Serialized Form
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Package moss
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Class moss.AtomTypeMgr
class AtomTypeMgr extends TypeMgr implements Serializable- serialVersionUID:
- 65536L
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Class moss.BondTypeMgr
class BondTypeMgr extends TypeMgr implements Serializable- serialVersionUID:
- 65536L
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Class moss.CanonicalForm
class CanonicalForm extends Object implements Serializable- serialVersionUID:
- 65538L
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Serialized Fields
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all
long all
all (remaining) ring flags of the current edge -
cedge
int cedge
the edge type for chain extensions -
chcnt
int chcnt
the number of variable length chains -
cnode
int cnode
the node type for chain extensions -
curr
long curr
the current ring flag -
dir
boolean dir
whether the graphs are to be treated as directed -
dst
int dst
the index of the current destination node -
edgecnt
int edgecnt
the number of new edges -
edges
Edge[] edges
(relevant) edges of the extension -
emap
int[] emap
the edge map for making a graph canonic -
emb
Embedding emb
the embedding that is extended (may benull
) -
fixed
int fixed
the number of fixed edges in a canonical form test -
frag
Fragment frag
the fragment that is extended -
idx
int idx
the current edge index in the source node -
max
int max
the maximum fragment size (number of nodes) -
mode
int mode
the extension mode (e.g.EDGE
,RING
) -
nmap
int[] nmap
the node map for making a graph canonic -
nodecnt
int nodecnt
the number of new nodes -
nodes
Node[] nodes
(relevant) nodes of the extension -
pmax
int pmax
the maximal position/position index of a ring edge -
pmin
int pmin
the minimal position/current position index of a ring edge -
pos1
int pos1
the current position 1 of equivalent edges for ring extensions -
pos2
int pos2
the current position 2 of equivalent edges for ring extensions -
rgmax
int rgmax
the maximum ring size (number of nodes/edges) -
rgmin
int rgmin
the minimum ring size (number of nodes/edges) -
size
int size
the number of nodes in a ring (positive) or chain (negative) -
src
int src
the index of the current source node -
sym
boolean sym
whether the current ring is locally symmetric -
type
int type
the type of the extension edge (fromEDGE.type
) -
word
int[] word
the code word for isCanonic/makeCanonic -
xemgr
ExtMgr xemgr
the extension edge manager (for extensions without embeddings)
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Class moss.CnFBreadth1
class CnFBreadth1 extends CanonicalForm implements Serializable- serialVersionUID:
- 65536L
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Class moss.CnFBreadth2
class CnFBreadth2 extends CanonicalForm implements Serializable- serialVersionUID:
- 65536L
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Class moss.CnFDepth
class CnFDepth extends CanonicalForm implements Serializable- serialVersionUID:
- 65536L
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Serialized Fields
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eqpos
int[] eqpos
the equivalent positions for a new ring edge -
path
int[] path
the indices of the edges on the rightmost path -
pei
int pei
the index of the next path edge
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Class moss.Ctab
class Ctab extends MoleculeNtn implements Serializable- serialVersionUID:
- 65536L
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Serialized Fields
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buf
int[] buf
the buffer for number reading
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Class moss.Edge
class Edge extends Object implements Serializable- serialVersionUID:
- 65538L
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Class moss.EdgePatternMgr
class EdgePatternMgr extends Object implements Serializable- serialVersionUID:
- 65536L
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Serialized Fields
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base
int base
the base support (largest possible support) -
bins
moss.EdgePattern[] bins
the hash table of the extension edges -
cnt
int cnt
the number of added edge patterns (full and partial) -
dir
boolean dir
whether edges are to be treated as directed -
supps
int[] supps
the support values for each edge type
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Class moss.Embedding
class Embedding extends Object implements Serializable- serialVersionUID:
- 65538L
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Class moss.ExtMgr
class ExtMgr extends Object implements Serializable- serialVersionUID:
- 65536L
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Serialized Fields
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bins
moss.ExtEdge[] bins
the hash table of the extension edges -
cnt
int cnt
the number of added extension edges (with reversals) -
curr
moss.ExtEdge curr
the current extension edge -
dir
boolean dir
whether edges are to be treated as directed -
exts
moss.ExtEdge[] exts
the table for access via the source node type
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Class moss.Fragment
class Fragment extends Object implements Serializable- serialVersionUID:
- 65541L
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Serialized Fields
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base
Fragment base
the base fragment (which was extended) -
bemb
Embedding bemb
the current base embedding (which was extended) -
chcnt
int chcnt
the number of variable length chains -
cnt
int cnt
the number of embeddings/graphs for the current graph -
cover
NamedGraph[] cover
the graph cover of the fragment -
curr
Embedding curr
the current embedding (cursor) -
dir
boolean dir
whether the fragment is directed -
dst
int dst
the index of the destination node of the (first) new edge -
flags
int flags
the property flags of the embedding (e.g.PERFECT
) -
graph
Graph graph
the fragment as a graph -
hash
int hash
the hash code of the fragment (or -1 if not computed yet) -
idx
int idx
the index of the (first) new edge -
list
Embedding list
the list of embeddings of the fragment -
max
int max
the maximal number of embeddings per graph -
ris
int[] ris
the indices of the nodes of new ring edges -
size
int size
the number of nodes in a ring or chain (positive: ring, negative: chain) -
src
int src
the index of the source node of the (first) new edge -
supp
int[] supp
the support and embedding counters for focus and complement -
tail
Embedding tail
the tail of the embedding list
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Class moss.FreeNtn
class FreeNtn extends Notation implements Serializable- serialVersionUID:
- 65536L
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Class moss.FreeTypeMgr
class FreeTypeMgr extends TypeMgr implements Serializable- serialVersionUID:
- 65536L
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Serialized Fields
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bins
moss.Type[] bins
the array of hash bins (name to code map) -
imap
moss.Type[] imap
the inverse map (code to name map) -
size
int size
the current number of types
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Class moss.Graph
class Graph extends Object implements Serializable- serialVersionUID:
- 65542L
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Serialized Fields
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coder
Recoder coder
an optional node type recoder -
dir
boolean dir
whether the graph is directed -
edgecnt
int edgecnt
the current number of edges (may be smaller than the array length) -
edges
Edge[] edges
the array of edges (may be only partially used) -
nodecnt
int nodecnt
the current number of nodes (may be smaller than the array length) -
nodes
Node[] nodes
the array of nodes (may be only partially used) -
ntn
Notation ntn
the notation for describing the graph
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Class moss.GraphReader
class GraphReader extends TableReader implements Serializable- serialVersionUID:
- 65538L
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Serialized Fields
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cabs
int cabs
the absolute support in the complement -
crel
float crel
the relative support in the complement -
desc
String desc
the description of the current graph -
edges
int edges
the number of edges of the current graph -
graph
Graph graph
the current graph -
mode
int mode
the read mode -
name
String name
the name/identifier of the current graph -
nodes
int nodes
the number of nodes of the current graph -
ntn
Notation ntn
the notation for parsing graph descriptions -
sabs
int sabs
the absolute support in the focus -
srel
float srel
the relative support in the focus -
value
float value
the value associated with the current graph
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Class moss.GraphWriter
class GraphWriter extends TableWriter implements Serializable- serialVersionUID:
- 65538L
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Serialized Fields
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cabs
int cabs
the absolute support in the complement -
crel
float crel
the relative support in the complement -
desc
String desc
the description of the current graph -
edges
int edges
the number of edges of the current graph -
graph
Graph graph
the current graph -
mode
int mode
the write mode -
name
String name
the name of the current graph -
nodes
int nodes
the number of nodes of the current graph -
ntn
Notation ntn
the notation for the graphs -
sabs
int sabs
the absolute support in the focus -
srel
float srel
the relative support in the focus -
value
float value
the value associated with the current graph
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Class moss.LineReader
class LineReader extends GraphReader implements Serializable- serialVersionUID:
- 65536L
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Serialized Fields
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pbrec
boolean pbrec
whether there is a pushed back record -
record
String[] record
the fields of a record
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Class moss.LineWriter
class LineWriter extends GraphWriter implements Serializable- serialVersionUID:
- 65536L
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Class moss.LiNoG
class LiNoG extends FreeNtn implements Serializable- serialVersionUID:
- 65536L
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Serialized Fields
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buf
StringBuilder buf
the buffer for reading and creating node descriptions -
coder
Recoder coder
the node type recoder for a graph to describe -
desc
StringBuilder desc
the buffer for creating graph descriptions -
graph
Graph graph
the parsed graph -
labels
int[] labels
the label to node index map
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Class moss.Miner
class Miner extends Object implements Serializable- serialVersionUID:
- 524291L
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Serialized Fields
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bins
moss.RepoElem[] bins
the repository of processed substructures (hash table) -
canonic
long canonic
for benchmarking: canonical form pruning counter -
chains
long chains
for benchmarking: invalid chains counter -
cnf
CanonicalForm cnf
the canonical form and restricted extension generator -
cnts
int[] cnts
the numbers of graphs in focus and complement -
coder
Recoder coder
the recoder for the node types -
comp
int comp
the maximum support in the complement as an absolute value -
conf
double conf
the minimum confidence of an association rule as a fraction -
curr
NamedGraph curr
the current insertion point for the focus -
duplic
long duplic
for benchmarking: duplicate fragments counter -
embcmp
long embcmp
for benchmarking: the number of comparisons with embeddings -
embcnt
long embcnt
for benchmarking: the number of created embeddings -
emblvl
int emblvl
the level at which to switch to embeddings -
epmgr
EdgePatternMgr epmgr
the edge pattern manager (if needed, for rule generation) -
equiv
long equiv
for benchmarking: equivalent frag. pruning counter -
error
Throwable error
the error status for the search process -
exseed
Graph exseed
the node types that are excluded as seeds -
extype
Graph extype
the excluded node types -
fcomp
double fcomp
the maximum support in the complement as a fraction -
frag
Fragment frag
the initial fragment (embedded seed structure) -
fragcmp
long fragcmp
for benchmarking: the number of fragment comparisons -
fragcnt
long fragcnt
for benchmarking: the number of created fragments -
fsupp
double fsupp
the minimum support in the focus as a fraction -
graphs
NamedGraph graphs
the list of graphs to mine (database) -
group
int group
the group for graphs with a value below the threshold -
invalid
long invalid
for benchmarking: invalid fragments counter -
isocnt
long isocnt
for benchmarking: the number of isomorphism tests -
lowsupp
long lowsupp
for benchmarking: insufficient support pruning counter -
masks
int[] masks
the masks for nodes and edges -
max
int max
the maximum size of substructures to report (number of nodes) -
maxdepth
int maxdepth
for benchmarking: the maximum depth of the search tree -
maxepg
int maxepg
the maximum number of embeddings per graph -
min
int min
the minimum size of substructures to report (number of nodes) -
mode
int mode
the search mode flags -
nodecnt
long nodecnt
for benchmarking: the number of search tree nodes -
nonclsd
long nonclsd
for benchmarking: non-closed fragments counter -
norm
CanonicalForm norm
the canonical form for normalizing the output -
openrgs
long openrgs
for benchmarking: open ring fragments counter -
pats
moss.GraphPattern pats
the list of found patterns for rule generation -
perfect
long perfect
for benchmarking: perfect extension pruning counter -
reader
GraphReader reader
the graph data set file reader -
recnt
int recnt
the size of the repository (number of substructures) -
repcnt
long repcnt
for benchmarking: the number of repository accesses -
rgmax
int rgmax
the maximum size of rings (number of nodes/edges) -
rgmin
int rgmin
the minimum size of rings (number of nodes/edges) -
ringord
long ringord
for benchmarking: ring order pruning counter -
seed
Graph seed
the seed structure to start the search from -
stop
boolean stop
whether to abort the search thread -
subcnt
int subcnt
the number of reported substructures -
supp
int supp
the minimum support in the focus as an absolute value -
tail
NamedGraph tail
the tail of the list of graphs (insertion point for complement) -
thresh
double thresh
the threshold for the split into focus and complement -
type
int type
the type of support to use -
vntn
Notation vntn
the notation for verbose output -
writer
GraphWriter writer
the substructure file writer
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Class moss.MoleculeNtn
class MoleculeNtn extends Notation implements Serializable- serialVersionUID:
- 65536L
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Serialized Fields
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desc
StringBuilder desc
the buffer for creating molecule descriptions
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Class moss.MoSS
class MoSS extends JFrame implements Serializable- serialVersionUID:
- 196608L
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Serialized Fields
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aborted
boolean aborted
whether the miner has been aborted -
abssupp
JCheckBox abssupp
whether to interpret the support as absolute numbers -
atarom
JCheckBox atarom
whether to match the atom aromaticity -
attype
JComboBox<String> attype
whether to ignore the atom type -
bdarom
JComboBox<String> bdarom
how to treat aromatic bonds -
bdtype
JComboBox<String> bdtype
whether to ignore the bond type -
buf
StringBuilder buf
the buffer for reading the configuration file -
canonic
JCheckBox canonic
whether to do canonical form pruning -
chains
JCheckBox chains
whether to find variable length carbon chains -
charge
JCheckBox charge
whether to match the atom charge -
chooser
JFileChooser chooser
the file chooser for selecting the input and output files -
closed
JCheckBox closed
whether to restrict the output to closed substructures -
equiv
JCheckBox equiv
whether to do equivalent sibling pruning -
exec
JButton exec
the execute/abort button -
exseed
JTextField exseed
the node types that are excluded for seeds -
exttype
JComboBox<String> exttype
the extension type -
extype
JTextField extype
the excluded node types -
fn_data
JTextField fn_data
the name of the input file -
fn_ids
JTextField fn_ids
the name of the graph identifier file -
fn_sub
JTextField fn_sub
the name of the substructure output file -
greedy
JCheckBox greedy
whether to use greedy algorithm for MIS computation -
infmt
JComboBox<String> infmt
the input format for the graphs -
invert
JCheckBox invert
whether to invert the split -
isprog
boolean isprog
whether started as a stand-alone program -
kekule
JCheckBox kekule
whether to convert Kekule representations -
level
JSpinner level
the level from which to use embeddings -
maxepg
JSpinner maxepg
the maximal number of embeddings per graph -
maxring
JSpinner maxring
the maximal size of a ring -
maxsize
JSpinner maxsize
the maximal size of a substructure -
maxsupp
JTextField maxsupp
the maximal support in the complement -
miner
Miner miner
the current substructure miner -
minring
JSpinner minring
the minimal size of a ring -
minsize
JSpinner minsize
the minimal size of a substructure -
minsupp
JTextField minsupp
the minimal support in the focus -
normal
JCheckBox normal
whether to normalize the output -
orbits
JCheckBox orbits
whether to do filter with node orbits -
owner
Component owner
the owner of this dialog box -
pane
JTabbedPane pane
the pane for the parameter tabs -
perfect
JComboBox<String> perfect
whether to do perfect extension pruning -
rclbls
JLabel[] rclbls
the labels that can be disabled in the tab -
ringext
JComboBox<String> ringext
the type of ring extensions -
rings
JCheckBox rings
whether to mark rings -
running
boolean running
whether the miner is currently running -
seed
JTextField seed
the seed structure to start the search from -
seedfmt
JComboBox<String> seedfmt
the seed format -
splbls
JLabel[] splbls
the labels that can be disabled in the tab -
start
long start
the start time for the miner thread -
stat
JTextField stat
the status line -
subfmt
JComboBox<String> subfmt
the output format for the substructures -
supptype
JComboBox<String> supptype
the support type -
thresh
JTextField thresh
the threshold for the split -
timer
Timer timer
the timer for updating the progress information -
unembed
JCheckBox unembed
whether to unembed siblings of the current search tree node -
verbose
JCheckBox verbose
whether to do verbose message output
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Class moss.MoSSPanel
class MoSSPanel extends JPanel implements Serializable- serialVersionUID:
- 131079L
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Class moss.MoSSTable
class MoSSTable extends AbstractTableModel implements Serializable- serialVersionUID:
- 131079L
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Serialized Fields
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buf
StringBuilder buf
the buffer for reading input lines -
format
String format
the format of the table -
mode
int mode
the mode of the table -
names
String[] names
the names of the columns of the table -
rowcnt
int rowcnt
the number of rows of the table
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Class moss.NamedGraph
class NamedGraph extends Graph implements Serializable- serialVersionUID:
- 65538L
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Serialized Fields
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group
int group
the marker for grouping (either 0 or 1, used as an array index) -
name
String name
the graph name/identifier -
succ
NamedGraph succ
the next graph in a list -
value
float value
the value associated with the graph
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Class moss.NEList
class NEList extends FreeNtn implements Serializable- serialVersionUID:
- 65536L
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Serialized Fields
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linog
LiNoG linog
linear notation for creating a description
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Class moss.NEListReader
class NEListReader extends GraphReader implements Serializable- serialVersionUID:
- 65536L
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Serialized Fields
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buf
StringBuilder buf
the buffer for an input field -
linog
Notation linog
the notation for line descriptions
-
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Class moss.NEListWriter
class NEListWriter extends GraphWriter implements Serializable- serialVersionUID:
- 65536L
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Class moss.Node
class Node extends Object implements Serializable- serialVersionUID:
- 65538L
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Serialized Fields
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deg
int deg
the current number of incident edges (node degree) -
edges
Edge[] edges
the array of incident edges (may not be fully used) -
mark
int mark
a marker for internal use (e.g. for a substructure) -
orbit
int orbit
the representative of the orbit of the node -
type
int type
the type (attribute/label) of a node (including flags)
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Class moss.Notation
class Notation extends Object implements Serializable- serialVersionUID:
- 65538L
-
Class moss.Recoder
class Recoder extends Object implements Serializable- serialVersionUID:
- 65536L
-
Serialized Fields
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bins
moss.RcType[] bins
the hash table for mapping types to codes (old codes to new) -
idx
int idx
the index of the current graph (for frequency counting) -
size
int size
the current number of types -
types
moss.RcType[] types
the types and their frequencies, sorted by their code
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Class moss.SDfileReader
class SDfileReader extends GraphReader implements Serializable- serialVersionUID:
- 65536L
-
Serialized Fields
-
buf
StringBuilder buf
the buffer for an input line -
smiles
Notation smiles
the notation for line descriptions
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Class moss.SDfileWriter
class SDfileWriter extends GraphWriter implements Serializable- serialVersionUID:
- 65536L
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Class moss.SLN
class SLN extends MoleculeNtn implements Serializable- serialVersionUID:
- 65536L
-
Serialized Fields
-
buf
StringBuilder buf
the buffer for creating atom descriptions -
coder
Recoder coder
the atom type recoder for a molecule to describe -
labels
int[] labels
the label to node index map -
mol
Graph mol
the parsed molecule
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Class moss.SMILES
class SMILES extends MoleculeNtn implements Serializable- serialVersionUID:
- 65536L
-
Serialized Fields
-
bonds
int[] bonds
the bond types of forward references -
buf
StringBuilder buf
the buffer for creating atom descriptions -
coder
Recoder coder
the atom type recoder for a molecule to describe -
labels
int[] labels
the label to node index map -
mol
Graph mol
the parsed molecule
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Class moss.TypeMgr
class TypeMgr extends Object implements Serializable- serialVersionUID:
- 65536L
-