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

A

abort() - Method in class moss.Miner
Abort the miner (if running as a thread).
ACTINIUM - Static variable in class moss.AtomTypeMgr
 
adapt(CanonicalForm, boolean) - Method in class moss.Fragment
Adapt the fragment (limited reordering of the edges and nodes).
ADAPTED - Static variable in class moss.Fragment
flag for an adapted fragment; this flag is set when a fragment gets adapted, so that the adaptation is not repeated
adaptRing(Fragment, boolean) - Method in class moss.CanonicalForm
Reorder the edges of a fragment with a ring extension.
adaptRing(Fragment, boolean) - Method in class moss.CnFBreadth1
Reorder the edges of a fragment with a ring extension.
adaptRing(Fragment, boolean) - Method in class moss.CnFBreadth2
Reorder the edges of a fragment with a ring extension.
adaptRing(Fragment, boolean) - Method in class moss.CnFDepth
Reorder the edges of a fragment with a ring extension.
add(String) - Method in class moss.AtomTypeMgr
Add an atom type.
add(String) - Method in class moss.BondTypeMgr
Add a bond type.
add(Edge) - Method in class moss.ExtMgr
Add an extension edge.
add(String) - Method in class moss.FreeTypeMgr
Add a type to the type map.
add(Component, GridBagConstraints) - Method in class moss.MoSSPanel
Add a component.
add(Embedding) - Method in class moss.OverlapGraph
Add an embedding to the overlap graph.
add(int) - Method in class moss.Recoder
Add a type to the recoder.
add(String) - Method in class moss.TypeMgr
Add a type to the type manager.
addButton(String) - Method in class moss.MoSSPanel
Add a button to a tab.
addButton(String, GridBagConstraints) - Method in class moss.MoSSPanel
Add a button to a tab.
addCheckBox(boolean) - Method in class moss.MoSSPanel
Add a check box to a tab.
addCheckBox(boolean, GridBagConstraints) - Method in class moss.MoSSPanel
Add a check box to a tab.
addComboBox(String[]) - Method in class moss.MoSSPanel
Add a combo box to a tab.
addComboBox(String[], GridBagConstraints) - Method in class moss.MoSSPanel
Add a combo box to a tab.
addEdge(int, int, int) - Method in class moss.Graph
Add an edge to the graph.
addEdge(Edge) - Method in class moss.Node
Add an edge to a node.
addEmb(Embedding) - Method in class moss.Fragment
Add an embedding (list) to the fragment.
addEmb(CanonicalForm) - Method in class moss.Fragment
Add an extension (as an embedding) to the fragment.
addFileInput(String) - Method in class moss.MoSSPanel
Add a file input field to a tab.
addFileInput(String, GridBagConstraints) - Method in class moss.MoSSPanel
Add a text input field to a tab.
addFiller(int) - Method in class moss.MoSSPanel
Add a filler.
addGraph(NamedGraph) - Method in class moss.Fragment
Add a graph to the cover of the fragment.
addGraph(NamedGraph) - Method in class moss.Miner
Add a graph to the database.
addHelp(String) - Method in class moss.MoSSPanel
Add a help text.
addLabel(String) - Method in class moss.MoSSPanel
Add a label to a tab.
addLabel(String, GridBagConstraints) - Method in class moss.MoSSPanel
Add a label to a tab.
addNode(int) - Method in class moss.Graph
Add a node to the graph, encode type if needed.
addNodeRaw(int) - Method in class moss.Graph
Add a node to the graph, do not encode the type.
addNumberInput(String) - Method in class moss.MoSSPanel
Add a text input field to a tab.
addNumberInput(String, GridBagConstraints) - Method in class moss.MoSSPanel
Add a text input field to a tab.
addSpinner(int, int, int, int) - Method in class moss.MoSSPanel
Add a spinner to a tab.
addSpinner(int, int, int, int, GridBagConstraints) - Method in class moss.MoSSPanel
Add a combo box to a tab.
addTextInput(String) - Method in class moss.MoSSPanel
Add a text input field to a tab.
addTextInput(String, GridBagConstraints) - Method in class moss.MoSSPanel
Add a text input field to a tab.
all - Variable in class moss.CanonicalForm
all (remaining) ring flags of the current edge
ALLEXTS - Static variable in class moss.CanonicalForm
extension mode flag: generate all extensions
ALLEXTS - Static variable in class moss.Miner
flag for generating all extensions
ALLORBS - Static variable in class moss.CanonicalForm
extension mode flag: use node orbits for all extensions; not only those leading to a new node
ALUMINUM - Static variable in class moss.AtomTypeMgr
 
AMERICUM - Static variable in class moss.AtomTypeMgr
 
ANTIMONY - Static variable in class moss.AtomTypeMgr
 
ARGON - Static variable in class moss.AtomTypeMgr
 
AROMATIC - Static variable in class moss.AtomTypeMgr
the flag indicating whether an atom is part of an aromatic ring
AROMATIC - Static variable in class moss.BondTypeMgr
bond type: aromatic
aromatize(Graph) - Static method in class moss.BondTypeMgr
Convert Kekulé representations to true aromatic rings.
AROMATIZE - Static variable in class moss.Miner
flag for converting Kekulé representations
ARSENIC - Static variable in class moss.AtomTypeMgr
 
ASTATINE - Static variable in class moss.AtomTypeMgr
 
AtomTypeMgr - Class in moss
Class for an atom type manager.
AtomTypeMgr() - Constructor for class moss.AtomTypeMgr
Create an atom type manager.

B

BARIUM - Static variable in class moss.AtomTypeMgr
 
base - Variable in class moss.Fragment
the base fragment (which was extended)
BASEMASK - Static variable in class moss.TypeMgr
the mask for the base type
bemb - Variable in class moss.Fragment
the current base embedding (which was extended)
BERKELIUM - Static variable in class moss.AtomTypeMgr
 
BERYLLIUM - Static variable in class moss.AtomTypeMgr
 
bins - Variable in class moss.ExtMgr
the hash table of the extension edges
bins - Variable in class moss.Miner
the repository of processed substructures (hash table)
BISMUTH - Static variable in class moss.AtomTypeMgr
 
BLANK - Static variable in class moss.TableReader
class/type flag: blank character
BOHRIUM - Static variable in class moss.AtomTypeMgr
 
BOLD - Static variable in class moss.MoSSPanel
the font for input text fields
BONDMASK - Static variable in class moss.BondTypeMgr
a mask for the type of a bond
BondTypeMgr - Class in moss
Class for a bond type manager.
BondTypeMgr() - Constructor for class moss.BondTypeMgr
Create a bond type manager.
BORON - Static variable in class moss.AtomTypeMgr
 
BRIDGE - Static variable in class moss.Edge
the mask to extract the bridge flag
BROMINE - Static variable in class moss.AtomTypeMgr
 

C

cabs - Variable in class moss.GraphReader
the absolute support in the complement
cabs - Variable in class moss.GraphWriter
the absolute support in the complement
CADMIUM - Static variable in class moss.AtomTypeMgr
 
CALCIUM - Static variable in class moss.AtomTypeMgr
 
CALIFORNIUM - Static variable in class moss.AtomTypeMgr
 
canonic - Variable in class moss.Miner
for benchmarking: canonical form pruning counter
CanonicalForm - Class in moss
Class for canonical forms of graphs and their restricted extensions.
CanonicalForm() - Constructor for class moss.CanonicalForm
Create a canonical form object.
CARBON - Static variable in class moss.AtomTypeMgr
 
cedge - Variable in class moss.CanonicalForm
the edge type for chain extensions
CERIUM - Static variable in class moss.AtomTypeMgr
 
CESIUM - Static variable in class moss.AtomTypeMgr
 
CHAIN - Static variable in class moss.CanonicalForm
extension mode flag: variable length chain
chain() - Method in class moss.CanonicalForm
Create a variable length chain extension.
CHAIN - Static variable in class moss.Fragment
flag for the result of an extension that is a chain start
CHAIN - Static variable in class moss.Node
the flag for a chain node (representing several equal nodes)
CHAINEXT - Static variable in class moss.Miner
flag for extensions by chains
chains - Variable in class moss.Miner
for benchmarking: invalid chains counter
chainsValid() - Method in class moss.Fragment
Check whether all variable length chains are valid.
CHARGEMASK - Static variable in class moss.AtomTypeMgr
the mask for extracting the charge from an atom type
CHARGESHIFT - Static variable in class moss.AtomTypeMgr
the shift value for extracting the charge from an atom type
chcnt - Variable in class moss.CanonicalForm
the number of variable length chains
chcnt - Variable in class moss.Fragment
the number of variable length chains
CHLORINE - Static variable in class moss.AtomTypeMgr
 
CHROMIUM - Static variable in class moss.AtomTypeMgr
 
CLASSES - Static variable in class moss.CanonicalForm
extension mode flag: use node equivalence classes
CLASSES - Static variable in class moss.Miner
flag for using node equivalence classes
clear() - Method in class moss.FreeTypeMgr
Clear the type map (remove all types).
clear() - Method in class moss.Graph
Clear a graph (remove all nodes and edges).
clear() - Method in class moss.OverlapGraph
Clear an overlap graph (remove all embeddings).
clear(int) - Method in class moss.Recoder
Clear the frequency and support of a type.
clearRings() - Method in class moss.Edge
Clear the ring flags of the edge.
clone() - Method in class moss.Graph
Create a clone of the graph.
clone() - Method in class moss.NamedGraph
Create a clone of this named graph.
CLOSED - Static variable in class moss.Fragment
flag for a closed fragment (no super-fragment has the same support)
CLOSED - Static variable in class moss.Miner
flag for restriction to closed fragments
CLOSERINGS - Static variable in class moss.Miner
flag for filtering open rings
cnf - Variable in class moss.Miner
the canonical form and restricted extension generator
CnFBreadth1 - Class in moss
Class for breadth-first search spanning tree canonical form and the corresponding maximum source extensions.
CnFBreadth1() - Constructor for class moss.CnFBreadth1
Create a breadth-first search spanning tree canonical form.
CnFBreadth2 - Class in moss
Class for breadth-first search spanning tree canonical form and the corresponding maximum source extensions.
CnFBreadth2() - Constructor for class moss.CnFBreadth2
Create a breadth-first search spanning tree canonical form.
CnFDepth - Class in moss
Class for a depth-first search spanning tree canonical form and the corresponding rightmost path extensions.
CnFDepth() - Constructor for class moss.CnFDepth
Create a depth-first search spanning tree canonical form.
cnode - Variable in class moss.CanonicalForm
the node type for chain extensions
cnt - Variable in class moss.ExtMgr
the number of extension edges
cnt - Variable in class moss.Fragment
the number of embeddings/graphs for the current graph
cnt - Variable in class moss.Notation
the number of unread/pushed back characters
cnts - Variable in class moss.Miner
the numbers of graphs in focus and complement
COBALT - Static variable in class moss.AtomTypeMgr
 
codeCharge(int) - Static method in class moss.AtomTypeMgr
Encode a charge for addition to an atom type.
codeHydros(int) - Static method in class moss.AtomTypeMgr
Encode hydrogens for addition to an atom type.
coder - Variable in class moss.Graph
an optional node type recoder
coder - Variable in class moss.Miner
the recoder for the node types
COMMENT - Static variable in class moss.TableReader
class/type flag: comment character
commit() - Method in class moss.Recoder
Commit a type code counting.
common(Embedding) - Method in class moss.Embedding
Find the (maximum) length of a common edge array prefix.
comp - Variable in class moss.Miner
the maximum support in the complement as an absolute value
compareEdge(Edge, Edge, int) - Method in class moss.CanonicalForm
Compare two edges with the precedence order of the canonical form.
compareEdge(Edge, Edge, int) - Method in class moss.CnFBreadth1
Compare two edges with the precedence order of the canonical form.
compareEdge(Edge, Edge, int) - Method in class moss.CnFBreadth2
Compare two edges with the precedence order of the canonical form.
compareEdge(Edge, Edge, int) - Method in class moss.CnFDepth
Compare two edges with the precedence order of the canonical form.
compareRing(Fragment) - Method in class moss.CanonicalForm
Compare the current ring extension to a fragment.
compareTo(Edge) - Method in class moss.Edge
Compare two edges (w.r.t.
compareTo(ExtList) - Method in class moss.ExtList
Compare to another extension list element.
compareTo(Node) - Method in class moss.Node
Compare two nodes (w.r.t.
compareToFrag(Fragment) - Method in class moss.CanonicalForm
Compare the current extension to a given fragment.
compareToFrag(Fragment) - Method in class moss.CnFBreadth1
Compare the current extension to a given fragment.
compareToFrag(Fragment) - Method in class moss.CnFBreadth2
Compare the current extension to a given fragment.
compareToFrag(Fragment) - Method in class moss.CnFDepth
Compare the current extension to a given fragment.
compareWord(Graph) - Method in class moss.CanonicalForm
Compare the current code word to the one of the given graph.
compareWord(Graph, int) - Method in class moss.CanonicalForm
Compare the current code word to the one of the given graph.
compareWord(Edge[], int) - Method in class moss.CanonicalForm
Compare the current code word to the one of the given edge array.
compareWord(Edge[], int) - Method in class moss.CnFBreadth1
Compare the current code word to the one of the given edge array.
compareWord(Edge[], int) - Method in class moss.CnFBreadth2
Compare the current code word to the one of the given edge array.
compareWord(Edge[], int) - Method in class moss.CnFDepth
Compare the current code word to the one of the given edge array.
COMPL - Static variable in class moss.Fragment
group identifier: complement
COMPL - Static variable in class moss.NamedGraph
group identifier: complement
computeSupport(int) - Method in class moss.Fragment
Compute the support of the fragment.
contains(int) - Method in class moss.Graph
Check whether a node type is contained in this graph.
contains(Graph) - Method in class moss.Graph
Check whether a graph is contained in this graph.
COPERNICIUM - Static variable in class moss.AtomTypeMgr
 
COPPER - Static variable in class moss.AtomTypeMgr
 
COPYRIGHT - Static variable in class moss.Miner
the copyright information for this program
costs - Variable in class moss.MaxComSub
the costs of the best sequence of edit operations transforming graph 1 into graph 2
count(int) - Method in class moss.Recoder
Count a type code.
cover - Variable in class moss.Fragment
the graph cover of the fragment
createCnF(String) - Static method in class moss.CanonicalForm
Create an extension object corresponding to a given name.
createNotation(String) - Static method in class moss.Notation
Create a graph notation corresponding to a given name.
createNumberInput(String) - Static method in class moss.MoSSPanel
Create a number input field.
createReader(Reader, int, String) - Static method in class moss.GraphReader
Create a graph reader for a given format and mode.
createWriter(Writer, int, String) - Static method in class moss.GraphWriter
Create a graph writer for a given format and mode.
crel - Variable in class moss.GraphReader
the relative support in the complement
crel - Variable in class moss.GraphWriter
the relative support in the complement
Ctab - Class in moss
Class for the connection table notation (Ctab, Elsevier MDL).
Ctab() - Constructor for class moss.Ctab
Create a connection table notation.
CURIUM - Static variable in class moss.AtomTypeMgr
 
curr - Variable in class moss.CanonicalForm
the current ring flag
curr - Variable in class moss.ExtMgr
the current extension edge
curr - Variable in class moss.Fragment
the current embedding (cursor)
curr - Variable in class moss.Miner
the current insertion point for the focus

D

DARMSTADTIUM - Static variable in class moss.AtomTypeMgr
 
decode() - Method in class moss.Graph
Decode the node types.
decode(Recoder) - Method in class moss.Node
Decode the node type.
decode(int) - Method in class moss.Recoder
Decode a type code, that is, retrieve the original type value.
DEFAULT - Static variable in class moss.Fragment
default flags that are set when a fragment is created
DEFAULT - Static variable in class moss.Miner
default search mode flags: edge extensions, embeddings, canonical form and full perfect extension pruning
deg - Variable in class moss.Node
the current number of incident edges (node degree)
desc - Variable in class moss.GraphReader
the description of the current graph
desc - Variable in class moss.GraphWriter
the description of the current graph
desc - Variable in class moss.MoleculeNtn
the buffer for creating molecule descriptions
describe(Graph) - Method in class moss.CanonicalForm
Create the code word for a given graph as a string.
describe(Graph, boolean) - Method in class moss.CanonicalForm
Create the code word for a given graph as a string.
describe(Graph, boolean) - Method in class moss.CnFBreadth1
Create the code word for a given graph as a string.
describe(Graph, boolean) - Method in class moss.CnFBreadth2
Create the code word for a given graph as a string.
describe(Graph, boolean) - Method in class moss.CnFDepth
Create the code word for a given graph as a string.
describe(Graph) - Method in class moss.Ctab
Create a description of a given molecule.
describe(Graph) - Method in class moss.LiNoG
Create a description of a given attributed graph.
describe(Graph) - Method in class moss.NEList
Create a string description of a graph.
describe(Graph) - Method in class moss.Notation
Create a string description of a graph.
describe(Graph) - Method in class moss.SLN
Create a description of a given molecule.
describe(Graph) - Method in class moss.SMILES
Create a string description of a molecule.
DESCRIPTION - Static variable in class moss.Miner
the program description
DOUBLE - Static variable in class moss.BondTypeMgr
bond type: double
DOWNGRADE - Static variable in class moss.BondTypeMgr
a mask, to be anded (bitwise &) with a bond type in order to downgrade an aromatic bond to a single bond
dst - Variable in class moss.CanonicalForm
the index of the current destination node
dst - Variable in class moss.Edge
the destination node of the edge
dst - Variable in class moss.ExtList
the index of the destination node
dst - Variable in class moss.Fragment
the index of the destination node of the (first) new edge
DUBNIUM - Static variable in class moss.AtomTypeMgr
 
duplic - Variable in class moss.Miner
for benchmarking: duplicate fragments counter
DYSPROSIUM - Static variable in class moss.AtomTypeMgr
 

E

EDGE - Static variable in class moss.CanonicalForm
extension mode flag: single edge
Edge - Class in moss
Class for edges of an attributed (labeled/typed) graph.
Edge(Node, Node, int) - Constructor for class moss.Edge
Create an edge of a given type between two nodes.
Edge(Node, Node, int, long) - Constructor for class moss.Edge
Create an edge of a given type between two nodes.
edge - Variable in class moss.ExtList
the type of the extension edge
edgecnt - Variable in class moss.CanonicalForm
the number of new edges
edgecnt - Variable in class moss.Graph
the current number of edges (may be smaller than the array length)
EDGEEXT - Static variable in class moss.Miner
flag for extensions by single edges
edgemap - Variable in class moss.MaxComSub
the mapping of the edges of graph 1 to graph 2
edgemgr - Variable in class moss.Notation
the manager for the edge types
edges - Variable in class moss.CanonicalForm
(relevant) edges of the extension
edges - Variable in class moss.Embedding
the array of edges (only references to the underlying graph)
edges - Variable in class moss.Graph
the array of edges (may be only partially used)
edges - Variable in class moss.GraphReader
the number of edges of the current graph
edges - Variable in class moss.GraphWriter
the number of edges of the current graph
edges - Variable in class moss.Node
the array of incident edges (may not be fully used)
EINSTEINIUM - Static variable in class moss.AtomTypeMgr
 
ELEMCNT - Static variable in class moss.AtomTypeMgr
the number of chemical elements (not all actually exist)
ELEMENTS - Static variable in class moss.AtomTypeMgr
the periodic table of elements; using the chemical element as an index for this table yields a printable element name
ELEMMASK - Static variable in class moss.AtomTypeMgr
the mask for the chemical element of an atom
emap - Variable in class moss.CanonicalForm
the edge map for making a graph canonic
emb - Variable in class moss.CanonicalForm
the embedding that is extended (may be null)
embcmp - Variable in class moss.Miner
for benchmarking: the number of comparisons with embeddings
embcnt - Variable in class moss.Miner
for benchmarking: the number of created embeddings
embed(int) - Method in class moss.Graph
Embed a single node into the graph.
embed(Graph) - Method in class moss.Graph
Embed a graph structure (find all its embeddings).
embed() - Method in class moss.Miner
Embed the seed structure into all graphs.
Embedding - Class in moss
Class for embeddings of substructures into graphs.
Embedding() - Constructor for class moss.Embedding
Dummy constructor.
Embedding(Graph, int) - Constructor for class moss.Embedding
Create a single node embedding.
Embedding(Graph, Node[], Edge[]) - Constructor for class moss.Embedding
Create an embedding from node and edge references.
Embedding(CanonicalForm) - Constructor for class moss.Embedding
Create an embedding from a canonical form.
Embedding(Embedding, Edge) - Constructor for class moss.Embedding
Extend a given embedding with a given edge.
emblvl - Variable in class moss.Miner
the level at which to switch to embeddings
encode(Recoder) - Method in class moss.Graph
Encode the node types with the given type recoder.
encode(Recoder) - Method in class moss.Node
Encode the node type.
encode(int) - Method in class moss.Recoder
Encode a type, that is, retrieve its code.
equals(Object) - Method in class moss.Edge
Check whether two edges are equal.
equals(Object) - Method in class moss.Embedding
Check whether two embeddings are equal.
equals(Object) - Method in class moss.Fragment
Check whether two fragments are equal.
equals(Object) - Method in class moss.Graph
Check whether another graph is equal to this graph.
equalsCanonic(Fragment) - Method in class moss.Fragment
Compare the (canonical) code words of two fragments.
equalsCanonic(Graph) - Method in class moss.Graph
Compare the (canonical) code words of two graphs.
equiv - Variable in class moss.Miner
for benchmarking: equivalent frag.
equivClasses(Graph) - Method in class moss.CanonicalForm
Find the node equivalence classes for a given graph.
equivSiblings() - Method in class moss.Fragment
Check whether a fragments can have equivalent siblings.
EQVARS - Static variable in class moss.CanonicalForm
extension mode flag: equivalent ring variants
EQVARS - Static variable in class moss.Miner
flag for extensions by equivalent variants of rings
ERBIUM - Static variable in class moss.AtomTypeMgr
 
EUROPIUM - Static variable in class moss.AtomTypeMgr
 
exclude(int) - Method in class moss.Recoder
Mark a type as excluded.
execute() - Method in class moss.MoSS
Execute the substructure search, that is, start a miner.
exseed - Variable in class moss.Miner
the node types that are excluded as seeds
extend(int, int, int, int) - Method in class moss.Embedding
Create all extensions of a given type of this embedding.
ExtList - Class in moss
Class for managing extension lists and their elements.
ExtList(int, int, int, int) - Constructor for class moss.ExtList
Create an extension list element for a single edge extension.
ExtList(int, int, int, int, int[], int) - Constructor for class moss.ExtList
Create an extension list element for a ring extension.
ExtMgr - Class in moss
Class for an extension edge manager.
ExtMgr(int, int) - Constructor for class moss.ExtMgr
Create an extension edge manager.
ExtMgr(int) - Constructor for class moss.ExtMgr
Create an extension edge manager.
exts - Variable in class moss.ExtMgr
the table for access via the source node type
extype - Variable in class moss.Miner
the excluded node types

F

fcomp - Variable in class moss.Miner
the maximum support in the complement as a fraction
FERMIUM - Static variable in class moss.AtomTypeMgr
 
FILL - Static variable in class moss.MoSSPanel
the grid bag constraints for fillers
first(int) - Method in class moss.ExtMgr
Initialize the traversal of extension edges.
firstEmb() - Method in class moss.Fragment
Get the first embedding of the fragment.
firstGraph() - Method in class moss.Fragment
Get the first graph containing the fragment.
FIXED - Static variable in class moss.CanonicalForm
flag for a fixed edge in the ring order test
fixed - Variable in class moss.CanonicalForm
the number of fixed edges in a canonical form test
FLAGMASK - Static variable in class moss.Edge
the mask for the edge flags (wildcard and ring)
FLAGMASK - Static variable in class moss.Node
the mask for the node flags (wildcard and chain)
FLAGMASK - Static variable in class moss.TypeMgr
the mask for the type flags
flags - Variable in class moss.Edge
the flags for rings and bridges
flags - Variable in class moss.Fragment
the property flags of the embedding (e.g.
FLDSEP - Static variable in class moss.TableReader
class/type flag: field separator
FLOURINE - Static variable in class moss.AtomTypeMgr
 
FOCUS - Static variable in class moss.Fragment
group identifier: focus
FOCUS - Static variable in class moss.NamedGraph
group identifier: focus
frag - Variable in class moss.CanonicalForm
the fragment that is extended
frag - Variable in class moss.Miner
the initial fragment (embedded seed structure)
fragcmp - Variable in class moss.Miner
for benchmarking: the number of fragment comparisons
fragcnt - Variable in class moss.Miner
for benchmarking: the number of created fragments
Fragment - Class in moss
Class for graph fragments (subgraphs and their embeddings).
Fragment() - Constructor for class moss.Fragment
Create an empty fragment.
Fragment(Graph) - Constructor for class moss.Fragment
Create a fragment from a graph.
Fragment(int) - Constructor for class moss.Fragment
Create an empty fragment with an embedding limit.
Fragment(Graph, int) - Constructor for class moss.Fragment
Create a fragment with an embedding limit from a graph.
Fragment(Graph, Graph) - Constructor for class moss.Fragment
Create a fragment from a graph and a subgraph.
Fragment(Graph, Graph, int) - Constructor for class moss.Fragment
Create a fragment from a graph and a subgraph.
Fragment(Fragment, int, int, int, int) - Constructor for class moss.Fragment
Create an extended fragment.
Fragment(CanonicalForm) - Constructor for class moss.Fragment
Create a fragment from an extension.
FRANCIUM - Static variable in class moss.AtomTypeMgr
 
FreeNtn - Class in moss
Class for free graph notations (with dynamic type managers).
FreeNtn() - Constructor for class moss.FreeNtn
 
FreeTypeMgr - Class in moss
Class for a node or edge type map.
FreeTypeMgr() - Constructor for class moss.FreeTypeMgr
Create a type map.
fsupp - Variable in class moss.Miner
the minimum support in the focus as a fraction

G

g1 - Variable in class moss.MaxComSub
the first graph of the pair for which to find the maximum common subgraph
g2 - Variable in class moss.MaxComSub
the second graph of the pair for which to find the maximum common subgraph
GADOLINIUM - Static variable in class moss.AtomTypeMgr
 
GALLIUM - Static variable in class moss.AtomTypeMgr
 
GERMANIUM - Static variable in class moss.AtomTypeMgr
 
getAbsCompl() - Method in class moss.GraphReader
Get the absolute complement support of the current substructure.
getAbsSupp() - Method in class moss.GraphReader
Get the absolute focus support of the current substructure.
getBase(int) - Static method in class moss.TypeMgr
Get the base type (remove flags).
getBaseType() - Method in class moss.Edge
Get the base type (attribute/label) of an edge.
getBaseType() - Method in class moss.Node
Get the base type (attribute/label) of a node.
getBond(int) - Static method in class moss.BondTypeMgr
Extract the raw bond type from a bond type.
getBondName(int) - Static method in class moss.BondTypeMgr
Get the name of the bond type.
getChainName() - Static method in class moss.AtomTypeMgr
Get the name of a chain atom.
getCharge(int) - Static method in class moss.AtomTypeMgr
Extract the charge from an atom type.
getChooser() - Method in class moss.MoSS
Get the file chooser (create if necessary).
getCode(String) - Method in class moss.AtomTypeMgr
Map an atom name to the corresponding code.
getCode(String) - Method in class moss.BondTypeMgr
Map a bond name to the corresponding code.
getCode(String) - Method in class moss.FreeTypeMgr
Map a type name to the corresponding type code.
getCode(String) - Method in class moss.TypeMgr
Map a type name to the corresponding type code.
getColumnCount() - Method in class moss.MoSSTable
Get the number of columns of the data table.
getColumnName(int) - Method in class moss.MoSSTable
Get the name of a column given its index.
getComplEmbCount() - Method in class moss.Fragment
Get the number of embeddings in the complement.
getComplSupport() - Method in class moss.Fragment
Get the complement support of a fragment.
getCosts() - Method in class moss.MaxComSub
Get the costs of the best sequence of edit operations.
getCurrent() - Method in class moss.Miner
Get the substructures that have been found up to now.
getDegree() - Method in class moss.ExtMgr
Get the maximum source node degree of the current extension edge.
getDegree() - Method in class moss.Node
Get the degree of the node.
getDelim() - Method in class moss.Notation
Get the delimiter character.
getDesc() - Method in class moss.GraphReader
Get a line description of the current graph.
getDesc() - Method in class moss.NEListReader
Get a (line) description of the current graph.
getDesc() - Method in class moss.SDfileReader
Get a (line) description of the current graph.
getDest() - Method in class moss.Edge
Get the destination node of the edge.
getDest() - Method in class moss.ExtMgr
Get the destination node type of the current extension edge.
getEdge(int) - Method in class moss.Graph
Get an edge by its index.
getEdge(int) - Method in class moss.Node
Get an edge of the node.
getEdgeCount() - Method in class moss.Graph
Get the number of edges of the graph.
getEdgeCount() - Method in class moss.GraphReader
Get the number of edges of the current graph.
getEdgeMap() - Method in class moss.MaxComSub
Get the mapping of the edges of graph 1 to the edges of graph 2.
getEdgeMgr() - Method in class moss.FreeNtn
Get the edge type manager.
getEdgeMgr() - Method in class moss.Graph
Get the edge type manager of the graph.
getEdgeMgr() - Method in class moss.Notation
Get the edge type manager.
getEdgeType(int) - Method in class moss.Graph
Get the type of an edge.
getElem(int) - Static method in class moss.AtomTypeMgr
Extract the chemical element from an atom type.
getElemName(int) - Static method in class moss.AtomTypeMgr
Extract the name of a chemical element from an atom type.
getEmbCount() - Method in class moss.Fragment
Get the number of embeddings (in both groups together).
getEmbCount(int) - Method in class moss.Fragment
Get the number of embeddings in the given group.
getError() - Method in class moss.Miner
Get the error status of the search process.
getFileName(String, JTextField) - Method in class moss.MoSS
Get a file name and store it in a text field.
getFocusEmbCount() - Method in class moss.Fragment
Get the number of embeddings in the focus.
getFocusSupport() - Method in class moss.Fragment
Get the focus support of a fragment.
getFreq(int) - Method in class moss.Recoder
Get the frequency of a type (number of occurrences).
getGraph() - Method in class moss.Fragment
Get the fragment as a (sub-)graph.
getGraph() - Method in class moss.GraphReader
Get the current graph or substructure.
getGraph() - Method in class moss.MaxComSub
Get the mapping of the edges of graph 1 to the edges of graph 2.
getGraph() - Method in class moss.TableReader
Get the current graph or substructure.
getGroup() - Method in class moss.Embedding
Get the group of the underlying graph.
getGroup() - Method in class moss.NamedGraph
Get the group of this graph.
getHydros(int) - Static method in class moss.AtomTypeMgr
Extract the hydrogens from an atom type.
getHydros() - Method in class moss.MoleculeNtn
Read shorthand hydrogen atoms.
getHydros(Node, Recoder) - Static method in class moss.MoleculeNtn
Get the number of adjacent hydrogen atoms (and mark them).
getMISExact() - Method in class moss.OverlapGraph
Find the size of a maximum independent node set (MIS).
getMISGreedy() - Method in class moss.OverlapGraph
Find the size of a maximum independent node set (MIS).
getMISSize() - Method in class moss.OverlapGraph
Find the size of a maximum independent node set (MIS).
getMISSize(boolean) - Method in class moss.OverlapGraph
Find the size of a maximum independent node set (MIS).
getMode() - Method in class moss.GraphReader
Get the mode of the graph reader.
getMode() - Method in class moss.GraphWriter
Get the mode of the graph writer.
getName(int) - Method in class moss.AtomTypeMgr
Map a code to the corresponding atom name.
getName(int) - Method in class moss.BondTypeMgr
Map a code to the corresponding bond name.
getName(int) - Method in class moss.FreeTypeMgr
Map a type code to the corresponding type name.
getName() - Method in class moss.GraphReader
Get the name of the current graph.
getName() - Method in class moss.NamedGraph
Get the name of this graph.
getName(int) - Method in class moss.TypeMgr
Map a type code to the corresponding type name.
getNode(int) - Method in class moss.Graph
Get a node by its index.
getNodeCount() - Method in class moss.Graph
Get the number of nodes of the graph.
getNodeCount() - Method in class moss.GraphReader
Get the number of nodes of the current graph.
getNodeMap() - Method in class moss.MaxComSub
Get the mapping of the nodes of graph 1 to the nodes of graph 2.
getNodeMgr() - Method in class moss.FreeNtn
Get the node type manager.
getNodeMgr() - Method in class moss.Graph
Get the node type manager of the graph.
getNodeMgr() - Method in class moss.Notation
Get the node type manager.
getNodeType(int) - Method in class moss.Graph
Get the type of a node.
getNodeTypeRaw(int) - Method in class moss.Graph
Get the type of a node.
getNotation() - Method in class moss.Graph
Get the notation of the graph.
getNotation() - Method in class moss.GraphReader
Get the notation of the graph reader.
getNotation() - Method in class moss.GraphWriter
Get the notation of the graph writer.
getRecoder() - Method in class moss.Graph
Get the recoder for the node types.
getRelCompl() - Method in class moss.GraphReader
Get the relative support of the current substructure.
getRelSupp() - Method in class moss.GraphReader
Get the relative focus support of the current substructure.
getRings() - Method in class moss.Edge
Get the ring flags of the edge.
getRowCount() - Method in class moss.MoSSTable
Get the number of rows of the table.
getSource() - Method in class moss.Edge
Get the source node of the edge.
getSupp(int) - Method in class moss.Recoder
Get the support of a type (number of containing graphs).
getSupport() - Method in class moss.Fragment
Get the support of a fragment (in both groups together).
getSupport(int) - Method in class moss.Fragment
Get the support of a fragment in the given group.
getType() - Method in class moss.Edge
Get the full type (attribute/label) of an edge.
getType() - Method in class moss.ExtMgr
Get the edge type of the current extension edge.
getType() - Method in class moss.Node
Get the full type (attribute/label) of a node.
getTypes(char) - Method in class moss.TableReader
Get the classes/types of a given character.
getValue() - Method in class moss.GraphReader
Get the value associated with the current graph.
getValue() - Method in class moss.NamedGraph
Get the value of this graph.
getValueAt(int, int) - Method in class moss.MoSSTable
Get the value of a table cell as an object.
getWildcard() - Static method in class moss.AtomTypeMgr
Get the name of a wildcard atom.
GOLD - Static variable in class moss.AtomTypeMgr
 
graph - Variable in class moss.Embedding
the graph referred to
graph - Variable in class moss.Fragment
the fragment as a graph
Graph - Class in moss
Class to represent attributed graphs for substructure mining.
Graph() - Constructor for class moss.Graph
Create/Initialize an empty graph.
Graph(Notation) - Constructor for class moss.Graph
Create a (empty) graph with default array sizes.
Graph(Notation, Recoder) - Constructor for class moss.Graph
Create a (empty) graph with default array sizes.
Graph(Notation, int, int) - Constructor for class moss.Graph
Create a (empty) graph with the given array sizes.
Graph(Notation, Recoder, int, int) - Constructor for class moss.Graph
Create a (empty) graph with the given array sizes.
Graph(Graph) - Constructor for class moss.Graph
Create a clone of a graph.
Graph(Graph, int, int, int, int) - Constructor for class moss.Graph
Create an extended graph (extended by one edge).
Graph(Fragment) - Constructor for class moss.Graph
Turn a fragment into a graph.
graph - Variable in class moss.GraphReader
the current graph
graph - Variable in class moss.GraphWriter
the current graph
GraphReader - Class in moss
Class for a reader for graph data sets.
GraphReader(Reader, int) - Constructor for class moss.GraphReader
Create a reader for a graph data set.
GRAPHS - Static variable in class moss.Fragment
support type: number of graphs that contain an embedding
GRAPHS - Static variable in class moss.GraphReader
read mode: graphs
GRAPHS - Static variable in class moss.GraphWriter
write mode: graphs
graphs - Variable in class moss.Miner
the list of graphs to mine (database)
GRAPHS - Static variable in class moss.MoSSTable
mode: graphs
GraphWriter - Class in moss
Class for a writer for graph data sets.
GraphWriter(Writer, int) - Constructor for class moss.GraphWriter
Create a writer for a graph data set.
GREEDY - Static variable in class moss.Fragment
support type flag: whether to use the greedy MIS algorithm
group - Variable in class moss.Miner
the group for graphs with a value below the threshold
group - Variable in class moss.NamedGraph
the marker for grouping (either 0 or 1, used as an array index)

H

HAFNIUM - Static variable in class moss.AtomTypeMgr
 
hasFixedTypes() - Method in class moss.FreeNtn
Whether this notation has a fixed set of (node and edge) types.
hasFixedTypes() - Method in class moss.MoleculeNtn
Whether this notation has a fixed set of (node and edge) types.
hasFixedTypes() - Method in class moss.Notation
Whether this notation has a fixed set of (node and edge) types.
hashCode() - Method in class moss.Embedding
Compute the hash code of the subgraph described by the embedding.
hashCode() - Method in class moss.Fragment
Compute the hash code of the fragment.
hashCode() - Method in class moss.Graph
Compute the hash code of the attributed graph.
hasOpenRings(int, int) - Method in class moss.Fragment
Check whether the fragment has open rings.
hasOpenRings(int, int) - Method in class moss.Graph
Check whether this subgraph has open rings.
hasOrbits() - Method in class moss.Fragment
Check whether the fragment has node orbit identifiers.
HASSIUM - Static variable in class moss.AtomTypeMgr
 
hasUnclosableRings(Fragment) - Method in class moss.CanonicalForm
Check whether a fragment contains unclosable rings.
hasUnclosableRings(Fragment) - Method in class moss.CnFBreadth1
Check whether a fragment contains unclosable rings.
hasUnclosableRings(Fragment) - Method in class moss.CnFBreadth2
Check whether a fragment contains unclosable rings.
hasUnclosableRings(Fragment) - Method in class moss.CnFDepth
Check whether a fragment contains unclosable rings.
hasUnclosableRings(CanonicalForm) - Method in class moss.Fragment
Check whether the fragment has unclosable rings.
HEADER - Static variable in class moss.TableWriter
the field names for the different file types
HELIUM - Static variable in class moss.AtomTypeMgr
 
HOLMIUM - Static variable in class moss.AtomTypeMgr
 
HYDROGEN - Static variable in class moss.AtomTypeMgr
 
HYDROMASK - Static variable in class moss.AtomTypeMgr
the mask for extracting the hydrogens from an atom type
HYDROSHIFT - Static variable in class moss.AtomTypeMgr
the shift value for extracting the hydrogens from an atom type

I

IDS - Static variable in class moss.MoSSTable
mode: identifiers
idx - Variable in class moss.CanonicalForm
the current edge index in the source node
idx - Variable in class moss.Fragment
the index of the (first) new edge
index() - Method in class moss.Embedding
Mark all nodes and edges with their index.
index() - Method in class moss.Graph
Mark all nodes and edges with their index.
INDIUM - Static variable in class moss.AtomTypeMgr
 
init(Fragment, Embedding) - Method in class moss.CanonicalForm
Initialize the extension generation process.
init(Fragment) - Method in class moss.CanonicalForm
Initialize the extension generation process.
init(Fragment, Embedding) - Method in class moss.CnFBreadth1
Initialize the extension generation process.
init(Fragment, Embedding) - Method in class moss.CnFBreadth2
Initialize the extension generation process.
init(Fragment, Embedding) - Method in class moss.CnFDepth
Initialize the extension generation process.
init(String[]) - Method in class moss.Miner
Initialize the miner from command line arguments.
initCanonic(Graph, int) - Method in class moss.CanonicalForm
Initialize a canonical form test or generation.
initFrag(Fragment) - Method in class moss.CanonicalForm
Initialize the extension generation process.
initVars() - Method in class moss.CanonicalForm
Initialize the generation of equivalent ring extension variants.
initVars() - Method in class moss.CnFBreadth1
Initialize the generation of equivalent ring extension variants.
initVars() - Method in class moss.CnFBreadth2
Initialize the generation of equivalent ring extension variants.
initVars() - Method in class moss.CnFDepth
Initialize the generation of equivalent ring extension variants.
invalid - Variable in class moss.Miner
for benchmarking: invalid fragments counter
IODINE - Static variable in class moss.AtomTypeMgr
 
IRIDIUM - Static variable in class moss.AtomTypeMgr
 
IRON - Static variable in class moss.AtomTypeMgr
 
isAromatic(int) - Static method in class moss.AtomTypeMgr
Check whether an atom type specifies an aromatic atom.
isAromatic(int) - Static method in class moss.BondTypeMgr
Check whether a bond type is aromatic.
isBridge() - Method in class moss.Edge
Check whether the edge is a bridge.
isCanExt(Graph) - Method in class moss.CanonicalForm
Check whether a given graph is a canonic extension of its base.
isCanonic(int, int, int) - Method in class moss.CanonicalForm
Internal recursive function for the canonical form test.
isCanonic(Graph, int) - Method in class moss.CanonicalForm
Check whether a given graph is canonic.
isCanonic(Graph) - Method in class moss.CanonicalForm
Check whether a given graph is canonic.
isCanonic(int, int, int) - Method in class moss.CnFBreadth1
Internal recursive function for the canonical form test.
isCanonic(int, int, int) - Method in class moss.CnFBreadth2
Internal recursive function for the canonical form test.
isCanonic(int, int, int) - Method in class moss.CnFDepth
Internal recursive function for the canonical form test.
isCanonic(CanonicalForm) - Method in class moss.Fragment
Check whether the fragment is in canonical form.
isCanonic(CanonicalForm, boolean) - Method in class moss.Fragment
Check whether the fragment is in canonical form.
isCanonic(CanonicalForm) - Method in class moss.Graph
Check whether a graph is canonic w.r.t.
isCanonic(CanonicalForm, int) - Method in class moss.Graph
Check whether a graph is canonic w.r.t.
isCellEditable(int, int) - Method in class moss.MoSSTable
Returns whether a table cell is editable.
isChain(int) - Static method in class moss.AtomTypeMgr
Check whether an atom type specifies a chain atom.
isChain() - Method in class moss.Node
Check whether this is a chain node.
isClosed(CanonicalForm) - Method in class moss.Fragment
Check whether the fragment is closed.
isConnected() - Method in class moss.Graph
Check whether the graph is connected.
isDouble(int) - Static method in class moss.BondTypeMgr
Check whether a bond type is double.
isEquivTo(Fragment) - Method in class moss.Fragment
Check whether two fragments are equivalent.
isExcluded(int) - Method in class moss.Recoder
Check whether a type is excluded.
isFixed() - Method in class moss.AtomTypeMgr
Check whether a type manager is fixed (is not extendable).
isFixed() - Method in class moss.BondTypeMgr
Check whether a type manager is fixed (is not extendable).
isFixed() - Method in class moss.FreeTypeMgr
Check whether a type manager is fixed (is not extendable).
isFixed() - Method in class moss.TypeMgr
Check whether a type manager is fixed (is not extendable).
isHarmful() - Method in class moss.OverlapGraph
Check whether this is a harmful overlap graph.
isInRing() - Method in class moss.Edge
Check whether the edge is part of a ring.
isLine() - Method in class moss.Ctab
Whether this is a line notation (single line description).
isLine() - Method in class moss.LiNoG
Whether this is a line notation (single line description).
isLine() - Method in class moss.NEList
Whether this is a line notation (single line description).
isLine() - Method in class moss.Notation
Whether this is a line notation (single line description).
isLine() - Method in class moss.SLN
Whether this is a line notation (single line description).
isLine() - Method in class moss.SMILES
Whether this is a line notation (single line description).
isMaximal(int) - Method in class moss.Recoder
Check whether a code has maximal frequency.
isocnt - Variable in class moss.Miner
for benchmarking: the number of isomorphism tests
isPerfect(boolean) - Method in class moss.Fragment
Check whether an extension is perfect.
isRing(int) - Static method in class moss.BondTypeMgr
Check whether a bond type specifies a ring bond.
isRingEdgeExt() - Method in class moss.Fragment
Check whether the fragment is the result of an extension by a ring edge.
isRingExt() - Method in class moss.Fragment
Check whether the fragment is the result of a ring extension.
isRingKey(Graph, Edge) - Method in class moss.CanonicalForm
Check whether a prefix is a ring key.
isSingle(int) - Static method in class moss.BondTypeMgr
Check whether a bond type is single.
isSpecial() - Method in class moss.Edge
Check whether this is a special edge (wildcard or ring).
isSpecial() - Method in class moss.Node
Check whether this is a special node (wildcard or chain).
isSpecial(int) - Static method in class moss.TypeMgr
Check whether a type code specifies a special type.
isTriple(int) - Static method in class moss.BondTypeMgr
Check whether a bond type is triple.
isType(int, char) - Method in class moss.TableReader
Check whether a given character is in a given class or of a given type.
isValid() - Method in class moss.Fragment
Check whether the valid flag is set.
isWildcard() - Method in class moss.Edge
Check whether this is a wildcard edge.
isWildcard() - Method in class moss.Node
Check whether this is a wildcard node.
isWildcard(int) - Static method in class moss.TypeMgr
Check whether a type code specifies a wildcard.
itemStateChanged(ItemEvent) - Method in class moss.MoSS
Handle the state change of the support type combo box.

K

KRYPTON - Static variable in class moss.AtomTypeMgr
 

L

LANTHANUM - Static variable in class moss.AtomTypeMgr
 
LAWRENCIUM - Static variable in class moss.AtomTypeMgr
 
LEAD - Static variable in class moss.AtomTypeMgr
 
LEFT - Static variable in class moss.MoSSPanel
the grid bag constraints for labels
LiNoG - Class in moss
Class for a simple line notation for (attributed) graphs
LiNoG() - Constructor for class moss.LiNoG
Create an attributed graph line notation object.
LiNoG(TypeMgr, TypeMgr) - Constructor for class moss.LiNoG
Create an attributed graph line notation object.
list - Variable in class moss.Fragment
the list of embeddings of the fragment
LITHIUM - Static variable in class moss.AtomTypeMgr
 
log - Variable in class moss.Miner
stream to write progress messages to
LOGIC - Static variable in class moss.Miner
flag for conversion to logic representation
lowsupp - Variable in class moss.Miner
for benchmarking: insufficient support pruning counter
LUTETIUM - Static variable in class moss.AtomTypeMgr
 

M

MAGNESIUM - Static variable in class moss.AtomTypeMgr
 
main(String[]) - Static method in class moss.AtomTypeMgr
Main function for testing some basic functionality.
main(String[]) - Static method in class moss.BondTypeMgr
Main function for testing some basic functionality.
main(String[]) - Static method in class moss.Ctab
Main function for testing basic functionality.
main(String[]) - Static method in class moss.Embedding
Main function for testing the overlap functions.
main(String[]) - Static method in class moss.Fragment
Main function for testing some basic functionality.
main(String[]) - Static method in class moss.Graph
Main function for testing some basic functionality.
main(String[]) - Static method in class moss.LiNoG
Main function for testing basic functionality.
main(String[]) - Static method in class moss.MaxComSub
Main function for basic testing basic functionality.
main(String[]) - Static method in class moss.Miner
Command line invocation of the molecular substructure miner.
main(String[]) - Static method in class moss.MoSS
Main function to invoke the user interface as a stand-alone program.
main(String[]) - Static method in class moss.NamedGraph
Main function for testing some basic functionality.
main(String[]) - Static method in class moss.NEList
Main function for testing basic functionality.
main(String[]) - Static method in class moss.NEListReader
Main function for testing basic functionality.
main(String[]) - Static method in class moss.OverlapGraph
Main function for testing some basic functionality.
main(String[]) - Static method in class moss.SDfileReader
Main function for testing basic functionality.
main(String[]) - Static method in class moss.SLN
Main function for testing basic functionality.
main(String[]) - Static method in class moss.SMILES
Main function for testing basic functionality.
main(String[]) - Static method in class moss.TableReader
Main function for testing basic functionality.
makeCanonic(int, int, int) - Method in class moss.CanonicalForm
Internal recursive function for making a given graph canonic.
makeCanonic(Graph, int) - Method in class moss.CanonicalForm
Make a given graph canonic.
makeCanonic(Graph) - Method in class moss.CanonicalForm
Make a given graph canonic.
makeCanonic(int, int, int) - Method in class moss.CnFBreadth1
Internal recursive function for making a given graph canonic.
makeCanonic(int, int, int) - Method in class moss.CnFBreadth2
Internal recursive function for making a given graph canonic.
makeCanonic(int, int, int) - Method in class moss.CnFDepth
Internal recursive function for making a given graph canonic.
makeCanonic(CanonicalForm) - Method in class moss.Fragment
Make the fragment canonic (minimize the code word).
makeCanonic(CanonicalForm, int) - Method in class moss.Fragment
Make the fragment canonic (minimize the code word).
makeCanonic(CanonicalForm) - Method in class moss.Graph
Make a graph canonic w.r.t.
makeCanonic(CanonicalForm, int) - Method in class moss.Graph
Make a graph canonic w.r.t.
makeEmbedding() - Method in class moss.CanonicalForm
Create an embedding from the current extension.
makeFragment() - Method in class moss.CanonicalForm
Create a fragment from the current extension.
makeMap(Graph, int) - Method in class moss.CanonicalForm
Build a map for reordering the nodes and edges.
makeWord(Graph) - Method in class moss.CanonicalForm
Create the code word for a given graph.
makeWord(Graph, int) - Method in class moss.CanonicalForm
Create the code word for the first edges of a given graph.
makeWord(Edge[], int) - Method in class moss.CanonicalForm
Create the (prefix of a) code word for a given edge array.
makeWord(Edge[], int) - Method in class moss.CnFBreadth1
Create the (prefix of a) code word for a given edge array.
makeWord(Edge[], int) - Method in class moss.CnFBreadth2
Create the (prefix of a) code word for a given edge array.
makeWord(Edge[], int) - Method in class moss.CnFDepth
Create the (prefix of a) code word for a given edge array.
MANGANESE - Static variable in class moss.AtomTypeMgr
 
map - Static variable in class moss.AtomTypeMgr
the map from element names (character pairs) to element codes
map(CanonicalForm) - Method in class moss.Fragment
Reorganize the fragment with a map from a canonical form.
map(CanonicalForm) - Method in class moss.Graph
Reorganize a graph with a map from a canonical form.
mark - Variable in class moss.Edge
a marker for internal use (e.g.
mark(int) - Method in class moss.Embedding
Mark all nodes and edges with a given value.
mark(int) - Method in class moss.Graph
Mark all nodes and edges with a given value.
mark - Variable in class moss.Node
a marker for internal use (e.g.
mark(int) - Method in class moss.Node
Recursive function to mark a connected component.
mark(Node) - Static method in class moss.Notation
Mark the visits of each node.
markBridge(boolean) - Method in class moss.Edge
Set or clear the bridge flag of the edge.
markBridges() - Method in class moss.Graph
Mark all edges that are bridges.
markPseudo(int) - Method in class moss.Graph
Mark pseudo-rings up to a given size.
markRing(boolean) - Method in class moss.Edge
Set or clear the ring type flag of the edge.
markRings(int, int) - Method in class moss.Graph
Mark rings in a given size range.
markRings(int, int, int) - Method in class moss.Graph
Mark rings in a given size range with a given type flag.
masks - Variable in class moss.Miner
the masks for nodes and edges
maskType(int) - Method in class moss.Edge
Mask the edge type with the given mask.
maskType(int) - Method in class moss.Node
Mask the edge type with the given mask.
maskTypes(int[]) - Method in class moss.Graph
Mask the node and edge types.
max - Variable in class moss.CanonicalForm
the maximum fragment size (number of nodes)
max - Variable in class moss.Fragment
the maximal number of embeddings per graph
max - Variable in class moss.Miner
the maximum size of substructures to report (number of nodes)
MaxComSub - Class in moss
Class for finding maximum common subgraphs.
MaxComSub(Graph, Graph) - Constructor for class moss.MaxComSub
Find the maximum common subgraph of two given graphs.
MaxComSub(Graph, Graph, boolean) - Constructor for class moss.MaxComSub
Find the maximum common subgraph of two given graphs.
maxdep - Variable in class moss.Miner
for benchmarking: the maximum depth of the search tree
maxepg - Variable in class moss.Miner
the maximum number of embeddings per graph
maximize(int) - Method in class moss.Recoder
Set frequency and support to a maximal value.
mcs - Variable in class moss.MaxComSub
the found maximum common subgraph (created on demand)
MEITNERIUM - Static variable in class moss.AtomTypeMgr
 
MENDELEVIUM - Static variable in class moss.AtomTypeMgr
 
MERCURY - Static variable in class moss.AtomTypeMgr
 
merge(ExtList, ExtList) - Static method in class moss.ExtList
Merge two sorted extension lists (and remove duplicates).
mergeExts(Fragment[], int) - Method in class moss.Fragment
Merge ring extensions that have the same initial edge.
MERGERINGS - Static variable in class moss.Miner
flag for merging ring extensions with the same first edge
MIDDLE - Static variable in class moss.MoSSPanel
the grid bag constraints for middle input fields
min - Variable in class moss.Miner
the minimum size of substructures to report (number of nodes)
MIN_IMAGE - Static variable in class moss.Fragment
support type: minimum number of different nodes mapped to
mine() - Method in class moss.Miner
Preprocess the graphs, embed the seed, and start the search.
Miner - Class in moss
Class for the molecular substructure miner.
Miner() - Constructor for class moss.Miner
Create an empty miner with default parameter settings.
MIS_HARM - Static variable in class moss.Fragment
support type: maximum independent set of harmful overlap graph
MIS_OLAP - Static variable in class moss.Fragment
support type: maximum independent set of normal overlap graph
mode - Variable in class moss.CanonicalForm
the extension mode (e.g.
mode - Variable in class moss.GraphReader
the read mode
mode - Variable in class moss.GraphWriter
the write mode
mode - Variable in class moss.Miner
the search mode flags
MoleculeNtn - Class in moss
Class for (linear) notations for molecules.
MoleculeNtn() - Constructor for class moss.MoleculeNtn
 
MOLYBDENUM - Static variable in class moss.AtomTypeMgr
 
moss - package moss
 
MoSS - Class in moss
Graphical user interface for the molecular substructure miner.
MoSS() - Constructor for class moss.MoSS
Create a user interface dialog box.
MoSS(Component) - Constructor for class moss.MoSS
Create a user interface for the molecular substructure miner.
MoSS(Component, boolean) - Constructor for class moss.MoSS
Create a user interface for the molecular substructure miner.
MoSSPanel - Class in moss
Class for a tab panel for the MoSS graphical user interface.
MoSSPanel() - Constructor for class moss.MoSSPanel
Create a MoSS tab panel.
MoSSTable - Class in moss
Class for data tables for molecular substructure mining.
MoSSTable(int, String) - Constructor for class moss.MoSSTable
Create a data table.

N

name - Variable in class moss.GraphReader
the name/identifier of the current graph
name - Variable in class moss.GraphWriter
the name of the current graph
name - Variable in class moss.NamedGraph
the graph name/identifier
NamedGraph - Class in moss
Class for attributed graphs with a name and a group.
NamedGraph(Notation) - Constructor for class moss.NamedGraph
Create a graph with an empty name and value and group 0.
NamedGraph(Notation, String) - Constructor for class moss.NamedGraph
Create a graph with value and group 0.
NamedGraph(Notation, String, float, int) - Constructor for class moss.NamedGraph
Create a graph of default size with a given name and group.
NamedGraph(Notation, int, int, String, float, int) - Constructor for class moss.NamedGraph
Create a graph with a given name, group and size.
NamedGraph(Graph) - Constructor for class moss.NamedGraph
Turn a graph into a named graph.
NamedGraph(Graph, String) - Constructor for class moss.NamedGraph
Turn a graph into a named graph.
NamedGraph(Graph, String, float, int) - Constructor for class moss.NamedGraph
Turn a graph into a named graph.
NamedGraph(NamedGraph) - Constructor for class moss.NamedGraph
Clone a named graph.
names - Static variable in class moss.BondTypeMgr
the table of bond names; using the bond type as an index for this table yields a printable bond description
NEList - Class in moss
Class for a simple node/edge list notation.
NEList() - Constructor for class moss.NEList
Create a list notation with empty type managers.
NEList(TypeMgr, TypeMgr) - Constructor for class moss.NEList
Create a list notation with given type managers.
NEListReader - Class in moss
Class for readers for a simple node/edge list format.
NEListReader(Reader, int) - Constructor for class moss.NEListReader
Create a reader for a simple node/edge list format.
NEListWriter - Class in moss
Class for writers for a simple node/edge list format.
NEListWriter(Writer, int) - Constructor for class moss.NEListWriter
Create a writer for a simple node/edge list format.
NEODYMIUM - Static variable in class moss.AtomTypeMgr
 
NEON - Static variable in class moss.AtomTypeMgr
 
NEPTUNIUM - Static variable in class moss.AtomTypeMgr
 
next() - Method in class moss.CanonicalForm
Create the next (restricted) extension of an embedding.
next() - Method in class moss.CnFBreadth1
Create the next extension.
next() - Method in class moss.CnFBreadth2
Create the next extension.
next() - Method in class moss.CnFDepth
Create the next extension.
next() - Method in class moss.ExtMgr
Get the next extension edge.
nextEmb() - Method in class moss.Fragment
Get the next embedding of the fragment.
nextFrag() - Method in class moss.CanonicalForm
Create the next (restricted) extension of a fragment.
nextFrag() - Method in class moss.CnFBreadth1
Create the next extended fragment.
nextFrag() - Method in class moss.CnFBreadth2
Create the next extended fragment.
nextFrag() - Method in class moss.CnFDepth
Create the next extended fragment.
nextGraph() - Method in class moss.Fragment
Get the next graph containing the fragment.
NICKEL - Static variable in class moss.AtomTypeMgr
 
NIOBIUM - Static variable in class moss.AtomTypeMgr
 
NITROGEN - Static variable in class moss.AtomTypeMgr
 
nmap - Variable in class moss.CanonicalForm
the node map for making a graph canonic
NOBELIUM - Static variable in class moss.AtomTypeMgr
 
node - Variable in class moss.ExtList
the type of the destination node
Node - Class in moss
Class for nodes of an attributed (labeled/typed) graph.
Node(int) - Constructor for class moss.Node
Create a node with a given type (attribute/label).
Node(int, int) - Constructor for class moss.Node
Create a node of a given type and given edge array size.
nodecnt - Variable in class moss.CanonicalForm
the number of new nodes
nodecnt - Variable in class moss.Graph
the current number of nodes (may be smaller than the array length)
nodecnt - Variable in class moss.Miner
for benchmarking: the number of search tree nodes
nodemap - Variable in class moss.MaxComSub
the mapping of the nodes of graph 1 to graph 2
nodemgr - Variable in class moss.Notation
the manager for the node types
nodes - Variable in class moss.CanonicalForm
(relevant) nodes of the extension
nodes - Variable in class moss.Embedding
the array of nodes (only references to the underlying graph)
nodes - Variable in class moss.Graph
the array of nodes (may be only partially used)
nodes - Variable in class moss.GraphReader
the number of nodes of the current graph
nodes - Variable in class moss.GraphWriter
the number of nodes of the current graph
nonclsd - Variable in class moss.Miner
for benchmarking: non-closed fragments counter
norm - Variable in class moss.Miner
the canonical form for normalizing the output
normalize(CanonicalForm) - Method in class moss.Graph
Normalize a graph w.r.t.
NORMFORM - Static variable in class moss.Miner
flag for normalized substructure output
NOSTATS - Static variable in class moss.Miner
flag for no search statistics output
Notation - Class in moss
Class for notations for attributed graphs.
Notation() - Constructor for class moss.Notation
 
ntn - Variable in class moss.Graph
the notation for describing the graph
ntn - Variable in class moss.GraphReader
the notation for parsing graph descriptions
ntn - Variable in class moss.GraphWriter
the notation for the graphs
NULL - Static variable in class moss.AtomTypeMgr
 
NULL - Static variable in class moss.BondTypeMgr
bond type: null bond, that is, a bond that does not actually connect two atoms

O

openrgs - Variable in class moss.Miner
for benchmarking: open ring fragments counter
opt() - Method in class moss.Graph
Optimize memory usage.
opt() - Method in class moss.Node
Optimize memory usage.
orbit - Variable in class moss.Node
the representative of the orbit of the node
ORBITS - Static variable in class moss.CanonicalForm
extension mode flag: use node orbits to filter (if known)
ORBITS - Static variable in class moss.Fragment
flag for valid orbit identifiers in the fragment graph
ORBITS - Static variable in class moss.Miner
flag for extension filtering with node orbits
OSMIUM - Static variable in class moss.AtomTypeMgr
 
OverlapGraph - Class in moss
Class to represent overlap graphs for embeddings.
OverlapGraph() - Constructor for class moss.OverlapGraph
Create a (empty) overlap graph with a default size.
OverlapGraph(boolean) - Constructor for class moss.OverlapGraph
Create a (empty) overlap graph with a default size.
OverlapGraph(boolean, int) - Constructor for class moss.OverlapGraph
Create a (empty) overlap graph with a given size.
overlaps(Embedding, boolean) - Method in class moss.Embedding
Check whether this embedding overlaps another.
overlaps(Embedding) - Method in class moss.Embedding
Check whether this embedding overlaps another.
overlapsHarmfully(Embedding) - Method in class moss.Embedding
Check whether this embedding overlaps another harmfully.
OXYGEN - Static variable in class moss.AtomTypeMgr
 

P

pack() - Method in class moss.Fragment
Pack the list of embeddings.
pack(int) - Method in class moss.Fragment
Pack the list of embeddings.
PACKED - Static variable in class moss.Fragment
flag for a packed list of embeddings
PALLADIUM - Static variable in class moss.AtomTypeMgr
 
parse(Reader) - Method in class moss.Ctab
Parse the description of a molecule.
parse(Reader) - Method in class moss.LiNoG
Parse a description of an attributed graph.
parse(Reader) - Method in class moss.NEList
Parse a description of an attributed graph.
parse(Reader) - Method in class moss.Notation
Parse a description of an attributed graph.
parse(Reader) - Method in class moss.SLN
Parse a description of a molecule.
parse(Reader) - Method in class moss.SMILES
Parse the description of a molecule.
parseGraph(Reader) - Static method in class moss.OverlapGraph
Parse a graph description.
PERFECT - Static variable in class moss.Fragment
flag for a perfect extension; set if the fragment was created by a perfect extension of its base fragment
perfect - Variable in class moss.Miner
for benchmarking: perfect extension pruning counter
PHOSPHORUS - Static variable in class moss.AtomTypeMgr
 
PLATINUM - Static variable in class moss.AtomTypeMgr
 
PLUTONIUM - Static variable in class moss.AtomTypeMgr
 
pmax - Variable in class moss.CanonicalForm
the maximal position/position index of a ring edge
pmin - Variable in class moss.CanonicalForm
the minimal position/current position index of a ring edge
POLONIUM - Static variable in class moss.AtomTypeMgr
 
pos1 - Variable in class moss.CanonicalForm
the current position 1 of equivalent edges for ring extensions
pos2 - Variable in class moss.CanonicalForm
the current position 2 of equivalent edges for ring extensions
POTASSIUM - Static variable in class moss.AtomTypeMgr
 
PR_CANONIC - Static variable in class moss.Miner
flag for canonical form pruning
PR_EQUIV - Static variable in class moss.Miner
flag for equivalent sibling extension pruning
PR_PARTIAL - Static variable in class moss.Miner
flag for partial perfect extension pruning
PR_PERFECT - Static variable in class moss.Miner
flag for full perfect extension pruning
PR_UNCLOSE - Static variable in class moss.Miner
flag for pruning fragments with unclosable rings
PRASEODYMIUM - Static variable in class moss.AtomTypeMgr
 
prepare(Fragment) - Method in class moss.CanonicalForm
Prepare the rings of a fragment for adaptation and order test.
prepare() - Method in class moss.Graph
Prepare a graph for frequent substructure mining.
prepareEmbed() - Method in class moss.Graph
Prepare a graph for embedding it into another.
PROMETHIUM - Static variable in class moss.AtomTypeMgr
 
PROTACTINIUM - Static variable in class moss.AtomTypeMgr
 

R

RADIUM - Static variable in class moss.AtomTypeMgr
 
RADON - Static variable in class moss.AtomTypeMgr
 
read(File) - Method in class moss.MoSSTable
Read table from an input stream.
read() - Method in class moss.Notation
Read the next character.
reader - Variable in class moss.Miner
the graph data set file reader
reader - Variable in class moss.Notation
the reader from which to read the graph description
readGraph() - Method in class moss.GraphReader
Read a graph.
readGraph() - Method in class moss.NEListReader
Read a graph.
readGraph() - Method in class moss.SDfileReader
Get the next graph description.
readGraph() - Method in class moss.TableReader
Read the next graph description.
readHeader() - Method in class moss.GraphReader
Read an (optional) header.
readHeader() - Method in class moss.NEListReader
Read an (optional) header.
readHeader() - Method in class moss.SDfileReader
Read an (optional) header.
readHeader() - Method in class moss.TableReader
Read an (optional) table header.
readLine() - Method in class moss.SDfileReader
Read the next input line.
recnt - Variable in class moss.Miner
the size of the repository (number of substructures)
Recoder - Class in moss
Class for recoders for node types.
Recoder() - Constructor for class moss.Recoder
Create a recoder of default size.
RECSEP - Static variable in class moss.TableReader
class/type flag: record separator
reembed() - Method in class moss.Fragment
Reembed a fragment, that is, recreate its embedding list.
removeCharge(int) - Static method in class moss.AtomTypeMgr
Remove the charge from an atom type.
removeExts(int) - Static method in class moss.AtomTypeMgr
Remove the extended information from an atom type.
removeHydros(int) - Static method in class moss.AtomTypeMgr
Remove the hydrogens from an atom type.
removeRings(Edge) - Static method in class moss.CanonicalForm
Remove the flags of all rings an edge is contained in.
repcnt - Variable in class moss.Miner
for benchmarking: the number of repository accesses
report(Fragment) - Method in class moss.Miner
Check and report a found fragment/substructure.
revert() - Method in class moss.Fragment
Revert the extension information of the fragment.
REVERTED - Static variable in class moss.Fragment
flag for reverted extension information
rgmax - Variable in class moss.CanonicalForm
the maximum ring size (number of nodes/edges)
rgmax - Variable in class moss.Miner
the maximum size of rings (number of nodes/edges)
rgmin - Variable in class moss.CanonicalForm
the minimum ring size (number of nodes/edges)
rgmin - Variable in class moss.Miner
the minimum size of rings (number of nodes/edges)
RHENIUM - Static variable in class moss.AtomTypeMgr
 
RHODIUM - Static variable in class moss.AtomTypeMgr
 
RIGHT - Static variable in class moss.MoSSPanel
the grid bag constraints for right input fields
RING - Static variable in class moss.CanonicalForm
extension mode flag: ring (must be marked)
ring() - Method in class moss.CanonicalForm
Create a ring extension.
RING - Static variable in class moss.Edge
the flag for the edge type to distinguish ring edges
ring - Variable in class moss.ExtList
the ring information (if needed)
RINGEXT - Static variable in class moss.Miner
flag for extensions by rings
RINGMASK - Static variable in class moss.Edge
the mask to extract the ring flags
ringord - Variable in class moss.Miner
for benchmarking: ring order pruning counter
ris - Variable in class moss.Fragment
the indices of the nodes of new ring edges
rno() - Method in class moss.TableReader
Get a string stating the current record number.
rno(int) - Method in class moss.TableReader
Get a string stating the current record number.
ROENTGENIUM - Static variable in class moss.AtomTypeMgr
 
RUBIDIUM - Static variable in class moss.AtomTypeMgr
 
run() - Method in class moss.Miner
Run the miner and clean up after the search finished.
run() - Method in class moss.MoSS
Create the user interface dialog box.
RUTHENIUM - Static variable in class moss.AtomTypeMgr
 
RUTHERFORDIUM - Static variable in class moss.AtomTypeMgr
 

S

sabs - Variable in class moss.GraphReader
the absolute support in the focus
sabs - Variable in class moss.GraphWriter
the absolute support in the focus
SAMARIUM - Static variable in class moss.AtomTypeMgr
 
SAMETYPE - Static variable in class moss.BondTypeMgr
a mask, to be anded (bitwise &) with a bond type in order to remove any distinction of bond types
SCANDIUM - Static variable in class moss.AtomTypeMgr
 
SDfileReader - Class in moss
Class for readers for structure-data files (SDfile, Elsevier MDL).
SDfileReader(Reader, int) - Constructor for class moss.SDfileReader
Create a reader for SDfiles.
SDfileWriter - Class in moss
Class for writers for structure-data files (SDfile, Elsevier MDL).
SDfileWriter(Writer, int) - Constructor for class moss.SDfileWriter
Create a writer for SDfiles.
SEABORGIUM - Static variable in class moss.AtomTypeMgr
 
seed - Variable in class moss.Miner
the seed structure to start the search from
SELENIUM - Static variable in class moss.AtomTypeMgr
 
setAbsCompl(int) - Method in class moss.GraphWriter
Set the absolute complement support of the current substructure.
setAbsSupp(int) - Method in class moss.GraphWriter
Set the absolute focus support of the current substructure.
setChainTypes(int, int) - Method in class moss.CanonicalForm
Set the node and edge type for chain extensions.
setChars(int, String) - Method in class moss.TableReader
Set the characters for a specific type/class.
setChars(String, String, String, String) - Method in class moss.TableReader
Set the characters for all types.
setChars(char, char) - Method in class moss.TableWriter
Set the record and field separators.
setClosed(boolean) - Method in class moss.Fragment
Set the flag for a closed fragment.
setCnF(CanonicalForm) - Method in class moss.Miner
Set the canonical form.
setEdgeMgr(TypeMgr) - Method in class moss.FreeNtn
Set the edge type manager.
setEdgeMgr(TypeMgr) - Method in class moss.MoleculeNtn
Set the edge type manager.
setEdgeMgr(TypeMgr) - Method in class moss.Notation
Set the edge type manager.
setEmbed(int, int) - Method in class moss.Miner
Set the embeddings parameters.
setExcluded(Graph, Graph) - Method in class moss.Miner
Set the excluded nodes and excluded seeds.
setExcluded(String, String, String) - Method in class moss.Miner
Set the excluded nodes and excluded seeds.
setExtMgr(ExtMgr) - Method in class moss.CanonicalForm
Set the extension edge manager.
setExtMode(int) - Method in class moss.CanonicalForm
Set the extension mode.
setGraph(Graph) - Method in class moss.GraphWriter
Set the current graph or substructure.
setGroup(int) - Method in class moss.NamedGraph
Set the group of this graph.
setGrouping(double, boolean) - Method in class moss.Miner
Set the grouping parameters.
setInput(GraphReader) - Method in class moss.Miner
Set the input reader.
setInput(String, String) - Method in class moss.Miner
Set the input reader.
setLimits(double, double) - Method in class moss.Miner
Set the support limits.
setLog(PrintStream) - Method in class moss.Miner
Sets the stream to which progress messages are written.
setMasks(int, int, int, int) - Method in class moss.Miner
Set the node and edge masks.
setMaxSize(int) - Method in class moss.CanonicalForm
Set the maximum fragment size (to limit extensions).
setMode(int) - Method in class moss.Miner
Set the search mode.
setName(String) - Method in class moss.GraphWriter
Set the name of the current graph.
setName(String) - Method in class moss.NamedGraph
Set the name of this graph.
setNodeMgr(TypeMgr) - Method in class moss.FreeNtn
Set the node type manager.
setNodeMgr(TypeMgr) - Method in class moss.MoleculeNtn
Set the node type manager.
setNodeMgr(TypeMgr) - Method in class moss.Notation
Set the node type manager.
setOutput(GraphWriter) - Method in class moss.Miner
Set the output writer.
setOutput(GraphWriter, Writer) - Method in class moss.Miner
Set the output writers.
setOutput(String, String) - Method in class moss.Miner
Set the output writer.
setOutput(String, String, String) - Method in class moss.Miner
Set the output writers.
setReader(Reader) - Method in class moss.Notation
Set the reader to read from.
setRelCompl(float) - Method in class moss.GraphWriter
Set the relative complement support of the current substructure.
setRelSupp(float) - Method in class moss.GraphWriter
Set the relative focus support of the current substructure.
setRingSizes(int, int) - Method in class moss.CanonicalForm
Set the ring sizes for ring extensions.
setRingSizes(int, int) - Method in class moss.Miner
Set the minimum and maximum ring size.
setSeed(Graph) - Method in class moss.Miner
Set the seed structure to start the search from.
setSeed(String, String) - Method in class moss.Miner
Set the seed structure to start the search from.
setSizes(int, int) - Method in class moss.Miner
Set the minimum and maximum fragment size.
setType(int) - Method in class moss.Miner
Set the support type.
setTypeMgrs(Notation) - Method in class moss.Notation
Set the type managers from another notation.
setValid(boolean) - Method in class moss.Fragment
Set or clear the valid flag.
setValue(float) - Method in class moss.GraphWriter
Set the value associated with the current graph.
setValue(float) - Method in class moss.NamedGraph
Set the value of this graph.
setValueAt(Object, int, int) - Method in class moss.MoSSTable
Set the value of a table cell from an object.
SIBLINGS - Static variable in class moss.Fragment
flag for possible equivalent siblings
SILICON - Static variable in class moss.AtomTypeMgr
 
SILVER - Static variable in class moss.AtomTypeMgr
 
SINGLE - Static variable in class moss.BondTypeMgr
bond type: single
size - Variable in class moss.CanonicalForm
the number of nodes in a ring (positive) or chain (negative)
size - Variable in class moss.Fragment
the number of nodes in a ring or chain (positive: ring, negative: chain)
size() - Method in class moss.Fragment
Get the size of the fragment.
size() - Method in class moss.FreeTypeMgr
Get the current number of types.
size() - Method in class moss.OverlapGraph
Get the size of the overlap graph (number of nodes).
size() - Method in class moss.Recoder
Get the size of the recoder.
SLN - Class in moss
Class for the SYBYL line notation (SLN, Tripos, Inc.).
SLN() - Constructor for class moss.SLN
Create a SYBYL line notation object.
SMALL - Static variable in class moss.MoSSPanel
the font for help text fields
SMILES - Class in moss
Class for the Simplified Molecular Input Line Entry System (SMILES, Daylight, Inc.).
SMILES() - Constructor for class moss.SMILES
Create a SMILES notation object.
SODIUM - Static variable in class moss.AtomTypeMgr
 
sort(ExtList) - Static method in class moss.ExtList
Sort an extension list (and remove duplicates).
sort() - Method in class moss.ExtMgr
Sort the extension edges lexicographically.
sort() - Method in class moss.Recoder
Sort types w.r.t. their frequency.
sortEdges() - Method in class moss.Node
Sort the edges that are incident to the node.
sortvec() - Method in class moss.ExtMgr
Sort the extension edges lexicographically.
SPECIAL - Static variable in class moss.TypeMgr
the flag for a special type
split() - Method in class moss.NamedGraph
Split a graph into its connected components.
src - Variable in class moss.CanonicalForm
the index of the current source node
src - Variable in class moss.Edge
the source node of the edge
src - Variable in class moss.ExtList
the index of the source node
src - Variable in class moss.Fragment
the index of the source node of the (first) new edge
srel - Variable in class moss.GraphReader
the relative support in the focus
srel - Variable in class moss.GraphWriter
the relative support in the focus
stack - Variable in class moss.Notation
the stack of unread/pushed back characters
stateChanged(ChangeEvent) - Method in class moss.MoSS
Handle the state change of the ring marking check box.
stats() - Method in class moss.Miner
Print statistics about the search.
STRONTIUM - Static variable in class moss.AtomTypeMgr
 
subcnt - Variable in class moss.Miner
the number of reported substructures
SUBS - Static variable in class moss.GraphReader
read mode: substructures
SUBS - Static variable in class moss.GraphWriter
write mode: substructures
SUBS - Static variable in class moss.MoSSTable
mode: substructures
succ - Variable in class moss.Embedding
the next embedding in a list of embeddings
succ - Variable in class moss.ExtList
the successor in a list
succ - Variable in class moss.NamedGraph
the next graph in a list
SULFUR - Static variable in class moss.AtomTypeMgr
 
supp - Variable in class moss.Fragment
the support and embedding counters for focus and complement
supp - Variable in class moss.Miner
the minimum support in the focus as an absolute value
SUPPMASK - Static variable in class moss.Fragment
the support type mask
sym - Variable in class moss.CanonicalForm
whether the current ring is locally symmetric

T

TableReader - Class in moss
Class for readers for simple table formats for graph data sets.
TableReader(Reader, int, Notation) - Constructor for class moss.TableReader
Create a table reader with default character flags.
TableWriter - Class in moss
Class for writers for simple table formats for graph data sets.
TableWriter(Writer, int, Notation) - Constructor for class moss.TableWriter
Create a simple table format writer.
tail - Variable in class moss.Fragment
the tail of the embedding list
tail - Variable in class moss.Miner
the tail of the list of graphs (insertion point for complement)
TANTALUM - Static variable in class moss.AtomTypeMgr
 
TECHNETIUM - Static variable in class moss.AtomTypeMgr
 
TELLURIUM - Static variable in class moss.AtomTypeMgr
 
TERBIUM - Static variable in class moss.AtomTypeMgr
 
term() - Method in class moss.Miner
Clean up after the search finished or was aborted.
THALLIUM - Static variable in class moss.AtomTypeMgr
 
THORIUM - Static variable in class moss.AtomTypeMgr
 
thresh - Variable in class moss.Miner
the threshold for the split into focus and complement
THULIUM - Static variable in class moss.AtomTypeMgr
 
TIN - Static variable in class moss.AtomTypeMgr
 
TITANIUM - Static variable in class moss.AtomTypeMgr
 
toLogic() - Method in class moss.NamedGraph
Create a Prolog description of this graph.
toString() - Method in class moss.Fragment
Create a string description of the fragment.
toString(Notation) - Method in class moss.Fragment
Create a string description of the fragment.
toString(CanonicalForm) - Method in class moss.Fragment
Create the code word of the fragment.
toString() - Method in class moss.Graph
Create a string description of the graph.
toString(Notation) - Method in class moss.Graph
Create a string description in the given notation.
toString(CanonicalForm) - Method in class moss.Graph
Create a code word for a given canonical form.
TRANSFORM - Static variable in class moss.Miner
flag for conversion to another description format
trim(Recoder) - Method in class moss.ExtMgr
Trim the extension edges.
trim(boolean) - Method in class moss.Graph
Trim a graph based on its encoding recoder.
trim(boolean, int) - Method in class moss.Recoder
Trim the recoder with a minimum support or frequency.
trim(int) - Method in class moss.Recoder
Trim the recoder with a minimum support.
trimFreq(int) - Method in class moss.Recoder
Trim the recoder with a minimum frequency.
trimSupp(int) - Method in class moss.Recoder
Trim the recoder with a minimum support.
TRIPLE - Static variable in class moss.BondTypeMgr
bond type: triple
TUNGSTEN - Static variable in class moss.AtomTypeMgr
 
type - Variable in class moss.CanonicalForm
the type of the extension edge (from EDGE.type)
type - Variable in class moss.Edge
the type of the edge, e.g.
type - Variable in class moss.Miner
the type of support to use
type - Variable in class moss.Node
the type (attribute/label) of a node (including flags)
TYPEMASK - Static variable in class moss.Edge
the mask for the base type
TYPEMASK - Static variable in class moss.Node
the mask for the base type
TypeMgr - Class in moss
Class for a node or edge type manager.
TypeMgr() - Constructor for class moss.TypeMgr
 

U

unembed() - Method in class moss.Fragment
Unembed a fragment, that is, remove all embeddings.
UNEMBED - Static variable in class moss.Miner
flag for unembedding siblings of the current search tree nodes
UNKNOWN - Static variable in class moss.AtomTypeMgr
atom type: unknown
UNKNOWN - Static variable in class moss.BondTypeMgr
bond type: unknown
unmark(Node) - Static method in class moss.Notation
Unmark a connected component.
unpack() - Method in class moss.Fragment
Unpack the list of embeddings.
unread(int) - Method in class moss.Notation
Unread/push back a character.
UPGRADE - Static variable in class moss.BondTypeMgr
a mask, to be anded (bitwise &) with a bond type in order to upgrade an aromatic bond to a double bond
URANIUM - Static variable in class moss.AtomTypeMgr
 
useOrbits() - Method in class moss.CanonicalForm
Whether node orbits are to be used to filter extensions.

V

VALID - Static variable in class moss.Fragment
flag for a valid fragment; invalid fragments can occur in ring mining with canonical form pruning: they are non-canonical fragments that have to processed nevertheless
validRing() - Method in class moss.CanonicalForm
Check whether the current ring extension is valid.
validRing() - Method in class moss.CnFBreadth1
Check whether the current ring extension is valid.
validRing() - Method in class moss.CnFBreadth2
Check whether the current ring extension is valid.
validRing() - Method in class moss.CnFDepth
Check whether the current ring extension is valid.
value - Variable in class moss.GraphReader
the value associated with the current graph
value - Variable in class moss.GraphWriter
the value associated with the current graph
value - Variable in class moss.NamedGraph
the value associated with the graph
VANADIUM - Static variable in class moss.AtomTypeMgr
 
variant() - Method in class moss.CanonicalForm
Create the next ring extension variant.
variant() - Method in class moss.CnFBreadth1
Create the next ring extension variant.
variant() - Method in class moss.CnFBreadth2
Create the next ring extension variant.
variant() - Method in class moss.CnFDepth
Create the next ring extension variant.
VERBOSE - Static variable in class moss.Miner
flag for verbose reporting
VERSION - Static variable in class moss.Miner
the version of this program
vntn - Variable in class moss.Miner
the notation for verbose output

W

WILDCARD - Static variable in class moss.Edge
the flag for a wildcard type
WILDCARD - Static variable in class moss.Node
the special code for a wildcard type
WILDCARD - Static variable in class moss.TypeMgr
the flag for a wildcard type
word - Variable in class moss.CanonicalForm
the code word for isCanonic/makeCanonic
wrids - Variable in class moss.Miner
the identifier file writer
write(Graph, Writer) - Method in class moss.LiNoG
Write a description of a graph.
write(Graph, Writer) - Method in class moss.MoleculeNtn
Write a description of a molecule.
write(Graph, Writer) - Method in class moss.NEList
Write a description of an attributed graph.
write(Graph, Writer) - Method in class moss.Notation
Write a description of an attributed graph.
writeGraph() - Method in class moss.GraphWriter
Write the current graph description.
writeGraph() - Method in class moss.NEListWriter
Write the current graph description.
writeGraph() - Method in class moss.SDfileWriter
Write a description of the current graph.
writeGraph() - Method in class moss.TableWriter
Write a description of the current graph.
writeGraphs() - Method in class moss.Miner
Write all graphs of the database.
writeHeader() - Method in class moss.GraphWriter
Write a header.
writeHeader() - Method in class moss.NEListWriter
Write a header.
writeHeader() - Method in class moss.SDfileWriter
Write a header.
writeHeader() - Method in class moss.TableWriter
Write a header.
writer - Variable in class moss.Miner
the substructure file writer

X

xemgr - Variable in class moss.CanonicalForm
the extension edge manager (for extensions without embeddings)
XENON - Static variable in class moss.AtomTypeMgr
 

Y

YTTERBIUM - Static variable in class moss.AtomTypeMgr
 
YTTRIUM - Static variable in class moss.AtomTypeMgr
 

Z

ZINC - Static variable in class moss.AtomTypeMgr
 
ZIRCONIUM - Static variable in class moss.AtomTypeMgr
 
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