BiopolymerResidue Class Reference

#include <Compound.h>

Inheritance diagram for BiopolymerResidue:

List of all members.

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

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Constructor & Destructor Documentation

BiopolymerResidue	(	Compound::Name	name,
		String	threeLetterCode,
		char	oneLetterCode
	)

Constructor for BiopolymerResidue.

Parameters:

name	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

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& 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.

BiopolymerResidue& setResidueName

(

const String &

name

)

Returns:

a reference to this BiopolymerResidue

Parameters:

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

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 RNA::RNA().

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