AminoAcid

Container that stores Atom's of amino acid. In addition the class provides a general information about amino acid residues.

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Class Summary

class AminoAcid
: public vector< Atom>
{

public:
int	getCA() const;
int	getN() const;
int	getC() const;
int	getO() const;
AminoAcid&	operator*=(const RigidTrans3& rt);
static float	getFreqOfOccurrence(RESIDUE_INDEX index);
static RESIDUE_INDEX	getResidueTypeIndx(const char cRes)
static char	getResidueType(const RESIDUE_INDEX indx) ;
static template < class ContainerAtom> vector< AminoAcid>	parsePDB(const ContainerAtom& i_contAtom);
static template < class TAtom> vector< AminoAcid>	parseFilePDB(const string& pdbFile);
protected:

}; // AminoAcid

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KEYWORD

AminoAcid, SeqScore

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AUTHORS

Maxim Shatsky (maxshats@math.tau.ac.il)

copyright: SAMBA Group , Tel-Aviv Univ. Israel, 1997, 1999, 2002

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CHANGES LOG

19.12.02 Changed to inherit from vector<Atom>. Added function 'parsePDB'. 16.01.03 Added new residue index OTHER, to support PCA, PTR ... 10.05.05 parsePDB was changed to differentiate between residues with the same residueId but different residueSeqId (for example, 45 and 45A)

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GOALS

Container that stores Atom's of amino acid. In addition, AminoAcid class should help to construct user-defined classes that deal with amino acid residues. For example it provides one-to-one mapping function from character that identifies the amino acid residue to index which defined in range of [0,19] (see USAGE for more details),for this purpose class provides global enum : RESIDUE_INDEX {ARG,LYS,GLU,GLN,ASP,ASN,PRO,GLY,SER, THR,HIS,ALA,ILE,LEU,VAL,PHE,CYS,MET,TYR,TRP,OTHER,MAX_AA};

AminoAcid can provide statistical information about amino acid residues, like "Frequency of Occurrence in Proteins".

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USAGE

See SeqScore. Complexity of all functions is O(1) besides: parsePDB - O(n)

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int getCA() const;

returns CA atom position (-1 if not found)

    int getCA() const;

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int getN() const;

returns N atom position (-1 if not found)

    int getN() const;

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int getC() const;

returns C atom position (-1 if not found)

    int getC() const;

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int getO() const;

returns O atom position (-1 if not found)

    int getO() const;

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AminoAcid& operator*=(const RigidTrans3& rt);

Applies a rigid transformation on all atom coordinates.

    AminoAcid& operator*=(const RigidTrans3& rt);

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float getFreqOfOccurrence(RESIDUE_INDEX index);

Returns frequency of occurrence of each amino acid residue in proteins taken from M.H.Klapper,Biochem.Biophys.Res.Commun.78:1018-1024,1977

    static float getFreqOfOccurrence(RESIDUE_INDEX index);

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RESIDUE_INDEX getResidueTypeIndx(const char cRes)

Receives one-letter abbreviation of amino acid residue. Returns index as appears in enum RESIDUE_INDEX.

    inline static RESIDUE_INDEX getResidueTypeIndx(const char cRes)

Function is currently defined inline.

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char getResidueType(const RESIDUE_INDEX indx) ;

Receives RESIDUE_INDEX and returns one-letter abbreviation of amino acid residue.

    inline static char getResidueType(const RESIDUE_INDEX indx)                                          
;

Function is currently defined inline.

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template < class ContainerAtom> vector< AminoAcid> parsePDB(const ContainerAtom& i_contAtom);

Parses PDB molecule container and extracts AminoAcid objects

    template < class ContainerAtom>
    static vector< AminoAcid> parsePDB(const ContainerAtom& i_contAtom);

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template < class TAtom> vector< AminoAcid> parseFilePDB(const string& pdbFile);

Parses PDB file and extracts AminoAcid objects possible to extract even 'alt' residues (alternative residue entries having the same id)

    template < class TAtom>
    static vector< AminoAcid> parseFilePDB(const string& pdbFile);

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All Members

public:
int	getCA() const;
int	getN() const;
int	getC() const;
int	getO() const;
AminoAcid&	operator*=(const RigidTrans3& rt);
static float	getFreqOfOccurrence(RESIDUE_INDEX index);
static RESIDUE_INDEX	getResidueTypeIndx(const char cRes)
static char	getResidueType(const RESIDUE_INDEX indx) ;
static template < class ContainerAtom> vector< AminoAcid>	parsePDB(const ContainerAtom& i_contAtom);
static template < class TAtom> vector< AminoAcid>	parseFilePDB(const string& pdbFile);
protected:

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Ancestors

Inheritance chain for AminoAcid:

vector

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Descendants

Class is not inherited by any others.

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