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java.lang.Objectorg.biojava.bio.structure.ChainImpl
public class ChainImpl
A Chain in a PDB file. It contains several groups which can be of type "amino", "hetatm", "nucleotide".
Field Summary | |
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static java.lang.String |
DEFAULT_CHAIN_ID
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Constructor Summary | |
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ChainImpl()
Constructs a ChainImpl object. |
Method Summary | |
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void |
addGroup(Group group)
add a group to this chain. |
java.lang.Object |
clone()
returns an identical copy of this Chain . |
Annotation |
getAnnotation()
get/set the Annotation of a Chain. |
Group |
getGroup(int position)
return the amino acid at position . |
Group |
getGroupByPDB(java.lang.String pdbresnum)
get a group by its PDB residue numbering. |
java.util.List |
getGroups()
return all groups of this chain . |
java.util.List |
getGroups(java.lang.String type)
return an array of all groups of a special type (e.g. |
Group[] |
getGroupsByPDB(java.lang.String pdbresnumStart,
java.lang.String pdbresnumEnd)
get all groups that are located between two PDB residue numbers |
int |
getLength()
get total length of chain, including HETATMs.. |
int |
getLengthAminos()
returns the length of the AminoAcids in chain, without HETATMs. |
java.lang.String |
getName()
get and set the name of this chain (Chain id in PDB file ). |
java.lang.String |
getSequence()
get amino acid sequence. |
java.lang.String |
getSwissprotId()
get the Swissprot id of this chains . |
void |
setAnnotation(Annotation anno)
get/set the Annotation of a Chain. |
void |
setName(java.lang.String nam)
get and set the name of this chain (Chain id in PDB file ). |
void |
setSwissprotId(java.lang.String sp_id)
set the Swissprot id of this chains . |
java.lang.String |
toString()
string representation. |
Methods inherited from class java.lang.Object |
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equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Field Detail |
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public static java.lang.String DEFAULT_CHAIN_ID
Constructor Detail |
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public ChainImpl()
Method Detail |
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public java.lang.Object clone()
clone
in interface Chain
clone
in class java.lang.Object
public void setAnnotation(Annotation anno)
Chain
setAnnotation
in interface Chain
anno
- the Annotation to be provided.public Annotation getAnnotation()
Chain
getAnnotation
in interface Chain
public void setSwissprotId(java.lang.String sp_id)
setSwissprotId
in interface Chain
sp_id
- a String specifying the swissprot id valuegetSwissprotId()
public java.lang.String getSwissprotId()
getSwissprotId
in interface Chain
setSwissprotId(java.lang.String)
public void addGroup(Group group)
Chain
addGroup
in interface Chain
group
- a Group objectpublic Group getGroup(int position)
getGroup
in interface Chain
position
- an int
public java.util.List getGroups(java.lang.String type)
getGroups
in interface Chain
type
- a String
public java.util.List getGroups()
getGroups
in interface Chain
public Group getGroupByPDB(java.lang.String pdbresnum) throws StructureException
Chain
getGroupByPDB
in interface Chain
pdbresnum
- the PDB residue number of the group
StructureException
public Group[] getGroupsByPDB(java.lang.String pdbresnumStart, java.lang.String pdbresnumEnd) throws StructureException
Chain
getGroupsByPDB
in interface Chain
pdbresnumStart
- PDB residue number of startpdbresnumEnd
- PDB residue number of end
StructureException
public int getLength()
Chain
getLength
in interface Chain
public int getLengthAminos()
Chain
getLengthAminos
in interface Chain
public void setName(java.lang.String nam)
setName
in interface Chain
nam
- a String specifying the name valuegetName()
public java.lang.String getName()
getName
in interface Chain
setName(java.lang.String)
public java.lang.String toString()
toString
in interface Chain
toString
in class java.lang.Object
public java.lang.String getSequence()
getSequence
in interface Chain
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