From ac39c9635955199269393e3c12e30a94e0001935 Mon Sep 17 00:00:00 2001
From: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Date: Thu, 3 Oct 2024 15:21:08 -0400
Subject: [PATCH] fix: use rdkit API to remove implicit hydrogens (#2278)

<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->

## Summary by CodeRabbit

- **New Features**
- Enhanced SMILES conversion process with improved implicit hydrogen
handling for atoms.

- **Bug Fixes**
- Removed outdated method that previously handled SMILES conversion,
streamlining the conversion process.

- **Tests**
- Removed a test related to the now-removed SMILES handling method,
reflecting updates in testing strategy.

- **Chores**
- Minor formatting adjustments and removal of unused imports for cleaner
code.

<!-- end of auto-generated comment: release notes by coderabbit.ai -->

---------

Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
---
 reacnetgenerator/_path.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/reacnetgenerator/_path.py b/reacnetgenerator/_path.py
index 90a781284..2db071a6e 100644
--- a/reacnetgenerator/_path.py
+++ b/reacnetgenerator/_path.py
@@ -264,6 +264,10 @@ def convertSMILES(self, atoms, bonds):
             d[number] = m.AddAtom(Chem.Atom(name))
         for atom1, atom2, level in bonds:
             m.AddBond(d[atom1], d[atom2], Chem.BondType(level))
+        # https://github.com/rdkit/rdkit/discussions/6613#discussioncomment-6688021
+        for a in m.GetAtoms():  # type:ignore
+            a.SetNoImplicit(True)
+            a.UpdatePropertyCache()
         name = Chem.MolToSmiles(m)
         return self._re(name)