Make zero LJ sigma check consistent with Sire.

OpenBioSim · Jun 4, 2024 · 0c22782 · 0c22782
1 parent dc50f26
commit 0c22782
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Showing 2 changed files with 8 additions and 8 deletions.
diff --git a/python/BioSimSpace/Align/_merge.py b/python/BioSimSpace/Align/_merge.py
@@ -693,8 +693,8 @@ def merge(
                     .molecule()
                 )
 
-    # Create a null LJParameter.
-    null_lj = _SireMM.LJParameter()
+    # Tolerance for zero sigma values.
+    null_lj_sigma = 1e-9
 
     # Atoms with zero LJ sigma values need to have their sigma values set to the
     # value from the other end state.
@@ -704,7 +704,7 @@ def merge(
         lj1 = atom.property("LJ1")
 
         # Lambda = 0 state has a zero sigma value.
-        if lj0.sigma() == null_lj.sigma():
+        if abs(lj0.sigma().value()) <= null_lj_sigma:
             # Use the sigma value from the lambda = 1 state.
             edit_mol = (
                 edit_mol.atom(atom.index())
@@ -713,7 +713,7 @@ def merge(
             )
 
         # Lambda = 1 state has a zero sigma value.
-        if lj1.sigma() == null_lj.sigma():
+        if abs(lj1.sigma().value()) <= null_lj_sigma:
             # Use the sigma value from the lambda = 0 state.
             edit_mol = (
                 edit_mol.atom(atom.index())

diff --git a/python/BioSimSpace/Sandpit/Exscientia/Align/_merge.py b/python/BioSimSpace/Sandpit/Exscientia/Align/_merge.py
@@ -739,8 +739,8 @@ def merge(
                     edit_mol.atom(idx).setProperty(name, atom.property(prop)).molecule()
                 )
 
-    # Create a null LJParameter.
-    null_lj = _SireMM.LJParameter()
+    # Tolerance for zero sigma values.
+    null_lj_sigma = 1e-9
 
     # Atoms with zero LJ sigma values need to have their sigma values set to the
     # value from the other end state.
@@ -750,7 +750,7 @@ def merge(
         lj1 = atom.property("LJ1")
 
         # Lambda = 0 state has a zero sigma value.
-        if lj0.sigma() == null_lj.sigma():
+        if abs(lj0.sigma().value()) <= null_lj_sigma:
             # Use the sigma value from the lambda = 1 state.
             edit_mol = (
                 edit_mol.atom(atom.index())
@@ -759,7 +759,7 @@ def merge(
             )
 
         # Lambda = 1 state has a zero sigma value.
-        if lj1.sigma() == null_lj.sigma():
+        if abs(lj1.sigma().value()) <= null_lj_sigma:
             # Use the sigma value from the lambda = 0 state.
             edit_mol = (
                 edit_mol.atom(atom.index())