public class SmilesGenerator
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
private int |
ac |
private boolean |
addAtomComment |
private Node[] |
atoms |
private BS |
bsAromatic |
private BS |
bsBondsDn |
private BS |
bsBondsUp |
private BS |
bsIncludingH |
private BS |
bsRingKeys |
private BS |
bsSelected |
private BS |
bsToDo |
private boolean |
explicitH |
(package private) boolean |
getAromatic |
private java.util.Map<java.lang.String,java.lang.Object[]> |
htRings |
private java.util.Map<java.lang.String,java.lang.Object[]> |
htRingsSequence |
private boolean |
isPolyhedral |
private boolean |
noBioComment |
private boolean |
noStereo |
private int |
nPairs |
private int |
nPairsMax |
private Node |
prevAtom |
private Node[] |
prevSp2Atoms |
private javajs.util.SB |
ringSets |
private SmilesStereo |
smilesStereo |
javajs.util.P3 |
stereoReference |
private boolean |
topologyOnly |
private VTemp |
vTemp |
Constructor and Description |
---|
SmilesGenerator() |
Modifier and Type | Method and Description |
---|---|
private void |
addBracketedBioName(javajs.util.SB sb,
Node atom,
java.lang.String atomName,
boolean addComment) |
private java.lang.String |
addStereoCheck(int atomIndex,
Node[] stereo,
int i,
java.lang.String s)
checks a group and either adds a new group to the growing
check string or returns null
|
private java.lang.String |
checkStereoPairs(Node atom,
int atomIndex,
Node[] stereo,
int stereoFlag) |
private void |
dumpRingKeys(javajs.util.SB sb,
java.util.Map<java.lang.String,java.lang.Object[]> ht) |
private java.lang.String |
getBioSmiles(BS bsSelected,
java.lang.String comment,
int flags) |
private char |
getBondStereochemistry(Edge bond,
Node atomFrom)
Retrieves the saved character based on the index of the bond.
|
private java.lang.String |
getRingCache(int i0,
int i1,
java.util.Map<java.lang.String,java.lang.Object[]> ht) |
protected static java.lang.String |
getRingKey(int i0,
int i1) |
private java.lang.String |
getRingPointer(int i) |
(package private) java.lang.String |
getSmiles(Node[] atoms,
int ac,
BS bsSelected,
java.lang.String comment,
int flags) |
private Node |
getSmilesAt(javajs.util.SB sb,
Node atom,
boolean allowConnectionsToOutsideWorld,
boolean allowBranches,
boolean explicitH,
boolean forceBrackets) |
private java.lang.String |
getSmilesComponent(Node atom,
BS bs,
boolean allowBioResidues,
boolean allowConnectionsToOutsideWorld,
boolean forceBrackets)
creates a valid SMILES string from a model.
|
private void |
setBondDirections()
Creates global BitSets bsBondsUp and bsBondsDown.
|
(package private) void |
sortBonds(Node atom,
Node refAtom,
javajs.util.P3 center) |
private java.lang.String |
sortInorganic(Node atom,
javajs.util.Lst<Edge> v,
VTemp vTemp)
We must sort the bond vector such that a diaxial pair is
first and last.
|
private Node[] atoms
private int ac
private BS bsSelected
private BS bsAromatic
private boolean explicitH
private javajs.util.SB ringSets
private VTemp vTemp
private int nPairs
private int nPairsMax
private BS bsBondsUp
private BS bsBondsDn
private BS bsToDo
private Node prevAtom
private Node[] prevSp2Atoms
private java.util.Map<java.lang.String,java.lang.Object[]> htRingsSequence
private java.util.Map<java.lang.String,java.lang.Object[]> htRings
private BS bsRingKeys
private BS bsIncludingH
private boolean topologyOnly
boolean getAromatic
private boolean addAtomComment
private boolean noBioComment
private boolean noStereo
public javajs.util.P3 stereoReference
private SmilesStereo smilesStereo
private boolean isPolyhedral
java.lang.String getSmiles(Node[] atoms, int ac, BS bsSelected, java.lang.String comment, int flags) throws InvalidSmilesException
InvalidSmilesException
private java.lang.String getBioSmiles(BS bsSelected, java.lang.String comment, int flags) throws InvalidSmilesException
InvalidSmilesException
private void addBracketedBioName(javajs.util.SB sb, Node atom, java.lang.String atomName, boolean addComment)
private java.lang.String getSmilesComponent(Node atom, BS bs, boolean allowBioResidues, boolean allowConnectionsToOutsideWorld, boolean forceBrackets) throws InvalidSmilesException
atom
- bs
- allowBioResidues
- allowConnectionsToOutsideWorld
- forceBrackets
- InvalidSmilesException
private char getBondStereochemistry(Edge bond, Node atomFrom)
bond
- atomFrom
- private void setBondDirections()
private Node getSmilesAt(javajs.util.SB sb, Node atom, boolean allowConnectionsToOutsideWorld, boolean allowBranches, boolean explicitH, boolean forceBrackets)
private java.lang.String sortInorganic(Node atom, javajs.util.Lst<Edge> v, VTemp vTemp)
atom
- v
- vTemp
- private java.lang.String checkStereoPairs(Node atom, int atomIndex, Node[] stereo, int stereoFlag)
private java.lang.String addStereoCheck(int atomIndex, Node[] stereo, int i, java.lang.String s)
atomIndex
- stereo
- i
- s
- private java.lang.String getRingCache(int i0, int i1, java.util.Map<java.lang.String,java.lang.Object[]> ht)
private java.lang.String getRingPointer(int i)
private void dumpRingKeys(javajs.util.SB sb, java.util.Map<java.lang.String,java.lang.Object[]> ht)
protected static java.lang.String getRingKey(int i0, int i1)