Additional tests, codecov

Author: Travis Hesketh

.coveragerc

@@ -0,0 +1,4 @@
+[run]
+omit =
+    pygen_structures/test/*
+    pygen_structures/_typing.py

.travis.yml

@@ -11,11 +11,12 @@ before_install:
   - conda config --set always_yes yes --set changeps1 no
   - conda update -q conda
   - conda info -a
-  - conda create -q -c rdkit -c omnia -n testenv python=$TRAVIS_PYTHON_VERSION 'rdkit>=2018.03' numpy pytest openmm
+  - conda create -q -c rdkit -c omnia -n testenv python=$TRAVIS_PYTHON_VERSION 'rdkit>=2018.03' numpy pytest pytest-cov codecov openmm
   - conda activate testenv
   - python --version
 install:
   - python setup.py install
-
 script:
-  - pytest
+  - pytest --cov-config .coveragerc --cov=pygen_structures
+after_success:
+  - codecov

pygen_structures/test/test_convenience_functions.py

@@ -0,0 +1,125 @@
+import os
+import pickle
+from pygen_structures import(
+    load_charmm_dir,
+    code_to_mol,
+    sequence_to_mol,
+    Molecule,
+)
+from pygen_structures.convenience_functions import pdb_to_mol
+
+RTF, PRM = load_charmm_dir()
+
+
+def test_load_charmm_dir():
+    pickle_dir = os.path.split(__file__)[0]
+    pickle_path = os.path.join(pickle_dir, 'charmm_dir.pkl')
+
+    with open(pickle_path, 'rb') as pickle_file:
+        rtf, prm = pickle.load(pickle_file)
+    assert(rtf.residues.keys() == RTF.residues.keys())
+    assert(rtf.patches.keys() == RTF.patches.keys())
+    assert(prm.bonds == PRM.bonds)
+    assert(prm.angles == PRM.angles)
+    assert(prm.dihedrals == PRM.dihedrals)
+    assert(prm.impropers == PRM.impropers)
+    assert(prm.cross_maps == PRM.cross_maps)
+
+
+def test_code_to_mol():
+    code = 'YEET'
+    molecule = code_to_mol(code, RTF)
+
+    sequence = ['TYR', 'GLU', 'GLU', 'THR']
+    residues = []
+    for index, residue_name in enumerate(sequence):
+        residue = RTF.residues[residue_name].to_residue(index)
+        residues.append(residue)
+    ref_molecule = Molecule('YEET', residues, RTF)
+    ref_molecule.finalize()
+
+    for residue, ref_residue in zip(molecule.residues, ref_molecule.residues):
+        assert(residue.name == ref_residue.name)
+        assert(set(residue.atoms) == set(ref_residue.atoms))
+        assert(set(residue.bonds) == set(ref_residue.bonds))
+        assert(set(residue.impropers) == set(ref_residue.impropers))
+        assert(set(residue.cross_maps) == set(ref_residue.cross_maps))
+
+
+def test_code_to_mol_terminal_patches():
+    code = 'NNEU-YEET-CT2'
+    molecule = code_to_mol(code, RTF)
+
+    sequence = ['TYR', 'GLU', 'GLU', 'THR']
+    patches = {'NNEU': ['FIRST'], 'CT2': ['LAST']}
+
+    residues = []
+    for index, residue_name in enumerate(sequence):
+        residue = RTF.residues[residue_name].to_residue(index)
+        residues.append(residue)
+    ref_molecule = Molecule('YEET', residues, RTF, patches)
+    ref_molecule.finalize()
+
+    for residue, ref_residue in zip(molecule.residues, ref_molecule.residues):
+        assert(residue.name == ref_residue.name)
+        assert(set(residue.atoms) == set(ref_residue.atoms))
+        assert(set(residue.bonds) == set(ref_residue.bonds))
+        assert(set(residue.impropers) == set(ref_residue.impropers))
+        assert(set(residue.cross_maps) == set(ref_residue.cross_maps))
+
+
+def test_code_to_mol_patches():
+    code = 'CAAC'
+    patches = {'DISU': [0, -1]}
+    molecule = code_to_mol(code, RTF, patches)
+
+    sequence = ['CYS', 'ALA', 'ALA', 'CYS']
+    residues = []
+    for index, residue_name in enumerate(sequence):
+        residue = RTF.residues[residue_name].to_residue(index)
+        residues.append(residue)
+    ref_molecule = Molecule('CAAC', residues, RTF, patches)
+    ref_molecule.finalize()
+
+    for residue, ref_residue in zip(molecule.residues, ref_molecule.residues):
+        assert(residue.name == ref_residue.name)
+        assert(set(residue.atoms) == set(ref_residue.atoms))
+        assert(set(residue.bonds) == set(ref_residue.bonds))
+        assert(set(residue.impropers) == set(ref_residue.impropers))
+        assert(set(residue.cross_maps) == set(ref_residue.cross_maps))
+
+
+def test_sequence_to_mol():
+    sequence = ['TYR', 'GLU', 'GLU', 'THR']
+    molecule = sequence_to_mol(sequence, RTF)
+
+    residues = []
+    for index, residue_name in enumerate(sequence):
+        residue = RTF.residues[residue_name].to_residue(index)
+        residues.append(residue)
+    ref_molecule = Molecule('YEET', residues, RTF)
+    ref_molecule.finalize()
+
+    for residue, ref_residue in zip(molecule.residues, ref_molecule.residues):
+        assert(residue.name == ref_residue.name)
+        assert(set(residue.atoms) == set(ref_residue.atoms))
+        assert(set(residue.bonds) == set(ref_residue.bonds))
+        assert(set(residue.impropers) == set(ref_residue.impropers))
+        assert(set(residue.cross_maps) == set(ref_residue.cross_maps))
+
+
+def test_pdb_to_mol():
+    code = 'AF'
+
+    ref_molecule = code_to_mol(code, RTF)
+    ref_molecule.to_pdb_file('AF.pdb')
+
+    molecule = pdb_to_mol('AF.pdb', RTF)
+    os.remove('AF.pdb')
+
+    for residue, ref_residue in zip(molecule.residues, ref_molecule.residues):
+        assert(residue.name == ref_residue.name)
+        assert(set(residue.atoms) == set(ref_residue.atoms))
+        assert(set(residue.bonds) == set(ref_residue.bonds))
+        assert(set(residue.impropers) == set(ref_residue.impropers))
+        assert(set(residue.cross_maps) == set(ref_residue.cross_maps))