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Fixes#1714 => Functionality for setting size of ghost atom #1911

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Fixes#1714 => Functionality for setting size of ghost atom #1911

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e22ba14
Functionality for setting size of ghost atom
peach280 Jan 26, 2025
645f5e8
Updated
peach280 Jan 27, 2025
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34 changes: 30 additions & 4 deletions avogadro/core/elements.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -26,8 +26,8 @@
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)
{
Expand Down Expand Up @@ -101,6 +101,8 @@
{
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);
Expand All @@ -111,9 +113,33 @@
}
}
} CustomElementTableInitializer;
void setCustomElementCovalentRadius(unsigned char atomicNumber, double radius)

Check notice

Code scanning / CodeQL

Unused static function Note

Static function setCustomElementCovalentRadius is unreachable
{
if (isCustomElement(atomicNumber)) {
CustomElementCovalentRadii[atomicNumber - CustomElementMin] = radius;
}
}

void setCustomElementVDWRadius(unsigned char atomicNumber, double radius)

Check notice

Code scanning / CodeQL

Unused static function Note

Static function setCustomElementVDWRadius is unreachable
{
if (isCustomElement(atomicNumber)) {
CustomElementVDWRadii[atomicNumber - CustomElementMin] = radius;
}
}
} // end anon namespace
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;
}
}
unsigned char Elements::elementCount()
{
return element_count;
Expand Down Expand Up @@ -235,7 +261,7 @@
if (atomicNumber < element_count)
return element_VDW[atomicNumber];
else if (isCustomElement(atomicNumber))
return CustomElementVDWRadius;
return CustomElementVDWRadii[atomicNumber - CustomElementMin];
else
return element_VDW[0];
}
Expand All @@ -245,7 +271,7 @@
if (atomicNumber < element_count)
return element_covalent[atomicNumber];
else if (isCustomElement(atomicNumber))
return CustomElementCovalentRadius;
return CustomElementCovalentRadii[atomicNumber - CustomElementMin];
else
return element_covalent[0];
}
Expand Down
3 changes: 2 additions & 1 deletion avogadro/core/elements.h
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Original file line number Diff line number Diff line change
Expand Up @@ -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.
Expand Down
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