SD File

Data input for both modules can be done via file upload, whereby the module for mere statistics reads in plain ASCI I files and the module For chemical data analysis takes the chemical structures in the Form of SD-files (cf. Chapter 2) as an input. In... 

While the protocol described above has proven very useful in its own right, it often serves as the first step in designing custom protocols for a team. Once a user is satisfied with the results returned by the ad hoc query, the next step is often to hardwire these queries into a protocol that provides one-button access to all the pertinent data for a project. Figure 5 shows such a protocol used to retrieve data for several assays in a Neuroscience project. This protocol highlights an additional filtering option that we make use of in many of our protocols. The text box ( selected cmpds from list ) (7) supports the input of a list of identification numbers (in our case either jnjnumber or batchid ). This allows data to be retrieved on select compounds as opposed to all those tested in the assays. This feature is very popular and involves the use of Perl within the Pipeline Pilot protocol. All this work is done on the server and the results are written to a SD file that can be downloaded to the desktop. At this stage either DIVA or Accord for Excel is typically used to view the files. 

Both DIVA and RS3 provide some functionality in terms of substructure searches (SSS), although it is somewhat limited. For example, DIVA searches can only be performed on data that have already been queried from the database ). This pre-queried data need to be readily available to DIVA either via RS3 or as an SD file. In the case of RS3, the inclusion of multiple data sources (e.g., searching the corporate database and an external vendor library) is not trivial. As a result, while DIVA and RS3 are very useful for SSS under certain conditions, they are not as robust when compared to the Pipeline Pilot protocol. 

Like the similarity protocol, the user interface for the Pipeline Pilot SSS protocol supports multiple databases and multiple probes in a single query. The input of the probe molecule(s) is accomplished using a SD file, which can be generated in most standard chemical drawing programs. This file is supplied as one of the inputs in the SSS interface. The use of identification numbers is not as applicable here as it is in the case of the similarity protocol since we are most likely not using existing molecules as substructures. Consequently, textbox input is not an option nor is the upload of a list of numbers in CSV or Excel format. 

REACCS RXN File which defines the reactien/lransldrmation OUTPUT Enumerated Library in SMILES format Library Subset (percent retum) as Web page and SD File... 

Although we have made use of SD files up to this point, at this stage we switch to SMILES files (19). This becomes necessary because even for small libraries the file size for a fully enumerated set can be quite large. For example, a sample library of just 2500 compounds resulted in 4.85 MB SD file while the SMILES file was only 384 KB. The one caveat with the SMILES format is that there is no standard for handling data fields. Our solution was to reformat the SD file type data field tags into the SMILES file,... 

One of the most widely used chemical structure-encoding schemas in the pharmaceutical industry is the MDL Connection Table (CT) File Format. Both Molfile and SD File are based on MDL CT File Format to represent chemical structures. A Molfile represents a single chemical structure. An SD File contains one to many records, each of which has a chemical structure and other data that are associated with the structure. MDL Connection Table File Format also supports RG File to describe a single Rgroup query, rxnfile, which contains structural information of a single reaction, RD File, which has one to many records, each of which has a reaction and data associated with the reaction, and lastly, MDL s newly developed XML representation of the above—XD File. The CT File Format definition can be downloaded from the MDL website http //www.mdl.com/downloads/public/ctfile/ctfile.jsp. 

Support SD file and XML file as input 1 week High Low Low... 

Brief Description This use case allows a Chemist to register single or multiple compounds interactively (not start from an SD File). At the end of the use case, the compounds are registered into the database and the Chemist receives sample identifiers for each compound. The Chemist must be authenticated and authorized to access this use case. 

Data Binder Since we are developing an object-oriented system, if the input is an SD File or an XML File, it must be converted to Java objects for processing efficiency reasons. This conversion is done by the Data Binder objects. 

In a compound registration system, compound data can be imported from data files such as SD File, XML File, or Mobile. Alternatively, data can be entered from the presentation layer using a structure drawing package such as ISISDraw or ChemDraw. These data, once imported to the system, need to be bound to the domain objects in order for the system to process them efficiently. To support a variety of data sources, a Data Binder API is needed to decouple the system from specific format of input data and make it easily extensible to support other data input formats down the road. Figure 12.17 is the class diagram of the Data Binder API. 

The SDFileBinder implementation takes an SD File as input, whereas the XMLFileBinder implementation takes an XML File as input. 

Parsing the SD File is a tricky job because the SD File is not a well-structured format, in contrast to XML. An SD File example with two records is as follows ... 

The source code of the SDFileBinder class binds the above SD File to a ChemicalLibrary object or a list of ChemicalSample objects, as follows ... 

Figure 12.19 is a sequence diagram that shows how the Front Controller, the Application Controller, and the Command objects interact with each other in the Load SD File transaction. 

After the user imports an SD File and submits the form, the Front Controller receives a request to upload the SD File. The Front Controller asks the Application Controller for the appropriate Command object that can handle the SD File upload request. The Application Controller returns a Data Input Command. The Front Controller invokes the execute() method on the DatalnputCommand object. The DatalnputCommand object invokes die SD File Binder s bind() method, which returns a List of ChemicalSample... 

Figure 12.19 The sequence diagram of Application Controller and DatalnputCommand in the Load SD File transaction.

The execute() method uses the DataBinder object as the request receiver to bind the input SD File or XML File to the ChemicalLibrary object. Because registering a compound or a library requires several interactions between the user and the system, the state has to be maintained between those interactions. As a result, the DatalnputCommand object saves the library object into a UserSession object for future access. 

Read SDFile ERROR Cannot open input SD File n ) ... 

Conformational models generated by other programs can be used for pharmacophore generation and in Catalyst databases by importing multiconformer structures stored, e.g., in SD file format. 

Imports data in SD file format, MDL molfile format, SMILES text strings, Daylight Chemical Information Systems Inc. s Thor Data Tree (TDT) format, and Tripos Inc. s Sybyl Line Notation (SLN) format. 

The new versions of DfW are compatible with Microsoft Windows. For the prediction of toxicity the chemical structure of a compound is input into the system with the use of ISIS/Draw (from MDL Information Systems) or by importing a mol-file or sd-file (Figure 2a). After the system has the structure, pushing the process button starts the prediction. During processing, the system searches and identifies all known toxicophores in the structure from all the different toxicological endpoints within seconds. After completion of the analysis, the system opens a result window. The result window contains the imported structure, a list of toxicological endpoints that the system has made a prediction for, the number and name of... 

All the results described above can be exported from DfW to other applications by generating a DEREK for Windows report in either rich text (rtf), tab delimited text, or modified sd file format (Figure 3). 

The most commonly used identifiers today include line notation identifiers (e.g., Simplified Molecular Input Line Entry System [SMILES] and International Chemical Identifier [InChls]), tabular identifiers (e.g., Molfile and Structure Definition [SD] file types), and portable mark-up language identifiers (e.g., Chemical Markup Language [CML] and FlexMol). Each identifier has its strengths and weaknesses as detailed in Chapter 5. Chapters 5 and 6 provide enough information to guide researchers in choosing the most appropriate formats for their individual use. 

Elsevier MDL CTFile Formats (MDL mol and SD file format) downloadable documentation on . 

LigPrep of Schrodinger can generate stereoisomers consistent with specified stereochemical information (e.g. parities in SD files) by varying the chirahties of the atoms for which chirahties are missing. Alternatively, the chirahties of aU chiral atoms may be varied. 

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