Class Avogadro::Core::Residue#
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class Residue#
The Residue class represents a chemical residue, used commonly in the PDB format.
Public Types
Public Functions
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Residue()#
Creates a new, empty residue.
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Residue(std::string &name)#
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Residue(std::string &name, Index &number)#
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Residue(std::string &name, Index &number, char &id)#
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virtual ~Residue()#
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inline std::string residueName() const#
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inline void setResidueName(std::string &name)#
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inline Index residueId() const#
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inline void setResidueId(Index &number)#
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inline char chainId() const#
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inline void setChainId(const char &id)#
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inline SecondaryStructure secondaryStructure() const#
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inline void setSecondaryStructure(const SecondaryStructure &ss)#
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inline AtomNameMap &atomNameMap()#
- Returns:
the atom map for the residue
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void resolveResidueBonds(Molecule &mol)#
Sets bonds to atoms in the residue based on data from residuedata header
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int getAtomicNumber(std::string name) const#
- Returns:
the atomic number of the atom with the name specified (e.g., “CA” = “C”)
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std::string getAtomName(const Atom atom) const#
- Returns:
the name of
atom
or an empty string if not in this residue
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std::string getAtomName(const Index index) const#
- Returns:
the name of atom
index
or an empty string if not in this residue
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bool hasAtomByIndex(Index index) const#
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inline void setHeterogen(bool heterogen)#
Set whether this residue is a “HET” / “HETATOM” ligand
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inline bool isHeterogen() const#
- Returns:
is this residue a heterogen (HET / HETATM)
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void setColor(const Vector3ub color)#
Set a custom color for this residue
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Vector3ub color() const#
- Returns:
the color set for this residue, or a default from the chain id
Protected Attributes
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std::string m_residueName#
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Index m_residueId#
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char m_chainId#
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AtomNameMap m_atomNameMap#
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bool m_heterogen#
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Vector3ub m_color#
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bool m_customColorSet#
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SecondaryStructure m_secondaryStructure#
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Residue()#