keyword stringclasses 7
values | repo_name stringlengths 8 98 | file_path stringlengths 4 244 | file_extension stringclasses 29
values | file_size int64 0 84.1M | line_count int64 0 1.6M | content stringlengths 1 84.1M ⌀ | language stringclasses 14
values |
|---|---|---|---|---|---|---|---|
3D | Autodesk/molecular-design-toolkit | moldesign/models/openbabel.py | .py | 3,300 | 86 | """ Energy models using OpenBabel's heuristic, highly approximate drug forcefields
"""
from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache Licen... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/models/toys.py | .py | 2,612 | 77 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/models/base.py | .py | 6,189 | 168 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/models/pyscf.py | .py | 22,179 | 542 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/models/openmm.py | .py | 16,925 | 400 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/orbitals/spherical.py | .py | 5,899 | 161 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/orbitals/atomic_basis_fn.py | .py | 4,085 | 120 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/orbitals/primitives.py | .py | 4,973 | 165 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/orbitals/cartesian.py | .py | 11,060 | 282 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/orbitals/__init__.py | .py | 271 | 14 | def toplevel(o):
__all__.append(o.__name__)
return o
__all__ = []
from .primitives import *
from .gaussians import *
from .orbitals import *
from .cartesian import *
from .spherical import *
from .atomic_basis_fn import *
from .basis import *
from .wfn import *
| Python |
3D | Autodesk/molecular-design-toolkit | moldesign/orbitals/orbitals.py | .py | 14,474 | 392 | """ Class definitions for atomic and molecular orbitals.
Notes:
In this documentation, we use the following conventions for labeling orbitals:
- atomic orbitals using lower case greek labels and subscripts, e.g.,
:math:`\left| \mu \right \rangle, F_{\nu \lambda}, etc.
- molecular orbitals use... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/orbitals/gaussians.py | .py | 5,009 | 154 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/orbitals/basis.py | .py | 4,187 | 121 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/orbitals/wfn.py | .py | 5,817 | 147 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/compute/compute.py | .py | 6,358 | 203 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with t... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/compute/configuration.py | .py | 10,041 | 283 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/compute/__init__.py | .py | 135 | 7 | __all__ = ['config']
from .compute import *
from .configuration import *
from .remote_procedure_calls import *
from . import packages
| Python |
3D | Autodesk/molecular-design-toolkit | moldesign/compute/packages.py | .py | 10,966 | 299 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/compute/remote_procedure_calls.py | .py | 5,016 | 128 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/forcefields/amber.py | .py | 1,415 | 50 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/forcefields/errors.py | .py | 6,575 | 167 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/forcefields/forcefieldbase.py | .py | 6,735 | 173 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/forcefields/__init__.py | .py | 173 | 12 | def toplevel(o):
__all__.append(o.__name__)
return o
__all__ = []
from . import errors
from .ffparams import *
from .forcefieldbase import *
from .amber import *
| Python |
3D | Autodesk/molecular-design-toolkit | moldesign/forcefields/ffparams.py | .py | 7,010 | 202 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/integrators/verlet.py | .py | 2,603 | 74 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/integrators/__init__.py | .py | 63 | 4 | from . import base
from .verlet import *
from .openmm import *
| Python |
3D | Autodesk/molecular-design-toolkit | moldesign/integrators/base.py | .py | 2,301 | 66 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/integrators/openmm.py | .py | 4,202 | 118 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/molecules/residue.py | .py | 17,344 | 487 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/molecules/bonds.py | .py | 7,733 | 236 | # coding: utf-8
from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/molecules/atomcollections.py | .py | 17,857 | 523 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/molecules/primary_structure.py | .py | 7,384 | 202 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/molecules/__init__.py | .py | 380 | 19 | def toplevel(o):
__all__.append(o.__name__)
return o
__all__ = []
from .properties import *
from .bond_graph import *
from .coord_arrays import *
from .atomcollections import *
from .bonds import *
from .atoms import *
from .biounits import *
from .residue import *
from .chain import *
from .primary_structure... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/molecules/chain.py | .py | 11,755 | 316 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/molecules/trajectory.py | .py | 16,080 | 451 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/molecules/bond_graph.py | .py | 3,993 | 115 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/molecules/molecule.py | .py | 45,660 | 1,213 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/molecules/biounits.py | .py | 7,897 | 239 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/molecules/coord_arrays.py | .py | 2,878 | 83 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/molecules/atoms.py | .py | 19,059 | 500 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/molecules/properties.py | .py | 3,962 | 117 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/_tests/test_minimizers.py | .py | 6,257 | 182 | import collections
import numpy as np
import pytest
import moldesign as mdt
from .helpers import assert_something_resembling_minimization_happened
from moldesign import units as u
from moldesign.compute import packages
__PYTEST_MARK__ = 'minimization'
@pytest.fixture(scope='function')
def harmonic_atom():
mol ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/_tests/test_objects.py | .py | 3,342 | 142 | import pickle
import pytest
import numpy as np
from moldesign.utils import Alias
from .object_fixtures import *
from .molecule_fixtures import *
from .object_fixtures import TESTDICT
__PYTEST_MARK__ = 'internal' # mark all tests in this module with this label (see ./conftest.py)
class ComposedClass(object):
... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/_tests/test_dna_primary_structure.py | .py | 2,948 | 109 | """ Tests introspection and methods for dna primary structure
"""
import itertools
import pytest
import moldesign as mdt
from moldesign import units as u
__PYTEST_MARK__ = 'internal' # mark all tests in this module with this label (see ./conftest.py)
fixture_types = {}
def typedfixture(*types, **kwargs):
""... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/_tests/test_pdb_processing.py | .py | 5,266 | 162 | """
This file collects tests relating to the many special cases we deal with when
trying to process biomolecular structures from the pdb.
These currently just test the specific cases that we've implemented fixes for
"""
import pytest
import moldesign as mdt
from .helpers import get_data_path
import parmed
from distu... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/_tests/molecule_fixtures.py | .py | 10,512 | 353 | import random
import pytest
import numpy as np
import moldesign as mdt
import moldesign.units as u
from moldesign.utils import exports
from .helpers import get_data_path
__all__ = ['molecule_standards']
molecule_standards = {}
def typedfixture(*types, **kwargs):
"""This is a decorator that lets us associate fi... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/_tests/test_openbabel_xface.py | .py | 2,159 | 71 | import pytest
import moldesign as mdt
from .molecule_fixtures import *
registered_types = {}
def typedfixture(*types, **kwargs):
"""This is a decorator that lets us associate fixtures with one or more arbitrary types.
We'll later use this type to determine what tests to run on the result"""
def fixtur... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/_tests/test_tools.py | .py | 3,739 | 126 | """ Tests topology manipulation tools
"""
import collections
import pytest
import moldesign as mdt
from moldesign import units as u
from .helpers import get_data_path, assert_almost_equal
from .molecule_fixtures import ligand3aid,pdb3aid,benzene,small_molecule,pdb1yu8, ligand_residue_3aid
registered_types = {}
d... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/_tests/test_trajectory.py | .py | 4,352 | 155 | import pytest
import numpy as np
import moldesign as mdt
from moldesign import units as u
from .object_fixtures import h2, h2_harmonic, h2_trajectory
@pytest.mark.internal
def test_frames_synched_with_trajectory(h2_trajectory):
traj = h2_trajectory
for iframe, frame in enumerate(traj):
assert frame... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/_tests/test_ambertools_xface.py | .py | 2,990 | 94 | import pytest
import moldesign as mdt
from . import helpers
from .molecule_fixtures import *
@pytest.mark.parametrize('fixturename', molecule_standards['hasmodel'])
def test_model_assigned(fixturename, request):
mol = request.getfixturevalue(fixturename)
assert mol.ff is not None
@pytest.mark.parametrize('... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/_tests/test_biopython_xface.py | .py | 649 | 25 | import io
import pytest
import Bio.PDB
import moldesign as mdt
from .helpers import get_data_path
from .molecule_fixtures import pdb3aid
@pytest.fixture
def biopy_3aid():
import gzip
parser = Bio.PDB.PDBParser()
s = gzip.open(get_data_path('3aid.pdb.gz'), 'r').read().decode('utf-8')
structure = parse... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/_tests/__init__.py | .py | 0 | 0 | null | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/_tests/test_io.py | .py | 8,850 | 307 | """ Tests for molecule creation and file i/o
"""
import io
import os
import subprocess
from future.utils import PY2, native_str
from builtins import str
import collections
import pathlib
import gzip
import bz2
import pickle
import numpy
import pytest
import moldesign as mdt
mdt.compute.config.engine_type = 'docker'
... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/_tests/object_fixtures.py | .py | 3,903 | 162 | """
This module is mostly _fixtures_ - functions that create various objects for downstream testing.
There are a few tests here too, mostly to make sure the objects are created correctly in the first
place.
"""
import collections
import numpy as np
import pytest
import moldesign as mdt
from .. import units as u
fro... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/_tests/test_gaussian_math.py | .py | 17,426 | 519 | """ Tests internal math routines
"""
import random
import itertools
import numpy as np
import pytest
import moldesign
from moldesign import units as u
from moldesign.mathutils import spherical_harmonics as harmonics
from . import helpers
from .molecule_fixtures import *
registered_types = {}
__PYTEST_MARK__ = ['m... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/_tests/test_openmm_xface.py | .py | 7,917 | 234 | import random
from itertools import product
import pytest
import numpy as np
import moldesign as mdt
from moldesign import units as u
from moldesign.compute import packages
from . import helpers
from .molecule_fixtures import *
# TODO: remove constraints from dynamics parameters - they should only live in the const... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/_tests/test_qmmm.py | .py | 2,650 | 103 | import pytest
import moldesign as mdt
from moldesign import units as u
from . import helpers
# Tests:
# 1. internal bonds on QM region are removed in all cases
# 2. wavefunction is perturbed for electrostatic embedding
# 3.
@pytest.fixture
def h2params():
mol = mdt.from_smiles('[H][H]')
mol.atoms[0].na... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/_tests/test_constraints.py | .py | 9,496 | 293 | """ Tests constraint routines
"""
from builtins import range
import pytest
import numpy as np
import moldesign as mdt
from moldesign import units as u
from .molecule_fixtures import *
from . import helpers
registered_types = {}
def typedfixture(*types, **kwargs):
"""This is a decorator that lets us associate fix... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/_tests/test_protein_primary_structure.py | .py | 8,144 | 256 | """ Tests introspection and methods for protein primary structure
"""
import itertools
import pytest
import moldesign as mdt
from moldesign import units as u
from .helpers import get_data_path
fixture_types = {}
def typedfixture(*types, **kwargs):
"""This is a decorator that lets us associate fixtures with one... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/_tests/test_molecules.py | .py | 11,254 | 364 | """ Test various functionalities around data structure consistency
"""
import pickle
from past.builtins import basestring
import pytest
import numpy as np
from moldesign import units as u
import moldesign as mdt
from .object_fixtures import *
from .molecule_fixtures import *
from . import helpers
__PYTEST_MARK__ =... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/_tests/helpers.py | .py | 8,008 | 249 | import io
from future.standard_library import install_aliases
install_aliases()
from builtins import range
from future.utils import PY2
import pytest
import os
import socket
import numpy as np
import moldesign as mdt
from moldesign import units as u
DEFSTEP = 0.000005*u.angstrom
def get_data_path(f):
"""
... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/_tests/test_copies.py | .py | 10,165 | 282 | from builtins import zip
import itertools
import numpy as np
import pytest
import moldesign as mdt
from moldesign import units as u
from .molecule_fixtures import *
from .object_fixtures import *
__PYTEST_MARK__ = 'internal' # mark all tests in this module with this label (see ./conftest.py)
def test_carbon_cop... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/_tests/test_cli.py | .py | 2,358 | 82 | from __future__ import print_function
import subprocess
import os
import pytest
import moldesign as mdt
from moldesign.external import pathlib
__PYTEST_MARK__ = 'io'
@pytest.fixture
def example_path(tmpdir):
path = pathlib.Path(str(tmpdir))
subprocess.check_call('python -m moldesign copyexamples',
... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/_tests/test_atom_containers.py | .py | 9,183 | 287 | from builtins import range
import itertools
import random
import pytest
import numpy as np
import moldesign as mdt
from moldesign import units as u
from . import helpers
from .molecule_fixtures import pdb3aid, ethylene_waterbox_2na_2cl
__PYTEST_MARK__ = 'internal' # mark all tests in this module with this label (s... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/_tests/test_wfn.py | .py | 3,128 | 78 | import pytest
import numpy as np
import moldesign as mdt
from moldesign import units as u
from moldesign.interfaces.pyscf_interface import basis_values
from .molecule_fixtures import *
from . import helpers
__PYTEST_MARK__ = 'wfn'
TESTSYSTEMS = ['h2_rhf_augccpvdz', 'h2_rhf_sto3g', 'acetylene_dft_631g']
def test_... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/_tests/test_config.py | .py | 3,146 | 105 | import os
import yaml
import pytest
import moldesign as mdt
from moldesign.compute import packages
from .molecule_fixtures import *
__PYTEST_MARK__ = ['internal', 'config']
# mark all tests in this module with this label (see ./conftest.py)
@pytest.fixture(scope='function')
def tempconfigfile(tmpdir):
tmpdir = ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/_tests/test_symmetry.py | .py | 5,256 | 189 | import pytest
import numpy as np
import moldesign as mdt
from moldesign import units as u
from moldesign.external import transformations
from .molecule_fixtures import *
@pytest.fixture
def linear():
expected = {'C1': 1,
'Cinf_v': 1}
a1 = mdt.Atom(1)
a1.position = [-1, 0, 0] * u.angstro... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/_tests/test_atom_bond_computed_properties.py | .py | 2,315 | 72 | import pytest
import moldesign as mdt
from moldesign import units as u
from .molecule_fixtures import *
from . import helpers
def test_forcefield_atom_term_access(protein_default_amber_forcefield):
mol = protein_default_amber_forcefield
for atom in mol.atoms:
assert atom.ff.ljepsilon.dimensionality ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/_tests/test_mathutils.py | .py | 7,600 | 253 | import itertools
import pytest
import numpy as np
from moldesign import mathutils
from moldesign import units as u
from moldesign.mathutils import spherical_harmonics as sh
from . import helpers
__PYTEST_MARK__ = ['internal', 'math', 'mathutils']
CONSTRUCTORS = []
IDS = []
# Couldn't figure out a way to do this... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/_tests/test_pdbfixer_xface.py | .py | 6,277 | 157 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/_tests/test_geometry.py | .py | 12,247 | 340 | """ Tests geometry routines
"""
from builtins import range
import random
import itertools
import pytest
import numpy as np
import moldesign as mdt
from moldesign import units as u
from . import helpers
registered_types = {}
__PYTEST_MARK__ = 'internal' # mark all tests in this module with this label (see ./conft... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/_tests/test_units.py | .py | 11,253 | 327 | """ Tests the unit system
"""
import pytest
import numpy as np
from moldesign import units
from moldesign import units as u
# mark all tests in this module with these label (see ./conftest.py)
__PYTEST_MARK__ = ['internal', 'units']
@pytest.mark.screening
def test_scalar_comparison_dimensionality_errors():
with... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/_tests/test_imports.py | .py | 646 | 28 | import pytest
import sys
__PYTEST_MARK__ = 'internal' # mark all tests in this module with this label (see ./conftest.py)
@pytest.mark.tryfirst
def test_lazy_imports():
import moldesign
for mod in 'simtk simtk.openmm pyscf pdbfixer scipy':
assert mod not in sys.modules
def test_package_install_c... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/_tests/test_atoms.py | .py | 7,153 | 254 | import pytest
import numpy as np
import moldesign as mdt
from moldesign import units as u
from .molecule_fixtures import *
from . import helpers
__PYTEST_MARK__ = 'internal'
def test_create_atom_with_element_as_name():
he_plus = mdt.Atom("He", position=np.ones(3) * u.nm, formal_charge=1*u.q_e)
assert he_pl... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/_tests/test_qm_xfaces.py | .py | 4,712 | 139 | """ Tests basic QM functionality and data structures
"""
import itertools
import pytest
import numpy as np
import moldesign as mdt
from moldesign import units as u
from . import helpers
from .molecule_fixtures import *
# TODO: automated method testing based on its metadata - i.e. test to make sure parameters are
# ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/_tests/conftest.py | .py | 541 | 20 |
def pytest_itemcollected(item):
marks = getattr(item.module, '__PYTEST_MARK__', None)
if marks is None:
return
if isinstance(marks, str):
marks = [marks]
for mark in marks:
item.add_marker(mark)
# TODO: nicer output strings for git commit status
# see https://docs.pytest.org/... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/_tests/test_alignments.py | .py | 5,314 | 149 | import random
import numpy as np
import pytest
import moldesign as mdt
from moldesign import geom
from moldesign.mathutils import normalized
from moldesign import units as u
from .molecule_fixtures import *
from .helpers import assert_almost_equal
__PYTEST_MARK__ = 'internal' # mark all tests in this module with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/geom/monitor.py | .py | 4,421 | 135 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/geom/symmetry.py | .py | 6,506 | 170 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/geom/coords.py | .py | 6,226 | 202 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/geom/setcoord.py | .py | 7,516 | 196 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/geom/grads.py | .py | 3,592 | 118 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/geom/__init__.py | .py | 262 | 14 | def toplevel(o):
__all__.append(o.__name__)
return o
__all__ = []
from .coords import *
from .grads import *
from .setcoord import *
from .constraints import *
from .symmetry import *
from .monitor import *
from .shake import *
from .alignment import *
| Python |
3D | Autodesk/molecular-design-toolkit | moldesign/geom/shake.py | .py | 3,447 | 103 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/geom/alignment.py | .py | 3,682 | 103 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/geom/constraints.py | .py | 13,871 | 401 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/_static_data/apply_copyright.sh | .sh | 729 | 22 | #!/bin/bash
for file in `grep -L "Copyright 2016 Autodesk Inc." *.py`; do
mv $file{.bak}
cat > $file <<EOF
# Copyright 2016 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License... | Shell |
3D | Autodesk/molecular-design-toolkit | moldesign/_static_data/scripts/generate_residue_templates.py | .py | 857 | 27 | #!/usr/bin/env python
""" A short script that assembles reasonable template geometries for standard amino acids
and DNA bases
"""
import moldesign as mdt
import json
protein = mdt.from_pdb('4F0A')
dna = mdt.build_bdna('ACTGAA')
residues = {}
for chain in list(protein.chains.values()) + list(dna.chains.values()):
... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/_static_data/scripts/generate_residue_data.py | .py | 4,363 | 137 | #!/usr/bin/env python
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law o... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/data/chemical_components.py | .py | 2,262 | 69 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/data/__init__.py | .py | 121 | 5 | from .data import *
from .atomic import *
from .biochemical import *
from .chemical_components import *
from .ff import * | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/data/atomic.py | .py | 1,571 | 45 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/data/ff.py | .py | 1,287 | 39 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/data/data.py | .py | 2,786 | 86 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | moldesign/data/biochemical.py | .py | 4,255 | 145 | from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Python |
3D | Autodesk/molecular-design-toolkit | docs/generate_package_api.py | .py | 4,738 | 157 | #!/usr/bin/env python
""" Auto-generate rst files for the MDT API.
This is more or less our customized replacement for sphinx-apidoc. The goal here is to
organize the auto-generated API documentation in a more user-focused way - to clearly group
the classes and functions exposed by various parts of the MDT *runtime* A... | Python |
3D | Autodesk/molecular-design-toolkit | docs/autogen_api.sh | .sh | 70 | 5 | #!/bin/bash
sphinx-apidoc -M -o _moldesign_api ../moldesign --force
| Shell |
3D | Autodesk/molecular-design-toolkit | docs/conf.py | .py | 10,517 | 320 | # -*- coding: utf-8 -*-
#
# Molecular Design Toolkit documentation build configuration file, created by
# sphinx-quickstart on Mon Apr 18 11:27:36 2016.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# autogene... | Python |
3D | Autodesk/molecular-design-toolkit | deployment/test-version-number.sh | .sh | 436 | 23 | #!/usr/bin/env bash
set -e
if [ -z "${CI_BRANCH}" ]; then
echo "Error: env var CI_BRANCH not set"
exit 1
fi
pyversion=$(python -m moldesign version | tail -n 1)
echo "Expecting moldesign==${CI_BRANCH}"
echo "Found moldesign==${pyversion}"
if [ "${pyversion}" == "${CI_BRANCH}" ]; then
echo "All good"
exit ... | Shell |
3D | Autodesk/molecular-design-toolkit | deployment/push-coverage.sh | .sh | 383 | 13 | #!/usr/bin/env bash
# combines coverage from all test environments and pushes it to coveralls.io
set -e
mkdir -p /opt/reports/env-coverage
if $(cp /opt/reports/env-coverage/coverage.* /opt/reports/); then
coverage combine /opt/reports/coverage.*
coveralls || echo "Failed to upload coverage to coveralls.io"
else
... | Shell |
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