Merge pull request #43 from ReactionMechanismGenerator/py3

The tests are passing with krsna's Openbabel 2.4.1a and ampayne's RMG 3.0.0b. 🎉 Coverage is down a touch (1.11%) but this is because some of our import shuffling - Addressing this coverage will be done in #45 but for now, we can merge this in.

.gitignore

@@ -11,6 +11,7 @@
 *.pyc
 *.so
 *.pyd
+*.symm
 *.coverage
 
 # Image files generated
@@ -29,6 +30,9 @@
 *.idea/
 
 # Gaussian scratch files and ase related io files
+*.symm
 *.ase
 *.com
 *.log
+*.ts
+*.kinetics

.travis.yml

@@ -1,11 +1,11 @@
 language: python
 python:
-  - "2.7"
+  - "3.7"
 install:
   - cd ..
   # Install miniconda
-  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then wget http://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh -O miniconda.sh; fi
-  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then wget http://repo.continuum.io/miniconda/Miniconda2-latest-MacOSX-x86_64.sh -O miniconda.sh; fi
+  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then wget http://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh; fi
+  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then wget http://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -O miniconda.sh; fi
   - bash miniconda.sh -b -p $HOME/miniconda
   - export PATH=$HOME/miniconda/bin:$PATH
   # Update conda
@@ -21,7 +21,7 @@ install:
   - conda env create -f environment.yml
   - source activate tst_env
   - conda list
-  - yes | conda uninstall --force openbabel
+  #- yes | conda uninstall --force openbabel
 
 script:
   - make unittests

Makefile

@@ -1,4 +1,6 @@
 unittest unittests test-unittest test-unittests:
 	nosetests --nocapture --nologcapture --all-modules --verbose --with-coverage  --cover-package=autotst 
 	rm -r species
-	rm -r ts
+	rm -r ts
+	rm -r test/species
+	rm -r test/ts

autotst/__init__.py

@@ -2,6 +2,7 @@
 # -*- coding: utf-8 -*-
 
 import os
+import rdkit
 
 __file_path = os.path.dirname(os.path.abspath(__file__))
 

autotst/calculator/gaussian.py

@@ -33,10 +33,6 @@
 import numpy as np
 from cclib.io import ccread
 
-import rmgpy
-from rmgpy.molecule import Molecule as RMGMolecule
-from rmgpy.reaction import Reaction as RMGReaction
-
 import autotst
 from autotst.reaction import Reaction, TS
 from autotst.species import Species, Conformer
@@ -46,6 +42,10 @@
 from ase.io.gaussian import read_gaussian, read_gaussian_out
 from ase.calculators.gaussian import Gaussian as ASEGaussian
 
+import rmgpy
+from rmgpy.molecule import Molecule as RMGMolecule
+from rmgpy.reaction import Reaction as RMGReaction
+
 
 class Gaussian():
 
@@ -158,7 +158,7 @@ def get_rotor_calc(self,
                 a, b, c, d = locked_torsion.atom_indices
                 addsec += 'D {0} {1} {2} {3} F\n'.format(a+1, b+1, c+1, d+1)
 
-        self.conformer.rmg_molecule.updateMultiplicity()
+        self.conformer.rmg_molecule.update_multiplicity()
         mult = self.conformer.rmg_molecule.multiplicity
 
         new_scratch = os.path.join(
@@ -207,7 +207,7 @@ def get_conformer_calc(self):
         assert isinstance(
             self.conformer, Conformer), "A Conformer object was not provided..."
 
-        self.conformer.rmg_molecule.updateMultiplicity()
+        self.conformer.rmg_molecule.update_multiplicity()
 
         label = "{}_{}".format(self.conformer.smiles, self.conformer.index)
 
@@ -252,7 +252,7 @@ def get_shell_calc(self):
         assert isinstance(self.conformer, TS), "A TS object was not provided..."
         assert self.conformer.direction.lower() in ["forward", "reverse"]
 
-        self.conformer.rmg_molecule.updateMultiplicity()
+        self.conformer.rmg_molecule.update_multiplicity()
 
         label = self.conformer.reaction_label + "_" + self.conformer.direction.lower() + "_shell_" + str(self.conformer.index)
 
@@ -267,10 +267,15 @@ def get_shell_calc(self):
             os.makedirs(new_scratch)
         except OSError:
             pass
-
-        ind1 = self.conformer.rmg_molecule.getLabeledAtom("*1").sortingLabel
-        ind2 = self.conformer.rmg_molecule.getLabeledAtom("*2").sortingLabel
-        ind3 = self.conformer.rmg_molecule.getLabeledAtom("*3").sortingLabel
+
+        #if self.conformer.reaction_family != "Some reaction family with 4 labeled atoms..."
+        if self.conformer.reaction_family.lower() in ["h_abstraction", "intra_h_migration", "r_addition_multiplebond"]:
+            ind1 = self.conformer.rmg_molecule.get_labeled_atoms("*1")[0].sorting_label
+            ind2 = self.conformer.rmg_molecule.get_labeled_atoms("*2")[0].sorting_label
+            ind3 = self.conformer.rmg_molecule.get_labeled_atoms("*3")[0].sorting_label
+        else:
+            logging.error("Reaction family {} is not supported...".format(self.conformer.reaction_family))
+            raise AssertionError
 
         combos = ""
         combos += "{0} {1} F\n".format(ind1+1, ind2+1)
@@ -321,7 +326,7 @@ def get_center_calc(self):
             a, b = combo
             addsec += "{0} {1} F\n".format(a + 1, b + 1)
 
-        self.conformer.rmg_molecule.updateMultiplicity()
+        self.conformer.rmg_molecule.update_multiplicity()
 
         label = self.conformer.reaction_label + "_" + self.conformer.direction.lower() + "_center_" + str(self.conformer.index)
 
@@ -369,7 +374,7 @@ def get_overall_calc(self):
 
         assert isinstance(self.conformer, TS), "A TS object was not provided..."
 
-        self.conformer.rmg_molecule.updateMultiplicity()
+        self.conformer.rmg_molecule.update_multiplicity()
 
         label = self.conformer.reaction_label + "_" + self.conformer.direction.lower() + "_" + str(self.conformer.index)
 
@@ -415,7 +420,7 @@ def get_irc_calc(self):
 
         assert isinstance(self.conformer, TS), "A TS object was not provided..."
 
-        self.conformer.rmg_molecule.updateMultiplicity()
+        self.conformer.rmg_molecule.update_multiplicity()
         label = self.conformer.reaction_label + "_irc_" + self.conformer.direction + "_" + str(self.conformer.index)
 
         new_scratch = os.path.join(
@@ -491,39 +496,39 @@ def validate_irc(self):
 
         pth1 = list()
         steps = list()
-        with open(irc_path) as outputFile:
-            for line in outputFile:
+        with open(irc_path) as output_file:
+            for line in output_file:
                 line = line.strip()
 
                 if line.startswith('Point Number:'):
                     if int(line.split()[2]) > 0:
                         if int(line.split()[-1]) == 1:
-                            ptNum = int(line.split()[2])
-                            pth1.append(ptNum)
+                            pt_num = int(line.split()[2])
+                            pth1.append(pt_num)
                         else:
                             pass
                 elif line.startswith('# OF STEPS ='):
-                    numStp = int(line.split()[-1])
-                    steps.append(numStp)
+                    num_step = int(line.split()[-1])
+                    steps.append(num_step)
         # This indexes the coordinate to be used from the parsing
         if steps == []:
             logging.error('No steps taken in the IRC calculation!')
             return False
         else:
             pth1End = sum(steps[:pth1[-1]])
             # Compare the reactants and products
-            ircParse = ccread(irc_path)
+            irc_parse = ccread(irc_path)
 
 
-            atomcoords = ircParse.atomcoords
-            atomnos = ircParse.atomnos
+            atomcoords = irc_parse.atomcoords
+            atomnos = irc_parse.atomnos
 
             mol1 = RMGMolecule()
-            mol1.fromXYZ(atomnos, atomcoords[pth1End])
+            mol1.from_xyz(atomnos, atomcoords[pth1End])
             mol2 = RMGMolecule()
-            mol2.fromXYZ(atomnos, atomcoords[-1])
+            mol2.from_xyz(atomnos, atomcoords[-1])
 
-            testReaction = RMGReaction(
+            test_reaction = RMGReaction(
                 reactants=mol1.split(),
                 products=mol2.split(),
             )
@@ -557,19 +562,19 @@ def validate_irc(self):
             for possible_reactant in possible_reactants:
                 reactant_list = []
                 for react in possible_reactant:
-                    reactant_list.append(react.toSingleBonds())
+                    reactant_list.append(react.to_single_bonds())
 
                 for possible_product in possible_products:
                     product_list = []
                     for prod in possible_product:
-                        product_list.append(prod.toSingleBonds())
+                        product_list.append(prod.to_single_bonds())
 
-                    targetReaction = RMGReaction(
+                    target_reaction = RMGReaction(
                         reactants=list(reactant_list),
                         products=list(product_list)
                     )
 
-                    if targetReaction.isIsomorphic(testReaction):
+                    if target_reaction.is_isomorphic(test_reaction):
                         logging.info("IRC calculation was successful!")
                         return True
             logging.info("IRC calculation failed for {} :(".format(irc_path))

autotst/calculator/gaussianTest.py

@@ -1,3 +1,32 @@
+#!/usr/bin/python
+# -*- coding: utf-8 -*-
+
+##########################################################################
+#
+#   AutoTST - Automated Transition State Theory
+#
+#   Copyright (c) 2015-2018 Prof. Richard H. West (r.west@northeastern.edu)
+#
+#   Permission is hereby granted, free of charge, to any person obtaining a
+#   copy of this software and associated documentation files (the 'Software'),
+#   to deal in the Software without restriction, including without limitation
+#   the rights to use, copy, modify, merge, publish, distribute, sublicense,
+#   and/or sell copies of the Software, and to permit persons to whom the
+#   Software is furnished to do so, subject to the following conditions:
+#
+#   The above copyright notice and this permission notice shall be included in
+#   all copies or substantial portions of the Software.
+#
+#   THE SOFTWARE IS PROVIDED 'AS IS', WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+#   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+#   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+#   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+#   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+#   FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+#   DEALINGS IN THE SOFTWARE.
+#
+##########################################################################
+
 import unittest
 
 import os, shutil
@@ -6,10 +35,6 @@
 import numpy as np
 from cclib.io import ccread
 
-import rmgpy
-from rmgpy.molecule import Molecule as RMGMolecule
-from rmgpy.reaction import Reaction as RMGReaction
-
 import autotst
 from autotst.reaction import Reaction, TS
 from autotst.species import Species, Conformer
@@ -22,8 +47,13 @@
 from ase.io.gaussian import read_gaussian, read_gaussian_out
 from ase.calculators.gaussian import Gaussian as ASEGaussian
 
+import rmgpy
+from rmgpy.molecule import Molecule as RMGMolecule
+from rmgpy.reaction import Reaction as RMGReaction
+
 class TestGaussian(unittest.TestCase):
     def setUp(self):
+        os.environ["PATH"] = os.path.expandvars("$AUTOTST/test/bin:") + os.environ["PATH"]
         rxn = Reaction(label='C+[O]O_[CH3]+OO')
         ts = rxn.ts["forward"][0]
         ts.get_molecules()

autotst/calculator/orca.py

@@ -124,7 +124,7 @@ def load_conformer_attributes(self):
         else:
             self.base = self.label
 
-        self.charge = self.conformer.rmg_molecule.getNetCharge()
+        self.charge = self.conformer.rmg_molecule.get_net_charge()
         self.mult = self.conformer.rmg_molecule.multiplicity
 
         try:
@@ -168,7 +168,7 @@ def write_fod_input(self,directory=None):
             f.write(self.coords)
             f.write('*\n')
 
-    def check_NormalTermination(self,path):
+    def check_normal_termination(self,path):
         """
         checks if an Orca job terminated normally.
         Returns True is normal termination and False if something went wrong.
@@ -190,7 +190,7 @@ def read_fod_log(self,path):
         """
         assert os.path.exists(path),'It seems {} is not a valid path'.format(path)
 
-        if self.check_NormalTermination(path):
+        if self.check_normal_termination(path):
             N_FOD = None
             for line in open(path,'r').readlines():
                 if 'N_FOD =' in line:

autotst/calculator/orcaTest.py

@@ -1,3 +1,32 @@
+#!/usr/bin/python
+# -*- coding: utf-8 -*-
+
+##########################################################################
+#
+#   AutoTST - Automated Transition State Theory
+#
+#   Copyright (c) 2015-2018 Prof. Richard H. West (r.west@northeastern.edu)
+#
+#   Permission is hereby granted, free of charge, to any person obtaining a
+#   copy of this software and associated documentation files (the 'Software'),
+#   to deal in the Software without restriction, including without limitation
+#   the rights to use, copy, modify, merge, publish, distribute, sublicense,
+#   and/or sell copies of the Software, and to permit persons to whom the
+#   Software is furnished to do so, subject to the following conditions:
+#
+#   The above copyright notice and this permission notice shall be included in
+#   all copies or substantial portions of the Software.
+#
+#   THE SOFTWARE IS PROVIDED 'AS IS', WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+#   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+#   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+#   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+#   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+#   FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+#   DEALINGS IN THE SOFTWARE.
+#
+##########################################################################
+
 import unittest
 
 import os
@@ -31,10 +60,10 @@ def test_write_fod_input(self):
         self.orca.write_fod_input()
         self.assertTrue(os.path.exists(os.path.join(self.orca.directory,'C_fod.inp')))
 
-    def test_check_NormalTermination(self):
+    def test_check_normal_termination(self):
         path = os.path.expandvars(
             "$AUTOTST/test/bin/log-files/C_fod.log")
-        self.assertTrue(self.orca.check_NormalTermination(path))
+        self.assertTrue(self.orca.check_normal_termination(path))
 
     def test_read_fod_log(self):
         path = os.path.expandvars(