Merge branch 'master' of https://github.com/mosdef-hub/gmso into lamm…

…ps_bonds_angles

.readthedocs.yml

@@ -0,0 +1,14 @@
+
+version: 2
+formats:
+  - htmlzip
+python:
+  version: 3.7
+  install:
+    - requirements: docs/requirements.txt
+  system_packages: true
+
+sphinx:
+  builder: html
+  configuration: docs/conf.py
+  fail_on_warning: false

docs/formats.rst

@@ -7,7 +7,7 @@ GROMACS
 -------
 The following methods are available for reading and writing GROMACS files.
 
-    .. autofunction:: gmso.external.read_gro
+    .. autofunction:: gmso.formats.read_gro
     .. autofunction:: gmso.formats.write_gro
 
 GSD

docs/requirements.txt

@@ -1,2 +1,6 @@
 sphinx
-sphinx_rtd_theme
+boltons
+lxml
+unyt
+pytest
+sphinx_rtd_theme

gmso/formats/top.py

@@ -13,7 +13,6 @@ def write_top(top, filename):
 
     _validate_compatibility(top)
     top_vars = _get_top_vars()
-    _assign_indices(top)
 
     with open(filename, 'w') as out_file:
         out_file.write(
@@ -131,15 +130,15 @@ def write_top(top, filename):
             '\n[ bonds ]\n'
             ';   ai     aj  funct   c0      c1\n'
         )
-        for bond_idx, bond in enumerate(top.bonds):
+        for bond in top.bonds:
             out_file.write(
                 '\t{0}'
                 '\t{1}'
                 '\t{2}'
                 '\t{3}'
                 '\t{4}\n'.format(
-                    bond.connection_members[0].idx,
-                    bond.connection_members[1].idx,
+                    top.sites.index(bond.connection_members[0]),
+                    top.sites.index(bond.connection_members[1]),
                     '1',
                     bond.connection_type.parameters['r_eq'].in_units(u.nm).value,
                     bond.connection_type.parameters['k'].in_units(
@@ -151,17 +150,17 @@ def write_top(top, filename):
             '\n[ angles ]\n'
             ';   ai     aj      ak      funct   c0      c1\n'
         )
-        for angle_idx, angle in enumerate(top.angles):
+        for angle in top.angles:
             out_file.write(
                 '\t{0}'
                 '\t{1}'
                 '\t{2}'
                 '\t{3}'
                 '\t{4}'
                 '\t{5}\n'.format(
-                    angle.connection_members[0].idx,
-                    angle.connection_members[1].idx,
-                    angle.connection_members[2].idx,
+                    top.sites.index(angle.connection_members[0]),
+                    top.sites.index(angle.connection_members[1]),
+                    top.sites.index(angle.connection_members[2]),
                     '1',
                     angle.connection_type.parameters['theta_eq'].in_units(u.degree).value,
                     angle.connection_type.parameters['k'].in_units(
@@ -173,7 +172,7 @@ def write_top(top, filename):
             '\n[ dihedrals ]\n'
             ';   ai     aj      ak      al  funct   c0      c1      c2\n'
         )
-        for dihedral_idx, dihedral in enumerate(top.dihedrals):
+        for dihedral in top.dihedrals:
             out_file.write(
                 '\t{0}'
                 '\t{1}'
@@ -186,10 +185,10 @@ def write_top(top, filename):
                 '\t{8}'
                 '\t{9}'
                 '\t{10}\n'.format(
-                    dihedral.connection_members[0].idx,
-                    dihderal.connection_members[1].idx,
-                    dihedral.connection_members[2].idx,
-                    dihedral.connection_members[3].idx,
+                    top.sites.index(dihedral.connection_members[0]),
+                    top.sites.index(dihedral.connection_members[1]),
+                    top.sites.index(dihedral.connection_members[2]),
+                    top.sites.index(dihedral.connection_members[3]),
                     '3',
                     dihedral.connection_type.parameters['c0'],
                     dihedral.connection_type.parameters['c1'],
@@ -246,11 +245,6 @@ def _get_top_vars():
     return top_vars
 
 
-def _assign_indices(top):
-    for idx, site in enumerate(top.sites):
-        site.idx = idx + 1
-
-
 def _lookup_atomic_number(atom_type):
     """Attempt to look up an atomic_number based on atom type information, 0 if non-element type"""
     try:

gmso/tests/base_test.py

@@ -5,8 +5,9 @@
 
 from gmso.core.box import Box
 from gmso.core.topology import Topology
-from gmso.core.element import Hydrogen
+from gmso.core.element import Hydrogen, Oxygen
 from gmso.core.site import Site
+from gmso.core.angle import Angle
 from gmso.core.atom_type import AtomType
 from gmso.core.forcefield import ForceField
 from gmso.external.convert_mbuild import from_mbuild
@@ -97,8 +98,34 @@ def water_system(self):
 
         packed_system = mb.fill_box(
                 compound=water,
-                n_compounds=10,
+                n_compounds=2,
                 box=mb.Box([2, 2, 2])
                 )
 
         return  from_mbuild(packed_system)
+
+    @pytest.fixture
+    def typed_water_system(self, water_system):
+        top = water_system
+
+        ff = ForceField(get_path('tip3p.xml'))
+
+        element_map = {"O": "opls_111", "H": "opls_112"}
+
+        for atom in top.sites:
+            atom.atom_type = ff.atom_types[atom.name]
+
+        for bond in top.bonds:
+            bond.connection_type = ff.bond_types["opls_111~opls_112"]
+
+        for subtop in top.subtops:
+            angle = Angle(
+                connection_members=[site for site in subtop.sites],
+                name="opls_112~opls_111~opls_112",
+                connection_type=ff.angle_types["opls_112~opls_111~opls_112"]
+            )
+            top.add_connection(angle)
+
+        top.update_topology()
+
+        return top

gmso/tests/test_top.py

@@ -15,10 +15,11 @@ def test_write_top(self, typed_ar_system):
         write_top(top, 'ar.top')
 
 
-    def test_pmd_loop(self, typed_ar_system):
-        top = typed_ar_system
-        write_top(top, 'ar.top')
-        pmd.load_file('ar.top')
+    @pytest.mark.parametrize('top', ['typed_ar_system',
+        'typed_water_system'])
+    def test_pmd_loop(self, top, request):
+        write_top(request.getfixturevalue(top), 'system.top')
+        pmd.load_file('system.top')
 
 
     def test_modified_potentials(self, ar_system):

setup.py

@@ -1,25 +1,35 @@
-from setuptools import setup
+from setuptools import setup, find_packages
 
 #####################################
-VERSION = "0.0.0"
-ISRELEASED = False 
+VERSION = "0.2.0"
+ISRELEASED = False
 if ISRELEASED:
     __version__ = VERSION
 else:
     __version__ = VERSION + '.dev0'
 #####################################
 
 
+requirements = [
+    'numpy',
+    'scipy',
+    'mbuild>=0.10.4',
+    'unyt>=2.4',
+    'boltons',
+    'lxml',
+]
+
+
 setup(
     name='gmso',
     version=__version__,
+    packages=find_packages(),
+    zip_safe=True,
     author='Matthew W Thompson, Justin Gilmer',
     author_email='[email protected], [email protected]',
-    url='https://github.com/mattwthompson/topology',
-    download_url='https://github.com/mattwthompson/topology/tarball/{}'.format(__version__),
-    package_dir={'gmso': 'gmso'},
+    url='https://github.com/mosdef-hub/gmso',
+    download_url='https://github.com/mosdef-hub/gmso/tarball/{}'.format(__version__),
     license="MIT",
-    zip_safe=False,
     keywords='gmso',
     classifiers=[
         'Development Status :: 1 - Planning',
@@ -35,5 +45,6 @@
         'Operating System :: Unix',
         'Operating System :: MacOS',
     ],
+    install_requires=requirements,
+    python_requires='>=3.6, <4',
 )
-