BiopolymerResidue Class Reference

#include <Compound.h>

Inheritance diagram for BiopolymerResidue:

List of all members.

Public Member Functions
	BiopolymerResidue (const Compound::Name &residueTypeName, const String &threeLetterCode, char oneLetterCode)
	Constructor for BiopolymerResidue.
BiopolymerResidue &	setOneLetterCode (char olc)
BiopolymerResidue &	setThreeLetterCode (const String &tlc)
BiopolymerResidue &	setResidueTypeName (const String &name)
char	getOneLetterCode () const
const String &	getThreeLetterCode () const
const String &	getResidueTypeName () const
bool	assignBiotypes (Ordinality::Residue ordinality=Ordinality::Any)
	Attempt to automatically assign a Biotype to each atom.
Compound::AtomIndex	getParentCompoundAtomIndex (AtomIndex residueAtomIndex) const
	SimTK_INSERT_DERIVED_HANDLE_DECLARATIONS (BiopolymerResidue, BiopolymerResidueRep, Compound)

---

Constructor & Destructor Documentation

BiopolymerResidue	(	const Compound::Name &	residueTypeName,
		const String &	threeLetterCode,
		char	oneLetterCode
	)

Constructor for BiopolymerResidue.

Parameters:

	residueTypeName	name for the type of BiopolymerResidue, e.g. "glycine"
	threeLetterCode	three letter code for the type of residue, e.g. "GLY". This name will be used in the ResidueType field when PDB files are created.
	oneLetterCode	one letter code for the type of residue. e.g 'G'. Use 'X' if the residue type is non-canonical.

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Member Function Documentation

bool assignBiotypes

(

Ordinality::Residue

ordinality = Ordinality::Any

)

Attempt to automatically assign a Biotype to each atom.

Biotype assignments for each atom in a compound are required to match atoms to force field parameters. Residue name and atom name, including synonyms, are used to identify Biotypes. Previous loading of relevant Biotypes from a force field definition may be required for the assignBiotypes() method to work.

Returns:

true if Biotypes were successfully assigned

Parameters:

ordinality

whether this residue is at the beginning, middle, or end of the Biopolymer chain.

Referenced by Protein::initialize(), and RNA::RNA().

char getOneLetterCode

(

)

const

Referenced by RibonucleosideResidue::withPhosphodiester().

Compound::AtomIndex getParentCompoundAtomIndex

(

AtomIndex

residueAtomIndex

)

const

const String& getResidueTypeName

(

)

const

const String& getThreeLetterCode

(

)

const

BiopolymerResidue& setOneLetterCode

(

char

olc

)

Returns:

a reference to this BiopolymerResidue

Parameters:

olc

The one-letter-code for this type of residue. Currently not used for anything.

BiopolymerResidue& setResidueTypeName

(

const String &

name

)

Returns:

a reference to this BiopolymerResidue

Parameters:

name

name for the type of BiopolymerResidue, e.g. "glycine"

BiopolymerResidue& setThreeLetterCode

(

const String &

tlc

)

Returns:

a reference to this BiopolymerResidue

Parameters:

tlc

three letter code for the type of residue, e.g. "GLY". This name will be used in the ResidueType field when PDB files are created.

SimTK_INSERT_DERIVED_HANDLE_DECLARATIONS	(	BiopolymerResidue	,
		BiopolymerResidueRep	,
		Compound
	)

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The documentation for this class was generated from the following file:

• Compound.h