◆ Adjustment
Enum values that control the adjustHydrogen function's behavior.
Enumerator |
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Add | Only add hydrogens to underbonded atoms.
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Remove | Only remove hydrogens from overbonded atoms.
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AddAndRemove | Add hydrogens to underbonded atoms and remove hydrogens from overbonded atoms.
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◆ removeAllHydrogens()
static void removeAllHydrogens |
( |
RWMolecule & |
molecule | ) |
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static |
Remove all hydrogen atoms from molecule.
◆ adjustHydrogens() [1/2]
Add/remove hydrogens on molecule to satisfy valency.
◆ adjustHydrogens() [2/2]
Add/remove hydrogens on atom to satisfy valency.
◆ valencyAdjustment()
static int valencyAdjustment |
( |
const RWAtom & |
atom | ) |
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static |
- Returns
- The number of bonds that need to be added or removed from atom to satisfy valency. A positive number indicates the number of bonds to add, a negative number indicates the number of bonds that need to be removed.
◆ extraHydrogenIndices()
static int extraHydrogenIndices |
( |
const RWAtom & |
atom, |
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int |
numberOfHydrogens, |
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std::vector< size_t > & |
indices |
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) |
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static |
Obtain the indices of hydrogens that can be removed from atom.
- Parameters
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atom | The atom from which to prune hydrogens. |
numberOfHydrogens | The maximum number of hydrogens to prune. |
indices | A vector that will be appended with the indices of the hydrogens to remove. |
- Returns
- The number of hydrogen indices appended to indices.
- Note
- This function modifies neither atom nor its parent molecule. It only pushes the indices of hydrogens to remove to the end of indices.
◆ generateNewHydrogenPositions()
static void generateNewHydrogenPositions |
( |
const RWAtom & |
atom, |
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int |
numberOfHydrogens, |
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std::vector< Vector3 > & |
positions |
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) |
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static |
Generate positions for numberOfHydrogens hydrogens bonded to atom.
- Parameters
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positions | Vector of positions that will be appended with numberOfHydrogens hydrogen locations. |
- Note
- There is nothing intelligent going on here. The new positions are randomly oriented and have a length that is the sum of atom's and hydrogen's covalent radii. Effort is made to prevent overlap with other bonded atoms, but this is not guaranteed.
The documentation for this class was generated from the following file: