Package | Description |
---|---|
org.biojava.bio.structure |
Interfaces and classes for protein structure (PDB).
|
org.biojava.bio.structure.io |
Input and Output of Structures
|
Modifier and Type | Interface and Description |
---|---|
interface |
AminoAcid
A
Group that represents an AminoAcid. |
Modifier and Type | Class and 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.
|
Modifier and Type | Method and Description |
---|---|
Group |
Structure.findGroup(java.lang.String chainId,
java.lang.String pdbResnum)
request a particular group from a structure.
|
Group |
StructureImpl.findGroup(java.lang.String chainName,
java.lang.String pdbResnum) |
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 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 instead
|
Group |
ChainImpl.getGroup(int position)
Deprecated.
use getAtomGroup or getSeqResGroup instead
|
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)
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,
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.
|
Modifier and Type | Method and 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> |
ChainImpl.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(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 instead
|
java.util.List<Group> |
ChainImpl.getGroups()
Deprecated.
use getAtomGroups instead
|
java.util.List<Group> |
Chain.getGroups(java.lang.String type)
Deprecated.
use getAtomGroups or getSeqResGroups instead
|
java.util.List<Group> |
ChainImpl.getGroups(java.lang.String type)
Deprecated.
use getAtomGroups instead
|
java.util.List<Group> |
Chain.getSeqResGroups()
Return all groups of this chain.
|
java.util.List<Group> |
ChainImpl.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(java.lang.String type)
Return a List of all groups of a special type (e.g.
|
Modifier and Type | Method and 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.
|
Modifier and Type | Method and 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.
|
Constructor and Description |
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AtomIterator(Group g)
Constructs an AtomIterator object.
|
StructureImpl(Group g)
construct a Structure object that only contains a single group
|
Modifier and Type | Method and 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).
|
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.
|