Package chemaxon.sss

Interface SearchConstants

All Known Implementing Classes:
MolSearch, MolSearchOptions, RGroupDecomposition, Search, SearchOptions, StandardizedMolSearch
@PublicApi public interface SearchConstants
Constants for structure searching

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    static final int
    ABS_STEREO_ALWAYS_ON
    Option for absolute stereo matching.
    static final int
    ABS_STEREO_CHIRAL_FLAG
    Option for absolute stereo matching.
    static final int
    ABS_STEREO_TABLE_OPTION
    Option for absolute stereo matching.
    static final int
    ATTACHED_DATA_MATCH_EXACT
    Option value constant for exact match of attached data.
    static final int
    ATTACHED_DATA_MATCH_GENERAL
    Option value constant for general match of attached data.
    static final int
    ATTACHED_DATA_MATCH_IGNORE
    Option value constant for ignoring attached data.
    static final int
    ATTACHMENT_ATOM
    Constant for attachment point representation in ligands: sets attachment points by attaching an any-atom.
    static final int
    ATTACHMENT_LABEL
    Constant for attachment point representation in ligands: sets attachment points by MolAtom.setExtraLabel(java.lang.String) Labels with R-group ID: "1" for R1, "2" for R2, ...
    static final int
    ATTACHMENT_MAP
    Constant for attachment point representation in ligands: sets attachment points by MolAtom.setAtomMap(int).
    static final int
    ATTACHMENT_NONE
    Constant for attachment point representation in ligands: none (no attachment point data).
    static final int
    ATTACHMENT_POINT
    Constant for attachment point representation in ligands: R-group attachment.
    static final int
    ATTACHMENT_RLABEL
    Constant for attachment point representation in ligands: sets attachment points by MolAtom.setExtraLabel(java.lang.String).
    static final int
    CHARGE_MATCHING_DEFAULT
    Option value constant for default charge searching (charged query matches only charged target, noncharged query matches all).
    static final int
    CHARGE_MATCHING_EXACT
    Option value constant for exact charge searching (charged query matches only charged target, noncharged query only matches noncharged).
    static final int
    CHARGE_MATCHING_IGNORE
    Option value constant for ignore charge searching (charge information is ignored during searching).
    static final float
    DEFAULT_DISSIMILARITY_THRESHOLD
    Default threshold value for similarity search.
    static final int
    DEFAULT_SEARCHTYPE
    Default search type equals SUBSTRUCTURE.
    static final String
    DISSIMILARITY_PROPERTY_NAME
    Name of the mrv/sdf property which stores the dissimilarity values.
    static final int
    DUPLICATE
    Duplicate search (formerly called perfect).
    static final int
    FULL
    Full structure search.
    static final int
    FULL_FRAGMENT
    Full fragment search (formerly called exact fragment).
    static final int
    HCOUNT_MATCHING_AUTO
    Default option for H count matching (setHCountMatching).
    static final int
    HCOUNT_MATCHING_EQUAL
    Option for H count matching.
    static final int
    HCOUNT_MATCHING_GREATER_OR_EQUAL
    Option for H count matching.
    static final int
    HIT_EXCLUDEDQ
    Hit constant denoting excluded query atom.
    static final int
    HIT_LP
    Hit constant denoting isolated lone-pair match.
    static final int
    HIT_MULTICENTER
    Hit constant denoting multicenter atoms in query.
    static final int
    HIT_NON_R
    Dummy hit constant used temporarily in BackTrack for denoting a non-R-node match.
    static final int
    HIT_ORDERING_NONE
    Option value constant.
    static final int
    HIT_ORDERING_UNDEF_R_MATCHING_GROUP_FIRST
    Option value constant.
    static final int
    HIT_R
    Hit constant denoting R-node matches in case of R-group search.
    static final int
    HIT_R_EMPTY_MATCH
    Hit constant denoting R-node empty match.
    static final int
    HIT_UNMAPABLE
    Hit constant denoting unmapable atoms in query (e.g.
    static final int
    IMPLICIT_H_MATCHING_DEFAULT
    Option value constant for default mode.
    static final int
    IMPLICIT_H_MATCHING_DISABLED
    Option value constant for indicate matching of an explicit hydrogen only to another explicit hydrogen.
    static final int
    IMPLICIT_H_MATCHING_ENABLED
    Option value constant for indicate matching between implicit and explicit hydrogens.
    static final int
    IMPLICIT_H_MATCHING_IGNORE
    Option value constant to indicate that hydrogens, either explicit or implicit, are ignored during searching.
    static final int
    ISOTOPE_MATCHING_DEFAULT
    Option value constant for default isotope searching (isotope query matches only isotope target, nonisotope query matches all).
    static final int
    ISOTOPE_MATCHING_EXACT
    Option value constant for exact isotope searching (isotope query matches only isotope target, nonisotope query only matches nonisotope).
    static final int
    ISOTOPE_MATCHING_IGNORE
    Option value constant for ignore isotope searching (isotope information is ignored during searching).
    static final int
    MARKUSH_HIT_INNER
    Option value constant for returning hit indices of the inner, compiled representation of a Markush target.
    static final int
    MARKUSH_HIT_ORIGINAL
    Option value constant for returning hit indices of the original Markush target.
    static final int
    MATCH_COUNT_BETWEEN
     
    static final int
    MATCH_COUNT_RELATION
     
    static final int
    NO_ABAS
    Substructure search that applies only screening.
    static final int
    NO_SCREEN
    Substructure search that applies only atom-by-atom search.
    static final int
    POSITION_ON_0TH_HEAVY_ATOM
    Hit constant denoting hit position of a non-heavy atom (e.g.
    static final int
    RADICAL_MATCHING_DEFAULT
    Option value constant for default radical searching (radical query matches only radical target, nonradical query matches all).
    static final int
    RADICAL_MATCHING_EXACT
    Option value constant for exact radical searching (radical query matches only radical target, nonradical query only matches nonradical).
    static final int
    RADICAL_MATCHING_IGNORE
    Option value constant for ignore radical searching (radical information is ignored during searching).
    static final String[]
    SEARCH_MODE_NAMES
    Deprecated, for removal: This API element is subject to removal in a future version.
    As of JChem 5.12, replaced by SEARCH_TYPE_NAMES.
    static final String[]
    SEARCH_TYPE_NAMES
    The names of the search types.
    static final int
    SIMILARITY
    Similarity search.
    static final int
    STEREO_DIASTEREOMER
    Option value constant for "diastereomer" stereo search type.
    static final int
    STEREO_ENANTIOMER
    Option value constant for "enantiomer" stereo search type.
    static final int
    STEREO_EXACT
    Option value constant for "exact" stereo search type.
    static final int
    STEREO_IGNORE
    Option value constant for "ignore" stereo search type.
    static final int
    STEREO_MODEL_COMPREHENSIVE
    Option value constant of the comprehensive stereo search model, which combines the advantages of local and global models.
    static final int
    STEREO_MODEL_DEFAULT
    For markush search in all cases and for non-markush duplicate search in query tables STEREO_MODEL_LOCAL, for non-markush duplicate search (with the exception of query tables) STEREO_MODEL_GLOBAL.
    static final int
    STEREO_MODEL_GLOBAL
    Option value constant of the global stereo search model, which considers global stereo information (global parity, global double bond stereo configuration, etc.).
    static final int
    STEREO_MODEL_LOCAL
    Option value constant for the local stereo search model, which only considers local stereo information (local parity, local double bond stereo configuration, etc.).
    static final int
    STEREO_SPECIFIC
    Option value constant for "specific" stereo search type.
    static final int
    SUBSTRUCTURE
    Substructure search that applies both screening and atom-by-atom search.
    static final int
    SUPERSTRUCTURE
    Superstructure search (Value=6)
    static final int
    TAUTOMER_SEARCH_DEFAULT
    Option value constant for indicating that tautomer duplicate search option is not explicitly set.
    static final int
    TAUTOMER_SEARCH_OFF
    Option value constant for switching tautomer searching off.
    static final int
    TAUTOMER_SEARCH_ON
    Option value constant for switching tautomer searching on.
    static final int
    TAUTOMER_SEARCH_ON_IGNORE_TAUTOMERSTEREO
    Option value constant for switching tautomer searching on without considering stereochemistry in tautomer regions.
    static final int
    UNDEF_R_MATCHING_ALL
    Option value constant.
    static final int
    UNDEF_R_MATCHING_GROUP
    Option value constant.
    static final int
    UNDEF_R_MATCHING_GROUP_H
    Option value constant.
    static final int
    UNDEF_R_MATCHING_GROUP_H_EMPTY
    Option value constant.
    static final int
    UNDEF_R_MATCHING_UNDEF_R
    Option value constant.
    static final int
    VAGUE_BOND_DEFAULT
    Option value constant for vague bond level HALF.
    static final int
    VAGUE_BOND_LEVEL_HALF
    Option value constant to handle some ambiguous aromaticity, 5-membered Kekule representation queries, like *1C=CC=C1 [C,N,O]1C=CC=C1 C1C=CC=C1 S1C=CC=C1.
    static final int
    VAGUE_BOND_LEVEL1
    Until 5.3 it was an option value constant to handle some ambiguous aromaticity, 5-membered Kekule representation queries.
    static final int
    VAGUE_BOND_LEVEL2
    Option value constant to vague handling of aromaticity; In the query all single ring bonds are replaced by "single or aromatic" and all double ring bonds are replaced by "double or aromatic" prior to search.
    static final int
    VAGUE_BOND_LEVEL3
    Option value constant to vague handling of aromaticity; In the query all single bonds are replaced by "single or aromatic" and all double bonds are replaced by "double or aromatic" prior to search.
    static final int
    VAGUE_BOND_LEVEL4
    Option value constant to vaguely handle bond types; All bond types are ignored (all bonds are replaced by "any" bonds prior to search.
    static final int
    VAGUE_BOND_OFF
    Option value constant to disable vague bond matching.

  • Field Details

    • DEFAULT_SEARCHTYPE

      static final int DEFAULT_SEARCHTYPE
      Default search type equals SUBSTRUCTURE.
      See Also:

    • NO_SCREEN

      static final int NO_SCREEN
      Substructure search that applies only atom-by-atom search. (Value=0)
      See Also:

    • NO_ABAS

      static final int NO_ABAS
      Substructure search that applies only screening. (Value=1)
      See Also:

    • SUBSTRUCTURE

      static final int SUBSTRUCTURE
      Substructure search that applies both screening and atom-by-atom search. (Value=2)
      See Also:

    • SIMILARITY

      static final int SIMILARITY
      Similarity search. (Value=3)
      See Also:

    • FULL

      static final int FULL
      Full structure search. (Prior to version 5.2 called EXACT.) Query and target must have the same heavy atom (non-H) network for matching. All other properties are otherwise evaluated the same way as substructure search. Please note that this search type is not suitable for equality check. For that, please use DUPLICATE search type. (Value=4)
      Since:
      JChem 5.2
      See Also:

    • DUPLICATE

      static final int DUPLICATE
      Duplicate search (formerly called perfect). Used for deciding absolute equality of molecular features (eg duplicate check before database insert). Equality is always subject to standardization in the database. Query features are not evaluated. (Value=5) For this search mode there is no search per minute license limitation in JChemBase, these searches are not counted.
      Since:
      JChem 5.2
      See Also:

    • SUPERSTRUCTURE

      static final int SUPERSTRUCTURE
      Superstructure search (Value=6)
      Since:
      JChem 3.0
      See Also:

    • FULL_FRAGMENT

      static final int FULL_FRAGMENT
      Full fragment search (formerly called exact fragment). Query must be FULL matching to a target fragment. (Value=7)
      Since:
      JChem 5.2
      See Also:

    • STEREO_SPECIFIC

      static final int STEREO_SPECIFIC
      Option value constant for "specific" stereo search type. Stereo information is considered during searching when it is explicitly specified in the query structure. That is, a part of the query structure with no specified stereo configuration matches only to both stereo and non-stereo parts of the target.

      This is the default option for substructure search.

      See Also:

    • STEREO_IGNORE

      static final int STEREO_IGNORE
      Option value constant for "ignore" stereo search type. Stereo information is entirely ignored during searching.
      See Also:

    • STEREO_EXACT

      static final int STEREO_EXACT
      Option value constant for "exact" stereo search type. Stereo information is matched exactly. That is, a part of the query structure with no specified stereo configuration matches only to a non-stereo part of the target. Similarly, a wiggly tetrahedral center of the query matches only to a wiggly tetrahedral center of the target, not to specific R/S configurations.

      This is the default option for duplicate search.

      See Also:

    • STEREO_DIASTEREOMER

      static final int STEREO_DIASTEREOMER
      Option value constant for "diastereomer" stereo search type. The diastereomer targets of a given query structure are also matched. It is only required that if a query atom has stereo information, then the matching target atom should also have specified stereo, but the two configurations are treated the same.
      See Also:

    • STEREO_ENANTIOMER

      static final int STEREO_ENANTIOMER
      Option value constant for "enantiomer" stereo search type. The enantiomer targets of a given query structure are also matched.
      See Also:

    • SEARCH_TYPE_NAMES

      static final String[] SEARCH_TYPE_NAMES
      The names of the search types.
      Since:
      JChem 5.12

    • SEARCH_MODE_NAMES

      @Deprecated(forRemoval=true) @SubjectToRemoval(date=JUL_01_2025) static final String[] SEARCH_MODE_NAMES
      Deprecated, for removal: This API element is subject to removal in a future version.
      As of JChem 5.12, replaced by SEARCH_TYPE_NAMES.
      The names of the search types.
      Since:
      JChem 3.0

    • DEFAULT_DISSIMILARITY_THRESHOLD

      static final float DEFAULT_DISSIMILARITY_THRESHOLD
      Default threshold value for similarity search. (Value=0.3)
      See Also:

    • DISSIMILARITY_PROPERTY_NAME

      static final String DISSIMILARITY_PROPERTY_NAME
      Name of the mrv/sdf property which stores the dissimilarity values.
      See Also:

    • HCOUNT_MATCHING_AUTO

      static final int HCOUNT_MATCHING_AUTO
      Default option for H count matching (setHCountMatching). The search tries to find out from the source of the query structure which H count matching option to use. (HCOUNT_MATCHING_EQUAL for smiles and smarts, and HCOUNT_MATCHING_GREATER_OR_EQUAL for mdl molfiles.)
      See Also:

    • HCOUNT_MATCHING_EQUAL

      static final int HCOUNT_MATCHING_EQUAL
      Option for H count matching. Means that a query atom with H count should only match a target atom with hydrogens (implicit or explicit) equal to the H count. This is the Daylight(smiles, smarts) behaviour.
      See Also:

    • HCOUNT_MATCHING_GREATER_OR_EQUAL

      static final int HCOUNT_MATCHING_GREATER_OR_EQUAL
      Option for H count matching. Means that a query atom with H count should only match a target atom with hydrogens (implicit or explicit) equal to or greater than the H count. One exception is H count = 0, which means no Hydrogens extra to those explicitly drawn. This is the MDL(sd, molfile) behaviour.
      See Also:

    • ABS_STEREO_TABLE_OPTION

      static final int ABS_STEREO_TABLE_OPTION
      Option for absolute stereo matching. Gets setting from property table.
      See Also:

    • ABS_STEREO_CHIRAL_FLAG

      static final int ABS_STEREO_CHIRAL_FLAG
      Option for absolute stereo matching. Chiral flag in molecule determines absolute configuration.
      See Also:

    • ABS_STEREO_ALWAYS_ON

      static final int ABS_STEREO_ALWAYS_ON
      Option for absolute stereo matching. Always treats chiral centers as abslute configuration.
      See Also:

    • MARKUSH_HIT_ORIGINAL

      static final int MARKUSH_HIT_ORIGINAL
      Option value constant for returning hit indices of the original Markush target. (Default.) For RgMolecule targets, the indices correspond to the graph union.
      Since:
      JChem 3.2
      See Also:

    • MARKUSH_HIT_INNER

      static final int MARKUSH_HIT_INNER
      Option value constant for returning hit indices of the inner, compiled representation of a Markush target.
      Since:
      JChem 3.2
      See Also:

    • TAUTOMER_SEARCH_OFF

      static final int TAUTOMER_SEARCH_OFF
      Option value constant for switching tautomer searching off.
      Since:
      JChem 5.4
      See Also:

    • TAUTOMER_SEARCH_ON

      static final int TAUTOMER_SEARCH_ON
      Option value constant for switching tautomer searching on.
      Since:
      JChem 5.4
      See Also:

    • TAUTOMER_SEARCH_DEFAULT

      static final int TAUTOMER_SEARCH_DEFAULT
      Option value constant for indicating that tautomer duplicate search option is not explicitly set. Default bahavior is TAUTOMER_SEARCH_OFF except in case of duplicate search in a database table created with "Duplicate search uses tautomers" option.
      Since:
      JChem 5.4
      See Also:

    • TAUTOMER_SEARCH_ON_IGNORE_TAUTOMERSTEREO

      static final int TAUTOMER_SEARCH_ON_IGNORE_TAUTOMERSTEREO
      Option value constant for switching tautomer searching on without considering stereochemistry in tautomer regions.
      Since:
      JChem 5.4
      See Also:

    • ISOTOPE_MATCHING_DEFAULT

      static final int ISOTOPE_MATCHING_DEFAULT
      Option value constant for default isotope searching (isotope query matches only isotope target, nonisotope query matches all).
      Since:
      JChem 3.2
      See Also:

    • ISOTOPE_MATCHING_EXACT

      static final int ISOTOPE_MATCHING_EXACT
      Option value constant for exact isotope searching (isotope query matches only isotope target, nonisotope query only matches nonisotope).
      Since:
      JChem 3.2
      See Also:

    • ISOTOPE_MATCHING_IGNORE

      static final int ISOTOPE_MATCHING_IGNORE
      Option value constant for ignore isotope searching (isotope information is ignored during searching).
      Since:
      JChem 3.2
      See Also:

    • CHARGE_MATCHING_DEFAULT

      static final int CHARGE_MATCHING_DEFAULT
      Option value constant for default charge searching (charged query matches only charged target, noncharged query matches all).
      Since:
      JChem 3.2
      See Also:

    • CHARGE_MATCHING_EXACT

      static final int CHARGE_MATCHING_EXACT
      Option value constant for exact charge searching (charged query matches only charged target, noncharged query only matches noncharged).
      Since:
      JChem 3.2
      See Also:

    • CHARGE_MATCHING_IGNORE

      static final int CHARGE_MATCHING_IGNORE
      Option value constant for ignore charge searching (charge information is ignored during searching). As of JChem 5.3, this option forces IMPLICIT_H_MATCHING_IGNORE in case of duplicate search.
      Since:
      JChem 3.2
      See Also:

    • RADICAL_MATCHING_DEFAULT

      static final int RADICAL_MATCHING_DEFAULT
      Option value constant for default radical searching (radical query matches only radical target, nonradical query matches all).
      Since:
      JChem 3.2
      See Also:

    • RADICAL_MATCHING_EXACT

      static final int RADICAL_MATCHING_EXACT
      Option value constant for exact radical searching (radical query matches only radical target, nonradical query only matches nonradical).
      Since:
      JChem 3.2
      See Also:

    • RADICAL_MATCHING_IGNORE

      static final int RADICAL_MATCHING_IGNORE
      Option value constant for ignore radical searching (radical information is ignored during searching).
      Since:
      JChem 3.2
      See Also:

    • VAGUE_BOND_OFF

      static final int VAGUE_BOND_OFF
      Option value constant to disable vague bond matching.
      Since:
      JChem 3.2
      See Also:

    • VAGUE_BOND_LEVEL1

      static final int VAGUE_BOND_LEVEL1
      Until 5.3 it was an option value constant to handle some ambiguous aromaticity, 5-membered Kekule representation queries. From 5.3 extends to 1-atom ligands of aromatic rings and 1 long connections between aromatic rings also (default from 5.3 to 15.9.14).
      Since:
      JChem 3.2
      See Also:

    • VAGUE_BOND_LEVEL_HALF

      static final int VAGUE_BOND_LEVEL_HALF
      Option value constant to handle some ambiguous aromaticity, 5-membered Kekule representation queries, like *1C=CC=C1 [C,N,O]1C=CC=C1 C1C=CC=C1 S1C=CC=C1. This is the default value before 5.3 and after 15.9.14.
      Since:
      JChem 5.3
      See Also:

    • VAGUE_BOND_DEFAULT

      static final int VAGUE_BOND_DEFAULT
      Option value constant for vague bond level HALF.
      Since:
      JChem 3.2
      See Also:

    • VAGUE_BOND_LEVEL2

      static final int VAGUE_BOND_LEVEL2
      Option value constant to vague handling of aromaticity; In the query all single ring bonds are replaced by "single or aromatic" and all double ring bonds are replaced by "double or aromatic" prior to search. (Caution: Not very efficient during fingerprint screening!)
      Since:
      JChem 3.2
      See Also:

    • VAGUE_BOND_LEVEL3

      static final int VAGUE_BOND_LEVEL3
      Option value constant to vague handling of aromaticity; In the query all single bonds are replaced by "single or aromatic" and all double bonds are replaced by "double or aromatic" prior to search. (Caution: very inefficient during fingerprint screening!)
      Since:
      JChem 3.2
      See Also:

    • VAGUE_BOND_LEVEL4

      static final int VAGUE_BOND_LEVEL4
      Option value constant to vaguely handle bond types; All bond types are ignored (all bonds are replaced by "any" bonds prior to search. (Caution: very inefficient during fingerprint screening!)
      Since:
      JChem 3.2
      See Also:

    • STEREO_MODEL_DEFAULT

      static final int STEREO_MODEL_DEFAULT
      For markush search in all cases and for non-markush duplicate search in query tables STEREO_MODEL_LOCAL, for non-markush duplicate search (with the exception of query tables) STEREO_MODEL_GLOBAL. Otherwise it is STEREO_MODEL_COMPREHENSIVE.
      Since:
      JChem 3.2.3
      See Also:

    • STEREO_MODEL_LOCAL

      static final int STEREO_MODEL_LOCAL
      Option value constant for the local stereo search model, which only considers local stereo information (local parity, local double bond stereo configuration, etc.). This model is suitable for substructure search. When a symmetric atom/bond with stereo configuration is specified in the query structure, then this model only allows it to be matched to target atoms/bonds with the specified stereo.

      For example, the query structure C[C@](C)(C)C does not match to CC(C)(C)C.

      Since:
      JChem 3.2.3
      See Also:

    • STEREO_MODEL_COMPREHENSIVE

      static final int STEREO_MODEL_COMPREHENSIVE
      Option value constant of the comprehensive stereo search model, which combines the advantages of local and global models. This model is suitable for all search types. Basically, it is similar to the local stereo model, except when the target is symmetric. In the case of symmetric target, the matching is accepted regardless of the stereo information.

      For example, the query structure C[C@](C)(C)C matches to CC(C)(C)C, C[C@@](C)(C)C, and {@link CCC[C@@](C)(CC)C(C)C}.

      Since:
      JChem 3.2.3
      See Also:

    • STEREO_MODEL_GLOBAL

      static final int STEREO_MODEL_GLOBAL
      Option value constant of the global stereo search model, which considers global stereo information (global parity, global double bond stereo configuration, etc.). This model is suitable for duplicate search, as well as full structure and full fragment search, because in these cases, the whole stereospecific substructure is always represented in both the query and the target structures. Therefore, a symmetric atom/bond with stereo configuration may match to an unspecified stereo atom/bond.

      For example, the query structure C[C@](C)(C)C matches to CC(C)(C)C.

      Since:
      JChem 3.2.3
      See Also:

    • IMPLICIT_H_MATCHING_DEFAULT

      static final int IMPLICIT_H_MATCHING_DEFAULT
      Option value constant for default mode. Its value is IMPLICIT_H_MATCHING_ENABLED in almost every cases. There is only one exception: in case of duplicate search against a query table in a database the default value is IMPLICIT_H_MATCHING_DISABLED.
      Since:
      JChem 5.0
      See Also:

    • IMPLICIT_H_MATCHING_ENABLED

      static final int IMPLICIT_H_MATCHING_ENABLED
      Option value constant for indicate matching between implicit and explicit hydrogens. In case of duplicate search the sum of implicit and explicit hydrogens of the query atom and the sum on the matched target atom must equal.
      Since:
      JChem 5.0
      See Also:

    • IMPLICIT_H_MATCHING_DISABLED

      static final int IMPLICIT_H_MATCHING_DISABLED
      Option value constant for indicate matching of an explicit hydrogen only to another explicit hydrogen. The number of implicit hydrogens (of the matching atoms) are not checked.
      Since:
      JChem 5.0
      See Also:

    • IMPLICIT_H_MATCHING_IGNORE

      static final int IMPLICIT_H_MATCHING_IGNORE
      Option value constant to indicate that hydrogens, either explicit or implicit, are ignored during searching. Hydrogens having special properties (radical, charge, isotope or more/less than one bond) are still considered.
      Option CHARGE_MATCHING_IGNORE forces IMPLICIT_H_MATCHING_IGNORE in case of duplicate search. In case of duplicate search against a query table in a database IMPLICIT_H_MATCHING_IGNORE is switched to IMPLICIT_H_MATCHING_DISABLED. Hydrogens receive the excluded atom hit index HIT_EXCLUDEDQ in this case.
      Since:
      JChem 5.3
      See Also:

    • UNDEF_R_MATCHING_ALL

      static final int UNDEF_R_MATCHING_ALL
      Option value constant. Undefined R-atom in query matches any atom in target.
      Since:
      JChem 5.1
      See Also:

    • UNDEF_R_MATCHING_UNDEF_R

      static final int UNDEF_R_MATCHING_UNDEF_R
      Option value constant. Undefined R-atom in query matches only an undefined R-atom in target.
      Since:
      JChem 5.1
      See Also:

    • UNDEF_R_MATCHING_GROUP

      static final int UNDEF_R_MATCHING_GROUP
      Option value constant. Undefined R-atom in query matches a group of one or more connected atoms, including at least one heavy atom.
      Since:
      JChem 5.2
      See Also:

    • UNDEF_R_MATCHING_GROUP_H

      static final int UNDEF_R_MATCHING_GROUP_H
      Option value constant. Undefined R-atom in query matches a group of one or more connected atoms, which can also be a single H atom.
      Since:
      JChem 5.3
      See Also:

    • UNDEF_R_MATCHING_GROUP_H_EMPTY

      static final int UNDEF_R_MATCHING_GROUP_H_EMPTY
      Option value constant. Undefined R-atom in query matches a group of one or more connected atoms, which can also be a single H atom or the empty set.
      Since:
      JChem 5.3
      See Also:

    • HIT_ORDERING_NONE

      static final int HIT_ORDERING_NONE
      Option value constant. Hit ordering type: no ordering.
      Since:
      JChem 5.4
      See Also:

    • HIT_ORDERING_UNDEF_R_MATCHING_GROUP_FIRST

      static final int HIT_ORDERING_UNDEF_R_MATCHING_GROUP_FIRST
      Option value constant. Hit ordering type for undefined R-atom matching. If this option is set then R-atom heavy group matches are given precedence in order of R-group ID.
      Since:
      JChem 5.4
      See Also:

    • POSITION_ON_0TH_HEAVY_ATOM

      static final int POSITION_ON_0TH_HEAVY_ATOM
      Hit constant denoting hit position of a non-heavy atom (e.g. implicit H, lone pair, ...) on the atom by index 0.
      Since:
      JChem 5.11.4
      See Also:

    • HIT_R

      static final int HIT_R
      Hit constant denoting R-node matches in case of R-group search.
      Since:
      JChem 5.3
      See Also:

    • HIT_MULTICENTER

      static final int HIT_MULTICENTER
      Hit constant denoting multicenter atoms in query.
      Since:
      JChem 5.3
      See Also:

    • HIT_UNMAPABLE

      static final int HIT_UNMAPABLE
      Hit constant denoting unmapable atoms in query (e.g. star atoms in polymerization).
      Since:
      JChem 5.3
      See Also:

    • HIT_LP

      static final int HIT_LP
      Hit constant denoting isolated lone-pair match.
      Since:
      JChem 5.3
      See Also:

    • HIT_R_EMPTY_MATCH

      static final int HIT_R_EMPTY_MATCH
      Hit constant denoting R-node empty match.
      Since:
      JChem 5.3
      See Also:

    • HIT_NON_R

      static final int HIT_NON_R
      Dummy hit constant used temporarily in BackTrack for denoting a non-R-node match.
      Since:
      JChem 5.3
      See Also:

    • HIT_EXCLUDEDQ

      static final int HIT_EXCLUDEDQ
      Hit constant denoting excluded query atom.
      • Excluded query atoms
      • Hydrogens receive this constant in case of ignoring hydrogens.
      Since:
      JChem 5.3
      See Also:

    • ATTACHMENT_NONE

      static final int ATTACHMENT_NONE
      Constant for attachment point representation in ligands: none (no attachment point data).
      See Also:

    • ATTACHMENT_POINT

      static final int ATTACHMENT_POINT
      Constant for attachment point representation in ligands: R-group attachment.
      See Also:

    • ATTACHMENT_MAP

      static final int ATTACHMENT_MAP
      Constant for attachment point representation in ligands: sets attachment points by MolAtom.setAtomMap(int). Maps with R-group ID: 1 for R1, 2 for R2, ...
      See Also:

    • ATTACHMENT_LABEL

      static final int ATTACHMENT_LABEL
      Constant for attachment point representation in ligands: sets attachment points by MolAtom.setExtraLabel(java.lang.String) Labels with R-group ID: "1" for R1, "2" for R2, ...
      See Also:

    • ATTACHMENT_RLABEL

      static final int ATTACHMENT_RLABEL
      Constant for attachment point representation in ligands: sets attachment points by MolAtom.setExtraLabel(java.lang.String). Labels with full R-atom name: "R1" for R1, "R2" for R2, ...
      See Also:

    • ATTACHMENT_ATOM

      static final int ATTACHMENT_ATOM
      Constant for attachment point representation in ligands: sets attachment points by attaching an any-atom.
      See Also:

    • MATCH_COUNT_BETWEEN

      static final int MATCH_COUNT_BETWEEN
      See Also:

    • MATCH_COUNT_RELATION

      static final int MATCH_COUNT_RELATION
      See Also:

    • ATTACHED_DATA_MATCH_IGNORE

      static final int ATTACHED_DATA_MATCH_IGNORE
      Option value constant for ignoring attached data.
      Since:
      JChem 5.2
      See Also:

    • ATTACHED_DATA_MATCH_GENERAL

      static final int ATTACHED_DATA_MATCH_GENERAL
      Option value constant for general match of attached data.
      Since:
      JChem 5.2
      See Also:

    • ATTACHED_DATA_MATCH_EXACT

      static final int ATTACHED_DATA_MATCH_EXACT
      Option value constant for exact match of attached data.
      Since:
      JChem 5.2
      See Also: