save XYZ in YAML file

ReactionMechanismGenerator · Jun 26, 2018 · 891a6a1 · 891a6a1
1 parent a8c2a36
commit 891a6a1
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Showing 2 changed files with 24 additions and 2 deletions.
diff --git a/rmgpy/cantherm/common.py b/rmgpy/cantherm/common.py
@@ -42,6 +42,7 @@
     from yaml import Dumper, Loader, SafeLoader
 
 import rmgpy.constants as constants
+from rmgpy.molecule.element import elementList
 from rmgpy.molecule.translator import toInChI, toInChIKey
 from rmgpy.thermo import NASA, NASAPolynomial, Wilhoit, ThermoData
 from rmgpy.statmech.conformer import Conformer
@@ -281,6 +282,7 @@ def __init__(self, species=None, author='', level_of_theory='', model_chemistry=
             self.InChI_Key = inchi_key
 
         self.conformer = species.conformer
+        self.update_xyz_string()
 
         if species.symmetryNumber != -1:
             self.symmetryNumber = species.symmetryNumber
@@ -327,6 +329,7 @@ def update_species_attributes(self, species):
             self.InChI = inchi
             self.InChI_Key = inchi_key
         self.conformer = species.conformer
+        self.update_xyz_string()
         if species.symmetryNumber != -1:
             self.symmetryNumber = species.symmetryNumber
         if species.transportData is not None:
@@ -338,6 +341,26 @@ def update_species_attributes(self, species):
         if species.thermo is not None:
             self.thermo = species.thermo
 
+    def update_xyz_string(self):
+        if self.conformer is not None and self.conformer.number is not None:
+            # generate an xyz-format string from the Conformer coordinates
+            xyz_string = '{0}\n{1}'.format(len(self.conformer.number.value_si), self.label)
+            for i, coorlist in enumerate(self.conformer.coordinates.value_si):
+                for element in elementList:
+                    if element.number == int(self.conformer.number.value_si[i]):
+                        element_symbol = element.symbol
+                        break
+                else:
+                    raise ValueError('Could not find element symbol corresponding to atom number {0}'.format(
+                        self.conformer.number.value_si[i]))
+                xyz_string += '\n{0} {1} {2} {3}'.format(element_symbol,
+                                                         coorlist[0],
+                                                         coorlist[1],
+                                                         coorlist[2])
+        else:
+            xyz_string = ''
+        self.xyz = xyz_string
+
     def as_dictionary(self):
         """
         Output all attributes of CanthermSpecies in a dictionary format

diff --git a/rmgpy/cantherm/statmech.py b/rmgpy/cantherm/statmech.py
@@ -57,7 +57,6 @@
 from rmgpy.statmech.torsion import Torsion, HinderedRotor, FreeRotor
 from rmgpy.statmech.conformer import Conformer
 from rmgpy.molecule import Molecule
-from rmgpy.molecule.element import elementList
 from rmgpy.molecule.converter import fromOBMol
 from rmgpy.exceptions import InputError, InvalidAdjacencyListError
 
@@ -505,7 +504,7 @@ def load(self, is_pdep=False):
 
         self.species.conformer = conformer
 
-    def load_species_from_database_file(self, is_pdep):
+    def load_species_from_database_file(self, is_pdep=False):
         """
         Load the species with all statMech data from the .yml file
         """