f! Make is_ts an attribute of the ArkaneSpecies class

arkane/common.py

@@ -70,7 +70,7 @@ def __init__(self, species=None, conformer=None, author='', level_of_theory='',
                  chemkin_thermo_string='', smiles=None, adjacency_list=None, inchi=None, inchi_key=None, xyz=None,
                  molecular_weight=None, symmetry_number=None, transport_data=None, energy_transfer_model=None,
                  thermo=None, thermo_data=None, label=None, datetime=None, RMG_version=None, reactants=None,
-                 products=None, reaction_label=None):
+                 products=None, reaction_label=None, is_ts=None):
         # reactants/products/reaction_label need to be in the init() to avoid error when loading a TS YAML file,
         # but we don't use them
         if species is None and conformer is None:
@@ -93,8 +93,8 @@ def __init__(self, species=None, conformer=None, author='', level_of_theory='',
         self.xyz = xyz
         self.molecular_weight = molecular_weight
         self.symmetry_number = symmetry_number
-        is_ts = isinstance(species, TransitionState)
-        if not is_ts:
+        self.is_ts = is_ts if is_ts is not None else isinstance(species, TransitionState)
+        if not self.is_ts:
             self.chemkin_thermo_string = chemkin_thermo_string
             self.smiles = smiles
             self.adjacency_list = adjacency_list
@@ -220,7 +220,7 @@ def load_yaml(self, path, species, pdep=False):
         try:
             if species.label != data['label']:
                 logging.debug('Found different labels for species: {0} in input file, and {1} in the .yml file. '
-                                'Using the label "{0}" for this species.'.format(species.label, data['label']))
+                              'Using the label "{0}" for this species.'.format(species.label, data['label']))
         except KeyError:
             # Lacking label in the YAML file is strange, but accepted
             logging.debug('Did not find label for species {0} in .yml file.'.format(species.label))
@@ -258,10 +258,11 @@ def load_yaml(self, path, species, pdep=False):
         self.adjacency_list = data['adjacency_list'] if 'adjacency_list' in data else None
         self.inchi = data['inchi'] if 'inchi' in data else None
         self.smiles = data['smiles'] if 'smiles' in data else None
-        if pdep and (self.transport_data is None or self.energy_transfer_model is None):
+        self.is_ts = data['is_ts'] if 'is_ts' in data else False
+        if pdep and not self.is_ts and (self.transport_data is None or self.energy_transfer_model is None):
             raise ValueError('Transport data and an energy transfer model must be given if pressure-dependent '
                              'calculations are requested. Check file {0}'.format(path))
-        if pdep and self.smiles is None and self.adjacency_list is None\
+        if pdep and not self.is_ts and self.smiles is None and self.adjacency_list is None\
                 and self.inchi is None and self.molecular_weight is None:
             raise ValueError('The molecular weight was not specified, and a structure was not given so it could '
                              'not be calculated. Specify either the molecular weight or structure if '