Merge pull request #141 from ReactionMechanismGenerator/xyz_to_smiles

xyz to smiles

arc/mainTest.py

@@ -175,12 +175,12 @@ def test_restart(self):
         self.assertEqual(arc1.freq_scale_factor, 0.986)
 
         with open(os.path.join(project_directory, 'output', 'thermo.info'), 'r') as f:
-            thermo_sft_ccsdtf12_bac = False
+            thermo_dft_ccsdtf12_bac = False
             for line in f.readlines():
                 if 'thermo_DFT_CCSDTF12_BAC' in line:
-                    thermo_sft_ccsdtf12_bac = True
+                    thermo_dft_ccsdtf12_bac = True
                     break
-        self.assertTrue(thermo_sft_ccsdtf12_bac)
+        self.assertTrue(thermo_dft_ccsdtf12_bac)
 
         with open(os.path.join(project_directory, 'arc_project_for_testing_delete_after_usage2.info'), 'r') as f:
             sts, n2h3, oet, lot, ap = False, False, False, False, False

arc/processor.py

@@ -73,8 +73,9 @@ def __init__(self, project, project_directory, species_dict, rxn_list, output, u
         if any([species.generate_thermo for species in self.species_dict.values()])\
                 and any(['ALL converged' in out['status'] for out in output.values()]):
             load_thermo_libs = True
-        rmgdb.load_rmg_database(rmgdb=self.rmgdb, load_thermo_libs=load_thermo_libs,
-                                load_kinetic_libs=load_kinetic_libs)
+        if any(['ALL converged' in spc_output_dict['status'] for spc_output_dict in output.values()]):
+            rmgdb.load_rmg_database(rmgdb=self.rmgdb, load_thermo_libs=load_thermo_libs,
+                                    load_kinetic_libs=load_kinetic_libs)
         t_min = t_min if t_min is not None else (300, 'K')
         t_max = t_max if t_max is not None else (3000, 'K')
         if isinstance(t_min, (int, float)):
@@ -221,9 +222,10 @@ def process(self):
                         thermo_job.execute(outputFile=output_file_path[1], plot=False)
                 try:
                     species.rmg_thermo = self.rmgdb.thermo.getThermoData(species.rmg_species)
-                except ValueError:
+                except (ValueError, AttributeError) as e:
                     logger.info('Could not retrieve RMG thermo for species {0}, possibly due to missing 2D structure '
-                                '(bond orders). Not including this species in the parity plots.'.format(species.label))
+                                '(bond orders). Not including this species in the parity plots.'
+                                '\nGot: {1}'.format(species.label, e.message))
                 else:
                     if species.generate_thermo:
                         species_list_for_thermo_parity.append(species)

environment.yml

@@ -4,6 +4,7 @@ channels:
   - rmg
   - omnia
   - conda-forge
+  - anaconda
 dependencies:
   - libgcc # [unix]
   - python
@@ -44,6 +45,7 @@ dependencies:
   - pymongo
   - mpmath
   - dde
+  - pydot-ng
   - pyyaml
   - paramiko >=2.4.2
   - cclib >=1.6

ipython/Tools/xyz_to_smiles.ipynb

@@ -0,0 +1,41 @@
+{
+  "cells": [
+    {
+      "cell_type": "markdown",
+      "metadata": {
+        "pycharm": {}
+      },
+      "source": "# ARC Tools\n### Convert xyz coordinates to SMILES"
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "pycharm": {}
+      },
+      "outputs": [],
+      "source": "from arc.species.converter import molecules_from_xyz\nfrom IPython.display import display\n\nxyz \u003d \"\"\"C\t0.7016210\t-0.8239730\t0.0000000\nO\t0.2212140\t-1.9437480\t0.0000000\nN\t0.0000000\t0.3448120\t0.0000000\nC\t-1.4542820\t0.3350170\t0.0000000\nC\t0.6543520\t1.6364050\t0.0000000\nH\t1.7968090\t-0.6524620\t0.0000000\nH\t-1.7802780\t-0.7056490\t0.0000000\nH\t-1.8463230\t0.8389980\t0.8932890\nH\t-1.8463230\t0.8389980\t-0.8932890\nH\t1.7395870\t1.4960250\t0.0000000\nH\t0.3783390\t2.2178500\t-0.8910160\nH\t0.3783390\t2.2178500\t0.8910160\"\"\"\n\ns_mol, b_mol \u003d molecules_from_xyz(xyz)\n\nprint \u0027SMILES: \u0027, b_mol.toSMILES()\n\ndisplay(b_mol)\n"
+    }
+  ],
+  "metadata": {
+    "kernelspec": {
+      "display_name": "Python 2",
+      "language": "python",
+      "name": "python2"
+    },
+    "language_info": {
+      "codemirror_mode": {
+        "name": "ipython",
+        "version": 2
+      },
+      "file_extension": ".py",
+      "mimetype": "text/x-python",
+      "name": "python",
+      "nbconvert_exporter": "python",
+      "pygments_lexer": "ipython2",
+      "version": "2.7.16"
+    }
+  },
+  "nbformat": 4,
+  "nbformat_minor": 2
+}

requirements.txt

@@ -3,11 +3,11 @@
 
 paramiko==2.4.2
 matplotlib==2.2.2
-numpy==1.11.3
+numpy==1.15.4
 cclib==1.6
 py3Dmol==0.8.0
 ase==3.15.0
-rdkit
+rdkit==2018.09.3
 openbabel
 pybel
 IPython