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Packages that use Group | |
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org.biojava.bio.structure | Interfaces and classes for protein structure (PDB). |
Uses of Group in org.biojava.bio.structure |
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Subinterfaces of Group in org.biojava.bio.structure | |
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interface |
AminoAcid
AminoAcid inherits most from Hetatom. |
Classes in org.biojava.bio.structure that implement Group | |
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class |
AminoAcidImpl
AminoAcid inherits most from Hetatom. |
class |
HetatomImpl
Generic Implementation of a Group interface. |
class |
NucleotideImpl
A nucleotide group is almost the same as a Hetatm group. |
Methods in org.biojava.bio.structure that return Group | |
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Group |
StructureImpl.findGroup(java.lang.String chainName,
java.lang.String pdbResnum)
|
Group |
Structure.findGroup(java.lang.String chainId,
java.lang.String pdbResnum)
request a particular group from a structure. |
Group |
StructureImpl.findGroup(java.lang.String chainId,
java.lang.String pdbResnum,
int modelnr)
|
Group |
Structure.findGroup(java.lang.String chainId,
java.lang.String pdbResnum,
int modelnr)
request a particular group from a structure. |
Group |
Chain.getGroup(int position)
return the amino acid at position X. |
Group |
ChainImpl.getGroup(int position)
return the amino acid at position . |
Group |
Chain.getGroupByPDB(java.lang.String pdbresnum)
get a group by its PDB residue numbering. |
Group |
ChainImpl.getGroupByPDB(java.lang.String pdbresnum)
|
Group[] |
Chain.getGroupsByPDB(java.lang.String pdbresnumStart,
java.lang.String pdbresnumEnd)
get all groups that are located between two PDB residue numbers |
Group[] |
ChainImpl.getGroupsByPDB(java.lang.String pdbresnumStart,
java.lang.String pdbresnumEnd)
|
Group |
Atom.getParent()
Returns the parent Group of the Atom returns null if the referenced object is not Group |
Group |
AtomImpl.getParent()
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Methods in org.biojava.bio.structure with parameters of type Group | |
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void |
Chain.addGroup(Group group)
add a group to this chain. |
void |
ChainImpl.addGroup(Group group)
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static void |
Calc.rotate(Group group,
double[][] rotationmatrix)
rotate a structure . |
static void |
Calc.rotate(Group group,
Matrix m)
rotate a group object |
void |
Atom.setParent(Group parent)
Sets the back-reference to its parent Group |
void |
AtomImpl.setParent(Group parent)
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static void |
Calc.shift(Group group,
Atom a)
shift a Group with a vector. |
Constructors in org.biojava.bio.structure with parameters of type Group | |
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AtomIterator(Group g)
Constructs an AtomIterator object. |
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StructureImpl(Group g)
construct a Structure object that only contains a single group |
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