A B C D E F G H I J K L M N O P Q R S T U V W Y Z _

A

actionPerformed(ActionEvent) - Method in class belka.BelkaManager
 
addActionListener(ActionListener) - Method in class belka.draw.InOutPanel
The function adds ActionListener to internal components.
addAfter(Atom) - Method in class belka.mol.Atom
Adds an atom after the current one.
addAfter(Chain) - Method in class belka.mol.Chain
Adds a chain after the current one.
addAfter(Molecule) - Method in class belka.mol.Molecule
Adds a molecule after the current one.
addAssembly(Assembly) - Method in class belka.mol.Chain
Adds an assembly to the end of assembly list for the current chain.
addAtom(Atom) - Method in class belka.mol.Assembly
Adds atom to the end of atom list of the current assembly.
addBefore(Atom) - Method in class belka.mol.Atom
Adds an atom before the current one.
addBefore(Chain) - Method in class belka.mol.Chain
Adds a chain before the current one.
addBefore(Molecule) - Method in class belka.mol.Molecule
Adds a molecule before the current one.
addBond(Bond) - Method in class belka.mol.Assembly
Adds peptide/phosphodiester bond.
addBond(Bond) - Method in class belka.mol.Atom
Adds a covalent bond to the end of covalent bond array for the current atom.
addChain(Chain) - Method in class belka.mol.Molecule
Adds a chain to the end of chain list for the current molecule.
addMolecule(Molecule) - Method in class belka.BelkaManager
 
addMoleculeToDraw(Molecule) - Method in class belka.draw.MolPanel
Adds a molecule to draw in the panel.
Adenine - Static variable in class belka.chem.Compound
Adenine
Al - Static variable in class belka.chem.Element
Aluminium, using double atomic radius for van der Waals radius.
Alanine - Static variable in class belka.chem.Compound
Alanine
ALICEBLUE_VAL - Static variable in class belka.CommandParser
 
align_nw(Chain, Chain) - Method in class belka.align.SeqAligner
Alignes two sets of assemblies (residues/nucleotides) with default parameters using Needleman-Wunsch method.
ALIGN_NW_VAL - Static variable in class belka.CommandParser
 
align_sw(Chain, Chain) - Method in class belka.align.SeqAligner
Alignes two sets of assemblies (residues/nucleotides) with default parameters using Smith-Waterman method.
ALIGN_SW_VAL - Static variable in class belka.CommandParser
 
ALIGNED_VAL - Static variable in class belka.CommandParser
 
ALL_VAL - Static variable in class belka.CommandParser
 
AND_VAL - Static variable in class belka.CommandParser
 
ANTIQUEWHITE_VAL - Static variable in class belka.CommandParser
 
applyToChains() - Method in class belka.align.SeqAligner
The function introduces gaps in chains to reflect the calculated alignment.
AQUA_VAL - Static variable in class belka.CommandParser
 
AQUAMARINE_VAL - Static variable in class belka.CommandParser
 
Ar - Static variable in class belka.chem.Element
Argon
Arginine - Static variable in class belka.chem.Compound
Arginine
arrayLeftDivide(Matrix) - Method in class Jama.Matrix
Element-by-element left division, C = A.\B
arrayLeftDivideEquals(Matrix) - Method in class Jama.Matrix
Element-by-element left division in place, A = A.\B
arrayRightDivide(Matrix) - Method in class Jama.Matrix
Element-by-element right division, C = A./B
arrayRightDivideEquals(Matrix) - Method in class Jama.Matrix
Element-by-element right division in place, A = A./B
arrayTimes(Matrix) - Method in class Jama.Matrix
Element-by-element multiplication, C = A.*B
arrayTimesEquals(Matrix) - Method in class Jama.Matrix
Element-by-element multiplication in place, A = A.*B
As - Static variable in class belka.chem.Element
Arsenic
Asparagine - Static variable in class belka.chem.Compound
Asparagine
Aspartate - Static variable in class belka.chem.Compound
Aspartate
Aspartate_or_Asparagine - Static variable in class belka.chem.Compound
Aspartate or asparagine (uncertain result of hydrolysis)
Assembly - Class in belka.mol
Abstract class describing behavior of an assembly.
Assembly() - Constructor for class belka.mol.Assembly
 
assembly() - Method in class belka.mol.Atom
Returns an assembly the atom belongs to.
assemblyList() - Method in class belka.mol.Chain
Returns list of assemblies.
assemblyMaySatisfy(Assembly) - Method in class belka.SelectExpression
Returns true if any atom in assembly may satisfy the expression, false otherwise.
ASSIGN_VAL - Static variable in class belka.CommandParser
 
Atom - Class in belka.mol
Abstract class describing behavior of an atom.
Atom() - Constructor for class belka.mol.Atom
 
ATOM_VAL - Static variable in class belka.CommandParser
 
atomList() - Method in class belka.mol.Assembly
Returns list of atoms.
atomMaySatisfy(Atom) - Method in class belka.SelectExpression
Returns true if the atom may satisfy the expression, false otherwise.
AZURE_VAL - Static variable in class belka.CommandParser
 

B

B - Static variable in class belka.chem.Element
Boron, using double atomic radius for van der Waals radius.
BACKBONE_VAL - Static variable in class belka.CommandParser
 
BACKGROUND_VAL - Static variable in class belka.CommandParser
 
Be - Static variable in class belka.chem.Element
Beryllium, using double atomic radius for van der Waals radius.
BEIGE_VAL - Static variable in class belka.CommandParser
 
belka - package belka
 
Belka - Class in <Unnamed>
Class containing main function to start Belka.
Belka() - Constructor for class Belka
 
belka.align - package belka.align
 
belka.chem - package belka.chem
 
belka.draw - package belka.draw
 
belka.geom - package belka.geom
 
belka.menu - package belka.menu
 
belka.mol - package belka.mol
 
belka.parser - package belka.parser
 
BelkaApplet - Class in <Unnamed>
Class called by browser to start Belka applet.
BelkaApplet() - Constructor for class BelkaApplet
 
BelkaManager - Class in belka
The object of this class manages the life of Belka as a program or applet.
BelkaManager(Container, String[], URL) - Constructor for class belka.BelkaManager
Object constructor meant to create object when Belka is used as an applet.
BelkaManager(Container, String[]) - Constructor for class belka.BelkaManager
Object constructor.
BISQUE_VAL - Static variable in class belka.CommandParser
 
BLACK_VAL - Static variable in class belka.CommandParser
 
BLANCHEDALMOND_VAL - Static variable in class belka.CommandParser
 
BLUE_VAL - Static variable in class belka.CommandParser
 
BLUEVIOLET_VAL - Static variable in class belka.CommandParser
 
Bond - Class in belka.mol
Abstract class describing behavior of a bond.
Bond() - Constructor for class belka.mol.Bond
 
bondArray() - Method in class belka.mol.Assembly
Returns array of peptide/phosphodiester bonds.
bondArray() - Method in class belka.mol.Atom
Returns array of covalent bonds.
Br - Static variable in class belka.chem.Element
Bromine
BROWN_VAL - Static variable in class belka.CommandParser
 
BURLYWOOD_VAL - Static variable in class belka.CommandParser
 

C

C - Static variable in class belka.chem.Element
Carbon
Ca - Static variable in class belka.chem.Element
Calcium, using double atomic radius for van der Walls radius.
CADETBLUE_VAL - Static variable in class belka.CommandParser
 
calculateModes(Molecule, double) - Method in class belka.geom.NormalModeCalculator
The functions generates a hessian matrix for provided molecule and calculates its eigen values and vectors.
calculateModes(Molecule, double, boolean) - Method in class belka.geom.NormalModeCalculator
The functions generates a hessian matrix for provided molecule and calculates its eigen values and vectors.
CARTOONS_VAL - Static variable in class belka.CommandParser
 
CENTER_VAL - Static variable in class belka.CommandParser
 
chain() - Method in class belka.mol.Assembly
Returns a chain the assembly belongs to.
Chain - Class in belka.mol
Abstract class describing behavior of a chain.
Chain() - Constructor for class belka.mol.Chain
 
CHAIN_VAL - Static variable in class belka.CommandParser
 
chainList() - Method in class belka.mol.Molecule
Returns list of chains.
chainMaySatisfy(Chain) - Method in class belka.SelectExpression
Returns true if any atom in chain may satisfy the expression, false otherwise.
CHARTREUSE_VAL - Static variable in class belka.CommandParser
 
CHOCOLATE_VAL - Static variable in class belka.CommandParser
 
chol() - Method in class Jama.Matrix
Cholesky Decomposition
CholeskyDecomposition - Class in Jama
Cholesky Decomposition.
CholeskyDecomposition(Matrix) - Constructor for class Jama.CholeskyDecomposition
Cholesky algorithm for symmetric and positive definite matrix.
Cl - Static variable in class belka.chem.Element
Chlorine
clone() - Method in class Jama.Matrix
Clone the Matrix object.
CLUSTER_VAL - Static variable in class belka.CommandParser
 
Co - Static variable in class belka.chem.Element
Cobalt, using double atomic radius for van der Waals radius.
COLOR_VAL - Static variable in class belka.CommandParser
 
CommandParser - Class in belka
Object of this class parses inputed commands.
CommandParser(String) - Constructor for class belka.CommandParser
Object constructor.
COMPARE_VAL - Static variable in class belka.CommandParser
 
Compound - Class in belka.chem
Objects of this class represent chemical compounds.
Compound(String, String, char, Color) - Constructor for class belka.chem.Compound
 
Compound(String) - Constructor for class belka.chem.Compound
 
cond() - Method in class Jama.Matrix
Matrix condition (2 norm)
cond() - Method in class Jama.SingularValueDecomposition
Two norm condition number
constructWithCopy(double[][]) - Static method in class Jama.Matrix
Construct a matrix from a copy of a 2-D array.
copy() - Method in class Jama.Matrix
Make a deep copy of a matrix
CORAL_VAL - Static variable in class belka.CommandParser
 
CORNFLOWERBLUE_VAL - Static variable in class belka.CommandParser
 
CORNSILK_VAL - Static variable in class belka.CommandParser
 
countAssemblies() - Method in class belka.mol.Chain
Returns number of assemblies in the chain.
countAssemblies() - Method in class belka.mol.Molecule
Returns number of assemblies in the molecule.
countAtoms() - Method in class belka.mol.Assembly
Returns number of atoms in the assembly.
countAtoms() - Method in class belka.mol.Chain
Returns number of atoms in the chain.
countAtoms() - Method in class belka.mol.Molecule
Returns number of atoms in the molecule.
countBonds() - Method in class belka.mol.Assembly
Returns number of peptide/phosphodiester bonds for the assembly.
countBonds() - Method in class belka.mol.Atom
Returns number of bonds for the atom.
countChains() - Method in class belka.mol.Molecule
Returns number of chains in the molecule.
countModels() - Method in class belka.mol.Molecule
Returns number of different NMR models in the molecule.
countMolecules() - Method in class belka.BelkaManager
 
CPK_VAL - Static variable in class belka.CommandParser
 
Cr - Static variable in class belka.chem.Element
Chromium, using double atomic radius for van der Waals radius.
create(Compound) - Static method in class belka.mol.Assembly
Static method to create a new assembly.
create(String, double, double, double, Element) - Static method in class belka.mol.Atom
Static method to create new atom
create(Atom, Atom) - Static method in class belka.mol.Bond
Static method to create a new bond
create(char) - Static method in class belka.mol.Chain
Static method to create a new chain.
create(String, String) - Static method in class belka.mol.Molecule
Static method to create a new molecule.
create(String) - Static method in class belka.mol.Molecule
Static method to create a new molecule.
createGap() - Static method in class belka.mol.Assembly
Static method to create a new assembly representing gap.
CRIMSON_VAL - Static variable in class belka.CommandParser
 
Cu - Static variable in class belka.chem.Element
Copper
CYAN_VAL - Static variable in class belka.CommandParser
 
Cysteine - Static variable in class belka.chem.Compound
Cysteine
Cytosine - Static variable in class belka.chem.Compound
Cytosine

D

DARKBLUE_VAL - Static variable in class belka.CommandParser
 
DARKCYAN_VAL - Static variable in class belka.CommandParser
 
DARKGOLDENROD_VAL - Static variable in class belka.CommandParser
 
DARKGRAY_VAL - Static variable in class belka.CommandParser
 
DARKGREEN_VAL - Static variable in class belka.CommandParser
 
DARKKHAKI_VAL - Static variable in class belka.CommandParser
 
DARKMAGENTA_VAL - Static variable in class belka.CommandParser
 
DARKOLIVEGREEN_VAL - Static variable in class belka.CommandParser
 
DARKORANGE_VAL - Static variable in class belka.CommandParser
 
DARKORCHID_VAL - Static variable in class belka.CommandParser
 
DARKRED_VAL - Static variable in class belka.CommandParser
 
DARKSALMON_VAL - Static variable in class belka.CommandParser
 
DARKSEAGREEN_VAL - Static variable in class belka.CommandParser
 
DARKSLATEBLUE_VAL - Static variable in class belka.CommandParser
 
DARKSLATEGRAY_VAL - Static variable in class belka.CommandParser
 
DARKTURQUOISE_VAL - Static variable in class belka.CommandParser
 
DARKVIOLET_VAL - Static variable in class belka.CommandParser
 
DEEPPINK_VAL - Static variable in class belka.CommandParser
 
DEEPSKYBLUE_VAL - Static variable in class belka.CommandParser
 
destroy() - Method in class belka.BelkaManager
The method nulls internal pointers and disassembles molecules to help garbage collector to clear memory.
destroy() - Method in class BelkaApplet
Destroys applet.
det() - Method in class Jama.LUDecomposition
Determinant
det() - Method in class Jama.Matrix
Matrix determinant
DIMGRAY_VAL - Static variable in class belka.CommandParser
 
disassemble() - Method in class belka.mol.Assembly
Disassembles assembly into null pointers to help garbage collector to free memory.
disassemble() - Method in class belka.mol.Atom
Disassembles atom into null pointers to help garbage collector to free memory.
disassemble() - Method in class belka.mol.Bond
Disassembles bond into null pointers to help garbage collector to free memory.
disassemble() - Method in class belka.mol.Chain
Disassembles chain into null pointers to help garbage collector to free memory.
disassemble() - Method in class belka.mol.Molecule
Disassembles molecule into null pointers to help garbage collector to free memory.
DISPLACEMENT_VAL - Static variable in class belka.CommandParser
 
Displacer - Class in belka.geom
The class calculates displacement vector between two given confomartions of a protein.
Displacer(Chain, Chain) - Constructor for class belka.geom.Displacer
Object constructor.
distance2To(Atom) - Method in class belka.mol.Atom
Returns squared distance to the given atom.
distanceTo(Atom) - Method in class belka.mol.Atom
Returns distance to the given atom.
DODGERBLUE_VAL - Static variable in class belka.CommandParser
 
DRAG_VAL - Static variable in class belka.CommandParser
 

E

ECHO_VAL - Static variable in class belka.CommandParser
 
eig() - Method in class Jama.Matrix
Eigenvalue Decomposition
EigenvalueDecomposition - Class in Jama
Eigenvalues and eigenvectors of a real matrix.
EigenvalueDecomposition(Matrix) - Constructor for class Jama.EigenvalueDecomposition
Check for symmetry, then construct the eigenvalue decomposition
Element - Class in belka.chem
Objects of this class represent chemical elements.
EXIT_VAL - Static variable in class belka.CommandParser
 
extractAfter() - Method in class belka.mol.Assembly
Extracts the assembly following the current one from the list.
extractAfter() - Method in class belka.mol.Molecule
Extracts the molecule following the current one from the list.
extractBefore() - Method in class belka.mol.Assembly
Extracts the assembly preceeding the current one from the list.
extractBefore() - Method in class belka.mol.Molecule
Extracts the molecule preceeding the current one from the list.

F

F - Static variable in class belka.chem.Element
Fluorine
Fe - Static variable in class belka.chem.Element
Iron, using double atomic radius for van der Waals radius.
findRigids() - Method in class belka.geom.RigidFinder
Returns number of rigid blocks the structure can be split in.
findRigids(double) - Method in class belka.geom.RigidFinder
Returns number of rigid blocks the structure can be split in.
findRigids(double, boolean, boolean, File) - Method in class belka.geom.RigidFinder
Returns number of rigid blocks the structure can be split in.
FIREBRICK_VAL - Static variable in class belka.CommandParser
 
fit(Atom[], Atom[]) - Method in class belka.geom.Kabscher
The function performs least-square fit of given atoms.
FIT_VAL - Static variable in class belka.CommandParser
 
fitCA(Chain, Chain) - Method in class belka.geom.Kabscher
The function performs least-square fit of C-alpha protein or P-phosphate nucleotide atoms and returns RMSD of the fit.
fitCA(Chain[], Chain[]) - Method in class belka.geom.Kabscher
The function performs least-square fit of C-alpha protein or P-phosphate nucleotide atoms and returns RMSD of the fit.
fitCA(Chain, Chain, boolean) - Method in class belka.geom.Kabscher
The function performs least-square fit of C-alpha protein or P-phosphate nucleotide atoms and returns RMSD of the fit.
fitCA(Chain[], Chain[], boolean) - Method in class belka.geom.Kabscher
The function performs least-square fit of C-alpha protein or P-phosphate nucleotide atoms and returns RMSD of the fit.
FLORALWHITE_VAL - Static variable in class belka.CommandParser
 
FORESTGREEN_VAL - Static variable in class belka.CommandParser
 
FORMAT_GROUP - Static variable in class belka.parser.FormatResolver
 
FORMAT_GROUP_EXTENSIONS - Static variable in class belka.parser.FormatResolver
Standard extensions for annotation/group file format
FORMAT_PDB - Static variable in class belka.parser.FormatResolver
 
FORMAT_PDB_EXTENSIONS - Static variable in class belka.parser.FormatResolver
Standard extensions for file in PDB format
FORMAT_PROJECT - Static variable in class belka.parser.FormatResolver
 
FORMAT_PROJECT_EXTENSIONS - Static variable in class belka.parser.FormatResolver
Standard extensions for project file format
FORMAT_UNKNOWN - Static variable in class belka.parser.FormatResolver
Constant to define PDB-file format
FormatResolver - Class in belka.parser
The class represents set of functions aimed to resolve format of file by extension.
FormatResolver() - Constructor for class belka.parser.FormatResolver
 
FROM_VAL - Static variable in class belka.CommandParser
 
FUCHSIA_VAL - Static variable in class belka.CommandParser
 

G

Ga - Static variable in class belka.chem.Element
Gallium
GAINSBORO_VAL - Static variable in class belka.CommandParser
 
Ge - Static variable in class belka.chem.Element
Germanium, using double atomic radius for van der Waals radius.
GeometryUtil - Class in belka.geom
The class does simple geometric calculations.
GeometryUtil() - Constructor for class belka.geom.GeometryUtil
 
get(int, int) - Method in class Jama.Matrix
Get a single element.
GET_VAL - Static variable in class belka.CommandParser
 
getAlignedAttribute() - Static method in class belka.mol.Assembly
Returns flag attribute of aligned assemblies.
getAliLength() - Method in class belka.align.SeqAligner
Returns lengths of alignment;
getAliSequence1() - Method in class belka.align.SeqAligner
Returns aligned part of first sequence.
getAliSequence2() - Method in class belka.align.SeqAligner
Returns aligned part of second sequence.
getAlternative() - Method in class belka.mol.Atom
Returns atom's alternate location indicator.
getAppletInfo() - Method in class BelkaApplet
Returns information about applet
getArray() - Method in class Jama.Matrix
Access the internal two-dimensional array.
getArrayCopy() - Method in class Jama.Matrix
Copy the internal two-dimensional array.
getAtomicNumber() - Method in class belka.chem.Element
Returns element's number in Mendeleev's periodic table, for example 26 for iron.
getCAAtom() - Method in class belka.mol.Assembly
Returns C-alpha atom or null if it is not found.
getColor() - Method in class belka.chem.Compound
Returns compound's color to be used to draw it.
getColor() - Method in class belka.chem.Element
Returns element's color to be used to draw it.
getColor() - Method in class belka.mol.Atom
Returns color of the sphere representing the atom on a screen.
getColor() - Method in class belka.mol.Bond
Returns color of the cylinder representing the bond on a screen.
getColumnDimension() - Method in class Jama.Matrix
Get column dimension.
getColumnPackedCopy() - Method in class Jama.Matrix
Make a one-dimensional column packed copy of the internal array.
getCompound() - Method in class belka.mol.Assembly
Returns assembly's compound.
getCompoundByName(String) - Static method in class belka.chem.Compound
Returns compound with given name.
getCompoundByShortName(String) - Static method in class belka.chem.Compound
Returns compound with short (three-letter) name.
getCovalentRadius() - Method in class belka.chem.Element
Returns element's covalent radius.
getD() - Method in class Jama.EigenvalueDecomposition
Return the block diagonal eigenvalue matrix
getDerivedX() - Method in class belka.mol.Atom
Returns derived atom's X coordinate.
getDerivedY() - Method in class belka.mol.Atom
Returns derived atom's Y coordinate.
getDerivedZ() - Method in class belka.mol.Atom
Returns derived atom's Z coordinate.
getDoublePivot() - Method in class Jama.LUDecomposition
Return pivot permutation vector as a one-dimensional double array
getElement() - Method in class belka.mol.Atom
Returns atom's chemical element.
getElementByName(String) - Static method in class belka.chem.Element
Returns element with given chemical name.
getElementBySign(String) - Static method in class belka.chem.Element
Returns element with given chemical sign.
getFAtom() - Method in class belka.mol.Bond
Returns first atom of the bond.
getGapExtend() - Method in class belka.align.SeqAligner
Returns current value of gap extension penatly.
getGapOpen() - Method in class belka.align.SeqAligner
Returns current value of gap open penatly.
getGroupAttribute(int) - Static method in class belka.mol.Assembly
Returns flag attribute for assemblies in particular group.
getGroupId() - Method in class belka.mol.Assembly
Returns group id or 0 if assembly is not assigned to any group.
getH() - Method in class Jama.QRDecomposition
Return the Householder vectors
getHelix3Attribute() - Static method in class belka.mol.Assembly
Returns flag attribute for residues in 3,10-helices.
getHelix4Attribute() - Static method in class belka.mol.Assembly
Returns flag attribute for residues in 4-helices.
getHelix5Attribute() - Static method in class belka.mol.Assembly
Returns flag attribute for residues in 5-helices.
getHelixAttribute() - Static method in class belka.mol.Assembly
Returns flag attribute for residues in helices.
getICode() - Method in class belka.mol.Assembly
Returns assembly's icode.
getId() - Method in class belka.mol.Chain
Returns chain's id.
getImagEigenvalues() - Method in class Jama.EigenvalueDecomposition
Return the imaginary parts of the eigenvalues
getInput() - Method in class belka.CommandParser
The function returns the input string of the parser.
getInput() - Method in class belka.draw.InOutPanel
Returns text inputed by user.
getL() - Method in class Jama.CholeskyDecomposition
Return triangular factor.
getL() - Method in class Jama.LUDecomposition
Return lower triangular factor
getLargestGroup() - Method in class belka.BelkaManager
The function returns the largest group id assigned to any assembly.
getLength1() - Method in class belka.align.SeqAligner
Returns lengths of first aligned sequence.
getLength2() - Method in class belka.align.SeqAligner
Returns lengths of second aligned sequence.
getLetterName() - Method in class belka.chem.Compound
Returns compound's one letter name, for example 'A' for Alanine.
getLetterName() - Method in class belka.mol.Assembly
Returns assembly's one letter name.
getMainAtom() - Method in class belka.mol.Assembly
Returns the main atom (CA for proteins and sugar P for nucleotides) in assembly or null if such atom can't be found.
getMainComponent() - Method in class belka.BelkaManager
Returns the main component to draw on
getMatrix(int, int, int, int) - Method in class Jama.Matrix
Get a submatrix.
getMatrix(int[], int[]) - Method in class Jama.Matrix
Get a submatrix.
getMatrix(int, int, int[]) - Method in class Jama.Matrix
Get a submatrix.
getMatrix(int[], int, int) - Method in class Jama.Matrix
Get a submatrix.
getModel() - Method in class belka.mol.Chain
Returns chain's model number.
getMoleculesToDraw() - Method in class belka.draw.MolPanel
Returs molecules drawn in the panel.
getName() - Method in class belka.chem.Compound
Returns compound's full name, for example "Alanine".
getName() - Method in class belka.chem.Element
Returns element's full name, for example "Iron".
getName() - Method in class belka.mol.Assembly
Returns assembly's name.
getName() - Method in class belka.mol.Atom
Returns atom's name.
getName() - Method in class belka.mol.Molecule
Returns molecule's name.
getNFitted() - Method in class belka.geom.Kabscher
Returns number of fitted atoms.
getNModes() - Method in class belka.geom.NormalModeCalculator
 
getNRigids() - Method in class belka.geom.RigidFinder
Returns number of found rigid blocks.
getNRigids() - Method in class BelkaApplet
Returns the number of rigid block found in all molecules.
getNumGaps() - Method in class belka.align.SeqAligner
Returns number of gaps in alignment.
getNumIdentical() - Method in class belka.align.SeqAligner
Returns number of identical residues in alignment.
getNumPositive() - Method in class belka.align.SeqAligner
Returns number of aligned residues with positive score.
getOccupancy() - Method in class belka.mol.Atom
Returns atom's occupancy.
getParsedAssemblyName() - Method in class belka.CommandParser
Returns parsed assembly name.
getParsedAssemblyNum() - Method in class belka.CommandParser
Returns parsed assembly number.
getParsedAtomName() - Method in class belka.CommandParser
Returns parsed atom name.
getParsedChainIds() - Method in class belka.CommandParser
Returns parsed chain id.
getParsedColor() - Method in class belka.CommandParser
Returns parsed color.
getParsedContent() - Method in class belka.CommandParser
Returns the parsed content of the command.
getParsedDouble() - Method in class belka.CommandParser
Returns parsed double number.
getParsedInt() - Method in class belka.CommandParser
Returns parsed integer number.
getParsedIntRangeEnd() - Method in class belka.CommandParser
Returns end of the parsed integer range.
getParsedIntRangeStart() - Method in class belka.CommandParser
Returns start of the parsed integer range.
getParsedMolName() - Method in class belka.CommandParser
Returns parsed molecule name.
getPDBCode() - Method in class belka.mol.Molecule
Returns molecule's PDB-code.
getPivot() - Method in class Jama.LUDecomposition
Return pivot permutation vector
getPreferredSize() - Method in class belka.draw.MolPanel
Return preferred size of a panel.
getQ() - Method in class Jama.QRDecomposition
Generate and return the (economy-sized) orthogonal factor
getR() - Method in class Jama.QRDecomposition
Return the upper triangular factor
getRadius() - Method in class belka.mol.Atom
Returns radius of the sphere representing the atom.
getRadius() - Method in class belka.mol.Bond
Returns radius of the cylinder representing the bond.
getRealEigenvalues() - Method in class Jama.EigenvalueDecomposition
Return the real parts of the eigenvalues
getRegularAttribute() - Static method in class belka.mol.Assembly
Returns flag attribute for residues in any secondary structure elements.
getRemainingContent() - Method in class belka.CommandParser
Returns the remaining content of the command.
getRMSD() - Method in class belka.geom.Kabscher
Returns RMSD of fit.
getRotation() - Method in class belka.geom.Kabscher
Returns rotation matrix.
getRotationCopy() - Method in class belka.geom.Kabscher
Returns copy of rotation matrix.
getRowDimension() - Method in class Jama.Matrix
Get row dimension.
getRowPackedCopy() - Method in class Jama.Matrix
Make a one-dimensional row packed copy of the internal array.
getS() - Method in class Jama.SingularValueDecomposition
Return the diagonal matrix of singular values
getSAtom() - Method in class belka.mol.Bond
Returns second atom of the bond.
getScore() - Method in class belka.align.SeqAligner
Returns score of the alignment.
getScoringMatrix() - Method in class belka.align.SeqAligner
Returns current scoring matrix.
getScreenRadius() - Method in class belka.mol.Atom
Returns radius of the sphere representing the atom on a screen.
getScreenRadius() - Method in class belka.mol.Bond
Returns radius of the cylinder representing the bond on a screen.
getScreenX() - Method in class belka.mol.Atom
Returns atom's X coordinate on a screen.
getScreenY() - Method in class belka.mol.Atom
Returns atom's Y coordinate on a screen.
getScreenZ() - Method in class belka.mol.Atom
Returns atom's Z coordinate on a screen.
getSelectedAttribute() - Static method in class belka.mol.Atom
Returns flag attribute for selected atom.
getSequence() - Method in class belka.mol.Chain
Returns sequence of the chain.
getSerialNum() - Method in class belka.mol.Assembly
Returns assembly's serial number.
getSerialNum() - Method in class belka.mol.Atom
Returns atom's serial number.
getSheetAttribute() - Static method in class belka.mol.Assembly
Returns flag attribute for residues in sheets.
getShortName() - Method in class belka.chem.Compound
Returns compound's short name (three-letter), for example "Ala".
getSign() - Method in class belka.chem.Element
Returns element's chemical sign, for example "Fe".
getSingularValues() - Method in class Jama.SingularValueDecomposition
Return the one-dimensional array of singular values
getSpentTime() - Method in class belka.geom.RigidFinder
Returns time in seconds spent on last call to function RigidFinder.findRigids(double,boolean,boolean,File).
getTemperature() - Method in class belka.mol.Atom
Returns atom's temperature factor.
getTranslation() - Method in class belka.geom.Kabscher
Returns translation vector.
getTranslationCopy() - Method in class belka.geom.Kabscher
Returns copy translation vector.
getTurnAttribute() - Static method in class belka.mol.Assembly
Returns flag attribute for residues in turn.
getU() - Method in class Jama.LUDecomposition
Return upper triangular factor
getU() - Method in class Jama.SingularValueDecomposition
Return the left singular vectors
getV() - Method in class Jama.EigenvalueDecomposition
Return the eigenvector matrix
getV() - Method in class Jama.SingularValueDecomposition
Return the right singular vectors
getVDWRadius() - Method in class belka.chem.Element
Returns element's van der Waals radius.
getX() - Method in class belka.mol.Atom
Returns atom's X coordinate.
getY() - Method in class belka.mol.Atom
Returns atom's Y coordinate.
getZ() - Method in class belka.mol.Atom
Returns atom's Z coordinate.
GHOSTWHITE_VAL - Static variable in class belka.CommandParser
 
Glutamate - Static variable in class belka.chem.Compound
Glutamate
Glutamate_or_Glutamine - Static variable in class belka.chem.Compound
Glutamate or glutamine (uncertain result of hydrolysis)
Glutamine - Static variable in class belka.chem.Compound
Glutamine
Glycine - Static variable in class belka.chem.Compound
Glycine
GOLD_VAL - Static variable in class belka.CommandParser
 
GOLDENROD_VAL - Static variable in class belka.CommandParser
 
GRAY_VAL - Static variable in class belka.CommandParser
 
GREEN_VAL - Static variable in class belka.CommandParser
 
GREENYELLOW_VAL - Static variable in class belka.CommandParser
 
GROUP_VAL - Static variable in class belka.CommandParser
 
GROUPMOL_VAL - Static variable in class belka.CommandParser
 
GroupParser - Class in belka.parser
Object of this class load annotation/group file either from file or URL.
GroupParser() - Constructor for class belka.parser.GroupParser
 
Guanine - Static variable in class belka.chem.Compound
Guanine

H

H - Static variable in class belka.chem.Element
Hydrogen
h2o - Static variable in class belka.chem.Compound
 
hasAlignment() - Method in class belka.align.SeqAligner
Returns true if the object has alignment, false otherwise.
hasAttribute(int) - Method in class belka.mol.Assembly
Returns true if the provide attribute matches to the attributes of the assembly.
hasAttribute(int) - Method in class belka.mol.Atom
Returns true if the provide attribute matches to the attributes of the atom.
hasMoreInput() - Method in class belka.CommandParser
Returns 'true' if there are more non-space characters in input line, 'false' otherwise.
He - Static variable in class belka.chem.Element
Helium
Histidine - Static variable in class belka.chem.Compound
Histidine
hoh - Static variable in class belka.chem.Compound
Water
HONEYDEW_VAL - Static variable in class belka.CommandParser
 
HOTPINK_VAL - Static variable in class belka.CommandParser
 
hypot(double, double) - Static method in class Jama.util.Maths
sqrt(a^2 + b^2) without under/overflow.

I

identity(int, int) - Static method in class Jama.Matrix
Generate identity matrix
INDIANRED_VAL - Static variable in class belka.CommandParser
 
INDIGO_VAL - Static variable in class belka.CommandParser
 
init() - Method in class BelkaApplet
Starts the Belka applet.
InOutPanel - Class in belka.draw
Panel for input commands and output messages
InOutPanel(String, boolean) - Constructor for class belka.draw.InOutPanel
Object constructor.
InOutPanel(String) - Constructor for class belka.draw.InOutPanel
Object constructor.
insertAfter(Assembly) - Method in class belka.mol.Assembly
Inserts an assembly after the current one.
insertBefore(Assembly) - Method in class belka.mol.Assembly
Inserts an assembly before the current one.
inverse() - Method in class Jama.Matrix
Matrix inverse or pseudoinverse
invert(double[][]) - Static method in class belka.geom.GeometryUtil
Function inverts given matrix.
isAligned() - Method in class belka.mol.Assembly
Returns true if assemblies is aligned, false otherwise.
isAndBoolean() - Method in class belka.SelectExpression
Returns true if boolean operation with next expression is 'and', false otherwise.
isC() - Method in class belka.mol.Atom
Returns 'true' if atom is carbon of mainchain, 'false' otherwise.
isCA() - Method in class belka.mol.Atom
Returns 'true' if atom is alpha carbon, 'false' otherwise.
isCB() - Method in class belka.mol.Atom
Returns 'true' if atom is CB carbon, 'false' otherwise.
isConnectedTo(Assembly) - Method in class belka.mol.Assembly
Returns true if assemblies are connected by peptide/phosphodiester bonds, false otherwise.
isFullRank() - Method in class Jama.QRDecomposition
Is the matrix full rank?
isGap() - Method in class belka.mol.Assembly
Returns true if the assembly represents gap.
isN() - Method in class belka.mol.Atom
Returns 'true' if atom is nitrogen of mainchain, 'false' otherwise.
isNonsingular() - Method in class Jama.LUDecomposition
Is the matrix nonsingular?
isO() - Method in class belka.mol.Atom
Returns 'true' if atom is oxygen of mainchain, 'false' otherwise.
Isoleucine - Static variable in class belka.chem.Compound
Isoleucine
isOrBoolean() - Method in class belka.SelectExpression
Returns true if boolean operation with next expression is 'or', false otherwise.
isSelected() - Method in class belka.mol.Atom
Returns atom's selection status.
isSPD() - Method in class Jama.CholeskyDecomposition
Is the matrix symmetric and positive definite?
IVORY_VAL - Static variable in class belka.CommandParser
 

J

Jama - package Jama
 
Jama.util - package Jama.util
 
JAR_VAL - Static variable in class belka.CommandParser
 

K

K - Static variable in class belka.chem.Element
Potassium
Kabscher - Class in belka.geom
The implementation of the Kabsch algorith for least-square fitting of two sets of points as describe in:
W.
Kabscher() - Constructor for class belka.geom.Kabscher
 
KHAKI_VAL - Static variable in class belka.CommandParser
 
Kr - Static variable in class belka.chem.Element
Krypton

L

LAVENDER_VAL - Static variable in class belka.CommandParser
 
LAVENDERBLUSH_VAL - Static variable in class belka.CommandParser
 
LAWNGREEN_VAL - Static variable in class belka.CommandParser
 
LEMONCHIFFON_VAL - Static variable in class belka.CommandParser
 
Leucine - Static variable in class belka.chem.Compound
Leucine
Leucine_or_Isoleucine - Static variable in class belka.chem.Compound
Leucine or isoleucine (uncertain result of mass-spec)
Li - Static variable in class belka.chem.Element
Lithium
LIGHTBLUE_VAL - Static variable in class belka.CommandParser
 
LIGHTCORAL_VAL - Static variable in class belka.CommandParser
 
LIGHTCYAN_VAL - Static variable in class belka.CommandParser
 
LIGHTGOLDENRODYELLOW_VAL - Static variable in class belka.CommandParser
 
LIGHTGRAY_VAL - Static variable in class belka.CommandParser
 
LIGHTGREEN_VAL - Static variable in class belka.CommandParser
 
LIGHTPINK_VAL - Static variable in class belka.CommandParser
 
LIGHTSALMON_VAL - Static variable in class belka.CommandParser
 
LIGHTSEAGREEN_VAL - Static variable in class belka.CommandParser
 
LIGHTSKYBLUE_VAL - Static variable in class belka.CommandParser
 
LIGHTSLATEGRAY_VAL - Static variable in class belka.CommandParser
 
LIGHTSTEELBLUE_VAL - Static variable in class belka.CommandParser
 
LIGHTYELLOW_VAL - Static variable in class belka.CommandParser
 
LIME_VAL - Static variable in class belka.CommandParser
 
LIMEGREEN_VAL - Static variable in class belka.CommandParser
 
LINEN_VAL - Static variable in class belka.CommandParser
 
LOAD_VAL - Static variable in class belka.CommandParser
 
loadFile(File, Molecule) - Method in class belka.parser.GroupParser
Loads annotation/group file and creates a molecule.
loadFile(URL, Molecule) - Method in class belka.parser.GroupParser
Loads annotation/group file from URL.
loadFile(File) - Method in class belka.parser.ProjectParser
Loads project-file and creates a molecule.
loadFile(URL) - Method in class belka.parser.ProjectParser
Loads project-file from URL.
lu() - Method in class Jama.Matrix
LU Decomposition
LUDecomposition - Class in Jama
LU Decomposition.
LUDecomposition(Matrix) - Constructor for class Jama.LUDecomposition
LU Decomposition
Lysine - Static variable in class belka.chem.Compound
Lysine

M

MAGENTA_VAL - Static variable in class belka.CommandParser
 
main(String[]) - Static method in class Belka
Starts the Belka.
MAROON_VAL - Static variable in class belka.CommandParser
 
Maths - Class in Jama.util
 
Maths() - Constructor for class Jama.util.Maths
 
Matrix - Class in Jama
Jama = Java Matrix class.
Matrix(int, int) - Constructor for class Jama.Matrix
Construct an m-by-n matrix of zeros.
Matrix(int, int, double) - Constructor for class Jama.Matrix
Construct an m-by-n constant matrix.
Matrix(double[][]) - Constructor for class Jama.Matrix
Construct a matrix from a 2-D array.
Matrix(double[][], int, int) - Constructor for class Jama.Matrix
Construct a matrix quickly without checking arguments.
Matrix(double[], int) - Constructor for class Jama.Matrix
Construct a matrix from a one-dimensional packed array
MEDIUMAQUAMARINE_VAL - Static variable in class belka.CommandParser
 
MEDIUMBLUE_VAL - Static variable in class belka.CommandParser
 
MEDIUMORCHID_VAL - Static variable in class belka.CommandParser
 
MEDIUMPURPLE_VAL - Static variable in class belka.CommandParser
 
MEDIUMSEAGREEN_VAL - Static variable in class belka.CommandParser
 
MEDIUMSLATEBLUE_VAL - Static variable in class belka.CommandParser
 
MEDIUMSPRINGGREEN_VAL - Static variable in class belka.CommandParser
 
MEDIUMTURQUOISE_VAL - Static variable in class belka.CommandParser
 
MEDIUMVIOLETRED_VAL - Static variable in class belka.CommandParser
 
MenuColor - Class in belka.menu
The class implements the menu 'Color' with items to change color of molecule structure on a screen.
MenuColor(BelkaManager) - Constructor for class belka.menu.MenuColor
Object constructor
MenuDisplay - Class in belka.menu
The class implements the menu 'Display' with items to change representation of molecule structure on a screen.
MenuDisplay(BelkaManager) - Constructor for class belka.menu.MenuDisplay
Object constructor
MenuFile - Class in belka.menu
The class implements the memu 'File' with items to load and save molecules to/from file.
MenuFile(BelkaManager) - Constructor for class belka.menu.MenuFile
Object constructor
MenuSelect - Class in belka.menu
The class implements the menu 'Select' with items to select sets of atoms in loaded molecules.
MenuSelect(BelkaManager) - Constructor for class belka.menu.MenuSelect
Object constructor
Methionine - Static variable in class belka.chem.Compound
Methionine
Mg - Static variable in class belka.chem.Element
Magnesium
MIDNIGHTBLUE_VAL - Static variable in class belka.CommandParser
 
MINTCREAM_VAL - Static variable in class belka.CommandParser
 
minus(Matrix) - Method in class Jama.Matrix
C = A - B
minusEquals(Matrix) - Method in class Jama.Matrix
A = A - B
MISTYROSE_VAL - Static variable in class belka.CommandParser
 
Mn - Static variable in class belka.chem.Element
Manganese, using double atomic radius for van der Waals radius.
MOCCASIN_VAL - Static variable in class belka.CommandParser
 
MODEL_VAL - Static variable in class belka.CommandParser
 
molecule() - Method in class belka.mol.Chain
Returns a molecule the chain belongs to.
Molecule - Class in belka.mol
Abstract class describing behavior of a molecule.
Molecule() - Constructor for class belka.mol.Molecule
 
MOLECULE_VAL - Static variable in class belka.CommandParser
 
moleculeList() - Method in class belka.BelkaManager
 
moleculeMaySatisfy(Molecule) - Method in class belka.SelectExpression
Returns true if any atom in molecule may satisfy the expression, false otherwise.
MolPanel - Class in belka.draw
Panel to draw structures of molecules.
MolPanel() - Constructor for class belka.draw.MolPanel
Object constructor.
multiply(double[][], double[][]) - Static method in class belka.geom.GeometryUtil
Function multiplies two given matrices.
multiply(double[][], double[]) - Static method in class belka.geom.GeometryUtil
Function multiplies given matrix and vector.
multiply(double[], double[][]) - Static method in class belka.geom.GeometryUtil
Function multiplies given matrix and vector.

N

N - Static variable in class belka.chem.Element
Nitrogen
Na - Static variable in class belka.chem.Element
Sodium
NAVAJOWHITE_VAL - Static variable in class belka.CommandParser
 
NAVY_VAL - Static variable in class belka.CommandParser
 
Ne - Static variable in class belka.chem.Element
Neon
next() - Method in class belka.mol.Assembly
Returns next assembly in list.
next() - Method in class belka.mol.Atom
Returns next atom in list.
next() - Method in class belka.mol.Chain
Returns next chain in list.
next() - Method in class belka.mol.Molecule
Returns next molecule in list.
next() - Method in class belka.SelectExpression
Returns next expression.
Ni - Static variable in class belka.chem.Element
Nickel
NMA_VAL - Static variable in class belka.CommandParser
 
NOCLUSTER_VAL - Static variable in class belka.CommandParser
 
NOREFINE_VAL - Static variable in class belka.CommandParser
 
norm1() - Method in class Jama.Matrix
One norm
norm2() - Method in class Jama.Matrix
Two norm
norm2() - Method in class Jama.SingularValueDecomposition
Two norm
NormalModeCalculator - Class in belka.geom
The class calculates normal model for given structure from Elastic Network Model (ENM), as described in Atilgan AR, Durell SR, Jernigan RL, Demirel MC, Keskin O, Bahar I, Anisotropy of fluctuation dynamics of proteins with an elastic network model.
NormalModeCalculator() - Constructor for class belka.geom.NormalModeCalculator
 
normF() - Method in class Jama.Matrix
Frobenius norm
normInf() - Method in class Jama.Matrix
Infinity norm
NOT_VAL - Static variable in class belka.CommandParser
 
numChainsSpecified() - Method in class belka.SelectExpression
The function returns the number of chains specified in selection.

O

O - Static variable in class belka.chem.Element
Oxygen
OCCUPANCY_VAL - Static variable in class belka.CommandParser
 
OFF_VAL - Static variable in class belka.CommandParser
 
OLDLACE_VAL - Static variable in class belka.CommandParser
 
OLIVE_VAL - Static variable in class belka.CommandParser
 
OLIVEDRAB_VAL - Static variable in class belka.CommandParser
 
ON_VAL - Static variable in class belka.CommandParser
 
OR_VAL - Static variable in class belka.CommandParser
 
ORANGE_VAL - Static variable in class belka.CommandParser
 
ORANGERED_VAL - Static variable in class belka.CommandParser
 
ORCHID_VAL - Static variable in class belka.CommandParser
 

P

P - Static variable in class belka.chem.Element
Phosphorus
paint(Graphics) - Method in class belka.draw.MolPanel
The function painting molecules.
PALEGOLDENROD_VAL - Static variable in class belka.CommandParser
 
PALEGREEN_VAL - Static variable in class belka.CommandParser
 
PALETURQUOISE_VAL - Static variable in class belka.CommandParser
 
PALEVIOLETRED_VAL - Static variable in class belka.CommandParser
 
PAPAYAWHIP_VAL - Static variable in class belka.CommandParser
 
parseCommand() - Method in class belka.CommandParser
Parses command and returns value of the current command.
parseExpression(String) - Method in class belka.CommandParser
Parses expression stating set of atoms.
parseFile(File) - Method in class belka.parser.PDBParser
Parses PDB-file and creates a molecule.
parseFile(URL) - Method in class belka.parser.PDBParser
Parses PDB-file from URL and creates molecules.
parseWord() - Method in class belka.CommandParser
Parses all symbols from the current position till next space character.
PDB_VAL - Static variable in class belka.CommandParser
 
PDBLOAD_VAL - Static variable in class belka.CommandParser
 
PDBParser - Class in belka.parser
Object of this class parses PDB-file either from file or from URL and creates a molecule.
PDBParser() - Constructor for class belka.parser.PDBParser
 
PEACHPUFF_VAL - Static variable in class belka.CommandParser
 
PERU_VAL - Static variable in class belka.CommandParser
 
Phenylalanine - Static variable in class belka.chem.Compound
Phenylalanine
PINK_VAL - Static variable in class belka.CommandParser
 
play(String) - Method in class BelkaApplet
The function executes set of commands inputed by 'script'.
PLUM_VAL - Static variable in class belka.CommandParser
 
plus(Matrix) - Method in class Jama.Matrix
C = A + B
plusEquals(Matrix) - Method in class Jama.Matrix
A = A + B
POWDERBLUE_VAL - Static variable in class belka.CommandParser
 
prev() - Method in class belka.mol.Assembly
Returns previous assembly in list.
prev() - Method in class belka.mol.Atom
Returns previous atom in list.
prev() - Method in class belka.mol.Chain
Returns previous chain in list.
prev() - Method in class belka.mol.Molecule
Returns previous molecule in list.
print(int, double) - Method in class belka.geom.Displacer
Returns string with values of displacement for each CA atom.
print(Chain[], Chain[]) - Method in class belka.geom.RigidFinder
Function prints information about rigid blocks into a string and returns it.
print(Molecule[]) - Method in class belka.parser.PDBParser
Prints PDB-file to a string buffer.
print(int, int) - Method in class Jama.Matrix
Print the matrix to stdout.
print(PrintWriter, int, int) - Method in class Jama.Matrix
Print the matrix to the output stream.
print(NumberFormat, int) - Method in class Jama.Matrix
Print the matrix to stdout.
print(PrintWriter, NumberFormat, int) - Method in class Jama.Matrix
Print the matrix to the output stream.
PRINT_VAL - Static variable in class belka.CommandParser
 
printHessian(File) - Method in class belka.geom.NormalModeCalculator
 
printModes(File) - Method in class belka.geom.NormalModeCalculator
 
printSimple() - Method in class belka.geom.Displacer
Returns string with values of displacement for each CA atom.
processEvent(AWTEvent) - Method in class belka.draw.MolPanel
Function to process events.
PROJECT_VAL - Static variable in class belka.CommandParser
 
ProjectParser - Class in belka.parser
Object of this class load project-file either from file or URL.
ProjectParser() - Constructor for class belka.parser.ProjectParser
 
Proline - Static variable in class belka.chem.Compound
Proline
PURPLE_VAL - Static variable in class belka.CommandParser
 
Pyrrolysine - Static variable in class belka.chem.Compound
Pyrrolysine (non-standard)

Q

qr() - Method in class Jama.Matrix
QR Decomposition
QRDecomposition - Class in Jama
QR Decomposition.
QRDecomposition(Matrix) - Constructor for class Jama.QRDecomposition
QR Decomposition, computed by Householder reflections.
QUIT_VAL - Static variable in class belka.CommandParser
 

R

random(int, int) - Static method in class Jama.Matrix
Generate matrix with random elements
rank() - Method in class Jama.Matrix
Matrix rank
rank() - Method in class Jama.SingularValueDecomposition
Effective numerical matrix rank
read(BufferedReader) - Static method in class Jama.Matrix
Read a matrix from a stream.
RED_VAL - Static variable in class belka.CommandParser
 
REFINE_VAL - Static variable in class belka.CommandParser
 
removeGaps() - Method in class belka.mol.Chain
Removes assemblies that are gaps from the list of assemblies.
removeMolecule(Molecule) - Method in class belka.BelkaManager
 
removeMoleculeToDraw(Molecule) - Method in class belka.draw.MolPanel
Removes molecule from the panel.
resetGroupId(int) - Method in class belka.mol.Chain
Resets group id for assemblies in the chain to the specified value.
resolveFileFormatByExtension(String) - Static method in class belka.parser.FormatResolver
The function resolves file format by its extension.
RIBBONS_VAL - Static variable in class belka.CommandParser
 
RigidFinder - Class in belka.geom
Objects of this class perform separation of a structure into several rigid blocks.
RigidFinder() - Constructor for class belka.geom.RigidFinder
Object constructor.
RigidFinder(Chain, Chain) - Constructor for class belka.geom.RigidFinder
Object constructor.
RigidFinder(Chain[], Chain[]) - Constructor for class belka.geom.RigidFinder
Object constructor.
RIGIDS_VAL - Static variable in class belka.CommandParser
 
ROSYBROWN_VAL - Static variable in class belka.CommandParser
 
rotate(double[][], double[]) - Method in class belka.mol.Molecule
The function transforms a molecule.
ROYALBLUE_VAL - Static variable in class belka.CommandParser
 
run() - Method in class belka.BelkaManager
The function waits for user input and processes command.
runCommand(String) - Method in class belka.BelkaManager
Runs the given command and updates screen view if necesary.
runCommand(String, boolean) - Method in class belka.BelkaManager
Runs the given command and updates screen view depending on value of update.
runScript(String) - Method in class belka.BelkaManager
Runs the script of command and updates screen view if necesary.

S

S - Static variable in class belka.chem.Element
Sulphur
SADDLEBROWN_VAL - Static variable in class belka.CommandParser
 
SALMON_VAL - Static variable in class belka.CommandParser
 
SANDYBROWN_VAL - Static variable in class belka.CommandParser
 
satisfy(Molecule, Chain, Assembly, Atom) - Method in class belka.SelectExpression
Checks if specified atom from specified assembly from specified chain from specified molecule satisfies the selection.
SAVE_VAL - Static variable in class belka.CommandParser
 
saveToFile(URL, Molecule) - Method in class belka.parser.GroupParser
Saves molecules into a annotation/group file.
saveToFile(File, Molecule) - Method in class belka.parser.GroupParser
Saves molecules into a annotation/group file.
saveToFile(Molecule[], URL) - Method in class belka.parser.PDBParser
Saves moleculs into a PDB-file.
saveToFile(Molecule[], File) - Method in class belka.parser.PDBParser
Saves molecules into a PDB-file.
saveToFile(Molecule, URL) - Method in class belka.parser.ProjectParser
Saves molecules into a project-file.
saveToFile(Molecule, File) - Method in class belka.parser.ProjectParser
Saves molecules into a project-file.
Sc - Static variable in class belka.chem.Element
Scandium, using double atomic radius for van der Walls radius.
scaleToPixels() - Static method in class belka.mol.Atom
Returns scale used to transform atomic coordinates to pixel coordiantes.
Se - Static variable in class belka.chem.Element
Selenium
SEAGREEN_VAL - Static variable in class belka.CommandParser
 
SEASHELL_VAL - Static variable in class belka.CommandParser
 
SELECT_VAL - Static variable in class belka.CommandParser
 
selectAllAtoms(boolean) - Method in class belka.mol.Assembly
Select or deselect all atoms in a assembly.
selectAllAtoms(boolean) - Method in class belka.mol.Chain
Select or deselect all atoms in a chain.
selectAllAtoms(boolean) - Method in class belka.mol.Molecule
Select or deselect all atoms in a molecule.
SELECTED_VAL - Static variable in class belka.CommandParser
 
SelectExpression - Class in belka
Object of this class represents an expression stating set of atoms.
SelectExpression(boolean) - Constructor for class belka.SelectExpression
Object constructor
SelectExpression(String, String, String, String, String, boolean) - Constructor for class belka.SelectExpression
Object constructor
SelectExpression(SelectExpression, boolean) - Constructor for class belka.SelectExpression
Object constructor
Selenocysteine - Static variable in class belka.chem.Compound
Selenocysteine (non-standard)
Selenomethionine - Static variable in class belka.chem.Compound
Selenomethionine (non-standard)
SeqAligner - Class in belka.align
Objects of this class perform sequence alignemnts by Needleman-Wunsch and Smith-Waterman algorithms.
SeqAligner() - Constructor for class belka.align.SeqAligner
Contructor of SeqAligner object with default values: scoring matrix: BLOSUM62 gap open penalty: -10 gap extend penalty: -1
SeqAligner(String, int, int) - Constructor for class belka.align.SeqAligner
Contructor of SeqAligner object with specified scoring matrix, gap open penalty, and gap extend penalty.
SEQUENCE_VAL - Static variable in class belka.CommandParser
 
Serine - Static variable in class belka.chem.Compound
Serine
set(int, int, double) - Method in class Jama.Matrix
Set a single element.
SET_VAL - Static variable in class belka.CommandParser
 
setAligned(boolean) - Method in class belka.mol.Assembly
Sets assembly's alignment attribute.
setAlternative(char) - Method in class belka.mol.Atom
Sets atom's alternate location indicator.
setAssembly(Assembly) - Method in class belka.mol.Atom
Sets assembly the atom belongs to.
setAssemblyAttribute(int) - Method in class belka.SelectExpression
Sets assembly attribute.
setAtomAttribute(int) - Method in class belka.SelectExpression
Sets atom attribute.
setBounds(int, int, int, int) - Method in class belka.draw.MolPanel
Sets bounds of the panel.
setChain(Chain) - Method in class belka.mol.Assembly
Sets a chain the assembly belongs to.
setColor(Color) - Method in class belka.mol.Atom
Sets atom's color on a screen.
setColor(Color) - Method in class belka.mol.Bond
Sets bond's color on a screen.
setDerivedX(double) - Method in class belka.mol.Atom
Sets derived atom's X coordinate.
setDerivedY(double) - Method in class belka.mol.Atom
Sets derived atom's Y coordinate.
setDerivedZ(double) - Method in class belka.mol.Atom
Sets derived atom's Z coordinate.
setGapExtend(int) - Method in class belka.align.SeqAligner
Sets new value for gap extention penatly.
setGapOpen(int) - Method in class belka.align.SeqAligner
Sets new value for gap open penatly.
setGroupId(int) - Method in class belka.mol.Assembly
Sets group id for the assembly.
setICode(char) - Method in class belka.mol.Assembly
Sets assembly's icode.
setMatrix(int, int, int, int, Matrix) - Method in class Jama.Matrix
Set a submatrix.
setMatrix(int[], int[], Matrix) - Method in class Jama.Matrix
Set a submatrix.
setMatrix(int[], int, int, Matrix) - Method in class Jama.Matrix
Set a submatrix.
setMatrix(int, int, int[], Matrix) - Method in class Jama.Matrix
Set a submatrix.
setModel(int) - Method in class belka.mol.Chain
Sets chain's model number.
setMolecule(Molecule) - Method in class belka.mol.Chain
Sets a molecule the chain belongs to.
setNextAnd(SelectExpression) - Method in class belka.SelectExpression
Sets next expression and boolean operation 'and' with it.
setNextOr(SelectExpression) - Method in class belka.SelectExpression
Sets next expression and boolean operation 'or' with it.
setOccupancy(double) - Method in class belka.mol.Atom
Sets atom's occupancy.
setRadius(double) - Method in class belka.mol.Atom
Sets radius of the sphere representing the atom.
setRadius(double) - Method in class belka.mol.Bond
Sets radius of the cylinder representing the bond.
setScoringMatrix(String) - Method in class belka.align.SeqAligner
Sets new scoring matrix.
setScreenRadius(double) - Method in class belka.mol.Atom
Sets radius of the sphere representing the atom on a screen.
setScreenRadius(double) - Method in class belka.mol.Bond
Sets radius of the cylinder representing the bond on a screen.
setScreenX(double) - Method in class belka.mol.Atom
Sets atom's X coordinate on a screen.
setScreenY(double) - Method in class belka.mol.Atom
Sets atom's Y coordinate on a screen.
setScreenZ(double) - Method in class belka.mol.Atom
Sets atom's Z coordinate on a screen.
setSelected(boolean) - Method in class belka.mol.Atom
Sets atom's selection status.
setSerialNum(int) - Method in class belka.mol.Assembly
Sets assembly's serial number.
setSerialNum(int) - Method in class belka.mol.Atom
Sets atom's serial number.
setTemperature(double) - Method in class belka.mol.Atom
Sets atom's temperature factor.
setText(String) - Method in class belka.draw.InOutPanel
Sets text to display
setUserInput(String) - Method in class belka.BelkaManager
To set user input to the manager.
SHAPELY_VAL - Static variable in class belka.CommandParser
 
Si - Static variable in class belka.chem.Element
Silicon
SIENNA_VAL - Static variable in class belka.CommandParser
 
SILVER_VAL - Static variable in class belka.CommandParser
 
SingularValueDecomposition - Class in Jama
Singular Value Decomposition.
SingularValueDecomposition(Matrix) - Constructor for class Jama.SingularValueDecomposition
Construct the singular value decomposition
SKYBLUE_VAL - Static variable in class belka.CommandParser
 
SLATEBLUE_VAL - Static variable in class belka.CommandParser
 
SLATEGRAY_VAL - Static variable in class belka.CommandParser
 
SNOW_VAL - Static variable in class belka.CommandParser
 
solve(Matrix) - Method in class Jama.CholeskyDecomposition
Solve A*X = B
solve(Matrix) - Method in class Jama.LUDecomposition
Solve A*X = B
solve(Matrix) - Method in class Jama.Matrix
Solve A*X = B
solve(Matrix) - Method in class Jama.QRDecomposition
Least squares solution of A*X = B
solveTranspose(Matrix) - Method in class Jama.Matrix
Solve X*A = B, which is also A'*X' = B'
SPACEFILL_VAL - Static variable in class belka.CommandParser
 
specifiesChain(Chain) - Method in class belka.SelectExpression
Checks if given chain is explicitly specified in selection.
specifiesChainAs(Chain, int) - Method in class belka.SelectExpression
Checks if given chain is explicitly specified in selection in specific order.
specifiesMolecule(Molecule) - Method in class belka.SelectExpression
Checks if given molecule is explicitly specified in selection.
SPLIT_VAL - Static variable in class belka.CommandParser
 
SPRINGGREEN_VAL - Static variable in class belka.CommandParser
 
STEELBLUE_VAL - Static variable in class belka.CommandParser
 
STRANDS_VAL - Static variable in class belka.CommandParser
 
substract(double[], double[]) - Static method in class belka.geom.GeometryUtil
Function substracts two given vectors.
substract(double[][], double[][]) - Static method in class belka.geom.GeometryUtil
Function substracts two given matrices.
summ(double[], double[]) - Static method in class belka.geom.GeometryUtil
Function summs two given vectors.
svd() - Method in class Jama.Matrix
Singular Value Decomposition

T

TAN_VAL - Static variable in class belka.CommandParser
 
TEAL_VAL - Static variable in class belka.CommandParser
 
TEMPERATURE_VAL - Static variable in class belka.CommandParser
 
THISTLE_VAL - Static variable in class belka.CommandParser
 
Threonine - Static variable in class belka.chem.Compound
Threonine
Thymine - Static variable in class belka.chem.Compound
Thymine
Ti - Static variable in class belka.chem.Element
Titanium, using double atomic radius for van der Waals radius.
times(double) - Method in class Jama.Matrix
Multiply a matrix by a scalar, C = s*A
times(Matrix) - Method in class Jama.Matrix
Linear algebraic matrix multiplication, A * B
timesEquals(double) - Method in class Jama.Matrix
Multiply a matrix by a scalar in place, A = s*A
TOMATO_VAL - Static variable in class belka.CommandParser
 
toString() - Method in class belka.mol.Assembly
Returns string representation of the assembly.
toString() - Method in class belka.mol.Atom
Returns string representation of the atom.
toString() - Method in class belka.mol.Bond
Returns string representation of the bond.
toString() - Method in class belka.mol.Chain
Returns string representation of the chain.
toString() - Method in class belka.mol.Molecule
Returns string representation of the molecule.
trace() - Method in class Jama.Matrix
Matrix trace.
TRACE_VAL - Static variable in class belka.CommandParser
 
transform(double[][], double[], double[]) - Static method in class belka.geom.GeometryUtil
Function transforms vector by given rotation matrix and translation vectory.
transpose() - Method in class Jama.Matrix
Matrix transpose.
Tryptophan - Static variable in class belka.chem.Compound
Tryptophan
TURQUOISE_VAL - Static variable in class belka.CommandParser
 
Tyrosine - Static variable in class belka.chem.Compound
Tyrosine

U

uminus() - Method in class Jama.Matrix
Unary minus
UNLOAD_VAL - Static variable in class belka.CommandParser
 
updateAssemblyPointers() - Method in class belka.mol.Chain
The function updates pointers to the first and last assemblies belonging to the chain.
updateMoleculeView() - Method in class belka.draw.MolPanel
The function updates the view of molecules.
Uracil - Static variable in class belka.chem.Compound
Uracil

V

V - Static variable in class belka.chem.Element
Vanadium, using double atomic radius for van der Waals radius.
Valine - Static variable in class belka.chem.Compound
Valine
VDW_VAL - Static variable in class belka.CommandParser
 
VIOLET_VAL - Static variable in class belka.CommandParser
 

W

WHEAT_VAL - Static variable in class belka.CommandParser
 
WHITE_VAL - Static variable in class belka.CommandParser
 
WHITESMOKE_VAL - Static variable in class belka.CommandParser
 
WIREFRAME_VAL - Static variable in class belka.CommandParser
 

Y

YELLOW_VAL - Static variable in class belka.CommandParser
 
YELLOWGREEN_VAL - Static variable in class belka.CommandParser
 

Z

ZAP_VAL - Static variable in class belka.CommandParser
 
Zn - Static variable in class belka.chem.Element
Zinc

_

_DOUBLE_NUM_VAL - Static variable in class belka.CommandParser
 
_ERROR_VAL - Static variable in class belka.CommandParser
 
_EXPRESSION_VAL - Static variable in class belka.CommandParser
 
_INTEGER_NUM_VAL - Static variable in class belka.CommandParser
 
_INTEGER_RANGE_VAL - Static variable in class belka.CommandParser
 
_NONE_VAL - Static variable in class belka.CommandParser
 
_USERCOLOR_VAL - Static variable in class belka.CommandParser
 

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