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Introduction

The jcsearch program is a command-line interface of the JChem chemical structure search. It is able to perform substructure, superstructure, full (formerly called exact), full fragment( formerly exact fragment), similarity, and duplicate (formerly perfect) searches, as well as match counts on the specified query and target molecules. These molecules can be specified as filenames, SMARTS/SMILES strings, or database tables (target only). A number of different molecular file formats are supported. Refer to the JChem Query Guide for a detailed description of search options and query features.
Note that the R-group decomposition functionality has been moved to a different script, the R-group Decomposition documentation contains specific information on this subject with examples.

Usage

For correct behavior, please prepare the usage of the jcsearch script or batch file as described in   Preparing the Usage of JChem Batch Files and Shell Scripts .
The program should be invoked in one of the following forms:

       jcsearch [options] [files...]
   or  jcsearch [options] DB:[table name]

With no file, or when file is -, it reads the standard input. When DB is specified, search is done in the database, using connection information saved by other JChem programs (e.g. jcman)
Options:

-h         this help message
-H         help on output file formats
-q query   SMARTS string or name of file that contains the query structure(s)
             (More than one can be specified in non-database mode. Please see
              options --and and --or.) For a detailed description about how
              to formulate queries, see the JChem Query Guide.
              In case of -t:d or --tautomer expects SMILES instead of SMARTS.
-t:<type>  search type.
      -t:s                         substructure search (default)
      -t:f                         full structure search
      -t:ff                        full fragment search
      -t:d                         duplicate search
      -t:i[:dissim_threshold]      similarity search
                                     (in case of mrv or sdf output, the
                                     dissimilarity value is stored as molecule
                                     property)
      -t:u                         superstructure search
                                     (default for query tables)
      -t:c                         count all hits
--hitColoring                  colors the hits depending on search type if the
                               output format is MRV.
--hitColor                     in case of hitColoring, specify color of hit
                               atoms and bonds
                                   examples: "red", "blue", "#00FF00" (green)
--hitHomologyColor             in case of hitColoring, specify color of homology
                               hit atoms and bonds
                                   examples: "red", "blue", "#00FF00" (green)
--nonHitColor                  in case of hitColoring, specify color of non-hit
                               atoms and bonds
                                   examples: "red", "blue", "#00FF00" (green)
--nonHitColor3D                in case of hitColoring in 3D molecules, specify
                               color of non-hit atoms and bonds
                                   examples: "red", "blue", "#00FF00" (green)
--removeUnusedDef              in case of markush search, remove unused R-group
                               definitions. Default value is false.
--markushScreening:y/n         specify if screening should be used in case of
                               markush search. Default value is y.
--haltOnError:y/n              specify how search should handle recoverable
                               errors: stop or log and continue if possible.
                               Default value is y for normal structure searches
                               and n for markush targets.
--markushDisplayMode:o/r/rhg   in case of markush searching and hit coloring,
                               specify the type of the resulting molecule.
      Values:
        o   Default: The results is shown on the given target structure.
        r   Markush reduction to hit : The markush structure is reduced
            according to the hit.
        rhg Markush reduction to hit and the homology groups
            are expanded according to the matching part of the query.
            which can also be a single H atom or the empty set
--align                      align or template based clean hits if DB option
                             has been set, and output format is MRV.
      --align:r              rotate: if query molecule has 0 dimension, it
                             will be cleaned in 2d for alignment.
      --align:p              partial clean (template based clean): if query
                             molecule has 0 dimension, same as rotate.
--similarity:s/d/o           specify which score is displayed within the
                             result of a similarity search.
      Values:
        s   Default: similarity score is displayed.
        d   Dissimilarity score is displayed.
        o   Neither similarity nor dissimilarity score is displayed.
--queryDisplay:n/y            specify whether query structure is displayed
                              within the result of a similarity search.
                              Default is n.
--displayLabelsAndBoxes:n/y   specify whether labels and bounding boxes for
                              the parts of the result of a similarity search
                              (target, query, score) are displayed. Default is n.
--queryAbsoluteStereo:y/n     All chiral atoms are absolute(y, default) or
                              consider chiral flag(n) in case of MDL mol files
                              w/o enhanced stereo labels. Has no effect in
                              database mode.
--targetAbsoluteStereo:y/n    All chiral atoms are absolute(y, default) or
                              consider chiral flag(n) in case of MDL mol files
                              w/o enhanced stereo labels. Has no effect in
                              database mode.
--DBAbsoluteStereo:T/C/A      In database mode, sets the above two
                              AbsoluteStereo flags.
                                T:(default) as set for table in database.
                                C: always check chiral flag(false)
                                A: always absolute stereo(true)
--orderSensitive              Switches on order sensitive search
--tautomerSearch:d/y/is/n     Tautomer search mode: d-default, y-on, is-on with
                               ignore stereo information in tautomer regions, n-off.
                              When set to d, tautomer search is off,
                              except in case of duplicate search in
                              a tautomer duplicate database table.
--exactAtomMatching:y/n       Exact atom matching (y) or not (n). Default is n.
                              (Deprecated.)
--exactQueryAtomMatching:y/n  Exact query atom matching (y) or not (n).
                              Default is n (except in case of duplicate search).
--exactBondMatching:y/n       Exact bond matching (y) or not (n).
                              Default is n (except in case of duplicate search).
--exactRadicalMatching:y/n    Exact radical matching (y) or not (n).
                              Default is n. (--radical is preferred instead.)
--exactIsotopeMatching:y/n    Exact isotope matching (y) or not (n).
                              Default is n. (--isotope is preferred instead.)
--exactChargeMatching:y/n     Exact charge matching (y) or not (n).
                              Default is n. (--charge is preferred instead.)
--charge:d/e/i                Charge matching mode: d-default,
                              e-exact, i-ignore
                              --charge:i forces --implicitHMatching:i in case of
                              duplicate search
--isotope:d/e/i               Isotope matching mode: d-default,
                              e-exact, i-ignore
--radical:d/e/i               Radical matching mode: d-default,
                              e-exact, i-ignore
--valence:d/i                 Valence matching mode: d-default, i-ignore
--vagueBond:n/h/1/2/3/4       Vague handling of bond types:
                               n - off
                               h - half: handling of certain 5-membered ambiguous
                                   aromatic rings like [C,N]1C=CC=C1 (default from version 15.9.14)
                               1 - handling of certain 5-membered ambiguous
                                   aromatic rings like [C,N]1C=CC=C1 and 1-atom-long
                                   aromatic ring ligands and bridging bonds
                                   between two aromatic rings(default in versions prior to 15.9.14)
                               2 - all single and double ring bonds
                                   match aromatic
                               3 - all single and double bonds
                                   match aromatic 
                               4 - ignore all bond types
--completeHG:y/n              Sets if only such structures can match on a
                              homology group that form an entire group. (e.g.
                              alkyl can't match on a cycloalkyl). default:y
--chekSpHyb                   Switch on sp hybridization checking.
--mix:d/i                     Handling of com, mix and for brackets: d-default,
                                i-ignore
--polymer:d/i                 Handling of polymer brackets: d-default,
                                i-ignore
--endGroupMatching:y/n        Polymer end groups must match: y-yes,
                                n-no (default: yes)
--transformMonomer:y/n        Polymer in their source based representation
                              are transformed to structure based : y-yes,
                                n-no (default: yes)
--phaseShift:y/n              Polymers match the phase shifted variant:
                              y-yes, n-no (default: yes)
--copolymerMatching:y/n       Polymers in copolymers can only be matched by
                              copolymers: y-yes, n-no (default: no)
--homologyNarrowTranslation:n/a/m  Query homology pseudo atoms are matching
                              on the represented group or only on pseudo:
                              n-none, a - all, m - marked atoms only
                              (default: none)
--homologyBroadTranslation:n/a/m  If specific atoms can match target
                              homology atoms:
                              n-none, a - all, m - marked atoms only
                              (default: none)
--doubleBondStereo:N/M/A      Double bond stereo Matching mode:None/Marked/All
                              Default is M.
--stereoSearchType:s/i/e/d/a  Sets the stereo search type.
                              Possible values:
                                s - stereo specific searching (default)
                                i - ignore stereo
                                e - exact stereo
                                d - diastereomer search
                                a - enantiomer search
--stereoModel:l/g/c           Sets the used stereo model (for tetrahedral and
                              double bond stereo). Possible values:
                              l - local, g - global, c - comprehensive
--ignoreTetrahedralStereo:y/n Option for ignoring tetrahedral stereo
                              during searching: y-yes ignore, n-no
                              (default: no)
--ignoreDoubleBondStereo:y/n  Option for ignoring double bond stereo
                              during searching: y-yes ignore, n-no
                              (default: no)
--ignoreCumuleneOrRingCisTransStereo:y/n   Option for ignoring cumulene or ring 
                              cis-trans stereo during searching: 
                              y-yes ignore, n-no (default: yes)
--ignoreAxialStereo:y/n       Option for ignoring axial stereo
                              during searching: y-yes ignore, n-no
                              (default: yes)
--ignoreSynAntiStereo:y/n     Option for ignoring syn-anti stereo
                              during searching: y-yes ignore, n-no
                              (default: yes)
--reactionUnpairedMap:All/unpairedOnly   Option for matching unpaired maps in
                                         reaction search:
                                   All(default): match to any atom map,
                                   unPairedOnly: match to unpaired map only.
--HCountMatching:G/E/A        Hydrogen count query property interpretation.
      Values:
        G    (greater or equal, mdl behavior) target atom must have H-s
             greater or equal to query H-s, in excess of explicit H-s.
             H0 means no extra H other than explicitly drawn.
        E    (equal, daylight behavior) target atom must have H-s equal to
             H count number.
        A    automatically determine whether G or E should be used, from the
             query source. (smiles and smarts source: E, all other: G).
--implicitHMatching:d/y/n/i   Describes the matching of implicit and
                              explicit hydrogens.
      Values:
        d   Default: its value is y in almost every cases.
            There is only one exception: its value is n in case of duplicate
            search against a query table in a database.
        y   Implicit and explicit hydrogens can match. 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.
        n   An explicit hydrogen matches only on another explicit hydrogen. The
            number of implicit hydrogens (of the matching atoms) are not checked.
        i   Implicit and explicit hydrogens are ignored. Hydrogens are excluded
            from the matching.
            For a more detailed explanation see:
             Search options apidoc
--ssrType:s/c   Describes the set of smallest rings to use for atom
                              property calculations.
      Values:
        s   Smallest set of smallest rings(SSSR), may vary depending on atom orders.
        c   Complete set of smallest rings(CSSR).
--keepQueryOrder              Does not rearrange the atoms of the query which
                              is done to achieve best search performance.
--markush:n/y                 Disable/enable special handling of
                              Markush targets. Default is n.
                              Enabling requires special license.
--hitIndexType:m/i            For Markush targets returns hits for the
                              original Markush diagram (m - default) or for the
                              inner compiled representation (i)(See --allHits).
--hitOrdering:n/g             Hit ordering type for undefined R-atom
                              atom-group matches.
                               Possible values:
                               n - none (default),
                               g - order hits by R-atom matches processed
                                   in the order of R-group numbers:
                                   1. heavy group, 2. H atom, 3. empty group
--optimizeQueries:y/n         Tries to speed up search when query molecule
                              contains special query features (atom lists,
                              bond lists) Default is y.
--distinctFirstAtomMatching:n/y   Disable/enable special findAll algorithm.
                              If set, the hits must have different first atoms.
                              Default is n.
--attachedDataMatch           Describes whether attached data
                              is compared.
      Values:
        i   Default: ignores attached data when checks matching.
        g   general: if attached data is present in query, it must be
            present in target as well.
        e   exact: existing attached data must match
            both in query and target.
--attachedDataMatchPrefixes   Comma separated list of name prefixes
                              (of attached data labels), that will be
                              compared. When not set or set to empty
                              string all attached data is checked.
                              Effective only when attachedDataMatch
                              is not set to 'i'.
--timeoutLimitMilliseconds    The search timeouts reaching this number
                               of milliseconds. Setting to -1 means no
                               timeout (Default 120000)
--exhaustiveModeLimit         Upon reaching this number of steps, the
                               search switches to exhaustive mode from
                               fast mode. Setting to -1 means never.
                               (Default -1)

--undefinedRAtom:g/gh/ghe/a/u     specify the matching of an undefined R-atom
                                  in the query. Effective only when
                                  --exactQueryAtomMatching is not set.
      Values:
        g   Default: Undefined R-atom matches a group of
            one or more connected atoms in target,
            including at least one heavy atom.
        gh  Undefined R-atom matches a group of
            one or more connected atoms in target,
            which can also be a single H atom.
        ghe Undefined R-atom matches a group of
            one or more connected atoms in target,
            which can also be a single H atom or the empty set
            (empty set match is allowed for isolated or
            one-attachment R-atoms only).
        a   Undefined R-atom matches any single atom in target.
        u   Undefined R-atom matches only an undefined R-atom in target.
--bridgingRAllowed:n/y        Forbid/allow different R-atoms matching
                              the same group. Default is n.
--RLigandEqualityCheck:y/n    Switch on/off the requirement that R-atoms
                              with the same R-group ID should match ligands
                              with the same structure. Default is y.
--maxResults:<n>              Limits the number of molecules returned.
-f format  output format (default: smiles). Run jcsearch -H for details.
      -f :T<column-name> write the value of the specified column of
                         matching targets
      -f :Tname          write the molecule names of matching targets
      -f :M<column-name1:...:column-namen>
                         write the values of the specified columns
                   together with the structure of matching targets
-o file    write output to file
-s SMILES  read input from SMILES string
-v         verbose
-vv        very verbose, stack trace on error
-0         skip coordinate calculation for SMILES input
-d         use Daylight-type aromatization (Huckel-rule) instead of
           the standard one. (This flag overrides flags -S and --standardize!)
-2[:[On][e]]  2D coordinate calculation (useful if the input is SMILES)
      -2      coordinate calculation with default options (O1)
      -2:O0   no optimization    -2:O1  optimize if needed
      -2:O2   optimize           -2:e   make double either (cis/trans) bonds
-n         List non-hits. For using with multiple targets, see options --and
           and --or.
--and      If two or more queries are present, all are required to match.
           (Default) For DB targets, only the first query is considered.
           If used together with option -n , a hit is returned if none of the
           query molecules match.
--or       If more than one queries are present, at least one is required to
           match. 
           If used together with option -n , a hit is returned if at least
           one query molecules does not match.
--allHits  Instead of checking the existence of matching, all matchings of
           the query molecule(s) are reported.
           Symbols used in hit arrays in place of specific query atoms:
            R    - R-group
            M    - multicenter
            U    - unmapable (e.g. polymer star atom)
            LP   - lone pair
            E    - R-atom matching the empty set
            EXCL - excluded query atom
-e, --expression <expression | file>   A Chemical Terms filtering expression
                                       for filtering hits. For syntax, see:
                                       Filtering expression syntax
-c, --config <file>                    User defined configuration XML file for
                                       Chemical Terms
-F <SQL statement>                     SQL query for filtering. The result should
  or --filterQuery <SQL statement>     contain the cd_id values. For syntax, see
       filterQuery documentation
--ignoreCTExceptions:n/y If set to y, only syntactical exceptions
                         will be thrown during search. Those molecules
                                 that return exception during evaluation
                         will be left out from hit list. Default is n.
-S, --standardize <file/string>      standardize query and target
                                     according to configuration file/string
-g, --ignore-error                   continue with next molecule on error

 

Filtering expression syntax

Option -e or --expression requires an additional parameter, a filtering expression formulated in ChemAxon's Chemical Terms language. (It can also be the name of a file containing the filtering expression.) Only targets (and hits in case of the --allHits option) satisfying the filtering expression are reported. Note that the filter expression applies to all query molecules if more than one are specified (in case the filter expression uses the query molecule at all).

The expression syntax is described in the Chemical Terms Language Reference. Search specific functions contained in the search context provide access to the query and the target molecules, the search hit array and its elements:

  • mol(), target(): both refer to the search target molecule
  • query(): refers to the search query molecule
  • m(int i): refers to the query atom index with atom map i
  • hit(), h(): both refer to the search hit array
  • hit(int i), h(int i): both refer to the i-th element of the search hit array, this is the target atom index matching the query atom with atom index i
  • hm(int i): refers to the target atom index matching the query atom with atom map i (shorthand for h(m(i)))


The default input molecule is the target molecule (e.g. mass() is the same as mass(target()), both refer to the molecule mass of the target molecule).

In most cases the function and plugin definitions provided by the built-in evaluator.xml are sufficient, but it is possible to specify a user-defined configuration xml in the --config parameter. The user-defined configuration is added to the definitions contained in the built-in evaluator.xml. The syntax is described in the Chemical Terms Language Reference, which includes a set of search filter examples . The short reference tables give a summary of the functions and plugins provided by the built-in configuration.

Examples

  1. Searching chlorobenzol in a SMILES file and sending the results to the standard output in SMILES format:

     jcsearch -q "c1ccccc1Cl" -f smiles input.smi
  2. Searching molecules with chlorobenzol and bromine at the same time. Output: smiles and molecule name (which is stored in input.smi, separated from the smiles by spaces .)

     jcsearch -q "c1ccccc1Cl" --and -q "Br" -f smiles:Tfield_0 input.smi
  3. Searching chlorobenzol in an SDfile file and writing the result (structures and all other data) into another SDfile:

     jcsearch -q "c1ccccc1Cl" -f sdf -o hits.sdf input.sdf
  4. Like the above, but reading the query from a molfile and displaying the results using mview:

     jcsearch -q clbenz.mol -f sdf input.sdf | mview -f ID -
  5. Like the above, but reading targets from a database table called molecules.

     jcsearch -q clbenz.mol -f sdf DB:molecules | mview -f ID -
  6. Listing atom numbers with less than -0.3 partial charge in a specific molecule.

     jcsearch --allHits -e "charge(h(0)) < -0.3" -q '[*]' '[O-]C(=O)CCCCCC(=O)CCCC([O-])=O'
  7. Listing carboxylic groups with acidic p K a value on the carboxylic OH greater than 4.

     jcsearch --allHits -e "pka('acidic',hm(1)) > 4" -q "[H][O:1]C=[O:2]" target.mol
  8. Filtering target molecules by both molecule mass and substructure search:

     jcsearch -e "mass() >= 250" -q query.mol targets.sdf
  9. Similiarity search, threshold should be between 0 (very similar) to 1 (not similar):

     jcsearch -q "CC(C)(O)C#N" input.smi -t:i:0.4
  10. Duplicate search, ignoring hydrogens:

     jcsearch -t:d --implicitHMatching:i -q Cc1c[nH]cn1 Cc1cnc[nH]1
  11. Duplicate search, ignoring charge (which in turn implies --implicitHMatching:i):

     jcsearch -t:d --charge:i -q SC1=CC=CC=C1 [SH2+]C1=CC=CC=C1