From 527b80b6299514d8db90c805769e06e95d1e243d Mon Sep 17 00:00:00 2001
From: Jackson Burns <jwburns@mit.edu>
Date: Mon, 1 Jul 2024 15:33:46 -0400
Subject: [PATCH] add newly defined functions to `pxd` files

as requested in: https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2687#discussion_r1661430047
---
 rmgpy/molecule/group.pxd     | 6 ++++++
 rmgpy/molecule/molecule.pxd  | 2 ++
 rmgpy/molecule/resonance.pxd | 4 ++++
 rmgpy/reaction.pxd           | 2 ++
 4 files changed, 14 insertions(+)

diff --git a/rmgpy/molecule/group.pxd b/rmgpy/molecule/group.pxd
index 83b4ae83c6..ada4072f78 100644
--- a/rmgpy/molecule/group.pxd
+++ b/rmgpy/molecule/group.pxd
@@ -31,6 +31,12 @@ cimport rmgpy.molecule.molecule as mol
 from cpython cimport bool
 ################################################################################
 
+cdef bool check_set(super_list, sub_list)
+
+cdef list add_cb_atom_to_ring(ring, cb_atom)
+
+cdef list merge_overlapping_benzene_rings(ring1, ring2, od)
+
 cdef class GroupAtom(Vertex):
 
     cdef public list atomtype
diff --git a/rmgpy/molecule/molecule.pxd b/rmgpy/molecule/molecule.pxd
index 335486f76f..d8bc24f4bb 100644
--- a/rmgpy/molecule/molecule.pxd
+++ b/rmgpy/molecule/molecule.pxd
@@ -36,6 +36,8 @@ from rmgpy.molecule.graph cimport Vertex, Edge, Graph
 ################################################################################
 cdef dict bond_orders 
 
+cdef tuple _skip_first(in_tuple)
+
 cdef class Atom(Vertex):
 
     cdef public Element element
diff --git a/rmgpy/molecule/resonance.pxd b/rmgpy/molecule/resonance.pxd
index e3b01db841..64662a797c 100644
--- a/rmgpy/molecule/resonance.pxd
+++ b/rmgpy/molecule/resonance.pxd
@@ -28,6 +28,10 @@
 from rmgpy.molecule.graph cimport Vertex, Edge, Graph
 from rmgpy.molecule.molecule cimport Atom, Bond, Molecule
 
+cdef int _sum_atom_ids(atom_list)
+
+cdef tuple _tuplize_bond(bond)
+
 cpdef list populate_resonance_algorithms(dict features=?)
 
 cpdef dict analyze_molecule(Graph mol, bint save_order=?)
diff --git a/rmgpy/reaction.pxd b/rmgpy/reaction.pxd
index 15feecef3f..c6c8b35601 100644
--- a/rmgpy/reaction.pxd
+++ b/rmgpy/reaction.pxd
@@ -38,6 +38,8 @@ cimport numpy as np
 
 ################################################################################
 
+cdef tuple get_sorting_key(spc)
+
 cdef class Reaction:
     cdef public int index
     cdef public str label