Package | Description |
---|---|
org.biojava.nbio.structure |
Interfaces and classes for protein structure (PDB).
|
Modifier and Type | Field and Description |
---|---|
static GroupType |
HetatomImpl.type
The GroupType is HETATM
|
static GroupType |
AminoAcidImpl.type
this is an Amino acid. type is "amino".
|
static GroupType |
NucleotideImpl.type
this is a "nucleotide", a special occurance of a Hetatom.
|
Modifier and Type | Method and Description |
---|---|
GroupType |
Chain.getPredominantGroupType()
Get the predominant
GroupType for a given Chain, following these
rules: if the ratio of number of residues of a certain
GroupType to total non-water residues is above the threshold
, then that GroupType is
returned if there is no GroupType that is above the
threshold then the GroupType with most members is chosen, logging
it
See also ChemComp.getPolymerType() and
ChemComp.getResidueType() which follow the PDB chemical component
dictionary and provide a much more accurate description of groups and
their linking. |
GroupType |
ChainImpl.getPredominantGroupType() |
static GroupType |
StructureTools.getPredominantGroupType(Chain c)
Deprecated.
use
Chain.getPredominantGroupType() instead. |
GroupType |
Group.getType()
|
GroupType |
HetatomImpl.getType()
|
GroupType |
AminoAcidImpl.getType() |
GroupType |
NucleotideImpl.getType() |
static GroupType |
GroupType.valueOf(String name)
Returns the enum constant of this type with the specified name.
|
static GroupType[] |
GroupType.values()
Returns an array containing the constants of this enum type, in
the order they are declared.
|
Modifier and Type | Method and Description |
---|---|
static Set<Group> |
StructureTools.getAllGroupsFromSubset(Atom[] atoms,
GroupType types)
Expand a set of atoms into all groups from the same structure.
|
List<Group> |
Chain.getAtomGroups(GroupType type)
|
List<Group> |
ChainImpl.getAtomGroups(GroupType type)
|
List<Group> |
Chain.getSeqResGroups(GroupType type)
|
List<Group> |
ChainImpl.getSeqResGroups(GroupType type)
|
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