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public interface Chain
Defines the interface for a Chain.
Method Summary | |
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void |
addGroup(Group group)
add a group to this chain. |
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 X. |
Group |
getGroupByPDB(String pdbresnum)
get a group by its PDB residue numbering. |
List |
getGroups()
return all groups of this chain. |
List |
getGroups(String type)
return an ArrayList of all groups of a special type (e.g. |
Group[] |
getGroupsByPDB(String pdbresnumStart,
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. |
String |
getName()
get and set the name of this chain (Chain id in PDB file ). |
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 |
setAnnotation(Annotation anno)
get/set the Annotation of a Chain. |
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 |
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Object clone()
void addGroup(Group group)
group
- a Group objectGroup getGroup(int position)
position
- an int
List getGroups(String type)
type
- a String
List getGroups()
Group getGroupByPDB(String pdbresnum) throws StructureException
pdbresnum
- the PDB residue number of the group
StructureException
Group[] getGroupsByPDB(String pdbresnumStart, String pdbresnumEnd) throws StructureException
pdbresnumStart
- PDB residue number of startpdbresnumEnd
- PDB residue number of end
StructureException
int getLength()
int getLengthAminos()
void setAnnotation(Annotation anno)
anno
- the Annotation to be provided.Annotation getAnnotation()
void setName(String name)
name
- a String specifying the name valuegetName()
String getName()
setName(java.lang.String)
String toString()
toString
in class Object
String getSequence()
void setSwissprotId(String sp_id)
sp_id
- a String specifying the swissprot id valuegetSwissprotId()
String getSwissprotId()
setSwissprotId(java.lang.String)
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