add coordination number and lone-pair regularization dimension tracking

Author: mjohnson541

rmgpy/molecule/group.pxd

@@ -53,6 +53,8 @@ cdef class GroupAtom(Vertex):
     cdef public list reg_dim_r
     cdef public list reg_dim_site
     cdef public list reg_dim_morphology
+    cdef public list reg_dim_ncoord
+    cdef public list reg_dim_p
 
     cpdef Vertex copy(self)
 

rmgpy/molecule/group.py

@@ -155,6 +155,8 @@ class GroupAtom(Vertex):
     `reg_dim_r`          ``list``            List of inRing values that are free dimensions in tree optimization
     `reg_dim_site`       ``list``            List of sites that are free dimensions in tree optimization
     `reg_dim_morphology` ``list``            List of morphologies that are free dimensions in tree optimization
+    `reg_dim_ncoord`     ``list``            List of coordination numbers that are free dimensions in tree optimization
+    `reg_dim_p`          ``list``            List of numbers of electron pairs that are free dimensions in tree optimization
     ==================== =================== ====================================
 
     Each list represents a logical OR construct, i.e. an atom will match the
@@ -184,6 +186,8 @@ def __init__(self, atomtype=None, radical_electrons=None, charge=None, label='',
         self.reg_dim_r = [[], []]
         self.reg_dim_site = [[], []]
         self.reg_dim_morphology = [[], []]
+        self.reg_dim_ncoord = [[],[]]
+        self.reg_dim_p = [[],[]]
 
     def __reduce__(self):
         """
@@ -1561,6 +1565,8 @@ def clear_reg_dims(self):
             atm.reg_dim_r = [[], []]
             atm.reg_dim_site = [[],[]]
             atm.reg_dim_morphology = [[],[]]
+            atm.reg_dim_ncoord = [[],[]]
+            atm.reg_dim_p = [[],[]]
         for bd in self.get_all_edges():
             bd.reg_dim = [[], []]