Modifier and Type | Class and Description |
---|---|
class |
AminoAcid
A AminoAcid is Monomer which stores additional amino acid specific
informations, like the N-terminus atom.
|
class |
BioPolymer
A BioPolymer is a subclass of a Polymer which is supposed to store
additional informations about the Polymer which are connected to BioPolymers.
|
class |
Crystal
Class representing a molecular crystal.
|
class |
Molecule
Represents the concept of a chemical molecule, an object composed of
atoms connected by bonds.
|
class |
Monomer
A Monomer is an AtomContainer which stores additional monomer specific
informations for a group of Atoms.
|
class |
Polymer
Subclass of Molecule to store Polymer specific attributes that a Polymer has.
|
class |
Ring
Class representing a ring structure in a molecule.
|
class |
Strand
A Strand is an AtomContainer which stores additional strand specific
informations for a group of Atoms.
|
Modifier and Type | Class and Description |
---|---|
class |
DebugAminoAcid
Debugging data class.
|
class |
DebugAtomContainer
Debugging data class.
|
class |
DebugBioPolymer
Debugging data class.
|
class |
DebugCrystal
Debugging data class.
|
class |
DebugMolecule
Debugging data class.
|
class |
DebugMonomer
Debugging data class.
|
class |
DebugPDBMonomer
Debugging data class.
|
class |
DebugPDBPolymer
Debugging data class.
|
class |
DebugPolymer
Debugging data class.
|
class |
DebugRing
Debugging data class.
|
class |
DebugStrand
Debugging data class.
|
Modifier and Type | Method and Description |
---|---|
static void |
AtomTools.add3DCoordinates1(AtomContainer atomContainer)
Generate coordinates for all atoms which are singly bonded and have
no coordinates.
|
static javax.vecmath.Point3d[] |
AtomTools.calculate3DCoordinatesForLigands(AtomContainer atomContainer,
IAtom refAtom,
int nwanted,
double length,
double angle)
Adds 3D coordinates for singly-bonded ligands of a reference atom (A).
|
Modifier and Type | Method and Description |
---|---|
static double[] |
HuLuIndexTool.getAtomWeights(AtomContainer atomContainer) |
static double |
HuLuIndexTool.getEAIDNumber(AtomContainer atomContainer)
Calculates the extended adjacency matrix index.
|
static double[][] |
HuLuIndexTool.getExtendedAdjacenyMatrix(AtomContainer atomContainer) |
Modifier and Type | Class and Description |
---|---|
class |
QueryAtomContainer |
Modifier and Type | Class and Description |
---|---|
class |
ChargeGroup
A ChargeGroup (CG) is a numbered collection of atoms in an MDMolecule.
|
class |
MDMolecule |
class |
Residue
A residue is a named, numbered collection of atoms in an MDMolecule.
|
Modifier and Type | Class and Description |
---|---|
class |
NNAminoAcid
Deprecated.
Use the
AminoAcid instead. |
class |
NNAtomContainer
Deprecated.
Use the
AtomContainer instead. |
class |
NNBioPolymer
Deprecated.
Use the
BioPolymer instead. |
class |
NNCrystal
Deprecated.
Use the
Crystal instead. |
class |
NNMolecule
Deprecated.
Use the
Molecule instead. |
class |
NNMonomer
Deprecated.
Use the
Monomer instead. |
class |
NNPDBMonomer
Deprecated.
Use the
PDBMonomer instead. |
class |
NNPDBPolymer
Deprecated.
Use the
PDBPolymer instead. |
class |
NNPolymer
Deprecated.
Use the
Polymer instead. |
class |
NNRing
Deprecated.
Use the
Ring instead. |
class |
NNStrand
Deprecated.
Use the
Strand instead. |
Modifier and Type | Class and Description |
---|---|
class |
PharmacophoreQuery
Represents a colleciton of pharmacophore groups and constraints.
|
Modifier and Type | Class and Description |
---|---|
class |
PDBMonomer
Represents the idea of an monomer as used in PDB files.
|
class |
PDBPolymer
An entry in the PDB database.
|
class |
PDBStrand
An entry in the PDB database.
|