CRDGEN-270 Add template for bicyclic pentane (#87)

Adds a template for C1C2CC1C2 aka bicycle (1.1.1) pentane. I had to change the ring system simplification logic slightly so that the template is picked up.
schrodinger · Mar 30, 2021 · f67ad5d · f67ad5d
1 parent 187419a
commit f67ad5d
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Showing 5 changed files with 3,247 additions and 2,496 deletions.
diff --git a/CoordgenFragmentBuilder.cpp b/CoordgenFragmentBuilder.cpp
@@ -1035,6 +1035,12 @@ void CoordgenFragmentBuilder::simplifyRingSystem(
                         /* disable rings that share too many atoms */
                         n++;
                     }
+                    if (r->fusionAtoms.at(ringCounter).size() == 3 &&
+                        r->size() == 4 &&
+                        fusedRing->size() == 4) {
+                        /* don't separate rings of bicyclo (1,1,1) pentane so we can use a template instead */
+                        n++;
+                    }
                 }
             }
             if (n == 1) /* ring is fused with only one ring,

diff --git a/CoordgenTemplates.cpp b/CoordgenTemplates.cpp
@@ -7,7 +7,7 @@
 //
 //   $SCHRODINGER/run mol_generator.py templates.mae
 //
-// generated using templates.mae version c17d2be57897d3e83435.
+// generated using templates.mae version 92d3dcc2b6d37e859c01.
 //
 
 
@@ -47,7 +47,7 @@ namespace schrodinger {
 
 std::vector<sketcherMinimizerMolecule*> coordgen_templates()
 {
-    std::vector<sketcherMinimizerMolecule*> molecules(80);
+    std::vector<sketcherMinimizerMolecule*> molecules(81);
     size_t i = 0;
 
 
@@ -4807,6 +4807,31 @@ std::vector<sketcherMinimizerMolecule*> coordgen_templates()
         ++i;
     }
 
+    {
+        auto molecule = new sketcherMinimizerMolecule();
+        std::array<std::tuple<int, float, float>, 5> atoms = {{
+            tuple<int, float, float>(6, -0.5833f, -0.0f),
+            tuple<int, float, float>(6, 0.0f, 0.5833f),
+            tuple<int, float, float>(6, 0.5833f, -0.0f),
+            tuple<int, float, float>(6, 0.0f, -0.5833f),
+            tuple<int, float, float>(6, 0.1458f, -0.0f)
+        }};
+        std::array<std::array<int, 3>, 6> bonds = {{
+            { 0, 1, 1 },
+            { 0, 3, 1 },
+            { 1, 2, 1 },
+            { 1, 4, 1 },
+            { 2, 3, 1 },
+            { 3, 4, 1 }
+        }};
+
+        add_atoms(molecule, atoms);
+        add_bonds(molecule, bonds);
+
+        molecules[i] = molecule;
+        ++i;
+    }
+
 
     return molecules;
 }

diff --git a/CoordgenTemplates.h b/CoordgenTemplates.h
@@ -9,7 +9,7 @@
 //
 //   $SCHRODINGER/run mol_generator.py templates.mae
 //
-// generated using templates.mae version c17d2be57897d3e83435.
+// generated using templates.mae version 92d3dcc2b6d37e859c01.
 //
-Original file line number
+Diff line change
@@ Expand Up / @@ -9,7 +9,7 @@ @@
     //
     //   $SCHRODINGER/run mol_generator.py templates.mae
     //
-    // generated using templates.mae version c17d2be57897d3e83435.
+    // generated using templates.mae version 92d3dcc2b6d37e859c01.
     //
@@ Expand Down @@