Package chemaxon.marvin.io.formats.smiles

Class SmartsAtomQuerifier

  • All Implemented Interfaces:
    chemaxon.marvin.modules.smarts.SmartsAtomTreeParserTreeConstants
    @PublicAPI
public class SmartsAtomQuerifier
extends Object
implements chemaxon.marvin.modules.smarts.SmartsAtomTreeParserTreeConstants
    Class for partial interpretation of smarts atoms. In MolAtom, queryString may contain a smarts query expression. This class parses the expression and decorates the MolAtom with those query properties and other features which can be put on the atom itself.
    Since:
    Marvin 3.4

    • Constructor Detail

      • SmartsAtomQuerifier

        public SmartsAtomQuerifier()
        Creates a new SmartsAtomQuerifier object.

    • Method Detail

      • isMarvinCompMode

        public boolean isMarvinCompMode()
        Marvin compatibility mode. If true(default), parsing corresponds marvin versions before 3.5: [!H!#6] is imported as heteroatom and [!H!#7!#8] as atom list. Otherwise, H means H count 1.
        Returns:
        the above marvin compatibility mode.

      • hasSMARTSPropsExcluding

        public static final boolean hasSMARTSPropsExcluding​(MolAtom atom,
                                                    String exclude)
        Tests whether it is a SMARTS query atom.
        Parameters:
        exclude - list of SMARTS properties to exclude
        Returns:
        true if it has SMARTS properties, false otherwise
        Since:
        Marvin 3.1.2

      • hasSMARTSProps

        public static final boolean hasSMARTSProps​(MolAtom atom)
        Tests whether it is a SMARTS query atom.
        Returns:
        true if it has SMARTS properties, false otherwise

      • setSMARTS

        public static void setSMARTS​(MolAtom atom,
                             String s)
                      throws SecurityException
        Sets SMARTS query string data.
        Parameters:
        s - the SMARTS string
        Throws:
        SecurityException - the SmilesImport cannot be loaded, possibly because of a misconfigured firewall

      • setMarvinCompMode

        public void setMarvinCompMode​(boolean marvinCompMode)
        Marvin compatibility mode. If true(default), parsing corresponds marvin versions before 3.5: [!H!#6] is imported as heteroatom and [!H!#7!#8] as atom list. Otherwise, H means H count 1.
        Parameters:
        marvinCompMode - marvin compatibility mode to set.

      • setQuerystr

        public static void setQuerystr​(MolAtom atom,
                               String s,
                               int options)
        Assigns the query properties string to this atom while setting all necessary atom and query properties. This is done through SmartsAtomQuerifier which parses the query string. For this reason this operation may be relatively costly. The remaining part of the query string (which could not be represented/assigned) is set to queryStr.

        In daylight smarts H is only considered as H atom when the atom expression has the syntax [<mass>H<charge><map>] (mass, charge and map are optional). If options is SMARTS_H_MARVIN_COMP_MODE and "H" is not in the form [<mass>H<charge><map>] then it may be interpreted as Hydrogen atom, not total H count! It is neccesary for backward compatibility.

        Parameters:
        s - the query string
        options - Possible values: SMARTS_H_MARVIN_COMP_MODE or SMARTS_H_DAYLIGHT_COMP_MODE. Instead of using this option, we recommend using unambiguous smarts queries: #1 for H atom and H1 for H count 1.
        Since:
        Marvin 3.5
        See Also:
        MolAtom.SMARTS_H_DAYLIGHT_COMP_MODE, MolAtom.SMARTS_H_MARVIN_COMP_MODE

      • setQuerystr

        public static void setQuerystr​(MolAtom atom,
                               String s)
        Assigns the query properties string to this atom while setting all necessary atom and query properties. This is done through SmartsAtomQuerifier which parses the query string. For this reason this operation may be relatively costly. The remaining part of the query string (which could not be represented/assigned) is set to queryStr.
        Parameters:
        s - the query string