static Atom[] |
Calc.centerAtoms(Atom[] atomSet) |
Center the atoms at the Centroid.
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static Atom |
Calc.createVirtualCBAtom(AminoAcid amino) |
creates a virtual C-beta atom.
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Chain |
Structure.findChain(java.lang.String chainId) |
request a particular chain from a structure.
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Chain |
Structure.findChain(java.lang.String chainId,
int modelnr) |
request a particular chain from a particular model
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Chain |
StructureImpl.findChain(java.lang.String chainId) |
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Chain |
StructureImpl.findChain(java.lang.String chainId,
int modelnr) |
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Group |
Structure.findGroup(java.lang.String chainId,
java.lang.String pdbResnum) |
request a particular group from a structure.
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Group |
Structure.findGroup(java.lang.String chainId,
java.lang.String pdbResnum,
int modelnr) |
request a particular group from a structure.
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Group |
StructureImpl.findGroup(java.lang.String chainName,
java.lang.String pdbResnum) |
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Group |
StructureImpl.findGroup(java.lang.String chainId,
java.lang.String pdbResnum,
int modelnr) |
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Atom |
Group.getAtom(int position) |
Get at atom by position.
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Atom |
Group.getAtom(java.lang.String name) |
Get an atom.
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Atom |
HetatomImpl.getAtom(int position) |
return an atom by its position in the internal List.
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Atom |
HetatomImpl.getAtom(java.lang.String name) |
get an atom throws StructureException if atom not found.
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Atom |
AminoAcid.getC() |
get C atom.
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Atom |
AminoAcidImpl.getC() |
get C atom.
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Atom |
AminoAcid.getCA() |
get CA atom.
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Atom |
AminoAcidImpl.getCA() |
get CA atom.
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Atom |
AminoAcid.getCB() |
get CB atom.
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Atom |
AminoAcidImpl.getCB() |
get CB atom.
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Chain |
Structure.getChainByPDB(java.lang.String chainId) |
request a chain by it's PDB code
by default takes only the first model
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Chain |
Structure.getChainByPDB(java.lang.String chainId,
int modelnr) |
request a chain by it's PDB code
by default takes only the first model
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Chain |
StructureImpl.getChainByPDB(java.lang.String chainId) |
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Chain |
StructureImpl.getChainByPDB(java.lang.String chainId,
int modelnr) |
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static double |
Calc.getDistance(Atom a,
Atom b) |
calculate distance between two atoms.
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Group |
Chain.getGroupByPDB(java.lang.String pdbresnum) |
get a group by its PDB residue numbering.
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Group |
ChainImpl.getGroupByPDB(java.lang.String pdbresnum) |
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Group[] |
Chain.getGroupsByPDB(java.lang.String pdbresnumStart,
java.lang.String pdbresnumEnd) |
Get all groups that are located between two PDB residue numbers.
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Group[] |
Chain.getGroupsByPDB(java.lang.String pdbresnumStart,
java.lang.String pdbresnumEnd,
boolean ignoreMissing) |
Get all groups that are located between two PDB residue numbers.
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Group[] |
ChainImpl.getGroupsByPDB(java.lang.String pdbresnumStart,
java.lang.String pdbresnumEnd) |
Get all groups that are located between two PDB residue numbers.
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Group[] |
ChainImpl.getGroupsByPDB(java.lang.String pdbresnumStart,
java.lang.String pdbresnumEnd,
boolean ignoreMissing) |
Get all groups that are located between two PDB residue numbers.
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Atom |
AminoAcid.getN() |
get N atom.
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Atom |
AminoAcidImpl.getN() |
get N atom.
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Atom |
AminoAcid.getO() |
get O atom.
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Atom |
AminoAcidImpl.getO() |
get O atom.
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static double |
Calc.getPhi(AminoAcid a,
AminoAcid b) |
phi angle.
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static double |
Calc.getPsi(AminoAcid a,
AminoAcid b) |
psi angle.
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static double |
SVDSuperimposer.getRMS(Atom[] atomSet1,
Atom[] atomSet2) |
Calculate the RMS (root mean square) deviation of two sets of atoms.
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static boolean |
Calc.isConnected(AminoAcid a,
AminoAcid b) |
test if two amino acids are connected, i.e.
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static void |
Calc.rotate(Group group,
double[][] rotationmatrix) |
rotate a structure .
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static void |
Calc.rotate(Structure structure,
double[][] rotationmatrix) |
Rotate a structure.
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static Atom |
Calc.substract(Atom a,
Atom b) |
substract two atoms ( a - b).
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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.
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