From fbdb87aee72648db04816c2cd0679060918b9231 Mon Sep 17 00:00:00 2001
From: rlaplaza <laplazasolanas@gmail.com>
Date: Wed, 4 Dec 2024 17:16:37 +0100
Subject: [PATCH] Added some minor fixes for edge cases where isomorphisms
 cannot be found

---
 navicat_marc/helpers.py |  2 +-
 navicat_marc/rmsd.py    | 14 +++++++++++---
 pyproject.toml          |  4 ++--
 3 files changed, 14 insertions(+), 6 deletions(-)

diff --git a/navicat_marc/helpers.py b/navicat_marc/helpers.py
index 084f62e..3371621 100755
--- a/navicat_marc/helpers.py
+++ b/navicat_marc/helpers.py
@@ -105,7 +105,7 @@ def molecules_from_file(filename, scale_factor=1.10, noh=True):
 def processargs(arguments):
     input_list = sys.argv
     input_str = " ".join(input_list)
-    version_str = "0.2.3"
+    version_str = "0.2.4"
     mbuilder = argparse.ArgumentParser(
         prog="navicat_marc",
         description="Analyse conformer ensembles to find the most representative structures.",
diff --git a/navicat_marc/rmsd.py b/navicat_marc/rmsd.py
index 7e011b5..ba4c498 100755
--- a/navicat_marc/rmsd.py
+++ b/navicat_marc/rmsd.py
@@ -50,9 +50,16 @@ def rmsd_matrix(mols, sort=False, truesort=False, normalize=True):
                         save_rotated_coordinates = rotated_coordinates
                     if np.isclose(0, min_res):
                         break
-                pos_ibj.append(save_ibj)
-                assert all(mols[i].atoms == mols[j].atoms[save_ibj])
-                mols[j].update(mols[j].atoms[save_ibj], save_rotated_coordinates)
+                if len(iviews) == 0:
+                    min_res, save_rotated_coordinates = kabsch_rmsd(
+                        mols[i].coordinates, mols[j].coordinates
+                    )
+                    assert all(mols[i].atoms == mols[j].atoms)
+                    mols[j].update(mols[j].atoms, save_rotated_coordinates)
+                else:
+                    pos_ibj.append(save_ibj)
+                    assert all(mols[i].atoms == mols[j].atoms[save_ibj])
+                    mols[j].update(mols[j].atoms[save_ibj], save_rotated_coordinates)
                 M[i, j] = M[j, i] = min_res
             if not sort and len(pos_ibj) > 0:
                 for k, ibj in enumerate(pos_ibj):
@@ -78,6 +85,7 @@ def rmsd_matrix(mols, sort=False, truesort=False, normalize=True):
         if not truesort:
             sort = False
     maxval = np.max(M)
+    max_idxs = np.unravel_index(M.argmax(), M.shape)
     if normalize:
         M = np.abs(M) / maxval
     return M, maxval
diff --git a/pyproject.toml b/pyproject.toml
index 57a0626..0794440 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "navicat_marc"
-version = "0.2.3"
+version = "0.2.4"
 authors = [
   { name="R. Laplaza", email="rlaplaza@duck.com" },
 ]
@@ -17,7 +17,7 @@ dependencies = [
   'networkx >= 3.0',
   'numpy >= 1.24.4',
   'scikit_learn >= 1.2.0',
-  'scipy >= 1.10.1',
+  'scipy == 1.10.1',
   'setuptools >= 65.4.1',
 ]
 classifiers = [