Merge pull request #167 from Autodesk/qmfixes

Pure-python orbital grids

NOTICES

@@ -1,37 +1,57 @@
-The Molecular Design Toolkit incorporates code from the following sources:
+This project incorporates code from the following sources:
 
-   Transformations.py
-------------------------------
-Copyright (c) 2006-2015, Christoph Gohlke
-Copyright (c) 2006-2015, The Regents of the University of California
-SOURCE CODE: moldesign/external/transformations.py
-DESCRIPTION: Included in its entirety, with minor modifications to imports
-LICENSE: moldesign/external/transformations.py
-WEBSITE: http://www.lfd.uci.edu/~gohlke/
+      Python
+--------------------------------
+Copyright (c) 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010,
+2011, 2012, 2013, 2014, 2015, 2016 Python Software Foundation; All Rights
+Reserved
+SOURCE CODE: moldesign/utils/utils.py (`methodcaller` class)
+DESCRIPTION: unmodified copy of the pure-python `methodcaller` class
+WEBSITE: https://www.python.org
+LICENSE: moldesign/external/licenses/python
+
+
+      PyQuante2
+--------------------------------
+By Rick Muller
+Copyright (c) 2013 PyQuante Development Team
+SOURCE CODE: moldesign/external/pyquante
+WEBSITE: http://pyquante.sourceforge.net/
+DESCRIPTION: Code for evaulating one-electron integrals of spherical gaussian basis
+functions. Except for the imports, the files are unmodified.
+LICENSE: moldesign/external/pyquante/LICENSE
 
 
-       Sphinx
+      Sphinx
 -------------------------
 Copyright (c) 2007-2016 by the Sphinx team
 SOURCE CODE: moldesign/utils/docparsers/google.py
 DESCRIPTION: Includes code derived from the Napoleon Google-style docstring parsers.
 Note that these routines have been heavily modified as described in the file.
-LICENSE: moldesign/utils/docparsers/sphinxlicense
 WEBSITE: http://sphinx-doc.org
+LICENSE: moldesign/utils/docparsers/sphinxlicense
 
 
-       Python
---------------------------------
-Copyright (c) 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010,
-2011, 2012, 2013, 2014, 2015, 2016 Python Software Foundation; All Rights
-Reserved
-SOURCE CODE: moldesign/utils/utils.py (`methodcaller` class)
-DESCRIPTION: unmodified copy of the pure-python `methodcaller` class
-LICENSE: moldesign/external/licenses/python
-WEBSITE: https://www.python.org
+      Symmol.f
+------------------------------------
+By Tullio Pilati and Alessandra Forni
+Released by the CCP14 Project
+SOURCE CODE: DockerMakefiles/buildfiles/symmol/symmol.f
+WEBSITE: http://www.ccp14.ac.uk
+LICENSE: None available
+
+
+      Transformations.py
+------------------------------
+Copyright (c) 2006-2015, Christoph Gohlke
+Copyright (c) 2006-2015, The Regents of the University of California
+SOURCE CODE: moldesign/external/transformations.py
+DESCRIPTION: Included in its entirety, with minor modifications to imports
+LICENSE: moldesign/external/transformations.py
+WEBSITE: http://www.lfd.uci.edu/~gohlke/
 
 
-   Versioneer
+      Versioneer
 -------------------------
 By Brian Warner
 SOURCE CODE: versioneer.py, moldesign/_version.py
@@ -40,11 +60,3 @@ LICENSE: To make Versioneer easier to embed, all its code is dedicated to the pu
 The _version.py that it creates is also in the public domain. Specifically, both are released
 under the Creative Commons "Public Domain Dedication" license (CC0-1.0), as described in
 https://creativecommons.org/publicdomain/zero/1.0/ 
-
-    Symmol.f
-------------------------------------
-By Tullio Pilati and Alessandra Forni
-Released by the CCP14 Project
-SOURCE CODE: docker_images/symmol/symmol.f
-WEBSITE: http://www.ccp14.ac.uk
-LICENSE: None available

moldesign/_static_data/pint_atomic_units.txt

@@ -3,11 +3,13 @@ atomic_time = hbar / hartree = t0
 kcalpermol = kcal / 6.0221412927e23
 kjpermol = kJ / 6.0221412927e23
 gpermol = g / 6.0221412927e23
-fs = femtosecond = 1.0 * femtosecond
-ps = picosecond = 1.0 * piscosecond
-amu = 1.0 * atomic_mass_units
-ang = 1.0 * angstrom
-eV = electron_volt
 debye = 0.393430307 * elementary_charge * bohr
 electron_charge = elementary_charge
-q_e = elementary_charge
+q_e = elementary_charge
+
+@system nano using international
+   nanometers
+   nanoseconds
+   atomic_mass_units
+@end
+

moldesign/_tests/conftest.py

@@ -1,8 +1,13 @@
 
 
 def pytest_itemcollected(item):
-    if hasattr(item.module, '__PYTEST_MARK__'):
-        item.add_marker(item.module.__PYTEST_MARK__)
+    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

moldesign/_tests/helpers.py

@@ -229,3 +229,20 @@ def assert_almost_equal(actual, desired, **kwargs):
                                                   reason='Network connection timed out')
 """ Decorator to disable tests that need internet if we can't connect to the network """
 
+
+def generate_grid(g, g2=None):
+    from moldesign import mathutils
+
+    if g2 is None: g2 = g
+    if not hasattr(g, 'alpha'):
+        alpha = min(min(p.alpha for p in g), min(p.alpha for p in g2))
+    else:
+        alpha = min(g.alpha, g2.alpha)
+
+    width = np.sqrt(1.0/alpha)
+    ranges = np.ones((3, 2))*5.0*width
+    ranges[:, 0] *= -1
+    ranges += ((g.center + g2.center)/2.0)[:, None]
+    grid = mathutils.VolumetricGrid(*ranges, npoints=64)
+    allpoints = grid.allpoints()
+    return allpoints, grid

moldesign/_tests/molecule_fixtures.py

@@ -4,10 +4,11 @@
 
 import moldesign as mdt
 import moldesign.units as u
+from moldesign.utils import exports
 from .helpers import get_data_path
 
-from moldesign.interfaces.openbabel import force_remote as openbabel_missing
 
+__all__ = ['molecule_standards']
 
 molecule_standards = {}
 
@@ -16,6 +17,7 @@ def typedfixture(*types, **kwargs):
     We'll later use this type to determine what tests to run on the result"""
 
     def fixture_wrapper(func):
+        __all__.append(func.__name__)
         for t in types:
             molecule_standards.setdefault(t, []).append(func.__name__)
         return pytest.fixture(**kwargs)(func)
@@ -56,29 +58,34 @@ def ethylene_waterbox_2na_2cl():
     return solvated
 
 
+@exports
 @pytest.fixture
 def random_atoms_from_3aid(pdb3aid):
     atoms = mdt.molecules.atomcollections.AtomList(random.sample(pdb3aid.atoms, 10))
     return atoms
 
 
+@exports
 @pytest.fixture(scope='session')
 def cached_small_molecule():
     mol = mdt.from_smiles('CNCOS(=O)C')
     mol.positions += 0.001*np.random.random(mol.positions.shape)*u.angstrom  # move out of minimum
     return mol
 
 
+@exports
 @pytest.fixture
 def small_molecule(cached_small_molecule):
     return cached_small_molecule.copy()
 
 
+@exports
 @pytest.fixture(scope='session')
 def cached_benzene():
     return mdt.from_smiles('c1ccccc1')
 
 
+@exports
 @pytest.fixture
 def benzene(cached_benzene):
     return cached_benzene.copy()
@@ -104,25 +111,30 @@ def heh_plus():
     return mol
 
 
+@exports
 @pytest.fixture(scope='session')
 def cached_ethylene():
     return mdt.from_smiles('C=C')
 
 
+@exports
 @pytest.fixture
 def ethylene(cached_ethylene):
     return cached_ethylene.copy()
 
 
+@exports
 @pytest.fixture(scope='session')
 def cached_pdb1yu8():
     return mdt.read(get_data_path('1yu8.pdb'))
 
+@exports
 @pytest.fixture
 def pdb1yu8():
     return mdt.read(get_data_path('1yu8.pdb'))
 
 
+@exports
 @pytest.fixture(scope='session')
 def cached_mol_from_xyz():
     return mdt.read("""43
@@ -173,11 +185,13 @@ def cached_mol_from_xyz():
     """, format='xyz')
 
 
+@exports
 @pytest.fixture
 def mol_from_xyz(cached_mol_from_xyz):
     return cached_mol_from_xyz.copy()
 
 
+@exports
 @pytest.fixture(scope='session')
 def cached_mol_from_sdf():
     return mdt.read("""
@@ -209,6 +223,7 @@ def cached_mol_from_sdf():
 $$$$
 """, format='sdf')
 
+@exports
 @pytest.fixture
 def mol_from_sdf(cached_mol_from_sdf):
     return cached_mol_from_sdf.copy()
@@ -224,6 +239,7 @@ def nucleic():
 ########################################################################################
 # Molecules with forcefields assigned - these use a session-scoped constructor w/ a copy factory
 
+@exports
 @pytest.fixture(scope='session')
 def cached_mol_parameterized_with_zeros(cached_small_molecule):
     return _param_small_mol(cached_small_molecule.copy(), 'zero')
@@ -234,6 +250,7 @@ def mol_with_zerocharge_params(cached_mol_parameterized_with_zeros):
     return cached_mol_parameterized_with_zeros.copy()
 
 
+@exports
 @pytest.fixture(scope='session')
 def cached_mol_parameterized_with_am1bcc(cached_small_molecule):
     """ We don't use this fixture directly, rather use another fixture that copies these results
@@ -247,6 +264,7 @@ def mol_with_am1bcc_params(cached_mol_parameterized_with_am1bcc):
     return cached_mol_parameterized_with_am1bcc.copy()
 
 
+@exports
 @pytest.fixture(scope='session')
 def cached_mol_parameterized_with_gasteiger(cached_small_molecule):
     """ We don't use this fixture directly, rather use another fixture that copies these results
@@ -271,6 +289,7 @@ def _param_small_mol(cached_small_molecule, chargemodel):
     return mol
 
 
+@exports
 @pytest.fixture(scope='session')
 def cached_protein_with_default_amber_ff(cached_pdb1yu8):
     """ We don't use this fixture directly, rather use another fixture that copies these results
@@ -288,14 +307,46 @@ def protein_default_amber_forcefield(cached_protein_with_default_amber_ff):
     return cached_protein_with_default_amber_ff.copy()
 
 
+@exports
 @pytest.fixture(scope='session')
-def cached_h2_rhfwfn():
+def cached_h2_rhf_sto3g():
     mol = h2()  # fixture is not cached, so just call it directly
     mol.set_energy_model(mdt.models.PySCFPotential, basis='sto-3g', theory='rhf')
     mol.calculate(requests=['forces'])
     return mol
 
 
+@exports
 @pytest.fixture
-def h2_rhfwfn(cached_h2_rhfwfn):
-    return cached_h2_rhfwfn.copy()
+def h2_rhf_sto3g(cached_h2_rhf_sto3g):
+    return cached_h2_rhf_sto3g.copy()
+
+
+@exports
+@pytest.fixture(scope='session')
+def cached_h2_rhf_augccpvdz():
+    mol = h2()
+    mol.set_energy_model(mdt.models.RHF, basis='aug-cc-pvdz')
+    mol.calculate()
+    return mol
+
+
+@exports
+@pytest.fixture
+def h2_rhf_augccpvdz(cached_h2_rhf_augccpvdz):
+    return cached_h2_rhf_augccpvdz.copy()
+
+
+@exports
+@pytest.fixture(scope='session')
+def cached_acetylene_dft_631g():
+    mol = mdt.from_smiles('C#C')
+    mol.set_energy_model(mdt.models.B3LYP, basis='6-31g')
+    mol.calculate()
+    return mol
+
+
+@exports
+@pytest.fixture
+def acetylene_dft_631g(cached_acetylene_dft_631g):
+    return cached_acetylene_dft_631g.copy()

moldesign/_tests/object_fixtures.py

@@ -18,11 +18,15 @@
 
 registered_types = {key:val[:] for key,val in molecule_standards.items()}
 
+__all__ = ['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 fixture_wrapper(func):
+        __all__.append(func.__name__)
         for t in types:
             registered_types.setdefault(t, []).append(func.__name__)
         return pytest.fixture(**kwargs)(func)
@@ -58,7 +62,7 @@ def simple_unit_array():
 
 @typedfixture('pickleable', 'equality')
 def unit_number():
-    return 391.23948 * u.ureg.kg * u.ang / u.alpha
+    return 391.23948 * u.ureg.kg * u.angstrom / u.alpha
 
 
 ######################################
@@ -104,13 +108,13 @@ def mol_bond_graph(h2):
 
 
 @typedfixture('pickleable')
-def mol_wfn(h2_rhfwfn):
-    return h2_rhfwfn.copy().wfn
+def mol_wfn(h2_rhf_sto3g):
+    return h2_rhf_sto3g.copy().wfn
 
 
 @typedfixture('pickleable')
-def mol_properties(h2_rhfwfn):
-    return h2_rhfwfn.copy().properties
+def mol_properties(h2_rhf_sto3g):
+    return h2_rhf_sto3g.copy().properties
 
 
 @typedfixture('trajectory')
@@ -153,3 +157,5 @@ def h2_harmonic_atoms(h2_harmonic):
                      registered_types['trajectory'] +
                      registered_types['atom'])
 pickleable = registered_types['pickleable'] + moldesign_objects
+
+__all__.extend(['moldesign_objects', 'pickleable'])