Merge pull request #451 from ReactionMechanismGenerator/ob3

Switch to OpenBabel 3

.github/workflows/cont_int.yml

@@ -1,27 +1,34 @@
 name: continuous integration
 
-on: [push]
+on:
+  push:
+  pull_request:
+    branches:
+      - master
+    types: [opened, synchronize, reopened, ready_for_review, review_requested]
 
 jobs:
   build:
     runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: [3.7, 3.8]
+    defaults:
+      run:
+        shell: bash -l {0}
 
     steps:
     - uses: actions/checkout@v2
 
-    - name: Set up miniconda Python ${{ matrix.python-version }}
+    - name: Set up miniconda Python 3.7
       uses: conda-incubator/setup-miniconda@v2
       with:
-        activate-environment: arc_env
         environment-file: environment.yml
-        python-version: ${{ matrix.python-version }}
+        activate-environment: arc_env
+        python-version: 3.7
         auto-activate-base: false
 
+    - name: Install codecov
+      run: conda install -y -c conda-forge codecov
+
     - name: Install dependencies
-      shell: bash -l {0}
       run: |
         export PYTHONPATH=$PYTHONPATH:$(pwd)
         conda activate arc_env
@@ -40,7 +47,6 @@ jobs:
         conda list
 
     - name: Lint with flake8
-      shell: bash -l {0}
       run: |
         conda install flake8
         # stop the build if there are Python syntax errors or undefined names
@@ -49,7 +55,6 @@ jobs:
         python -m flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
 
     - name: Test with nosetests
-      shell: bash -l {0}
       run: |
         cd ..
         cd RMG-Py

arc/species/conformers.py

@@ -43,8 +43,8 @@
 from itertools import product
 from typing import List, Optional, Tuple, Union
 
-import openbabel as ob
-import pybel as pyb
+from openbabel import openbabel as ob
+from openbabel import pybel as pyb
 from rdkit import Chem
 from rdkit.Chem.rdchem import EditableMol as RDMol
 

arc/species/conformersTest.py

@@ -142,7 +142,7 @@ def test_generate_conformers_with_openbabel(self):
                                                         force_field='MMFF94s', print_logs=False, diastereomers=None,
                                                         n_confs=1, return_all_conformers=False)
         self.assertEqual(len(lowest_confs), 1)
-        self.assertAlmostEqual(lowest_confs[0]['FF energy'], -0.7460169669694667)
+        self.assertAlmostEqual(lowest_confs[0]['FF energy'], -0.7418115656748858)
         expected_xyz = {'symbols': ('C', 'C', 'H', 'H', 'H', 'O', 'H', 'H', 'O'),
                         'isotopes': (12, 12, 1, 1, 1, 16, 1, 1, 16),
                         'coords': ((-1.06401, 0.15134, -0.02907),
@@ -535,7 +535,7 @@ def test_openbabel_force_field(self):
         xyzs, energies = conformers.openbabel_force_field(label='', mol=spc.mol, num_confs=1,
                                                           force_field='GAFF', method='diverse')
         self.assertEqual(len(xyzs), 1)
-        self.assertAlmostEqual(energies[0], 2.9310163, 3)
+        self.assertAlmostEqual(energies[0], 2.931930, 3)
 
     def test_openbabel_force_field_on_rdkit_conformers(self):
         """Test Open Babel force field on RDKit conformers"""
@@ -576,8 +576,8 @@ def test_openbabel_force_field_on_rdkit_conformers(self):
                                     (0.59336, 1.16044, 0.53412),
                                     (2.51642, -0.38757, 0.25036))}]
         self.assertEqual(len(energies), 2)
-        self.assertAlmostEqual(energies[0], 0.2446742680965306)
-        self.assertAlmostEqual(energies[1], -0.7460169699282158)
+        self.assertAlmostEqual(energies[0], 3.4958104235174376)
+        self.assertAlmostEqual(energies[1], -0.7028477774918569)
         # Only symbols instead of the coordinate values are compared.
         # This is due to the unknown behavior of OpenBabel optimization function.
         # With the same iteration number and same initial xyz, the optimized xyzs can
@@ -2065,8 +2065,8 @@ def test_determine_chirality(self):
                                         (5, 4, 6, 7): 204.57856732311797}}]
         mol = ARCSpecies(label='C(O)(S)NC=CO', smiles='C(O)(S)NC=CO', xyz=confs[0]['xyz']).mol  # preserves atom order
         confs = conformers.determine_chirality(conformers=confs, label='C(O)(S)NC=CO', mol=mol)
-        self.assertEqual(confs[0]['chirality'], {(3,): 'NR', (4,): 'S', (5, 6): 'E'})
-        self.assertEqual(confs[1]['chirality'], {(3,): 'NR', (4,): 'R', (5, 6): 'Z'})
+        self.assertEqual(confs[0]['chirality'], {(0,): 'R', (3,): 'NR', (4, 5): 'E'})
+        self.assertEqual(confs[1]['chirality'], {(0,): 'S', (3,): 'NR', (4, 5): 'Z'})
 
     def test_get_lowest_diastereomers(self):
         """Test the getting the lowest diasteroemrs from a given conformers list"""

arc/species/converter.py

@@ -6,8 +6,8 @@
 import os
 from typing import Dict, Iterable, List, Optional, Tuple, Union
 
-import pybel
 import qcelemental as qcel
+from openbabel import pybel
 from rdkit import Chem
 from rdkit.Chem import rdMolTransforms as rdMT
 from rdkit.Chem.rdchem import AtomValenceException

arc/species/converterTest.py

@@ -3086,10 +3086,10 @@ def test_xyz_to_smiles(self):
         # self.assertEqual(mol11.to_smiles(), 'N(N)[N+](=O)[O-]')  # gives None
         self.assertEqual(mol12.to_smiles(), '[O]N=O')
         # self.assertEqual(mol13.to_smiles(), 'C[N+]([NH-])=O')  # gives None
-        self.assertEqual(mol14.to_smiles(), 'OS(=O)[O]')
+        self.assertEqual(mol14.to_smiles(), '[O]S(=O)O')
         self.assertEqual(mol15.to_smiles(), '[N-]=[N+]=N')
         self.assertEqual(mol16.to_smiles(), '[O]N=C')
-        self.assertEqual(mol17.to_smiles(), 'OS(=O)(=O)O')
+        self.assertEqual(mol17.to_smiles(), '[O-][S+](=O)(O)O')
         self.assertEqual(mol18.to_smiles(), 'O=S(=O)=O')
         self.assertEqual(mol19.to_adjacency_list(), """multiplicity 2
 1 N u1 p1 c0 {4,S} {5,S}
@@ -3624,7 +3624,7 @@ def test_add_lone_pairs_by_atom_valance(self):
 4 H u0 p0 c0 {2,S}"""
         mol2 = Molecule().from_adjacency_list(adjlist=adj2)
         converter.add_lone_pairs_by_atom_valance(mol2)
-        self.assertEqual(mol2.to_smiles(), 'N[N]')
+        self.assertEqual(mol2.to_smiles(), '[N]N')
         mol2.multiplicity = 1
         converter.add_lone_pairs_by_atom_valance(mol2)
         self.assertEqual(mol2.to_smiles(), '[N-]=[NH2+]')

arc/species/speciesTest.py

@@ -1118,6 +1118,7 @@ def test_check_xyz_isomorphism(self):
                   Cl  -0.5031634975   -0.0109430036    0.0
                   H    1.5281481620   -0.8718549847    0.0"""
         spc6 = ARCSpecies(label='[CH]Cl', smiles='[CH]Cl', xyz=xyz6)
+        self.assertEqual(spc6.get_xyz(), str_to_xyz(xyz6))
 
     def test_scissors(self):
         """Test the scissors method in Species"""

arc/species/xyz_to_2d.py

@@ -5,7 +5,7 @@
 
 import numpy as np
 
-import pybel
+from openbabel import pybel
 from rdkit import Chem
 from rdkit.Chem import GetPeriodicTable
 

arc/species/zmatTest.py

@@ -290,12 +290,12 @@ def setUpClass(cls):
 
     def test_get_atom_connectivity_from_mol(self):
         """Test listing an atom's connectivity in a molecule"""
-        mol = ARCSpecies(label='c1cc1O', smiles='c1cc1O').mol
+        mol = ARCSpecies(label='OC1CC1', smiles='OC1CC1').mol
         connectivity = dict()
         for i, atom in enumerate(mol.atoms):
             connectivity[i] = zmat.get_atom_connectivity_from_mol(mol, atom)
-        expected_connectivity = {0: [1, 2, 4, 5], 1: [0, 2, 6, 7], 2: [1, 0, 3, 8], 3: [2, 9],
-                                 4: [0], 5: [0], 6: [1], 7: [1], 8: [2], 9: [3]}
+        expected_connectivity = {0: [1, 4], 1: [0, 2, 3, 5], 2: [1, 3, 6, 7], 3: [2, 1, 8, 9],
+                                 4: [0], 5: [1], 6: [2], 7: [2], 8: [3], 9: [3]}
         self.assertEqual(connectivity, expected_connectivity)
 
     def test_get_connectivity(self):
@@ -311,12 +311,12 @@ def test_get_connectivity(self):
                                         1: [0], 2: [3], 4: [0], 6: [5], 7: [5]})
 
         connectivity = zmat.get_connectivity(
-            mol=ARCSpecies(label='phenanthrene', smiles='c1=ccc2c3cc=ccc3ccc2c1', xyz=self.phenanthrene).mol)
+            mol=ARCSpecies(label='phenanthrene', smiles='C1=CCC2=C3CC=CCC3=CC=C2C1', xyz=self.phenanthrene).mol)
         self.assertEqual(connectivity[2], [1, 3, 16, 17])
         self.assertEqual(len(list(connectivity.keys())), 28)
 
         connectivity = zmat.get_connectivity(
-            mol=ARCSpecies(label='crazy', smiles='CSC(CCO)(Cc1ccc(NO)cc1)C(O[CH2])(COO)C', xyz=self.crazy).mol)
+            mol=ARCSpecies(label='crazy', smiles='OCCC(C(COO)(O[CH2])C)(Cc1ccc(cc1)NO)SC', xyz=self.crazy).mol)
         self.assertEqual(len(list(connectivity.keys())), 46)
 
         connectivity = zmat.get_connectivity(mol=ARCSpecies(label='N', smiles='[N]').mol)
@@ -342,15 +342,15 @@ def test_get_atom_order_from_mol(self):
         self.assertEqual(symbols, ['N', 'N', 'N', 'H', 'H', 'H', 'H', 'H'])
 
         atom_order = zmat.get_atom_order_from_mol(
-            ARCSpecies(label='phenanthrene', smiles='c1=ccc2c3cc=ccc3ccc2c1', xyz=self.phenanthrene).mol)
+            ARCSpecies(label='phenanthrene', smiles='C1=CCC2=C3CC=CCC3=CC=C2C1', xyz=self.phenanthrene).mol)
         self.assertEqual(atom_order, [0, 1, 13, 2, 12, 3, 11, 4, 10, 5, 9, 6, 8, 7, 14,
                                       15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27])
         symbols = [self.phenanthrene['symbols'][atom_index] for atom_index in atom_order]
         self.assertEqual(symbols, ['C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C',
                                    'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'])
 
         atom_order = zmat.get_atom_order_from_mol(
-            ARCSpecies(label='crazy', smiles='CSC(CCO)(Cc1ccc(NO)cc1)C(O[CH2])(COO)C', xyz=self.crazy).mol)
+            ARCSpecies(label='crazy', smiles='OCCC(C(COO)(O[CH2])C)(Cc1ccc(cc1)NO)SC', xyz=self.crazy).mol)
         self.assertEqual(atom_order, [0, 1, 2, 3, 6, 15, 4, 7, 23, 20, 16, 5, 8, 14, 21, 17, 9, 13, 22, 10, 11,
                                       12, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38,
                                       39, 40, 41, 42, 43, 44, 45])
@@ -360,7 +360,7 @@ def test_get_atom_order_from_mol(self):
                                    'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'])
 
         atom_order = zmat.get_atom_order_from_mol(
-            ARCSpecies(label='crazy', smiles='CSC(CCO)(Cc1ccc(NO)cc1)C(O[CH2])(COO)C', xyz=self.crazy).mol,
+            ARCSpecies(label='crazy', smiles='OCCC(C(COO)(O[CH2])C)(Cc1ccc(cc1)NO)SC', xyz=self.crazy).mol,
             constraints_dict={})
         self.assertEqual(atom_order, [0, 1, 2, 3, 6, 15, 4, 7, 23, 20, 16, 5, 8, 14, 21, 17, 9, 13, 22, 10, 11,
                                       12, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38,

environment.yml

@@ -2,16 +2,13 @@ name: arc_env
 channels:
   - defaults
   - rmg
-  - anaconda
-  - omnia
   - conda-forge
 dependencies:
   - cairo
   - cairocffi
   - rmg::cantera >=2.3.0
-  - cclib >=1.6
+  - conda-forge::cclib >=1.6.3
   - rmg::chemprop
-  - codecov
   - coolprop
   - coverage
   - cython >=0.25.2
@@ -23,16 +20,16 @@ dependencies:
   - jupyter
   - rmg::lpsolve55
   - markupsafe
-  - matplotlib >=2.2.2
-  - mock
+  - matplotlib >=1.5
   - rmg::mopac
   - mpmath
+  - rmg::muq2
   - networkx
   - nose
   - rmg::numdifftools
-  - numpy >=1.15.4
-  - openbabel
-  - pandas >=1.0.1
+  - numpy >=1.10.0
+  - conda-forge::openbabel >= 3
+  - pandas
   - psutil
   - rmg::pydas >=1.0.2
   - pydot
@@ -46,12 +43,13 @@ dependencies:
   - rmg::rdkit >=2020.03.3.0
   - scikit-learn
   - scipy
-  - sphinx_rtd_theme
   - rmg::symmetry
+  - xlrd
   - xlwt
-  - paramiko >=2.6.0
-  - py3dmol >= 0.8.0
-  - ase >=3.15.0
-  - ipython
-  - sphinx
-  - qcelemental
+  - anaconda::sphinx_rtd_theme
+  - anaconda::paramiko >=2.6.0
+  - conda-forge::py3dmol >= 0.8.0
+  - conda-forge::ase >=3.15.0
+  - anaconda::ipython
+  - anaconda::sphinx
+  - conda-forge::qcelemental