rename package to VOID

learningmatter-mit · Aug 18, 2020 · 390e0e3 · 390e0e3
1 parent 596aaa2
commit 390e0e3
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Showing 65 changed files with 69 additions and 69 deletions.
diff --git a/moldocker/__init__.py → VOID/__init__.py b/moldocker/__init__.py → VOID/__init__.py
diff --git a/moldocker/dockers/__init__.py → VOID/dockers/__init__.py b/moldocker/dockers/__init__.py → VOID/dockers/__init__.py
diff --git a/moldocker/dockers/base.py → VOID/dockers/base.py b/moldocker/dockers/base.py → VOID/dockers/base.py
@@ -2,8 +2,8 @@
 from typing import List
 from pymatgen.core import Structure, Molecule
 
-from moldocker.structure import Complex
-from moldocker.object import ParseableObject
+from VOID.structure import Complex
+from VOID.object import ParseableObject
 
 
 ATTEMPTS = 50

diff --git a/moldocker/dockers/batch.py → VOID/dockers/batch.py b/moldocker/dockers/batch.py → VOID/dockers/batch.py
@@ -1,8 +1,8 @@
 import numpy as np
 
 from .base import Docker
-from moldocker.structure import Complex
-from moldocker.utils.geometry import random_rotation_matrices
+from VOID.structure import Complex
+from VOID.utils.geometry import random_rotation_matrices
 
 
 class BatchDocker(Docker):

diff --git a/moldocker/dockers/mcdocker.py → VOID/dockers/mcdocker.py b/moldocker/dockers/mcdocker.py → VOID/dockers/mcdocker.py
@@ -1,8 +1,8 @@
 import numpy as np
 
-from moldocker.structure import Complex
-from moldocker.mcarlo import Metropolis, Action
-from moldocker.dockers import Docker
+from VOID.structure import Complex
+from VOID.mcarlo import Metropolis, Action
+from VOID.dockers import Docker
 
 
 class MonteCarloDocker(Metropolis, Docker):

diff --git a/moldocker/dockers/serial.py → VOID/dockers/serial.py b/moldocker/dockers/serial.py → VOID/dockers/serial.py
@@ -1,8 +1,8 @@
 import numpy as np
 
 from .base import Docker
-from moldocker.structure import Complex
-from moldocker.utils.geometry import random_rotation_matrices
+from VOID.structure import Complex
+from VOID.utils.geometry import random_rotation_matrices
 
 
 class SerialDocker(Docker):

diff --git a/moldocker/dockers/subdock.py → VOID/dockers/subdock.py b/moldocker/dockers/subdock.py → VOID/dockers/subdock.py
@@ -1,6 +1,6 @@
 import numpy as np
 
-from moldocker.object import ParseableObject
+from VOID.object import ParseableObject
 
 
 MAX_SUBDOCK = 1

diff --git a/moldocker/dockers/success.py → VOID/dockers/success.py b/moldocker/dockers/success.py → VOID/dockers/success.py
@@ -1,8 +1,8 @@
 import numpy as np
 
-from moldocker.structure import Complex
-from moldocker.dockers.serial import SerialDocker
-from moldocker.dockers.mcdocker import MonteCarloDocker
+from VOID.structure import Complex
+from VOID.dockers.serial import SerialDocker
+from VOID.dockers.mcdocker import MonteCarloDocker
 
 
 class SuccessDocker(SerialDocker):

diff --git a/moldocker/dockers/tests/__init__.py → VOID/dockers/tests/__init__.py b/moldocker/dockers/tests/__init__.py → VOID/dockers/tests/__init__.py
diff --git a/moldocker/dockers/tests/test_batch.py → VOID/dockers/tests/test_batch.py b/moldocker/dockers/tests/test_batch.py → VOID/dockers/tests/test_batch.py
@@ -1,11 +1,11 @@
 import numpy as np
 import unittest as ut
 
-from moldocker.dockers import BatchDocker
-from moldocker.samplers import OriginSampler
-from moldocker.fitness import MinDistanceFitness
+from VOID.dockers import BatchDocker
+from VOID.samplers import OriginSampler
+from VOID.fitness import MinDistanceFitness
 
-from moldocker.tests.test_inputs import load_structure, load_molecule
+from VOID.tests.test_inputs import load_structure, load_molecule
 
 
 class TestBatch(ut.TestCase):

diff --git a/moldocker/dockers/tests/test_docker.py → VOID/dockers/tests/test_docker.py b/moldocker/dockers/tests/test_docker.py → VOID/dockers/tests/test_docker.py
@@ -1,10 +1,10 @@
 import numpy as np
 import unittest as ut
 
-from moldocker.dockers import Docker
-from moldocker.samplers import OriginSampler
+from VOID.dockers import Docker
+from VOID.samplers import OriginSampler
 
-from moldocker.tests.test_inputs import load_structure, load_molecule
+from VOID.tests.test_inputs import load_structure, load_molecule
 
 
 @ut.skip("does not execute this class")

diff --git a/moldocker/dockers/tests/test_mcdocker.py → VOID/dockers/tests/test_mcdocker.py b/moldocker/dockers/tests/test_mcdocker.py → VOID/dockers/tests/test_mcdocker.py
@@ -1,12 +1,12 @@
 import numpy as np
 import unittest as ut
 
-from moldocker.structure import Complex
-from moldocker.dockers import MonteCarloDocker
-from moldocker.samplers import OriginSampler
-from moldocker.fitness import MinDistanceFitness
+from VOID.structure import Complex
+from VOID.dockers import MonteCarloDocker
+from VOID.samplers import OriginSampler
+from VOID.fitness import MinDistanceFitness
 
-from moldocker.tests.test_inputs import load_structure, load_molecule
+from VOID.tests.test_inputs import load_structure, load_molecule
 
 
 class TestMCDocker(ut.TestCase):

diff --git a/moldocker/dockers/tests/test_subdocker.py → VOID/dockers/tests/test_subdocker.py b/moldocker/dockers/tests/test_subdocker.py → VOID/dockers/tests/test_subdocker.py
@@ -1,12 +1,12 @@
 import numpy as np
 import unittest as ut
 
-from moldocker.structure import Complex
-from moldocker.dockers import BatchDocker, Subdocker
-from moldocker.samplers import OriginSampler
-from moldocker.fitness import MinDistanceFitness
+from VOID.structure import Complex
+from VOID.dockers import BatchDocker, Subdocker
+from VOID.samplers import OriginSampler
+from VOID.fitness import MinDistanceFitness
 
-from moldocker.tests.test_inputs import load_structure, load_molecule
+from VOID.tests.test_inputs import load_structure, load_molecule
 
 
 class TestSubdocker(ut.TestCase):

diff --git a/moldocker/fitness/__init__.py → VOID/fitness/__init__.py b/moldocker/fitness/__init__.py → VOID/fitness/__init__.py
diff --git a/moldocker/fitness/base.py → VOID/fitness/base.py b/moldocker/fitness/base.py → VOID/fitness/base.py
@@ -1,4 +1,4 @@
-from moldocker.object import ParseableObject
+from VOID.object import ParseableObject
 
 
 class Fitness(ParseableObject):

diff --git a/moldocker/fitness/target.py → VOID/fitness/target.py b/moldocker/fitness/target.py → VOID/fitness/target.py
diff --git a/moldocker/fitness/threshold.py → VOID/fitness/threshold.py b/moldocker/fitness/threshold.py → VOID/fitness/threshold.py
diff --git a/moldocker/fitness/union.py → VOID/fitness/union.py b/moldocker/fitness/union.py → VOID/fitness/union.py
diff --git a/moldocker/io/cif.py → VOID/io/cif.py b/moldocker/io/cif.py → VOID/io/cif.py
diff --git a/moldocker/io/stdout.py → VOID/io/stdout.py b/moldocker/io/stdout.py → VOID/io/stdout.py
diff --git a/moldocker/io/tests/__init__.py → VOID/io/tests/__init__.py b/moldocker/io/tests/__init__.py → VOID/io/tests/__init__.py
diff --git a/moldocker/io/tests/test_cif.py → VOID/io/tests/test_cif.py b/moldocker/io/tests/test_cif.py → VOID/io/tests/test_cif.py
@@ -2,8 +2,8 @@
 import shutil
 import unittest as ut
 
-from moldocker.io import cif
-from moldocker.tests.test_inputs import load_structure, load_molecule, inpath
+from VOID.io import cif
+from VOID.tests.test_inputs import load_structure, load_molecule, inpath
 
 
 class TestCif(ut.TestCase):

diff --git a/moldocker/mcarlo/__init__.py → VOID/mcarlo/__init__.py b/moldocker/mcarlo/__init__.py → VOID/mcarlo/__init__.py
diff --git a/moldocker/mcarlo/base.py → VOID/mcarlo/base.py b/moldocker/mcarlo/base.py → VOID/mcarlo/base.py
@@ -1,4 +1,4 @@
-from moldocker.object import ParseableObject
+from VOID.object import ParseableObject
 
 
 NUM_STEPS = 50

diff --git a/moldocker/mcarlo/mcmc.py → VOID/mcarlo/mcmc.py b/moldocker/mcarlo/mcmc.py → VOID/mcarlo/mcmc.py
diff --git a/moldocker/mcarlo/metropolis.py → VOID/mcarlo/metropolis.py b/moldocker/mcarlo/metropolis.py → VOID/mcarlo/metropolis.py
diff --git a/moldocker/mcarlo/tests/__init__.py → VOID/mcarlo/tests/__init__.py b/moldocker/mcarlo/tests/__init__.py → VOID/mcarlo/tests/__init__.py
diff --git a/moldocker/mcarlo/tests/test_markovchain.py → VOID/mcarlo/tests/test_markovchain.py b/moldocker/mcarlo/tests/test_markovchain.py → VOID/mcarlo/tests/test_markovchain.py
@@ -1,8 +1,8 @@
 import numpy as np
 import unittest as ut
 
-from moldocker.mcarlo import MarkovChainMC, Action
-from moldocker.fitness import Fitness
+from VOID.mcarlo import MarkovChainMC, Action
+from VOID.fitness import Fitness
 
 
 class ExampleMCMC(MarkovChainMC):

diff --git a/moldocker/mcarlo/tests/test_metropolis.py → VOID/mcarlo/tests/test_metropolis.py b/moldocker/mcarlo/tests/test_metropolis.py → VOID/mcarlo/tests/test_metropolis.py
@@ -1,7 +1,7 @@
 import numpy as np
 import unittest as ut
 
-from moldocker.mcarlo import Metropolis, Action
+from VOID.mcarlo import Metropolis, Action
 
 
 def example_fitness(number):

diff --git a/moldocker/mcarlo/tests/test_montecarlo.py → VOID/mcarlo/tests/test_montecarlo.py b/moldocker/mcarlo/tests/test_montecarlo.py → VOID/mcarlo/tests/test_montecarlo.py
@@ -1,10 +1,10 @@
 import numpy as np
 import unittest as ut
 
-from moldocker.mcarlo import MonteCarlo
-from moldocker.fitness import Fitness
+from VOID.mcarlo import MonteCarlo
+from VOID.fitness import Fitness
 
-from moldocker.tests.test_inputs import load_structure, load_molecule
+from VOID.tests.test_inputs import load_structure, load_molecule
 
 
 class ExampleMC(MonteCarlo):

diff --git a/moldocker/object.py → VOID/object.py b/moldocker/object.py → VOID/object.py
diff --git a/moldocker/samplers/__init__.py → VOID/samplers/__init__.py b/moldocker/samplers/__init__.py → VOID/samplers/__init__.py
diff --git a/moldocker/samplers/base.py → VOID/samplers/base.py b/moldocker/samplers/base.py → VOID/samplers/base.py
@@ -1,6 +1,6 @@
 import numpy as np
 
-from moldocker.object import ParseableObject
+from VOID.object import ParseableObject
 
 
 class Sampler(ParseableObject):

diff --git a/moldocker/samplers/random.py → VOID/samplers/random.py b/moldocker/samplers/random.py → VOID/samplers/random.py
diff --git a/moldocker/samplers/tests/__init__.py → VOID/samplers/tests/__init__.py b/moldocker/samplers/tests/__init__.py → VOID/samplers/tests/__init__.py
diff --git a/moldocker/samplers/tests/test_random.py → VOID/samplers/tests/test_random.py b/moldocker/samplers/tests/test_random.py → VOID/samplers/tests/test_random.py
@@ -1,8 +1,8 @@
 import numpy as np
 import unittest as ut
 
-from moldocker.samplers import RandomSampler
-from moldocker.tests.test_inputs import load_structure, load_molecule
+from VOID.samplers import RandomSampler
+from VOID.tests.test_inputs import load_structure, load_molecule
 
 
 class TestRandomSampler(ut.TestCase):

diff --git a/moldocker/samplers/tests/test_sampler.py → VOID/samplers/tests/test_sampler.py b/moldocker/samplers/tests/test_sampler.py → VOID/samplers/tests/test_sampler.py
@@ -1,8 +1,8 @@
 import numpy as np
 import unittest as ut
 
-from moldocker.samplers import OriginSampler
-from moldocker.tests.test_inputs import load_structure, load_molecule
+from VOID.samplers import OriginSampler
+from VOID.tests.test_inputs import load_structure, load_molecule
 
 
 class TestSampler(ut.TestCase):

diff --git a/moldocker/samplers/tests/test_voronoi.py → VOID/samplers/tests/test_voronoi.py b/moldocker/samplers/tests/test_voronoi.py → VOID/samplers/tests/test_voronoi.py
@@ -1,8 +1,8 @@
 import numpy as np
 import unittest as ut
 
-from moldocker.samplers import VoronoiSampler, VoronoiClustering
-from moldocker.tests.test_inputs import load_structure, load_molecule
+from VOID.samplers import VoronoiSampler, VoronoiClustering
+from VOID.tests.test_inputs import load_structure, load_molecule
 
 
 class TestVoronoi(ut.TestCase):

diff --git a/moldocker/samplers/voronoi.py → VOID/samplers/voronoi.py b/moldocker/samplers/voronoi.py → VOID/samplers/voronoi.py
@@ -10,7 +10,7 @@
 from pymatgen.analysis.bond_valence import BVAnalyzer
 
 from .base import Sampler
-from moldocker.io.stdout import suppress_stdout
+from VOID.io.stdout import suppress_stdout
 
 
 PROBE_RADIUS = 0.1

diff --git a/moldocker/structure/__init__.py → VOID/structure/__init__.py b/moldocker/structure/__init__.py → VOID/structure/__init__.py
diff --git a/moldocker/structure/complex.py → VOID/structure/complex.py b/moldocker/structure/complex.py → VOID/structure/complex.py
@@ -2,7 +2,7 @@
 from pymatgen.core import Molecule, Structure
 
 from .molecule import MoleculeTransformer
-from moldocker.utils.geometry import random_rotation_matrices
+from VOID.utils.geometry import random_rotation_matrices
 
 
 class Complex:

diff --git a/moldocker/structure/molecule.py → VOID/structure/molecule.py b/moldocker/structure/molecule.py → VOID/structure/molecule.py
diff --git a/moldocker/structure/tests/__init__.py → VOID/structure/tests/__init__.py b/moldocker/structure/tests/__init__.py → VOID/structure/tests/__init__.py
diff --git a/moldocker/structure/tests/test_complex.py → VOID/structure/tests/test_complex.py b/moldocker/structure/tests/test_complex.py → VOID/structure/tests/test_complex.py
@@ -1,9 +1,9 @@
 import numpy as np
 import unittest as ut
 
-from moldocker.structure import Complex
-from moldocker.utils.geometry import rotation_matrix
-from moldocker.tests.test_inputs import load_structure, load_molecule
+from VOID.structure import Complex
+from VOID.utils.geometry import rotation_matrix
+from VOID.tests.test_inputs import load_structure, load_molecule
 
 
 class TestComplex(ut.TestCase):

diff --git a/...ocker/structure/tests/test_transformer.py → VOID/structure/tests/test_transformer.py b/...ocker/structure/tests/test_transformer.py → VOID/structure/tests/test_transformer.py
@@ -1,9 +1,9 @@
 import numpy as np
 import unittest as ut
 
-from moldocker.structure import MoleculeTransformer
-from moldocker.utils.geometry import rotation_matrix
-from moldocker.tests.test_inputs import load_molecule
+from VOID.structure import MoleculeTransformer
+from VOID.utils.geometry import rotation_matrix
+from VOID.tests.test_inputs import load_molecule
 
 
 class TestTransformer(ut.TestCase):

diff --git a/moldocker/tests/__init__.py → VOID/tests/__init__.py b/moldocker/tests/__init__.py → VOID/tests/__init__.py
diff --git a/moldocker/tests/files/AFI.cif → VOID/tests/files/AFI.cif b/moldocker/tests/files/AFI.cif → VOID/tests/files/AFI.cif
diff --git a/moldocker/tests/files/ammonium.xyz → VOID/tests/files/ammonium.xyz b/moldocker/tests/files/ammonium.xyz → VOID/tests/files/ammonium.xyz
diff --git a/moldocker/tests/files/molecule.xyz → VOID/tests/files/molecule.xyz b/moldocker/tests/files/molecule.xyz → VOID/tests/files/molecule.xyz
diff --git a/moldocker/tests/test_inputs.py → VOID/tests/test_inputs.py b/moldocker/tests/test_inputs.py → VOID/tests/test_inputs.py
diff --git a/moldocker/utils/__init__.py → VOID/utils/__init__.py b/moldocker/utils/__init__.py → VOID/utils/__init__.py
diff --git a/moldocker/utils/geometry.py → VOID/utils/geometry.py b/moldocker/utils/geometry.py → VOID/utils/geometry.py
diff --git a/moldocker/utils/parser/__init__.py → VOID/utils/parser/__init__.py b/moldocker/utils/parser/__init__.py → VOID/utils/parser/__init__.py
diff --git a/moldocker/utils/parser/base.py → VOID/utils/parser/base.py b/moldocker/utils/parser/base.py → VOID/utils/parser/base.py
@@ -2,7 +2,7 @@
 
 
 class Parser:
-    DESCRIPTION = """moldocker: a package to dock molecules
+    DESCRIPTION = """VOID: a package to dock molecules
         to materials.
     """
 

diff --git a/moldocker/utils/parser/dock.py → VOID/utils/parser/dock.py b/moldocker/utils/parser/dock.py → VOID/utils/parser/dock.py
@@ -1,5 +1,5 @@
 from .base import Parser
-from moldocker import dockers, samplers, fitness
+from VOID import dockers, samplers, fitness
 
 
 class DockParser(Parser):

diff --git a/moldocker/utils/parser/tests/__init__.py → VOID/utils/parser/tests/__init__.py b/moldocker/utils/parser/tests/__init__.py → VOID/utils/parser/tests/__init__.py
diff --git a/moldocker/utils/parser/tests/test_dock.py → VOID/utils/parser/tests/test_dock.py b/moldocker/utils/parser/tests/test_dock.py → VOID/utils/parser/tests/test_dock.py
@@ -1,7 +1,7 @@
 import numpy as np
 import unittest as ut
 
-from moldocker.utils.parser import DockParser
+from VOID.utils.parser import DockParser
 
 
 class TestParser(ut.TestCase):

diff --git a/moldocker/utils/parser/tests/test_parser.py → VOID/utils/parser/tests/test_parser.py b/moldocker/utils/parser/tests/test_parser.py → VOID/utils/parser/tests/test_parser.py
@@ -1,7 +1,7 @@
 import numpy as np
 import unittest as ut
 
-from moldocker.utils.parser.base import Parser
+from VOID.utils.parser.base import Parser
 
 
 class TestParser(ut.TestCase):

diff --git a/moldocker/utils/setup.py → VOID/utils/setup.py b/moldocker/utils/setup.py → VOID/utils/setup.py
@@ -1,7 +1,7 @@
 import os
 import json
 from pymatgen.core import Structure, Molecule
-from moldocker import dockers, samplers, fitness
+from VOID import dockers, samplers, fitness
 
 
 class SetupRun:

diff --git a/moldocker/utils/structure.py → VOID/utils/structure.py b/moldocker/utils/structure.py → VOID/utils/structure.py
diff --git a/moldocker/utils/tests/__init__.py → VOID/utils/tests/__init__.py b/moldocker/utils/tests/__init__.py → VOID/utils/tests/__init__.py
diff --git a/moldocker/utils/tests/test_setup.py → VOID/utils/tests/test_setup.py b/moldocker/utils/tests/test_setup.py → VOID/utils/tests/test_setup.py
@@ -2,9 +2,9 @@
 import unittest as ut
 from argparse import Namespace
 
-from moldocker.utils.setup import SetupRun
-from moldocker import dockers, samplers, fitness
-from moldocker.tests.test_inputs import load_structure, load_molecule
+from VOID.utils.setup import SetupRun
+from VOID import dockers, samplers, fitness
+from VOID.tests.test_inputs import load_structure, load_molecule
 
 
 thisdir = os.path.dirname(os.path.abspath(__file__))

diff --git a/moldocker/utils/timing.py → VOID/utils/timing.py b/moldocker/utils/timing.py → VOID/utils/timing.py
diff --git a/scripts/dock.py b/scripts/dock.py
@@ -2,9 +2,9 @@
 import os
 import logging
 
-from moldocker.utils.parser import DockParser
-from moldocker.utils.setup import SetupRun
-from moldocker.io.cif import write_cif
+from VOID.utils.parser import DockParser
+from VOID.utils.setup import SetupRun
+from VOID.io.cif import write_cif
 
 
 if __name__ == "__main__":

diff --git a/setup.py b/setup.py
@@ -10,16 +10,16 @@ def read(fname):
 
 
 setup(
-    name="moldocker",
+    name="VOID",
     version="1.0.0",
     author="Daniel Schwalbe-Koda",
     email="[email protected]",
-    url="https://github.com/dskoda/moldocker",
+    url="https://github.com/learningmatter-mit/VOID",
     packages=find_packages("."),
     scripts=["scripts/dock.py",],
     python_requires=">=3.5",
     install_requires=["numpy", "networkx", "pymatgen>=2020.3.2", "scikit-learn"],
     license="MIT",
-    description="Tools to dock molecules to crystal structures",
+    description="Voronoi Organic-Inorganic Docking",
     long_description=read("README.md"),
 )