add: generalize stoichiometry for all outputs thanks to cclib 1.6

devtools/conda-recipe/build.sh

@@ -1,3 +1,3 @@
 #!/bin/bash
-pip install apscheduler cclib flask flask-sslify markdown gunicorn requests GitHub-Flask requests_oauthlib
+pip install apscheduler 'cclib>=1.6' flask flask-sslify markdown gunicorn requests GitHub-Flask requests_oauthlib
 $PYTHON setup.py install

docs/templates.rst

@@ -86,7 +86,7 @@ during the templating:
       extension.
    -  ``{{ filename }}``: Filename, with extension.
    -  ``{{ filepath }}``: Full path to the file.
-   -  ``{{ stoichiometry }}``. (Gaussian only).
+   -  ``{{ stoichiometry }}``. Self-explanatory.
    -  ``{{ imaginary_freqs }}``: Number of negative frequencies.
    -  ``{{ mean_of_electrons }}``: Mean of ``alphaelectrons`` and
       ``betaelectrons``.

environment-pymol.yml

@@ -10,7 +10,7 @@ dependencies:
   - libglu
   - pip:
     - apscheduler
-    - cclib
+    - cclib>=1.6
     - flask
     - flask-sslify
     - markdown

environment.yml

@@ -4,7 +4,7 @@ dependencies:
 - numpy
 - pip:
   - apscheduler
-  - cclib
+  - cclib>=1.6
   - flask
   - flask-sslify
   - markdown

esigen/io.py

@@ -57,7 +57,6 @@ class ccDataExtended(ccData_optdone_bool):
     _attributes = ccData_optdone_bool._attributes.copy()
     _attributes.update(
         {# Gaussian only
-         'stoichiometry':       Attribute(str,   'stoichiometry',                    'N/A'),
          'solvent':             Attribute(str,   'solvent',                          'N/A'),
          'thermalenergy':       Attribute(float, 'electronic + thermal energies',    'N/A'),
          'zeropointenergy':     Attribute(float, 'electronic + zero-point energies', 'N/A'),
@@ -74,7 +73,7 @@ class ccDataExtended(ccData_optdone_bool):
          })
     _attrlist = sorted(_attributes.keys())
     _properties = ['mean_of_electrons', 'atoms', 'coordinates', 'electronic_energy',
-                   'imaginary_freqs', 'cartesians', 'nsteps']
+                   'imaginary_freqs', 'cartesians', 'nsteps', 'stoichiometry']
 
     def as_dict(self):
         """
@@ -117,6 +116,11 @@ def nsteps(self):
         if hasattr(self, 'scfenergies'):
             return self.scfenergies.shape[0]
 
+    @property
+    def stoichiometry(self):
+        from cclib.method import Nuclear
+        return Nuclear(self).stoichiometry()
+
     @property
     def has_coordinates(self):
         return hasattr(self, 'atomnos') and hasattr(self, 'atomcoords')