From 19fb5cba1003ba46700f97da829aa2e5e294422e Mon Sep 17 00:00:00 2001
From: peach280 <vaishnavibhandari.128@gmail.com>
Date: Sun, 5 Jan 2025 00:00:16 +0530
Subject: [PATCH] Functionality for setting size of ghost atom

---
 avogadro/core/elements.cpp | 22 ++++++++++++++++++----
 1 file changed, 18 insertions(+), 4 deletions(-)

diff --git a/avogadro/core/elements.cpp b/avogadro/core/elements.cpp
index 002c6d6a3e..26deb509ae 100644
--- a/avogadro/core/elements.cpp
+++ b/avogadro/core/elements.cpp
@@ -26,8 +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)
 {
@@ -101,6 +101,8 @@ 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);
@@ -113,7 +115,19 @@ class InitializeCustomElementTables
 } CustomElementTableInitializer;
 
 } // end anon namespace
+void Elements::setCustomElementCovalentRadius(unsigned char atomicNumber, double radius)
+{
+  if (isCustomElement(atomicNumber)) {
+    CustomElementCovalentRadii[atomicNumber - CustomElementMin] = radius;
+  }
+}
 
+void Elements::setCustomElementVDWRadius(unsigned char atomicNumber, double radius)
+{
+  if (isCustomElement(atomicNumber)) {
+    CustomElementVDWRadii[atomicNumber - CustomElementMin] = radius;
+  }
+}
 unsigned char Elements::elementCount()
 {
   return element_count;
@@ -235,7 +249,7 @@ 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 +259,7 @@ 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];
 }