Package | Description |
---|---|
org.biojava.bio.structure |
Interfaces and classes for protein structure (PDB).
|
org.biojava.bio.structure.align |
Classes for the super-imposition of structures.
|
org.biojava.bio.structure.align.pairwise |
Classes for the pairwise alignment of structures.
|
org.biojava.bio.structure.gui.util |
Some utility classes for the protein structure GUIs.
|
org.biojava.bio.structure.io |
Input and Output of Structures
|
Modifier and Type | Method and Description |
---|---|
static Atom[] |
Calc.centerAtoms(Atom[] atomSet)
Center the atoms at the Centroid.
|
static Atom |
Calc.createVirtualCBAtom(AminoAcid amino)
creates a virtual C-beta atom.
|
Chain |
Structure.findChain(java.lang.String chainId)
request a particular chain from a structure.
|
Chain |
StructureImpl.findChain(java.lang.String chainId) |
Chain |
Structure.findChain(java.lang.String chainId,
int modelnr)
request a particular chain from a particular model
|
Chain |
StructureImpl.findChain(java.lang.String chainId,
int modelnr) |
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) |
Atom |
Group.getAtom(int position)
Get at atom by position.
|
Atom |
HetatomImpl.getAtom(int position)
return an atom by its position in the internal List.
|
Atom |
Group.getAtom(java.lang.String name)
Get an atom.
|
Atom |
HetatomImpl.getAtom(java.lang.String name)
get an atom throws StructureException if atom not found.
|
Atom |
AminoAcid.getC()
get C atom.
|
Atom |
AminoAcidImpl.getC()
get C atom.
|
Atom |
AminoAcid.getCA()
get CA atom.
|
Atom |
AminoAcidImpl.getCA()
get CA atom.
|
Atom |
AminoAcid.getCB()
get CB atom.
|
Atom |
AminoAcidImpl.getCB()
get CB atom.
|
Chain |
Structure.getChainByPDB(java.lang.String chainId)
request a chain by it's PDB code
by default takes only the first model
|
Chain |
StructureImpl.getChainByPDB(java.lang.String chainId) |
Chain |
Structure.getChainByPDB(java.lang.String chainId,
int modelnr)
request a chain by it's PDB code
by default takes only the first model
|
Chain |
StructureImpl.getChainByPDB(java.lang.String chainId,
int modelnr) |
static double |
Calc.getDistance(Atom a,
Atom b)
calculate distance between two atoms.
|
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.
|
Atom |
AminoAcid.getN()
get N atom.
|
Atom |
AminoAcidImpl.getN()
get N atom.
|
Atom |
AminoAcid.getO()
get O atom.
|
Atom |
AminoAcidImpl.getO()
get O atom.
|
static double |
Calc.getPhi(AminoAcid a,
AminoAcid b)
phi angle.
|
static double |
Calc.getPsi(AminoAcid a,
AminoAcid b)
psi angle.
|
static double |
SVDSuperimposer.getRMS(Atom[] atomSet1,
Atom[] atomSet2)
Calculate the RMS (root mean square) deviation of two sets of atoms.
|
static boolean |
Calc.isConnected(AminoAcid a,
AminoAcid b)
test if two amino acids are connected, i.e.
|
static void |
Calc.rotate(Group group,
double[][] rotationmatrix)
rotate a structure .
|
static void |
Calc.rotate(Structure structure,
double[][] rotationmatrix)
Rotate a structure.
|
static Atom |
Calc.substract(Atom a,
Atom b)
substract two atoms ( a - b).
|
static double |
Calc.torsionAngle(Atom a,
Atom b,
Atom c,
Atom d)
torsion angle
= angle between the normal vectors of the
two plains a-b-c and b-c-d.
|
Constructor and Description |
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SVDSuperimposer(Atom[] atomSet1,
Atom[] atomSet2)
Create a SVDSuperimposer object and calculate a SVD superimposition of two sets of atoms.
|
Modifier and Type | Method and Description |
---|---|
void |
StructurePairAligner.align(Atom[] ca1,
Atom[] ca2,
StrucAligParameters params)
calculate the protein structure superimposition, between two sets of atoms.
|
void |
StructurePairAligner.align(Structure s1,
Structure s2)
calculate the alignment between the two full structures with default parameters
|
void |
StructurePairAligner.align(Structure s1,
Structure s2,
StrucAligParameters params)
calculate the alignment between the two full structures with user provided parameters
|
Modifier and Type | Method and Description |
---|---|
void |
AlternativeAlignment.calculateSuperpositionByIdx(Atom[] ca1,
Atom[] ca2) |
void |
AlternativeAlignment.finish(StrucAligParameters params,
Atom[] ca1,
Atom[] ca2) |
void |
AlternativeAlignment.refine(StrucAligParameters params,
Atom[] ca1,
Atom[] ca2)
Refinement procedure based on superposition and dynamic programming.
|
Modifier and Type | Method and Description |
---|---|
Structure |
PDBServerPanel.getStructure1() |
Structure |
PDBDirPanel.getStructure1() |
Structure |
StructurePairSelector.getStructure1() |
Structure |
PDBUploadPanel.getStructure1() |
Structure |
PDBServerPanel.getStructure2() |
Structure |
PDBDirPanel.getStructure2() |
Structure |
StructurePairSelector.getStructure2() |
Structure |
PDBUploadPanel.getStructure2() |
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).
|