources/generate-nts/1-w3dna/TA.pdb 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% rename from dnarbd/resources/generate-nts/build.tcl rename to mrdna/resources/generate-nts/build.tcl 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% rename from dnarbd/resources/generate-nts/charmm36/top_all36_na.rtf 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% rename from dnarbd/resources/jj-nar-dna-pmf-20Mg-200Na.dat 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% rename from dnarbd/resources/json/bend-000.json 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% rename from dnarbd/resources/json/bend-030.json rename to mrdna/resources/json/bend-030.json diff --git a/dnarbd/resources/json/bend-060.json b/mrdna/resources/json/bend-060.json similarity index 100% rename from dnarbd/resources/json/bend-060.json rename to mrdna/resources/json/bend-060.json 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 rename to mrdna/resources/json/bend-090.json 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 rename to mrdna/resources/json/bend-120.json 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 rename to mrdna/resources/json/bend-150.json 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 9cf1532cacc6a7d692ae82a570ab068742a8ca2f..4a43ce4dd38ff22e5f14b6b5b517a3d9e314aef7 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',