Report:MMS/Search Interface/The Command Line Interface/Full Search
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Performing a Full Search
If the user is satisfied that his query was drawn correctly, and after reviewing the results of the sample search, determines that it is it is retrieving desired structures as hits, he or she can feel safe in conducting the full search. The full structure search will be the most expensive part of using MMS.
As was seen as part of the sample search output, there are a few different stages of activity that take place during an MMS structure search. These are the RE or “retrieve candidates” search (also known as a fragment search), the SB or “bit screen” search, and the AA or “atom-by-atom” search stages. The in-depth meanings of these abbreviations are:
RE search - a fragment search to retrieve candidates (a broader search than the AA search). As of 10/2010, the RE search will also by default begin the SB search, as the SB search will identify a broader results set.
SB search – bit screen searching, used to perform searches for queries defined atoms and/or bonds
AA search – an atom-by-atom search on the candidates produced by the RE search (this would be too time-and resource-consuming if a limited number of candidates were not retrieved by a fragment search first)
While running a sample search, the first stage of a RE and SB search is performed at exactly the same way as it would be during a full search. To save time, once a sample search has been conducted, the user may simply type the command AA along with the results set number of the original candidate results set (or “r” number) that was given in the sample search output (in the earlier figure showing the sample search output, the RE/SB results were said to be stored in the results set R09). Typing the AA command will save computing time by performing only the necessary last stage of a full search on an already completed candidate retrieval process. If the RE/SB search must be conducted again for any reason, the user can type the command SEARCH FULL to conduct a full RE/SB investigation, and then an AA search automatically. The results of the full search performed with the previously discussed query are shown below. Note that only 5 search results were returned from a full search, when a range of 2-126 was predicted by the sample search.
Full Search in JChem
After a user has linked the JChem platform to the MMS database, they can conduct a Markush structure search through the JChem interface. First, users must define the domain of the query: searching the entire database is the default domain, but users can also choose to conduct the search within specific lists of records. The user then selects to add a "detail field." Under the "detail field" menu, they select the "vmns" option, and from the "vmns" menu they select "Markush structure." Users can upload a structure query drawn in MarvinSketch. Users then define the search type (i.e. full structure or substructure), and they define other structure query options (stereochemistry, atom matching, tautomer, and vague bond). Finally, users can add additional search terms in text fields, connected by Boolean operators to the structure query, in order to further narrow the search.
The query results will display the relevant Markush structures that correspond with the query, as well as the number of possible enumerations for each of the structures.
According the the Markush structures guide on the ChemAxon website, "the following query features are supported in the query when searching Markush targets":
- Tetrahedral and double bond E/Z stereochemistry
- Query atoms, including atom lists, not lists, generic query atoms (A, Q, M, etc.)
- Query bond types, including any, single/aromatic, etc.
- Atom query properties: a(aromatic), A(aliphatic), R(part of a ring), R0 (not part of a ring), D<n> (number of explicit connections)
- Bond topology query properties (chain/ring)
- Link nodes
- Position variation bonds
- Explicit H atoms in query only match explicit Hydrogens in the Markush target.
Simple R-group queries are supported when searching Markush targets:
- [That do] not have R-logic
- [That do] not contain nested R-group definitions
- [Where] an R-group is referenced only once
- [Where] number of enumerates does not exceed 100
- ↑ Borne, Philip, Laurence Favier, and Catherine Roesch. MMS User Manual. Chapter 4, "Searching and Answer Display." Questel Website, http://www.questel.com/en/customersupport/manual.htm. Accessed on January 29, 2007.
- ↑ "Workshop Manual: MMS for Beginners." published January 2010. Questel user guide.
- ↑ Personal e-mail correspondence with MMS representative, October 29, 2010.
- ↑ 4.0 4.1 "Special search types: Markush structures." ChemAxon website, http://www.chemaxon.com/jchem/doc/user/query_markush.html. Accessed June 28, 2011.