From a1e49931a90ede00483732ed647b55a9181fc92f Mon Sep 17 00:00:00 2001
From: Klaus Weinbauer <51136324+klausweinbauer@users.noreply.github.com>
Date: Wed, 15 May 2024 14:19:05 +0200
Subject: [PATCH] Change how implicit hydrogens are added (#11)

* change how implicit hydroges are added to the graph
---
 fgutils/utils.py | 8 +++++---
 pyproject.toml   | 2 +-
 2 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/fgutils/utils.py b/fgutils/utils.py
index fa1efdd..20e6063 100644
--- a/fgutils/utils.py
+++ b/fgutils/utils.py
@@ -41,9 +41,11 @@ def add_implicit_hydrogens(graph: nx.Graph) -> nx.Graph:
         if n_sym not in ["R", "H"]
     ]
     for n_id, n_sym in nodes:
-        assert (
-            n_sym in valence_table.keys()
-        ), "Element {} not found in valence table.".format(n_sym)
+        if n_sym not in valence_table.keys():
+            # No hydrogens are added if element is not in dict. These atoms
+            # are most likley not part of a functional group anyway so skipping
+            # hydrogens is fine
+            continue
         bond_cnt = sum([b for _, _, b in graph.edges(n_id, data="bond")])  # type: ignore
         # h_cnt can be negative; aromaticity is complicated, we just ignore that
         valence = valence_table[n_sym]
diff --git a/pyproject.toml b/pyproject.toml
index e4b809a..9918c45 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "fgutils"
-version = "0.0.15"
+version = "0.0.16"
 authors = [{name="Klaus Weinbauer", email="klaus@bioinf.uni-leipzig.de"}]
 description = "Library to get functional groups from molecular graphs."
 readme = "README.md"