org.jmol.smiles

Class SmilesMatcher

java.lang.Object

org.jmol.smiles.SmilesMatcher

All Implemented Interfaces:

SmilesMatcherInterface

public class SmilesMatcher
extends java.lang.Object
implements SmilesMatcherInterface

Originating author: Nicholas Vervelle A class to handle a variety of SMILES/SMARTS-related functions, including: -- determining if two SMILES strings are equivalent -- determining the molecular formula of a SMILES or SMARTS string -- searching for specific runs of atoms in a 3D model -- searching for specific runs of atoms in a SMILES description -- generating valid (though not canonical) SMILES and bioSMILES strings -- getting atom-atom correlation maps to be used with biomolecular alignment methods

The original SMILES description can been found at the SMILES Home Page. Specification for this implementation can be found in package.html.

 
 public methods:
 
 int areEqual  -- checks a SMILES string against a reference (-1 for error; 0 for no finds; >0 for number of finds)
 
 BitSet[] find  -- finds one or more occurances of a SMILES or SMARTS string within a SMILES string
 
 int[][] getCorrelationMaps  -- returns correlated arrays of atoms
 
 String getLastError  -- returns any error that was last encountered.
 
 String getMolecularFormula   -- returns the MF of a SMILES or SMARTS string
 
 String getRelationship -- returns isomeric relationship
 
 String getSmiles  -- returns a standard SMILES string or a
                  Jmol BIOSMILES string with comment header.
 
 BitSet getSubstructureSet  -- returns a single BitSet with all found atoms included
   
   
   in Jmol script:
   
   string2.find("SMILES", string1)
   string2.find("SMARTS", string1)
   
   e.g.
   
     print "CCCC".find("SMILES", "C[C]")
 
   select search("smartsString")
   
   All bioSMARTS strings begin with ~ (tilde).
   
 
 

Author:

Bob Hanson

Field Summary

Fields

Modifier and Type	Field and Description
private static int	MODE_ARRAY
private static int	MODE_BITSET
private static int	MODE_MAP

Constructor Summary

Constructors

Constructor and Description
SmilesMatcher()

Method Summary

Modifier and Type	Method and Description
boolean	areEqual(java.lang.String smiles, SmilesSearch molecule) for JUnit test, mainly
int	areEqual(java.lang.String smiles1, java.lang.String smiles2)
private static int	countStereo(java.lang.String s)
private BS[]	find(java.lang.String pattern, SmilesSearch search, boolean isSmarts, boolean matchAllAtoms, boolean firstMatchOnly)
BS[]	find(java.lang.String pattern, java.lang.String smiles, boolean isSmarts, boolean firstMatchOnly) Searches for all matches of a pattern within a SMILES string.
int[][]	getCorrelationMaps(java.lang.String pattern, Node[] atoms, int ac, BS bsSelected, boolean isSmarts, boolean firstMatchOnly) Rather than returning bitsets, this method returns the sets of matching atoms in array form so that a direct atom-atom correlation can be made.
java.lang.String	getLastException()
java.lang.String	getMolecularFormula(java.lang.String pattern, boolean isSmarts)
java.lang.String	getRelationship(java.lang.String smiles1, java.lang.String smiles2)
java.lang.String	getSmiles(Node[] atoms, int ac, BS bsSelected, boolean asBioSmiles, boolean bioAllowUnmatchedRings, boolean bioAddCrossLinks, java.lang.String bioComment, boolean explicitH)
BS	getSubstructureSet(java.lang.String pattern, Node[] atoms, int ac, BS bsSelected, boolean isSmarts, boolean firstMatchOnly) Returns a bitset matching the pattern within atoms.
BS[]	getSubstructureSetArray(java.lang.String pattern, Node[] atoms, int ac, BS bsSelected, BS bsAromatic, boolean isSmarts, boolean firstMatchOnly) Returns a vector of bitsets indicating which atoms match the pattern.
void	getSubstructureSets(java.lang.String[] smarts, Node[] atoms, int ac, int flags, BS bsSelected, javajs.util.Lst<BS> ret, javajs.util.Lst<BS>[] vRings) called by ForceFieldMMFF.setAtomTypes
private java.lang.Object	match(java.lang.String pattern, Node[] atoms, int ac, BS bsSelected, BS bsAromatic, boolean isSmarts, boolean matchAllAtoms, boolean firstMatchOnly, int mode)
java.lang.String	reverseChirality(java.lang.String smiles)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

MODE_BITSET

private static final int MODE_BITSET

See Also:

Constant Field Values

MODE_ARRAY

private static final int MODE_ARRAY

See Also:

Constant Field Values

MODE_MAP

private static final int MODE_MAP

See Also:

Constant Field Values

Constructor Detail

SmilesMatcher

public SmilesMatcher()

Method Detail

getLastException

public java.lang.String getLastException()

Specified by:

getLastException in interface SmilesMatcherInterface

getMolecularFormula

public java.lang.String getMolecularFormula(java.lang.String pattern,
                                            boolean isSmarts)
                                     throws java.lang.Exception

Specified by:

getMolecularFormula in interface SmilesMatcherInterface

Throws:

java.lang.Exception

getSmiles

public java.lang.String getSmiles(Node[] atoms,
                                  int ac,
                                  BS bsSelected,
                                  boolean asBioSmiles,
                                  boolean bioAllowUnmatchedRings,
                                  boolean bioAddCrossLinks,
                                  java.lang.String bioComment,
                                  boolean explicitH)
                           throws java.lang.Exception

Specified by:

getSmiles in interface SmilesMatcherInterface

Throws:

java.lang.Exception

areEqual

public int areEqual(java.lang.String smiles1,
                    java.lang.String smiles2)
             throws java.lang.Exception

Specified by:

areEqual in interface SmilesMatcherInterface

Throws:

java.lang.Exception

areEqual

public boolean areEqual(java.lang.String smiles,
                        SmilesSearch molecule)
                 throws java.lang.Exception

for JUnit test, mainly

Parameters:

smiles -

molecule -

Returns:

true only if the SMILES strings match and there are no errors

Throws:

java.lang.Exception

find

public BS[] find(java.lang.String pattern,
                 java.lang.String smiles,
                 boolean isSmarts,
                 boolean firstMatchOnly)
          throws java.lang.Exception

Searches for all matches of a pattern within a SMILES string. If SMILES (not isSmarts), requires that all atoms be part of the match.

Specified by:

find in interface SmilesMatcherInterface

Parameters:

pattern - SMILES or SMARTS pattern.

smiles -

isSmarts - TRUE for SMARTS strings, FALSE for SMILES strings

firstMatchOnly -

Returns:

number of occurances of pattern within smiles

Throws:

java.lang.Exception

getRelationship

public java.lang.String getRelationship(java.lang.String smiles1,
                                        java.lang.String smiles2)
                                 throws java.lang.Exception

Specified by:

getRelationship in interface SmilesMatcherInterface

Throws:

java.lang.Exception

reverseChirality

public java.lang.String reverseChirality(java.lang.String smiles)

Specified by:

reverseChirality in interface SmilesMatcherInterface

getSubstructureSet

public BS getSubstructureSet(java.lang.String pattern,
                             Node[] atoms,
                             int ac,
                             BS bsSelected,
                             boolean isSmarts,
                             boolean firstMatchOnly)
                      throws java.lang.Exception

Returns a bitset matching the pattern within atoms.

Specified by:

getSubstructureSet in interface SmilesMatcherInterface

Parameters:

pattern - SMILES or SMARTS pattern.

atoms -

ac -

bsSelected -

isSmarts -

firstMatchOnly -

Returns:

BitSet indicating which atoms match the pattern.

Throws:

java.lang.Exception

getSubstructureSets

public void getSubstructureSets(java.lang.String[] smarts,
                                Node[] atoms,
                                int ac,
                                int flags,
                                BS bsSelected,
                                javajs.util.Lst<BS> ret,
                                javajs.util.Lst<BS>[] vRings)
                         throws java.lang.Exception

called by ForceFieldMMFF.setAtomTypes

Specified by:

getSubstructureSets in interface SmilesMatcherInterface

Throws:

java.lang.Exception

getSubstructureSetArray

public BS[] getSubstructureSetArray(java.lang.String pattern,
                                    Node[] atoms,
                                    int ac,
                                    BS bsSelected,
                                    BS bsAromatic,
                                    boolean isSmarts,
                                    boolean firstMatchOnly)
                             throws java.lang.Exception

Returns a vector of bitsets indicating which atoms match the pattern.

Specified by:

getSubstructureSetArray in interface SmilesMatcherInterface

Parameters:

pattern - SMILES or SMARTS pattern.

atoms -

ac -

bsSelected -

bsAromatic -

isSmarts -

firstMatchOnly -

Returns:

BitSet Array indicating which atoms match the pattern.

Throws:

java.lang.Exception

getCorrelationMaps

public int[][] getCorrelationMaps(java.lang.String pattern,
                                  Node[] atoms,
                                  int ac,
                                  BS bsSelected,
                                  boolean isSmarts,
                                  boolean firstMatchOnly)
                           throws java.lang.Exception

Rather than returning bitsets, this method returns the sets of matching atoms in array form so that a direct atom-atom correlation can be made.

Specified by:

getCorrelationMaps in interface SmilesMatcherInterface

Parameters:

pattern - SMILES or SMARTS pattern.

atoms -

ac -

bsSelected -

isSmarts -

firstMatchOnly -

Returns:

a set of atom correlations

Throws:

java.lang.Exception

find

private BS[] find(java.lang.String pattern,
                  SmilesSearch search,
                  boolean isSmarts,
                  boolean matchAllAtoms,
                  boolean firstMatchOnly)
           throws java.lang.Exception

Throws:

java.lang.Exception

match

private java.lang.Object match(java.lang.String pattern,
                               Node[] atoms,
                               int ac,
                               BS bsSelected,
                               BS bsAromatic,
                               boolean isSmarts,
                               boolean matchAllAtoms,
                               boolean firstMatchOnly,
                               int mode)
                        throws java.lang.Exception

Throws:

java.lang.Exception

countStereo

private static int countStereo(java.lang.String s)