started adding ether trappe-ua to forcefield

foyer/tests/implemented_trappe_tests.txt

@@ -8,3 +8,9 @@ methane
 methanol
 neopentane
 propane
+dimethylether
+aldehyde_1
+aldehyde_2
+aldehyde_3
+aldehyde_4
+methyl_acrylate

foyer/tests/test_trappe.py

@@ -1,14 +1,16 @@
 import glob
 import itertools as it
 import os
-
+from scipy.constants import N_A, k, calorie
 import parmed as pmd
 from pkg_resources import resource_filename
 import pytest
 
 from foyer import Forcefield
 from foyer.tests.utils import atomtype
 
+from numpy.testing import assert_almost_equal
+
 TRAPPE_UA = Forcefield(name='trappe-ua')
 
 TRAPPE_TESTFILES_DIR = resource_filename('foyer', 'trappe_validation')
@@ -45,12 +47,199 @@ def find_correctly_implemented(self):
 
     @pytest.mark.parametrize('mol_name', correctly_implemented)
     def test_atomtyping(self, mol_name, testfiles_dir=TRAPPE_TESTFILES_DIR):
-        files = glob.glob(os.path.join(testfiles_dir, mol_name, '*'))
+        files = glob.glob(os.path.join(testfiles_dir, mol_name, '*.mol2'))
         for mol_file in files:
             _, ext = os.path.splitext(mol_file)
             mol2_path = os.path.join(testfiles_dir, mol_name, mol_file)
             structure = pmd.load_file(mol2_path, structure=True)
         atomtype(structure, TRAPPE_UA, non_atomistic=True)
 
+@pytest.fixture
+def trappe_ref(request):
+    # load raw trappe csv file and process slightly
+    container = {
+        '(pseudo)atom': [],
+        'stretch': [],
+        'bend': [],
+        'torsion': [],
+    }
+    # split csv file into sections
+    csv_file = os.path.join(TRAPPE_TESTFILES_DIR,
+                            request.param)
+    with open(csv_file, 'r') as inf:
+        for line in inf:
+            if line.startswith('#'):
+                section_clue = line.split(",")[1]
+                section = container[section_clue]
+                line = next(inf)
+                while not line == '\n':
+                    # slurp until newline hit
+                    section.append(line)
+                    try:
+                        line = next(inf)
+                    except StopIteration:
+                        break
+
+    return container
+
+
+@pytest.fixture
+def mol2file(request):
+    # load a mol2 file and apply foyer's trappe-ua forcefield
+    fname = request.param
+    molfile = glob.glob(os.path.join(TRAPPE_TESTFILES_DIR, fname, '*'))[0]
+    structure = pmd.load_file(molfile, structure=True)
+
+    return TRAPPE_UA.apply(structure,
+                           assert_angle_params=False,
+                           assert_dihedral_params=False,
+    )
+
+
+def parmed2trappe(val):
+    # convert kcal/mol (parmed units) to K/k_B (trappe units)
+    return val * calorie / (k * N_A / 1000.)
+
+def angle_parmed2trappe(val):
+    # trappe angle units need doubling
+    return 2 * parmed2trappe(val)
+
+def assert_dihedrals_match(foyer_d, reference_params):
+    # Check that a dihedral from foyer matches the text in the csv file
+    # foyer_d - parmed rb_torsion
+    # reference_params - dihedral parameters from trappe csv file
+    def conv1(t):
+        # convert RB to original Trappe dihedral form:
+        # V = c0 + c1(1 + cos phi) + c1(1 - cos 2phi) + c3(1 + cos 3phi)
+        R0, R1, R2, R3 = t.c0, t.c1, t.c2, t.c3
+        c0 = - R0 + R1 + R2 + R3
+        c1 = - R1 - 3/4. * R3
+        c2 = - 0.5 * R2
+        c3 = - 1/4. * R3
+
+        return c0, c1, c2, c3
+
+    def conv2(t):
+        # convert RB to second Trappe dihedral form:
+        # V = c0 + c1 cos phi + c2 cos 2phi + c3 cos 3phi + c4 cos 4phi
+        R0, R1, R2, R3, R4 = t.c0, t.c1, t.c2, t.c3, t.c4
+        print(list(map(lambda x: x * calorie, [R0, R1, R2, R3, R4])))
+        c0 = - R0 + 0.5 * R2 + 3/8. * R4
+        c1 = - R1 - 3/4. * R3
+        c2 = 0.5 * R2 + 0.5 * R4
+        c3 = - 1/4. * R3
+        c4 = 1/8. * R4
+
+        return [parmed2trappe(v) for v in [c0, c1, c2, c3, c4]]
+
+    reference_params = list(map(float, reference_params))
+    # check parameters in *foyer_d* match the raw text from trappe
+    # trappe's params are in one of two functional forms.....
+    if len(reference_params) == 5:
+        # using later form, has an extra column
+        foyer_params = conv2(foyer_d.type)
+    elif len(reference_params) == 4:
+        # using original dihedral form
+        foyer_params = conv1(foyer_d.type)
+
+    assert_almost_equal(foyer_params, reference_params, decimal=3)
+
+class TestTrappeReferences(object):
+    @staticmethod
+    def check_atoms(ref, struc):
+        ref_atoms = sorted(ref['(pseudo)atom'],
+                           key=lambda x: int(x.split(',')[0]))
+        for ref_atom, foyer_atom in zip(ref_atoms, struc.atoms):
+            _, _, _, epsilon, sigma, charge = ref_atom.strip().split(',')
+
+            assert_almost_equal(foyer_atom.charge, float(charge))
+            assert_almost_equal(foyer_atom.sigma, float(sigma))
+            assert_almost_equal(parmed2trappe(foyer_atom.epsilon),
+                                float(epsilon),
+                                decimal=3)
+
+    @staticmethod
+    def check_bonds(ref, struc):
+        ref_bonds = ref['stretch']
+        # organise foyer's bonds into dict of indices
+        bond_dict = {}
+        for b in struc.bonds:
+            i, j = sorted((b.atom1.idx, b.atom2.idx))
+            bond_dict[i+1, j+1] = b
+
+        # iterate reference file bonds
+        # lookup foyer bond and compare length
+        for ref_bond in ref_bonds:
+            _, desc, _, length = ref_bond.strip().split(',')
+            i, j = map(int, desc.strip("\"\'").split('-'))
+            foyer_bond = bond_dict[i, j]
+
+            assert_almost_equal(foyer_bond.type.req, float(length))
+            # trappe is fixed bond length, no point in K comparison
+
+    @staticmethod
+    def check_angles(ref, struc):
+        ref_angles = ref['bend']
+        assert len(ref_angles) == len(struc.angles)
+
+        angle_dict = {}
+        for a in struc.angles:
+            i, j, k = a.atom1.idx, a.atom2.idx, a.atom3.idx
+            if k < i:
+                i, j, k = k, j, i
+            angle_dict[i+1, j+1, k+1] = a
+
+        for ref_angle in ref_angles:
+            _, desc, _, angle, k_angle = ref_angle.strip().split(',')
+            i, j, k = map(int, desc.strip("\"\'").split('-'))
+
+            foyer_angle = angle_dict[i, j, k]
+
+            assert_almost_equal(foyer_angle.type.theteq,
+                                float(angle),
+                                decimal=4)
+            assert_almost_equal(angle_parmed2trappe(foyer_angle.type.k),
+                                float(k_angle),
+                                decimal=3)
+
+    @staticmethod
+    def check_dihedrals(ref, struc):
+        ref_dihedrals = ref['torsion']
+
+        assert len(ref_dihedrals) == len(struc.rb_torsions)
+
+        dih_dict = {}
+        for d in struc.rb_torsions:
+            i, j, k, l = d.atom1.idx, d.atom2.idx, d.atom3.idx, d.atom4.idx
+
+            if l < i:
+                i, j, k, l = l, k, j, i
+            dih_dict[i+1, j+1, k+1, l+1] = d
+
+        for ref_d in ref_dihedrals:
+            _, desc, _, *params = ref_d.strip().split(',')
+            i, j, k, l = map(int, desc.strip("\"\'").split('-'))
+            if l < i:
+                i, j, k, l = l, k, j, i
+
+            foyer_d = dih_dict[i, j, k, l]
+
+            assert_dihedrals_match(foyer_d, params)
+
+    @pytest.mark.parametrize('trappe_ref,mol2file', [
+        ('butadiene/trappe_parameters_94.csv', 'butadiene'),
+        ('isoprene/trappe_parameters_95.csv', 'isoprene'),
+        ('methyl_acrylate/trappe_parameters_96.csv', 'methyl_acrylate'),
+    ], indirect=True)
+    def test_trappe_reference(self, trappe_ref, mol2file):
+        self.check_atoms(trappe_ref, mol2file)
+
+        self.check_bonds(trappe_ref, mol2file)
+
+        self.check_angles(trappe_ref, mol2file)
+
+        self.check_dihedrals(trappe_ref, mol2file)
+
+
 if __name__ == '__main__':
     TestTraPPE().find_correctly_implemented()

foyer/trappe_validation/aldehyde_1/aldehyde_1.mol2

@@ -0,0 +1,16 @@
+@<TRIPOS>MOLECULE
+RES
+3 2 1 0 1
+SMALL
+USER_CHARGES
+@<TRIPOS>CRYSIN
+    5.0000     5.0000     5.0000    90.0000    90.0000    90.0000  1  1
+@<TRIPOS>ATOM
+       1 _CH3         0.0000     0.0000     0.0000 CH3_sp3-Cald      1 RES       -0.043000
+       2 _HC          0.0000     0.0000     0.0000 CH_ald        1 RES        0.525000
+       3 O            0.0000     0.0000     0.0000 O_ald         1 RES       -0.482000
+@<TRIPOS>BOND
+       1        1        2 1
+       2        3        2 1
+@<TRIPOS>SUBSTRUCTURE
+       1 RES             1 RESIDUE    0 1    ROOT      0

foyer/trappe_validation/aldehyde_2/aldehyde_2.mol2

@@ -0,0 +1,18 @@
+@<TRIPOS>MOLECULE
+RES
+4 3 1 0 1
+SMALL
+USER_CHARGES
+@<TRIPOS>CRYSIN
+    5.0000     5.0000     5.0000    90.0000    90.0000    90.0000  1  1
+@<TRIPOS>ATOM
+       1 _CH3         0.0000     0.0000     0.0000 CH3_sp3       1 RES        0.000000
+       2 _CH2         0.0000     0.0000     0.0000 CH2_sp3-Cald      1 RES       -0.043000
+       3 _HC          0.0000     0.0000     0.0000 CH_ald        1 RES        0.525000
+       4 O            0.0000     0.0000     0.0000 O_ald         1 RES       -0.482000
+@<TRIPOS>BOND
+       1        1        2 1
+       2        2        3 1
+       3        3        4 1
+@<TRIPOS>SUBSTRUCTURE
+       1 RES             1 RESIDUE    0 1    ROOT      0

foyer/trappe_validation/aldehyde_3/aldehyde_3.mol2

@@ -0,0 +1,20 @@
+@<TRIPOS>MOLECULE
+RES
+5 4 1 0 1
+SMALL
+USER_CHARGES
+@<TRIPOS>CRYSIN
+    5.0000     5.0000     5.0000    90.0000    90.0000    90.0000  1  1
+@<TRIPOS>ATOM
+       1 _CH3         0.0000     0.0000     0.0000 CH3_sp3       1 RES        0.000000
+       2 _CH3         0.0000     0.0000     0.0000 CH3_sp3       1 RES        0.000000
+       3 _HC          0.0000     0.0000     0.0000 CH_sp3-Cald      1 RES       -0.043000
+       4 _HC          0.0000     0.0000     0.0000 CH_ald        1 RES        0.525000
+       5 O            0.0000     0.0000     0.0000 O_ald         1 RES       -0.482000
+@<TRIPOS>BOND
+       1        2        3 1
+       2        3        1 1
+       3        4        3 1
+       4        4        5 1
+@<TRIPOS>SUBSTRUCTURE
+       1 RES             1 RESIDUE    0 1    ROOT      0

foyer/trappe_validation/aldehyde_4/aldehyde_4.mol2

@@ -0,0 +1,22 @@
+@<TRIPOS>MOLECULE
+RES
+6 5 1 0 1
+SMALL
+USER_CHARGES
+@<TRIPOS>CRYSIN
+    5.0000     5.0000     5.0000    90.0000    90.0000    90.0000  1  1
+@<TRIPOS>ATOM
+       1 _CH3         0.0000     0.0000     0.0000 CH3_sp3       1 RES        0.000000
+       2 _CH3         0.0000     0.0000     0.0000 CH3_sp3       1 RES        0.000000
+       3 _CH3         0.0000     0.0000     0.0000 CH3_sp3       1 RES        0.000000
+       4 C            0.0000     0.0000     0.0000 C_sp3-Cald      1 RES       -0.043000
+       5 _HC          0.0000     0.0000     0.0000 CH_ald        1 RES        0.525000
+       6 O            0.0000     0.0000     0.0000 O_ald         1 RES       -0.482000
+@<TRIPOS>BOND
+       1        1        4 1
+       2        2        4 1
+       3        3        4 1
+       4        4        5 1
+       5        5        6 1
+@<TRIPOS>SUBSTRUCTURE
+       1 RES             1 RESIDUE    0 1    ROOT      0

foyer/trappe_validation/butadiene/butadiene.mol2

@@ -0,0 +1,18 @@
+@<TRIPOS>MOLECULE
+RES
+4 3 1 0 1
+SMALL
+NO_CHARGES
+@<TRIPOS>CRYSIN
+    9.5000     5.0000     5.0000    90.0000    90.0000    90.0000  1  1
+@<TRIPOS>ATOM
+       1 _CH2         0.0000     0.0000     0.0000 CH2_sp2       1 RES     
+       2 _HC          1.5000     0.0000     0.0000 CH_sp2-Csp2      1 RES     
+       3 _HC          3.0000     0.0000     0.0000 CH_sp2-Csp2      1 RES     
+       4 _CH2         4.5000     0.0000     0.0000 CH2_sp2       1 RES     
+@<TRIPOS>BOND
+       1        1        2 1
+       2        2        3 1
+       3        3        4 1
+@<TRIPOS>SUBSTRUCTURE
+       1 RES             1 RESIDUE    0 1    ROOT      0

foyer/trappe_validation/butadiene/trappe_parameters_94.csv

@@ -0,0 +1,19 @@
+"1,3-butadiene"
+
+#,(pseudo)atom,type,"epsilon/kB [K]","sigma [Ang.]","charge [e]"
+1,CH2,[CH2]=CHx,85.0,3.675,0.000
+4,CH2,[CH2]=CHx,85.0,3.675,0.000
+2,CH,CHx=[CH](sp2)-CHy(sp2),52.0,3.710,0.000
+3,CH,CHx=[CH](sp2)-CHy(sp2),52.0,3.710,0.000
+
+#,stretch,type,"length [Ang.]"
+1,"'1 - 2'",CHx=CHy,1.3300
+2,"'2 - 3'",CHx-CHy,1.5400
+3,"'3 - 4'",CHx=CHy,1.3300
+
+#,bend,type,"theta [degrees]","k_theta/kB [K/rad^2]"
+1,"'1 - 2 - 3'",CHx=(CH)-CHx,119.70,70420
+2,"'2 - 3 - 4'",CHx=(CH)-CHx,119.70,70420
+
+#,torsion,type,"c0/kB [K]","c1/kB [K]","c2/kB [K]","c3/kB [K]","c4/kB [K]"
+1,"'1 - 2 - 3 - 4'",CH2=(CH)-(CH)=CH2,2034.58,531.57,-1239.35,460.04,196.38

foyer/trappe_validation/dimethylether/dme.mol2

@@ -0,0 +1,14 @@
+@<TRIPOS>MOLECULE
+DME
+3 2 1 0 1
+SMALL
+USER_CHARGES
+@<TRIPOS>ATOM
+       1 _CH3        12.5360     1.0140    22.0490 CH3_eth       1 DME        0.265000
+       2 O           13.5570     1.3980    22.8620 O_eth         1 DME        0.000000
+       3 _CH3        13.5710     2.7160    23.1980 CH3_eth       1 DME        0.265000
+@<TRIPOS>BOND
+       1        1        2 1
+       2        2        3 1
+@<TRIPOS>SUBSTRUCTURE
+       1 DME             1 RESIDUE    0 1    ROOT      0

foyer/trappe_validation/isoprene/isoprene.mol2

@@ -0,0 +1,20 @@
+@<TRIPOS>MOLECULE
+RES
+5 4 1 0 1
+SMALL
+NO_CHARGES
+@<TRIPOS>CRYSIN
+    9.5000     6.5000     5.0000    90.0000    90.0000    90.0000  1  1
+@<TRIPOS>ATOM
+       1 _CH2         3.0000     1.5000     0.0000 CH2_sp2       1 RES     
+       2 C            3.0000     0.0000     0.0000 C_sp2-Csp2      1 RES     
+       3 _HC          1.5000     0.0000     0.0000 CH_sp2-Csp2      1 RES     
+       4 _CH2         0.0000     0.0000     0.0000 CH2_sp2       1 RES     
+       5 _CH3         4.5000     0.0000     0.0000 CH3_sp3       1 RES     
+@<TRIPOS>BOND
+       1        2        1 1
+       2        2        5 1
+       3        3        2 1
+       4        4        3 1
+@<TRIPOS>SUBSTRUCTURE
+       1 RES             1 RESIDUE    0 1    ROOT      0