java.lang.Object
de.grogra.ext.pdb.model.Protein
- All Implemented Interfaces:
IProtein
- Author:
- fdill, mdube The protein contains the sequences as a vector. It also provides a text output. RH20060629 changed variable name 'enum' to 'e' to avoid problems with java 1.5
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
addAminoSequence
(AminoSequence sequence) getAcidName
(int sequence, int acid) getAtomName
(int sequence, int acid, int atom) getElement
(int sequence, int acid, int atom) getName()
int
getNumberOfAcids
(int sequence) int
getNumberOfAtoms
(int sequence, int acid) int
int
getResSeqNr
(int sequence, int acid) float
getXCoord
(int sequence, int acid, int atom) float
getYCoord
(int sequence, int acid, int atom) float
getZCoord
(int sequence, int acid, int atom) void
text output for testing
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Constructor Details
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Protein
- Parameters:
proteinName
- - the name of the protein
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Protein
public Protein()
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Method Details
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addAminoSequence
- Parameters:
sequence
- - a sequence to be added to this protein
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textOutput
public void textOutput()text output for testing -
getAminoSequences
- Returns:
- - a vector containing the amino sequences of the type @link AminoSequence of this protein
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getName
- Returns:
- - the name of the protein
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getAcidName
- Specified by:
getAcidName
in interfaceIProtein
- See Also:
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getResSeqNr
public int getResSeqNr(int sequence, int acid) - Specified by:
getResSeqNr
in interfaceIProtein
- See Also:
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getXCoord
public float getXCoord(int sequence, int acid, int atom) -
getYCoord
public float getYCoord(int sequence, int acid, int atom) -
getZCoord
public float getZCoord(int sequence, int acid, int atom) -
getElement
- Specified by:
getElement
in interfaceIProtein
- See Also:
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getAtomName
- Specified by:
getAtomName
in interfaceIProtein
- See Also:
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getNumberOfSequences
public int getNumberOfSequences()- Specified by:
getNumberOfSequences
in interfaceIProtein
- See Also:
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getNumberOfAcids
public int getNumberOfAcids(int sequence) - Specified by:
getNumberOfAcids
in interfaceIProtein
- See Also:
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getNumberOfAtoms
public int getNumberOfAtoms(int sequence, int acid) - Specified by:
getNumberOfAtoms
in interfaceIProtein
- See Also:
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