Functionality for setting size of ghost atom

Signed-off-by: Vaishnavi Bhandari <[email protected]>
OpenChemistry · Jan 26, 2025 · e22ba14 · e22ba14
1 parent 05d2dd0
commit e22ba14
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Showing 3 changed files with 21 additions and 6 deletions.
diff --git a/avogadro/core/elements.cpp b/avogadro/core/elements.cpp
@@ -26,9 +26,8 @@ static std::vector<std::string> CustomElementSymbols;
 static std::vector<std::string> CustomElementNames;
 
 // Match carbon's radii
-static double CustomElementCovalentRadius = element_covalent[6];
-static double CustomElementVDWRadius = element_VDW[6];
-
+static std::vector<double> CustomElementCovalentRadii;
+static std::vector<double> CustomElementVDWRadii;
 inline std::string encodeCustomElement(unsigned char atomicNumber)
 {
   std::string result;
@@ -101,6 +100,8 @@ class InitializeCustomElementTables
   {
     CustomElementSymbols.resize(CustomElementCount);
     CustomElementNames.resize(CustomElementCount);
+    CustomElementCovalentRadii.resize(CustomElementCount, element_covalent[6]); 
+    CustomElementVDWRadii.resize(CustomElementCount, element_VDW[6]); 
     std::string suffix;
     for (unsigned char i = CustomElementMin; i <= CustomElementMax; ++i) {
       suffix = encodeCustomElement(i);
@@ -111,7 +112,19 @@ class InitializeCustomElementTables
     }
   }
 } CustomElementTableInitializer;
+void setCustomElementCovalentRadius(unsigned char atomicNumber, double radius)
+{
+  if (isCustomElement(atomicNumber)) {
+    CustomElementCovalentRadii[atomicNumber - CustomElementMin] = radius;
+  }
+}
 
+void setCustomElementVDWRadius(unsigned char atomicNumber, double radius)
+{
+  if (isCustomElement(atomicNumber)) {
+    CustomElementVDWRadii[atomicNumber - CustomElementMin] = radius;
+  }
+}
 } // end anon namespace
 
 unsigned char Elements::elementCount()
@@ -235,7 +248,7 @@ double Elements::radiusVDW(unsigned char atomicNumber)
   if (atomicNumber < element_count)
     return element_VDW[atomicNumber];
   else if (isCustomElement(atomicNumber))
-    return CustomElementVDWRadius;
+    return CustomElementVDWRadii[atomicNumber - CustomElementMin];
   else
     return element_VDW[0];
 }
@@ -245,7 +258,7 @@ double Elements::radiusCovalent(unsigned char atomicNumber)
   if (atomicNumber < element_count)
     return element_covalent[atomicNumber];
   else if (isCustomElement(atomicNumber))
-    return CustomElementCovalentRadius;
+    return CustomElementCovalentRadii[atomicNumber - CustomElementMin];
   else
     return element_covalent[0];
 }

diff --git a/avogadro/core/elements.h b/avogadro/core/elements.h
@@ -76,7 +76,8 @@ class AVOGADROCORE_EXPORT Elements
 
   /** @return the mass of the element with the supplied @p atomicNumber. */
   static double mass(unsigned char atomicNumber);
-
+  static void setCustomElementVDWRadius(unsigned char atomicNumber, double radius);
+  static void setCustomElementCovalentRadius(unsigned char atomicNumber, double radius);
   /**
    * @return the Van der Waals radius of the element with the supplied
    * @p atomicNumber.

diff --git a/tests/qtgui/CMakeLists.txt b/tests/qtgui/CMakeLists.txt
@@ -43,6 +43,7 @@ if(PYTHON_EXECUTABLE AND AVOGADRO_DATA)
 #    InputGeneratorWidget
   )
 endif()
+# link_directories(/usr/lib)
 
 # Build up the source file names.
 set(testSrcs "")