org.biojava.bio.structure
Interface Chain

All Known Implementing Classes:

ChainImpl

public interface Chain

Method Summary

void	addGroup(Group group) add a group to this chain
Group	getGroup(int position) return the amino acid at position X
ArrayList	getGroups(String type) return an ArrayList of all groups of a special type (e.g.
int	getLength() get total length of chain, including HETATMs.
int	getLengthAminos() returns the length of the AminoAcids in chain, without HETATMs.
String	getName()
String	getSequence() return the amino acid sequqence of this chain ( all aminos even if they do not have 3D data ...)
String	getSwissprotId() get the Swissprot id of this chains
void	setName(String name) get and set the name of this chain (Chain id in PDB file )
void	setSwissprotId(String sp_id) set the Swissprot id of this chains
String	toString() string representation

Method Detail

addGroup

public void addGroup(Group group)

add a group to this chain

getGroup

public Group getGroup(int position)

return the amino acid at position X

getGroups

public ArrayList getGroups(String type)

return an ArrayList of all groups of a special type (e.g. amino, hetatm, nucleotide)

getLength

public int getLength()

get total length of chain, including HETATMs.

getLengthAminos

public int getLengthAminos()

returns the length of the AminoAcids in chain, without HETATMs. note: not all amino acids need to have 3D coords, in fact in could be that none has! so length always corresponds to Sequence ( = uniprot,swissprot) length

setName

public void setName(String name)

get and set the name of this chain (Chain id in PDB file )

getName

public String getName()

toString

public String toString()

string representation

getSequence

public String getSequence()

return the amino acid sequqence of this chain ( all aminos even if they do not have 3D data ...)

setSwissprotId

public void setSwissprotId(String sp_id)

set the Swissprot id of this chains

getSwissprotId

public String getSwissprotId()

get the Swissprot id of this chains