Modifier and Type | Class and Description |
---|---|
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 |
Molecule
Represents the concept of a chemical molecule, an object composed of
atoms connected by bonds.
|
class |
Polymer
Subclass of Molecule to store Polymer specific attributes that a Polymer has.
|
Modifier and Type | Method and Description |
---|---|
IMolecule |
Molecule.clone() |
IMolecule |
MoleculeSet.getMolecule(int number)
Returns the Molecule at position
number in the
container. |
Modifier and Type | Method and Description |
---|---|
void |
Reaction.addAgent(IMolecule agent)
Adds an agent to this reaction.
|
void |
MoleculeSet.addMolecule(IMolecule molecule)
Adds an molecule to this container.
|
void |
Reaction.addProduct(IMolecule product)
Adds a product to this reaction.
|
void |
Reaction.addProduct(IMolecule product,
Double coefficient)
Adds a product to this reaction.
|
void |
Reaction.addReactant(IMolecule reactant)
Adds a reactant to this reaction.
|
void |
Reaction.addReactant(IMolecule reactant,
Double coefficient)
Adds a reactant to this reaction with a stoichiometry coefficient.
|
Double |
Reaction.getProductCoefficient(IMolecule product)
Returns the stoichiometry coefficient of the given product.
|
Double |
Reaction.getReactantCoefficient(IMolecule reactant)
Returns the stoichiometry coefficient of the given reactant.
|
void |
MoleculeSet.setMolecules(IMolecule[] molecules) |
boolean |
Reaction.setProductCoefficient(IMolecule product,
Double coefficient)
Sets the coefficient of a a product to a given value.
|
boolean |
Reaction.setReactantCoefficient(IMolecule reactant,
Double coefficient)
Sets the coefficient of a a reactant to a given value.
|
Modifier and Type | Class and Description |
---|---|
class |
DebugBioPolymer
Debugging data class.
|
class |
DebugMolecule
Debugging data class.
|
class |
DebugPDBPolymer
Debugging data class.
|
class |
DebugPolymer
Debugging data class.
|
Modifier and Type | Method and Description |
---|---|
IMolecule |
DebugMolecule.clone() |
IMolecule |
DebugMoleculeSet.getMolecule(int number) |
Modifier and Type | Method and Description |
---|---|
void |
DebugReaction.addAgent(IMolecule agent) |
void |
DebugMoleculeSet.addMolecule(IMolecule molecule) |
void |
DebugReaction.addProduct(IMolecule product) |
void |
DebugReaction.addProduct(IMolecule product,
Double coefficient) |
void |
DebugReaction.addReactant(IMolecule reactant) |
void |
DebugReaction.addReactant(IMolecule reactant,
Double coefficient) |
Double |
DebugReaction.getProductCoefficient(IMolecule product) |
Double |
DebugReaction.getReactantCoefficient(IMolecule reactant) |
void |
DebugMoleculeSet.setMolecules(IMolecule[] molecules) |
boolean |
DebugReaction.setProductCoefficient(IMolecule product,
Double coefficient) |
boolean |
DebugReaction.setReactantCoefficient(IMolecule reactant,
Double coefficient) |
Modifier and Type | Method and Description |
---|---|
static double |
VABCVolume.calculate(IMolecule molecule)
Calculates the volume for the given
IMolecule . |
Modifier and Type | Method and Description |
---|---|
static void |
PathTools.breadthFirstSearch(IAtomContainer atomContainer,
List<IAtom> sphere,
IMolecule molecule)
Performs a breadthFirstSearch in an AtomContainer starting with a
particular sphere, which usually consists of one start atom.
|
static void |
PathTools.breadthFirstSearch(IAtomContainer atomContainer,
List<IAtom> sphere,
IMolecule molecule,
int max)
Performs a breadthFirstSearch in an AtomContainer starting with a
particular sphere, which usually consists of one start atom.
|
Modifier and Type | Interface and Description |
---|---|
interface |
IBioPolymer
A BioPolymer is a subclass of a Polymer which is supposed to store
additional informations about the Polymer which are connected to BioPolymers.
|
interface |
IPDBPolymer
A PDBPolymer is a subclass of a BioPolymer which is supposed to store
additional informations about the BioPolymer which are connected to BioPolymers.
|
interface |
IPolymer
Subclass of Molecule to store Polymer specific attributes that a Polymer has.
|
Modifier and Type | Method and Description |
---|---|
IMolecule |
IMolecule.clone() |
IMolecule |
IMoleculeSet.getMolecule(int number)
Returns the Molecule at position
number in the
container. |
Modifier and Type | Method and Description |
---|---|
void |
IReaction.addAgent(IMolecule agent)
Adds an agent to this reaction.
|
void |
IMoleculeSet.addMolecule(IMolecule molecule)
Adds an IMolecule to this container.
|
void |
IReaction.addProduct(IMolecule product)
Adds a product to this reaction.
|
void |
IReaction.addProduct(IMolecule product,
Double coefficient)
Adds a product to this reaction.
|
void |
IReaction.addReactant(IMolecule reactant)
Adds a reactant to this reaction.
|
void |
IReaction.addReactant(IMolecule reactant,
Double coefficient)
Adds a reactant to this reaction with a stoichiometry coefficient.
|
Double |
IReaction.getProductCoefficient(IMolecule product)
Returns the stoichiometry coefficient of the given product.
|
Double |
IReaction.getReactantCoefficient(IMolecule reactant)
Returns the stoichiometry coefficient of the given reactant.
|
void |
IMoleculeSet.setMolecules(IMolecule[] molecules)
Sets the molecules in the IMoleculeSet, removing previously added
IMolecule's.
|
boolean |
IReaction.setProductCoefficient(IMolecule product,
Double coefficient)
Sets the coefficient of a a product to a given value.
|
boolean |
IReaction.setReactantCoefficient(IMolecule reactant,
Double coefficient)
Sets the coefficient of a a reactant to a given value.
|
Modifier and Type | Method and Description |
---|---|
IMolecule |
MDLV3000Reader.readMolecule(IChemObjectBuilder builder) |
Modifier and Type | Method and Description |
---|---|
void |
XYZWriter.writeMolecule(IMolecule mol)
writes a single frame in XYZ format to the Writer.
|
void |
SMILESWriter.writeMolecule(IMolecule molecule)
Writes the content from molecule to output.
|
void |
PDBWriter.writeMolecule(IMolecule molecule)
Writes a single frame in PDB format to the Writer.
|
void |
Mol2Writer.writeMolecule(IMolecule mol)
Writes a single frame in XYZ format to the Writer.
|
Modifier and Type | Method and Description |
---|---|
void |
GaussianInputWriter.writeMolecule(IMolecule mol)
Writes a molecule for input for Gaussian.
|
Modifier and Type | Method and Description |
---|---|
IMolecule |
PubChemXMLHelper.parseMolecule(org.xmlpull.v1.XmlPullParser parser,
IChemObjectBuilder builder) |
Modifier and Type | Method and Description |
---|---|
void |
PubChemXMLHelper.parseAtomCharges(org.xmlpull.v1.XmlPullParser parser,
IMolecule molecule) |
void |
PubChemXMLHelper.parseAtomElements(org.xmlpull.v1.XmlPullParser parser,
IMolecule molecule) |
void |
PubChemXMLHelper.parserAtomBlock(org.xmlpull.v1.XmlPullParser parser,
IMolecule molecule) |
void |
PubChemXMLHelper.parserBondBlock(org.xmlpull.v1.XmlPullParser parser,
IMolecule molecule) |
void |
PubChemXMLHelper.parserCompoundInfoData(org.xmlpull.v1.XmlPullParser parser,
IMolecule molecule) |
void |
PubChemXMLHelper.parserCoordBlock(org.xmlpull.v1.XmlPullParser parser,
IMolecule molecule) |
Modifier and Type | Method and Description |
---|---|
boolean |
IsomorphismTester.isIsomorphic(IMolecule mol2)
Checks whether a given molecule is isomorphic with the one
that has been assigned to this IsomorphismTester at contruction time
|
boolean |
IsomorphismTester.isIsomorphic(IMolecule mol1,
IMolecule mol2)
Checks whether a given molecule is isomorphic with the one
that has been assigned to this IsomorphismTester at contruction time
|
Constructor and Description |
---|
IsomorphismTester(IMolecule mol)
Constructor for the IsomorphismTester object
|
Modifier and Type | Method and Description |
---|---|
IMolecule |
StructureDiagramGenerator.getMolecule()
Returns the molecule, usually used after a call of generateCoordinates()
|
IMolecule |
RingPlacer.getMolecule() |
Modifier and Type | Method and Description |
---|---|
IAtomContainer |
AtomPlacer.getInitialLongestChain(IMolecule molecule)
Search an aliphatic molecule for the longest chain.
|
IAtomContainer |
AtomPlacer.getLongestUnplacedChain(IMolecule molecule,
IAtom startAtom)
Search a molecule for the longest unplaced, aliphatic chain in it.
|
void |
StructureDiagramGenerator.setMolecule(IMolecule molecule)
Assings a molecule to be layed out.
|
void |
RingPlacer.setMolecule(IMolecule molecule) |
void |
StructureDiagramGenerator.setMolecule(IMolecule mol,
boolean clone)
Assings a molecule to be layed out.
|
Constructor and Description |
---|
StructureDiagramGenerator(IMolecule molecule)
Creates an instance of this class while assigning a molecule to be layed
out.
|
Modifier and Type | Method and Description |
---|---|
org.xmlcml.cml.element.CMLMolecule |
Convertor.cdkMoleculeToCMLMolecule(IMolecule structure) |
Modifier and Type | Method and Description |
---|---|
static IMolecule |
Convertor.model2Molecule(com.hp.hpl.jena.rdf.model.Model model,
IChemObjectBuilder builder)
|
Modifier and Type | Method and Description |
---|---|
static com.hp.hpl.jena.rdf.model.Model |
Convertor.molecule2Model(IMolecule molecule)
Converts a
IMolecule into a Model representation using the CDK OWL. |
Modifier and Type | Class and Description |
---|---|
class |
MDMolecule |
Modifier and Type | Method and Description |
---|---|
IMolecule |
ModelBuilder3D.generate3DCoordinates(IMolecule molecule,
boolean clone)
Generate 3D coordinates with force field information.
|
IMolecule |
TemplateExtractor.removeLoopBonds(IMolecule molecule,
int position) |
Modifier and Type | Method and Description |
---|---|
IRingSet |
ForceFieldConfigurator.assignAtomTyps(IMolecule molecule)
Method assigns atom types to atoms (calculates sssr and aromaticity)
|
IMolecule |
ModelBuilder3D.generate3DCoordinates(IMolecule molecule,
boolean clone)
Generate 3D coordinates with force field information.
|
IMolecule |
TemplateExtractor.removeLoopBonds(IMolecule molecule,
int position) |
Modifier and Type | Class and Description |
---|---|
class |
NNBioPolymer
Deprecated.
Use the
BioPolymer instead. |
class |
NNMolecule
Deprecated.
Use the
Molecule instead. |
class |
NNPDBPolymer
Deprecated.
Use the
PDBPolymer instead. |
class |
NNPolymer
Deprecated.
Use the
Polymer instead. |
Modifier and Type | Method and Description |
---|---|
static IMolecule |
SMSDNormalizer.makeDeepCopy(IAtomContainer container)
Returns deep copy of the molecule
|
Modifier and Type | Class and Description |
---|---|
class |
PDBPolymer
An entry in the PDB database.
|
Constructor and Description |
---|
MoleculeSignature(IMolecule molecule,
int height)
Creates a signature with a maximum height of
height
for molecule molecule . |
Modifier and Type | Method and Description |
---|---|
IMolecule |
Molecule.clone() |
IMolecule |
MoleculeSet.getMolecule(int number)
Returns the Molecule at position
number in the
container. |
Modifier and Type | Method and Description |
---|---|
void |
Reaction.addAgent(IMolecule agent)
Adds an agent to this reaction.
|
void |
MoleculeSet.addMolecule(IMolecule molecule)
Adds an molecule to this container.
|
void |
Reaction.addProduct(IMolecule product)
Adds a product to this reaction.
|
void |
Reaction.addProduct(IMolecule product,
Double coefficient)
Adds a product to this reaction.
|
void |
Reaction.addReactant(IMolecule reactant)
Adds a reactant to this reaction.
|
void |
Reaction.addReactant(IMolecule reactant,
Double coefficient)
Adds a reactant to this reaction with a stoichiometry coefficient.
|
Double |
Reaction.getProductCoefficient(IMolecule product)
Returns the stoichiometry coefficient of the given product.
|
Double |
Reaction.getReactantCoefficient(IMolecule reactant)
Returns the stoichiometry coefficient of the given reactant.
|
void |
MoleculeSet.setMolecules(IMolecule[] molecules) |
boolean |
Reaction.setProductCoefficient(IMolecule product,
Double coefficient)
Sets the coefficient of a a product to a given value.
|
boolean |
Reaction.setReactantCoefficient(IMolecule reactant,
Double coefficient)
Sets the coefficient of a a reactant to a given value.
|
Modifier and Type | Method and Description |
---|---|
IMolecule |
DeduceBondSystemTool.fixAromaticBondOrders(IMolecule molecule)
Added missing bond orders based on atom type information.
|
IMolecule |
FixBondOrdersTool.kekuliseAromaticRings(IMolecule molecule)
kekuliseAromaticRings - function to add double/single bond order information for molecules having rings containing all atoms marked SP2 or Planar3 hybridisation.
|
IMolecule |
SmilesParser.parseSmiles(String smiles)
Parses a SMILES string and returns a Molecule object.
|
Modifier and Type | Method and Description |
---|---|
IMolecule |
DeduceBondSystemTool.fixAromaticBondOrders(IMolecule molecule)
Added missing bond orders based on atom type information.
|
boolean |
DeduceBondSystemTool.isOK(IMolecule m)
Determines if, according to the algorithms implemented in this class, the given
molecule has properly distributed double bonds.
|
IMolecule |
FixBondOrdersTool.kekuliseAromaticRings(IMolecule molecule)
kekuliseAromaticRings - function to add double/single bond order information for molecules having rings containing all atoms marked SP2 or Planar3 hybridisation.
|
Modifier and Type | Method and Description |
---|---|
void |
Isomorphism.init(IMolecule reactant,
IMolecule product,
boolean removeHydrogen,
boolean cleanAndConfigureMolecule)
initialize query and target molecules.
|
Modifier and Type | Method and Description |
---|---|
abstract void |
AbstractMCS.init(IMolecule source,
IMolecule target,
boolean removeHydrogen,
boolean cleanAndConfigureMolecule)
initialize query and target molecules.
|
Modifier and Type | Method and Description |
---|---|
static IMolecule |
ExtAtomContainerManipulator.makeDeepCopy(IMolecule container)
Retrurns deep copy of the molecule
|
static IMolecule |
ExtAtomContainerManipulator.removeHydrogensExceptSingleAndPreserveAtomID(IAtomContainer atomContainer)
Returns IAtomContainer without Hydrogen.
|
Modifier and Type | Method and Description |
---|---|
static IMolecule |
ExtAtomContainerManipulator.makeDeepCopy(IMolecule container)
Retrurns deep copy of the molecule
|
Modifier and Type | Method and Description |
---|---|
IMolecule |
SingleStructureRandomGenerator.generate()
Generates a random structure based on the atoms in the given IAtomContainer.
|
IMolecule |
RandomGenerator.getMolecule()
Returns the molecule which reflects the current state of this
stochastic structure generator.
|
IMolecule |
RandomGenerator.proposeStructure()
Proposes a structure which can be accepted or rejected by an external
entity.
|
Modifier and Type | Method and Description |
---|---|
static List |
VicinitySampler.sample(IMolecule ac)
Choose any possible quadruple of the set of atoms
in ac and establish all of the possible bonding schemes according to
Faulon's equations.
|
void |
RandomGenerator.setMolecule(IMolecule molecule)
Assigns a starting structure to this generator.
|
Constructor and Description |
---|
RandomGenerator(IMolecule molecule)
Constructs a RandomGenerator with a given starting structure.
|
Modifier and Type | Method and Description |
---|---|
static IMolecule |
MoleculeFactory.loadMolecule(String inFile) |
static IMolecule |
MoleculeFactory.makeAdenine() |
Modifier and Type | Method and Description |
---|---|
IRingSet |
AtomTypeTools.assignAtomTypePropertiesToAtom(IMolecule molecule) |
IRingSet |
AtomTypeTools.assignAtomTypePropertiesToAtom(IMolecule molecule,
boolean aromaticity)
Method assigns certain properties to an atom.
|
static void |
CDKUtilities.fixAromaticityForXLogP(IMolecule m) |
static boolean |
CDKUtilities.fixNitroGroups2(IMolecule m) |
static void |
CDKUtilities.fixSulphurH(IMolecule m) |
IAtomContainer |
StructureResonanceGenerator.getContainer(IMolecule molecule,
IAtom atom)
Get the container which the atom is found on resonance from a IMolecule.
|
IAtomContainer |
StructureResonanceGenerator.getContainer(IMolecule molecule,
IBond bond)
Get the container which the bond is found on resonance from a IMolecule.
|
IAtomContainerSet |
StructureResonanceGenerator.getContainers(IMolecule molecule)
Get the container which is found resonance from a IMolecule.
|
List<IAtom>[] |
HOSECodeGenerator.getSpheres(IMolecule ac,
IAtom root,
int noOfSpheres,
boolean ringsize)
This method is intended to be used to get the atoms around an atom in spheres.
|
IMoleculeSet |
StructureResonanceGenerator.getStructures(IMolecule molecule)
Get the resonance structures from an IMolecule.
|
static int |
DataFeaturesTool.getSupportedDataFeatures(IMolecule molecule)
Determines the features present in the given IMolecule.
|
Modifier and Type | Method and Description |
---|---|
static boolean |
MoleculeFeaturesTool.hasElementSymbols(IMolecule molecule) |
static boolean |
MoleculeFeaturesTool.hasFormalCharges(IMolecule molecule) |
static boolean |
MoleculeFeaturesTool.hasGraphRepresentation(IMolecule molecule)
Checks whether all bonds have exactly two atoms.
|
static boolean |
MoleculeFeaturesTool.hasPartialCharges(IMolecule molecule) |
Modifier and Type | Method and Description |
---|---|
static ArrayList<IMoleculeSet> |
ReactionSchemeManipulator.getMoleculeSet(IMolecule origenMol,
IMolecule finalMol,
IReactionScheme reactionScheme)
Extract the list of molecules taking part in the IReactionScheme to originate a
product given a reactant.
|
Modifier and Type | Method and Description |
---|---|
ValidationReport |
ValidatorEngine.validateMolecule(IMolecule subject) |
ValidationReport |
IValidator.validateMolecule(IMolecule subject) |
ValidationReport |
BasicValidator.validateMolecule(IMolecule subject) |
ValidationReport |
AbstractValidator.validateMolecule(IMolecule subject) |