Package | Description |
---|---|
org.openscience.cdk | |
org.openscience.cdk.debug | |
org.openscience.cdk.graph.invariant | |
org.openscience.cdk.libio.md | |
org.openscience.cdk.protein.data |
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 |
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 |
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 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 |
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 |
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.
|
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