Uses of Interface
org.biojava.bio.structure.Group
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Packages that use Group Package Description org.biojava.bio.structure Interfaces and classes for protein structure (PDB).org.biojava.bio.structure.io Input and Output of Structures -
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Uses of Group in org.biojava.bio.structure
Subinterfaces of Group in org.biojava.bio.structure Modifier and Type Interface Description interface
AminoAcid
AGroup
that represents an AminoAcid.Classes in org.biojava.bio.structure that implement Group Modifier and Type Class Description 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 Modifier and Type Method Description Group
Structure. findGroup(java.lang.String chainId, java.lang.String pdbResnum)
request a particular group from a structure.Group
Structure. findGroup(java.lang.String chainId, java.lang.String pdbResnum, int modelnr)
request a particular group from a structure.Group
StructureImpl. findGroup(java.lang.String chainName, java.lang.String pdbResnum)
Group
StructureImpl. findGroup(java.lang.String chainId, java.lang.String pdbResnum, int modelnr)
Group
Chain. getAtomGroup(int position)
return the Group at position X.Group
ChainImpl. getAtomGroup(int position)
return the group at position .Group
Chain. getGroup(int position)
Deprecated.use getAtomGroup or getSeqResGroup insteadGroup
ChainImpl. getGroup(int position)
Deprecated.use getAtomGroup or getSeqResGroup insteadGroup
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[]
Chain. getGroupsByPDB(java.lang.String pdbresnumStart, java.lang.String pdbresnumEnd, boolean ignoreMissing)
Get all groups that are located between two PDB residue numbers.Group[]
ChainImpl. 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, boolean ignoreMissing)
Get all groups that are located between two PDB residue numbers.Group
Atom. getParent()
Returns the parent Group of the Atom.Group
AtomImpl. getParent()
Group
Chain. getSeqResGroup(int position)
return the Group at position X.Group
ChainImpl. getSeqResGroup(int position)
return the Group at position X.Group
GroupIterator. next()
get next Group.Methods in org.biojava.bio.structure that return types with arguments of type Group Modifier and Type Method Description java.util.List<Group>
Chain. getAtomGroups()
Return all groups that have been specified in the ATOM section of this chain .java.util.List<Group>
Chain. getAtomGroups(java.lang.String type)
Return a List of all groups of a special type (e.g.java.util.List<Group>
ChainImpl. getAtomGroups()
Return all groups that have been specified in the ATOM section of this chain .java.util.List<Group>
ChainImpl. getAtomGroups(java.lang.String type)
Get the Groups of a certain type, that are listed int the ATOM records of the PDB file.java.util.List<Group>
Chain. getGroups()
Deprecated.use getAtomGroups or getSeqResGroups insteadjava.util.List<Group>
Chain. getGroups(java.lang.String type)
Deprecated.use getAtomGroups or getSeqResGroups insteadjava.util.List<Group>
ChainImpl. getGroups()
Deprecated.use getAtomGroups insteadjava.util.List<Group>
ChainImpl. getGroups(java.lang.String type)
Deprecated.use getAtomGroups insteadjava.util.List<Group>
Chain. getSeqResGroups()
Return all groups of this chain.java.util.List<Group>
Chain. getSeqResGroups(java.lang.String type)
Return a List of all groups of a special type (e.g.java.util.List<Group>
ChainImpl. getSeqResGroups()
Return all groups of this chain.java.util.List<Group>
ChainImpl. getSeqResGroups(java.lang.String type)
Return a List of all groups of a special type (e.g.Methods in org.biojava.bio.structure with parameters of type Group Modifier and Type Method Description void
Chain. addGroup(Group group)
add a group to the list of ATOM record group of this chain.void
ChainImpl. addGroup(Group group)
add a group to the list of ATOM record group of this chain.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)
static void
Calc. shift(Group group, Atom a)
Shift a Group with a vector.Method parameters in org.biojava.bio.structure with type arguments of type Group Modifier and Type Method Description void
Chain. setAtomGroups(java.util.List<Group> groups)
Set all groups that have been specified in the ATOM section of this chain .void
ChainImpl. setAtomGroups(java.util.List<Group> groups)
Set all groups that have been specified in the ATOM section of this chain .void
Chain. setSeqResGroups(java.util.List<Group> seqResGroups)
Set the list of SeqResGroups for this chain.void
ChainImpl. setSeqResGroups(java.util.List<Group> groups)
Set the list of SeqResGroups for this chain.Constructors in org.biojava.bio.structure with parameters of type Group Constructor Description AtomIterator(Group g)
Constructs an AtomIterator object.StructureImpl(Group g)
construct a Structure object that only contains a single group -
Uses of Group in org.biojava.bio.structure.io
Method parameters in org.biojava.bio.structure.io with type arguments of type Group Modifier and Type Method Description boolean
SeqRes2AtomAligner. align(java.util.List<Group> seqRes, java.util.List<Group> atomRes)
aligns two chains of groups, where the first chain is representing the list of amino acids as obtained from the SEQRES records, and the second chain represents the groups obtained from the ATOM records (and containing the actual ATOM information).java.lang.String
SeqRes2AtomAligner. getFullAtomSequence(java.util.List<Group> groups)
returns the full sequence of the Atom records of a chain with X instead of HETATMSs.
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