Package org.openscience.cdk.tools

Class ProteinBuilderTool

java.lang.Object

org.openscience.cdk.tools.ProteinBuilderTool

public class ProteinBuilderTool
extends Object

Class that facilitates building protein structures. Building DNA and RNA is done by a complementary class NucleicAcidBuilderTool (to be written).

Source code:

main

Belongs to CDK module:

pdb

Constructor Summary

Constructors

Constructor	Description
ProteinBuilderTool()

Method Summary

Modifier and Type	Method	Description
static IBioPolymer	addAminoAcidAtCTerminus(IBioPolymer protein, IAminoAcid aaToAdd, IStrand strand, IAminoAcid aaToAddTo)	Builds a protein by connecting a new amino acid at the C-terminus of the given strand.
static IBioPolymer	addAminoAcidAtNTerminus(IBioPolymer protein, IAminoAcid aaToAdd, IStrand strand, IAminoAcid aaToAddTo)	Builds a protein by connecting a new amino acid at the N-terminus of the given strand.
static IBioPolymer	createProtein(String sequence)	Creates a BioPolymer from a sequence of amino acid as identified by a the sequence of their one letter codes.
static IBioPolymer	createProtein(String sequence, IChemObjectBuilder builder)	Creates a BioPolymer from a sequence of amino acid as identified by a the sequence of their one letter codes.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ProteinBuilderTool

public ProteinBuilderTool()

Method Detail

addAminoAcidAtNTerminus

public static IBioPolymer addAminoAcidAtNTerminus(IBioPolymer protein,
                                                  IAminoAcid aaToAdd,
                                                  IStrand strand,
                                                  IAminoAcid aaToAddTo)

Builds a protein by connecting a new amino acid at the N-terminus of the given strand.

Parameters:

protein - protein to which the strand belongs

aaToAdd - amino acid to add to the strand of the protein

strand - strand to which the protein is added

addAminoAcidAtCTerminus

public static IBioPolymer addAminoAcidAtCTerminus(IBioPolymer protein,
                                                  IAminoAcid aaToAdd,
                                                  IStrand strand,
                                                  IAminoAcid aaToAddTo)

Builds a protein by connecting a new amino acid at the C-terminus of the given strand. The acidic oxygen of the added amino acid is removed so that additional amino acids can be added savely. But this also means that you might want to add an oxygen at the end of the protein building!

Parameters:

protein - protein to which the strand belongs

aaToAdd - amino acid to add to the strand of the protein

strand - strand to which the protein is added

createProtein

public static IBioPolymer createProtein(String sequence)
                                 throws CDKException

Creates a BioPolymer from a sequence of amino acid as identified by a the sequence of their one letter codes. It uses the DefaultChemObjectBuilder to create a data model.

For example:

 BioPolymer protein = ProteinBuilderTool.createProtein("GAGA");
 

Throws:

CDKException

See Also:

createProtein(String)

createProtein

public static IBioPolymer createProtein(String sequence,
                                        IChemObjectBuilder builder)
                                 throws CDKException

Creates a BioPolymer from a sequence of amino acid as identified by a the sequence of their one letter codes. It uses the given IChemObjectBuilder to create a data model.

For example:

 BioPolymer protein = ProteinBuilderTool.createProtein(
     "GAGA", SilentChemObjectBuilder.getInstance()
 );
 

Throws:

CDKException

See Also:

createProtein(String)