SimTK::AminoAcidResidue Class Reference

amino acid residue building block for protein polypeptide chain molecules More...

#include <Protein.h>

Inheritance diagram for SimTK::AminoAcidResidue:

List of all members.

Classes
class	Alanine
class	Arginine
class	Asparagine
class	Aspartate
class	BetaBranchedAminoAcidResidue
class	BetaUnbranchedAminoAcidResidue
class	Cysteine
class	Glutamate
class	Glutamine
class	Glycine
class	Histidine
class	HNAminoAcidResidue
	AminoAcidResidue differs from HNAminoAcidResidue in lacking "HN" proton, so Proline can be derived. More...
class	Isoleucine
class	Leucine
class	Lysine
class	Methionine
class	Phenylalanine
class	Proline
class	Serine
class	Threonine
class	Tryptophan
class	Tyrosine
class	Valine
Public Member Functions
	AminoAcidResidue (String name, String threeLetterCode="Unk", char oneLetterCode= '?')
AminoAcidResidue &	setDefaultPhiAngle (Angle phi)
	Set default (initial) phi dihedral angle (rotation about N-CA bond)
AminoAcidResidue &	setDefaultPsiAngle (Angle psi)
Static Public Member Functions
static AminoAcidResidue	create (char oneLetterCode)
	Factory method for creating caninical amino acid residues.
static AminoAcidResidue	create (const PdbResidue &)
	Factory method for creating caninical amino acid residues.

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Detailed Description

amino acid residue building block for protein polypeptide chain molecules

AminoAcidResidue has three unsatisfied BondCenters: 1) "bondN" at the amino nitrogen, for the preceding amino acid residue 2) "boncC" at the carbonyl carbon, for the next amino acid residue 3) "bondCA" at the alpha carbon, for the side chain

The decision of which atoms bond to bond centers bond1, bond2, bond3 etc., depends upon several criteria: 1) chirality - in quadravalent atoms (e.g. alpha carbon), bonds 2, 3, 4 are aranged clockwise when viewed down bond 1. 2) inboard bond - unless explicitly changed, bond1 is the inboard bond for a given compound 3) dihedral angle definition - the dihedral angle for bond1 is defined relative to the plane containing bond2. bonds2,3,4... are defined relative to bond1

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Constructor & Destructor Documentation

SimTK::AminoAcidResidue::AminoAcidResidue	(	String	name,
		String	threeLetterCode = "Unk",
		char	oneLetterCode = '?'
	)		[inline, explicit]

Parameters:

name	name of this type of amino acid. e.g. "glycine"
threeLetterCode	three letter code. Might appear in ResidueName field of PDB files
oneLetterCode	one letter code (use 'X' for non-canonical residues)

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Member Function Documentation

static AminoAcidResidue SimTK::AminoAcidResidue::create

(

char

oneLetterCode

)

[static]

Factory method for creating caninical amino acid residues.

Parameters:

oneLetterCode

one letter code of desired amino acid residue, e.g. "W" for tryptophan

static AminoAcidResidue SimTK::AminoAcidResidue::create

(

const PdbResidue &

)

[static]

Factory method for creating caninical amino acid residues.

AminoAcidResidue& SimTK::AminoAcidResidue::setDefaultPhiAngle

(

Angle

phi

)

[inline]

Set default (initial) phi dihedral angle (rotation about N-CA bond)

Phi and psi angles are offset 180 degrees from other dihedral definitions

AminoAcidResidue& SimTK::AminoAcidResidue::setDefaultPsiAngle

(

Angle

psi

)

[inline]

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

• Protein.h