From 67fc0708e55e90fcc20672fecedd737292aefd80 Mon Sep 17 00:00:00 2001
From: Dan Nealschneider <dan.nealschneider@schrodinger.com>
Date: Wed, 6 May 2026 02:57:28 -0700
Subject: [PATCH] CIPLabeler performance: Store vector of bonds (#9250)

* CIPLabeler performance: Store vector of bonds

CIPLabelling refers to bonds by index over and over again. This
causes a measurable hit in performance in findConfigs() because
we iterate over a bitset of "allowed" bonds. For very large
molecules with many bonds, this can be a rate-limiting step!

This affects many PDB-sized structures.

2J3N goes from 0.7s to 0.25s with this change.

I had another example for which the findBondWithIdx() call was
taking 500ms of a 700ms call (after the performance update
in #9171 was implemented)

* yikes, XXL reserve

thanks, greg

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>

---------

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
---
 Code/GraphMol/CIPLabeler/CIPMol.cpp | 9 ++++++---
 Code/GraphMol/CIPLabeler/CIPMol.h   | 1 +
 2 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/Code/GraphMol/CIPLabeler/CIPMol.cpp b/Code/GraphMol/CIPLabeler/CIPMol.cpp
index ed7c1798d..043b65cb1 100644
--- a/Code/GraphMol/CIPLabeler/CIPMol.cpp
+++ b/Code/GraphMol/CIPLabeler/CIPMol.cpp
@@ -16,7 +16,10 @@
 namespace RDKit {
 namespace CIPLabeler {
 
-CIPMol::CIPMol(ROMol &mol) : d_mol{mol} {}
+CIPMol::CIPMol(ROMol &mol) : d_mol{mol} {
+  d_bonds.reserve(mol.getNumBonds());
+  std::ranges::copy(mol.bonds(), std::back_inserter(d_bonds));
+}
 
 boost::rational<int> CIPMol::getFractionalAtomicNum(Atom *atom) const {
   PRECONDITION(atom, "bad atom")
@@ -36,7 +39,7 @@ CXXAtomIterator<MolGraph, Atom *> CIPMol::atoms() const {
   return d_mol.atoms();
 }
 
-Bond *CIPMol::getBond(int idx) const { return d_mol.getBondWithIdx(idx); };
+Bond *CIPMol::getBond(int idx) const { return d_bonds[idx]; };
 
 CIPMolSpan<Bond *, ROMol::OEDGE_ITER> CIPMol::getBonds(Atom *atom) const {
   PRECONDITION(atom, "bad atom")
@@ -108,4 +111,4 @@ int CIPMol::getBondOrder(Bond *bond) const {
 };
 
 }  // namespace CIPLabeler
-}  // namespace RDKit
\ No newline at end of file
+}  // namespace RDKit
diff --git a/Code/GraphMol/CIPLabeler/CIPMol.h b/Code/GraphMol/CIPLabeler/CIPMol.h
index eda543846..bedd335a2 100644
--- a/Code/GraphMol/CIPLabeler/CIPMol.h
+++ b/Code/GraphMol/CIPLabeler/CIPMol.h
@@ -97,6 +97,7 @@ class CIPMol {
   ROMol &d_mol;
   std::vector<RDKit::Bond::BondType> d_kekulized_bonds;
   std::vector<boost::rational<int>> d_atomnums;
+  std::vector<RDKit::Bond* > d_bonds;
 };
 
 }  // namespace CIPLabeler