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Packages that use StructureException | |
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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. |
Uses of StructureException in org.biojava.bio.structure |
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Methods in org.biojava.bio.structure that throw StructureException | |
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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 |
StructureImpl.findChain(java.lang.String chainId)
|
Chain |
Structure.findChain(java.lang.String chainId)
request a particular chain from a structure. |
Chain |
StructureImpl.findChain(java.lang.String chainId,
int modelnr)
|
Chain |
Structure.findChain(java.lang.String chainId,
int modelnr)
request a particular chain from a particular model |
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. |
Atom |
HetatomImpl.getAtom(int position)
return an atom by its position in the internal List. |
Atom |
Group.getAtom(int position)
get at atom by position. |
Atom |
HetatomImpl.getAtom(java.lang.String name)
get an atom throws StructureException if atom not found. |
Atom |
Group.getAtom(java.lang.String name)
get an atom throws StructureException if atom not found. |
Atom |
AminoAcidImpl.getC()
get C atom. |
Atom |
AminoAcid.getC()
get C atom. |
Atom |
AminoAcidImpl.getCA()
get CA atom. |
Atom |
AminoAcid.getCA()
get CA atom. |
Atom |
AminoAcidImpl.getCB()
get CB atom. |
Atom |
AminoAcid.getCB()
get CB atom. |
Chain |
StructureImpl.getChainByPDB(java.lang.String chainId)
|
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,
int modelnr)
|
Chain |
Structure.getChainByPDB(java.lang.String chainId,
int modelnr)
request a chain by it's PDB code by default takes only the first model |
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)
|
Atom |
AminoAcidImpl.getN()
get N atom. |
Atom |
AminoAcid.getN()
get N atom. |
Atom |
AminoAcidImpl.getO()
get O atom. |
Atom |
AminoAcid.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) 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. |
Constructors in org.biojava.bio.structure that throw StructureException | |
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SVDSuperimposer(Atom[] atomSet1,
Atom[] atomSet2)
|
Uses of StructureException in org.biojava.bio.structure.align |
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Methods in org.biojava.bio.structure.align that throw StructureException | |
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void |
StructurePairAligner.align(Atom[] ca1,
Atom[] ca2,
StrucAligParameters params)
calculate the actual protein structure superimposition. |
void |
StructurePairAligner.align(Structure s1,
Structure s2)
|
void |
StructurePairAligner.align(Structure s1,
Structure s2,
StrucAligParameters params)
|
Uses of StructureException in org.biojava.bio.structure.align.pairwise |
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Methods in org.biojava.bio.structure.align.pairwise that throw StructureException | |
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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. |
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