Class Protein

java.lang.Object

org.episteme.natural.chemistry.Molecule

org.episteme.natural.biology.Protein

All Implemented Interfaces:

Serializable, Commented, ComprehensiveIdentification, Identified<Identification>, Named

public class Protein
extends Molecule

Represents a protein structure composed of polypeptide chains.

Since:

1.0

Author:

Silvere Martin-Michiellot, Gemini AI (Google DeepMind)

See Also:

• Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	Protein.Chain
static class	Protein.Residue

Field Summary

Fields inherited from class Molecule

traits

Constructor Summary

Constructors

Constructor	Description
Protein(String pdbId)

Method Summary

Modifier and Type	Method	Description
void	addChain(Protein.Chain chain)
Protein.Chain	getChain(String chainId)
List<Protein.Chain>	getChains()
String	getPdbId()
void	setSequence(String sequence)	Sets the sequence for this protein.

Methods inherited from class Molecule

addAtom, addBond, getAtomCount, getAtoms, getBondCount, getBonds, getBondsFor, getFormula, getId, getMolecularWeight, getName, getNeighbors, getTraits, setName, toString

Methods inherited from class Object

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

Methods inherited from interface Commented

getComments, getTrait, setComments

Methods inherited from interface ComprehensiveIdentification

getTrait, setTrait

Constructor Details

Protein

public Protein(String pdbId)

Method Details

getPdbId

public String getPdbId()

addChain

public void addChain(Protein.Chain chain)

getChains

public List<Protein.Chain> getChains()

setSequence

public void setSequence(String sequence)

Sets the sequence for this protein. Creates a single default chain if the sequence is provided.

Parameters:

sequence - the protein sequence (one-letter codes)

getChain

public Protein.Chain getChain(String chainId)