SS-1: Tutorial Branch

molecular_interaction_rules/molecular_database.py

@@ -113,6 +113,7 @@
 
 ## Organosulfur
 
+from molecular_interaction_rules.molecules.non_aromatic.organosulfur.dithiolane import Dithiolane
 from molecular_interaction_rules.molecules.non_aromatic.organosulfur.dimethyl_sulfone import DimethylSulfone
 from molecular_interaction_rules.molecules.non_aromatic.organosulfur.dimethyl_sulfoxide import DimethylSulfoxide
 from molecular_interaction_rules.molecules.non_aromatic.organosulfur.dimethyl_trithiocarbonate import DimethylTrithiocarbonate

molecular_interaction_rules/molecules/non_aromatic/organosulfur/diothiolane.py

@@ -0,0 +1,75 @@
+#!/usr/bin/env python3
+#
+# Lennard-Jones-Drill-2: Dithiolane
+# ---------------------------------
+
+# Imports
+# -------
+
+import textwrap
+
+class Dithiolane(object):
+
+    def __init__(self):
+
+        self.resi_name = 'MESH'
+
+    def get_monomer_a_species(self):
+
+        '''
+
+        Get the Monomer A Species
+
+        '''
+
+        monomer_a_species = {
+        }
+
+        return monomer_a_species
+
+    def get_sulphur_hetereoatom(self):
+
+        zmatrix = '''\
+            S11
+            S12  S11  2.1492
+            C11  S12  1.8415    S11   94.9681
+            C12  C11  1.5287    S12  108.1008    S11  -28.2456
+            H11  C12  1.1043    C11  110.1289    S12  173.1128
+            H12  C12  1.1009    C11  109.8789    S12  -66.6192
+            C13  S11  1.8415    S12   94.9680    C11   -0.0003
+            H13  C13  1.1011    S11  106.2198    S12  148.9234
+            H14  C13  1.1009    S11  109.4742    S12  -92.8470
+            H15  C11  1.1011    S12  106.2199    S11 -148.9227
+            H16  C11  1.1009    S12  109.4741    S11   92.8477
+            X11  S11  1.0000    S12   90.0000    C11    0.0000
+        '''
+
+        atom_name = []
+        return textwrap.dedent(zmatrix), atom_name
+
+    def get_monomer_a(self):
+
+        zmatrix = '''\
+        '''
+
+        atom_name = [
+        ]
+
+        return textwrap.dedent(zmatrix), atom_name
+
+    def get_monomer_b_species(self):
+
+        monomer_b_species = {
+        }
+
+        return monomer_b_species
+
+    def get_monomer_b(self):
+
+        zmatrix = '''\
+        '''
+
+        atom_name = [
+        ]
+
+        return textwrap.dedent(zmatrix), atom_name