From aaf14455b5048cd295352973e4d8f7655bea5db2 Mon Sep 17 00:00:00 2001
From: Emmanuel Noutahi <emmanuel.noutahi@hotmail.ca>
Date: Mon, 6 May 2024 11:59:26 -0400
Subject: [PATCH] start adding spacialscore

---
 env.yml                       |  4 ++--
 medchem/complexity/_calc.py   | 20 ++++++++++++++++++++
 medchem/complexity/_filter.py |  4 +++-
 pyproject.toml                | 10 +++++-----
 4 files changed, 30 insertions(+), 8 deletions(-)

diff --git a/env.yml b/env.yml
index 5073505..80aacb6 100644
--- a/env.yml
+++ b/env.yml
@@ -15,8 +15,8 @@ dependencies:
   - networkx
 
   # Chemistry
-  - rdkit
-  - datamol >=0.10
+  - rdkit >=2023.09.3
+  - datamol >=0.12
 
   # Optional
   - lilly-medchem-rules
diff --git a/medchem/complexity/_calc.py b/medchem/complexity/_calc.py
index 7e0459e..066c88c 100644
--- a/medchem/complexity/_calc.py
+++ b/medchem/complexity/_calc.py
@@ -1,5 +1,6 @@
 import math
 
+import contextlib
 from rdkit.Chem.rdmolops import GetMolFrags
 from rdkit.Chem.rdmolops import FindPotentialStereo
 from rdkit.Chem import FindMolChiralCenters
@@ -299,3 +300,22 @@ def TWC(mol: dm.Mol, log10: bool = True):
         except ValueError:
             return float("nan")
     return twc
+
+
+def SPS(mol: dm.Mol, normalize=True):
+    """Calculates the SpacialScore descriptor, as described in:
+    [1] Krzyzanowski, A.; Pahl, A.; Grigalunas, M.; Waldmann, H. Spacial Score─A Comprehensive Topological Indicator for Small-Molecule Complexity. J. Med. Chem. 2023. https://doi.org/10.1021/acs.jmedchem.3c00689.
+
+    Args:
+        normalize: whether to normalize the score by the number of heavy atoms (nSPS).
+    """
+
+    score = None
+    with contextlib.suppress(ImportError):
+        mol = dm.to_mol(mol)
+        from rdkit.Chem import SpacialScore
+
+        score = SpacialScore.SPS(mol, normalize=normalize)
+    if score is None:
+        raise ValueError("SpacialScore is not available in your RDKit version, please update to 2023.09.1")
+    return score
diff --git a/medchem/complexity/_filter.py b/medchem/complexity/_filter.py
index 85f0f22..261f834 100644
--- a/medchem/complexity/_filter.py
+++ b/medchem/complexity/_filter.py
@@ -15,6 +15,7 @@
 from ._calc import BaroneCT
 from ._calc import SMCM
 from ._calc import TWC
+from ._calc import SPS
 
 
 class ComplexityFilter:
@@ -39,7 +40,8 @@ class ComplexityFilter:
         "whitlock": WhitlockCT,  # whitlock complexity index
         "barone": BaroneCT,  # barone complexity index
         "smcm": SMCM,  # synthetic and molecular complexity
-        "twc": TWC,  # Total walk count complexity
+        "twc": TWC,  # Total walk count complexity,
+        "spacialscore": SPS,
     }
 
     def __init__(
diff --git a/pyproject.toml b/pyproject.toml
index dc2cbcd..b512390 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -38,7 +38,7 @@ dependencies = [
     "pandas",
     "networkx",
     "datamol >=0.10",
-    "rdkit",
+    "rdkit >=2023.09.3",
 ]
 
 [project.scripts]
@@ -87,17 +87,17 @@ omit = ["medchem/__init__.py", "medchem/_version.py"]
 output = "coverage.xml"
 
 [tool.ruff]
-ignore = [
+lint.ignore = [
     "E501", # Never enforce `E501` (line length violations).
 ]
-line-length = 110
+line-length = 120
 target-version = "py311"
 
-[tool.ruff.per-file-ignores]
+[tool.ruff.lint.per-file-ignores]
 "__init__.py" = [
     "F401", # imported but unused
     "E402", # Module level import not at top of file
 ]
 
-[tool.ruff.pycodestyle]
+[tool.ruff.lint.pycodestyle]
 max-doc-length = 150