From ef2547c17f82edf03fda2a0fa924d56c9c2de123 Mon Sep 17 00:00:00 2001
From: Klaus Weinbauer <51136324+klausweinbauer@users.noreply.github.com>
Date: Mon, 15 Apr 2024 14:43:41 +0200
Subject: [PATCH] v0.0.8 (#3)

* Update README.md

* Update test-and-lint.yml

* prepare release v0.0.7

* fix issue in implicit hydrogen computation

* allow non-carbon atoms to belong to no functional group

* fix linting

* prepare release v0.0.8

---------

Co-authored-by: Klaus Weinbauer <klaus@becks.bioinf.uni-leipzig.de>
---
 fgutils/query.py   |  9 ---------
 fgutils/utils.py   |  2 +-
 pyproject.toml     |  2 +-
 test/test_utils.py | 35 +++++++++++++++++++++++++++++++++++
 4 files changed, 37 insertions(+), 11 deletions(-)

diff --git a/fgutils/query.py b/fgutils/query.py
index b31502c..ae813e4 100644
--- a/fgutils/query.py
+++ b/fgutils/query.py
@@ -99,15 +99,6 @@ def __get_functional_groups(self, graph: nx.Graph) -> list[tuple[str, list[int]]
                     elif i in unidentified_ids:
                         unidentified_ids.remove(i)
                 groups.append((node.fgconfig.name, indices))
-        if len(unidentified_ids) > 0:
-            raise RuntimeError(
-                "Could not find a functional group for atom(s) {}.".format(
-                    [
-                        "{}@{}".format(graph.nodes[i]["symbol"], i)
-                        for i in unidentified_ids
-                    ]
-                )
-            )
         return groups
 
     def get(self, value) -> list[tuple[str, list[int]]]:
diff --git a/fgutils/utils.py b/fgutils/utils.py
index f5e94a8..b543ad4 100644
--- a/fgutils/utils.py
+++ b/fgutils/utils.py
@@ -42,8 +42,8 @@ def add_implicit_hydrogens(graph: nx.Graph) -> nx.Graph:
             n_sym in valence_table.keys()
         ), "Element {} not found in valence table.".format(n_sym)
         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
         h_cnt = int(8 - valence_table[n_sym] - bond_cnt)
-        assert h_cnt >= 0, "Negative hydrogen count."
         for h_id in range(len(graph), len(graph) + h_cnt):
             graph.add_node(h_id, symbol="H")
             graph.add_edge(n_id, h_id, bond=1)
diff --git a/pyproject.toml b/pyproject.toml
index 532d594..ae11187 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "fgutils"
-version = "0.0.7"
+version = "0.0.8"
 authors = [{name="Klaus Weinbauer", email="klaus@bioinf.uni-leipzig.de"}]
 description = "Library to get functional groups from molecular graphs."
 readme = "README.md"
diff --git a/test/test_utils.py b/test/test_utils.py
index 5d6b6f1..69dc986 100644
--- a/test/test_utils.py
+++ b/test/test_utils.py
@@ -36,3 +36,38 @@ def test_add_implicit_hydrogens_3():
     assert 6 == len(graph)
     _assert_Hs(graph, 1, 3)
     _assert_Hs(graph, 4, 1)
+
+
+def test_sulfur_ring():
+    graph = parse("C:1N:C:S:C:1")
+    graph = add_implicit_hydrogens(graph)
+    assert 8 == len(graph)
+    _assert_Hs(graph, 0, 1)
+    _assert_Hs(graph, 1, 0)
+    _assert_Hs(graph, 2, 1)
+    _assert_Hs(graph, 3, 0)
+    _assert_Hs(graph, 4, 1)
+
+
+def test_nitrogen_5ring():
+    graph = parse("C:1C:N(H):C:C:1")
+    graph = add_implicit_hydrogens(graph)
+    assert 10 == len(graph)
+    _assert_Hs(graph, 0, 1)
+    _assert_Hs(graph, 1, 1)
+    _assert_Hs(graph, 2, 1)
+    _assert_Hs(graph, 3, 0)
+    _assert_Hs(graph, 4, 1)
+    _assert_Hs(graph, 5, 1)
+
+
+def test_nitrogen_6ring():
+    graph = parse("C:1C:C:N:C:C:1")
+    graph = add_implicit_hydrogens(graph)
+    assert 11 == len(graph)
+    _assert_Hs(graph, 0, 1)
+    _assert_Hs(graph, 1, 1)
+    _assert_Hs(graph, 2, 1)
+    _assert_Hs(graph, 3, 0)
+    _assert_Hs(graph, 4, 1)
+    _assert_Hs(graph, 5, 1)