4b. Import/export procedures
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Import/export compounds from SMILES
Import smiles
The functionality is available both through the Cerius2 graphical user interface (via the SDK SMILES card in the COMBI-CHEM I card deck) or from the TCL command interface. The import facility contains both an internal file-reader for SMILES and access to the Daylight file-reader (if the Daylight toolkit is available). It also contains a Daylight exporter.
Clicking the Load Smiles menu item on the SDK SMILES card opens the Load Smiles control panel.
The Load Smiles control panel enables you to use the Daylight SMILES reader (which requires the appropriate license from Daylight) or the SMILES reader that is implemented in Cerius2.
The Coordinates From popup includes these options for calculating the coordinates of the model from the SMILES string:
The File Contains popup has the following options:
The Model Space popup controls whether to input the SMILES strings into the same model space in Cerius2 or to create a new model space for each SMILES string.
The Hydrogen Fill popup controls whether to add hydrogen atoms to the molecules after reading the SMILES strings.
Export smiles
The Save Smiles menu item on the SDK SMILES card provides the SMILES export capabilities. The saved files contain either only SMILES strings or SMILES and a model name. The Save Smiles item on the SDK SMILES card opens the Save SMILES control panel
Note
SMARTS Search
This Smarts Search panel allows you to specify a SMARTS and search for matches in the current model. Pattern matches can be counted, selected, or highlighted in the model.
When a selection is chosen, other operations such as rendering can be performed on the matching atoms. When Match only unique atoms is checked, only non-overlapping sets of matches are returned. That is, no two result sets will contain the same atom. For example, when searching for c1ccccc1 in naphthalene, only one phenyl ring will be matched.
Tcl commands for SMARTS substructure searching
The following commands can be used from the command line or from C2·Tcl scripts.
SDK_SMILES/SSEARCH_FROM_MODEL [] [-UNIQUE]
Examples:
set nhits [SDK_SMILES/SSEARCH_FROM_MODEL c1ccccc1]
set nhits [SDK_SMILES/SSEARCH_FROM_MODEL Model(4) c1ccccc1]
set nhits [SDK_SMILES/SSEARCH_FROM_MODEL Model(4) c1ccccc1 -UNIQUE]
SDK_SMILES/SSEARCH_FROM_SMILES <smiles-string> <smarts-string> [-UNIQUE]
Examples:
set nhits [SDK_SMILES/SSEARCH_FROM_SMILES c1ccc2ccccc2c1 c1ccccc1]
SMARTS table derivations
The following derivations can be entered as column headers in the study table:
==daysss(Structure, ) and
==daysss_unique(Structure, )
For example:
==daysss(Structure, "c1ccccc1")
==daysss_unique(Structure, "[C;H1]NOH")
More information about Daylight
From Daylight Chemical Information Systems, Inc.:
Limitations
The SMARTS substructure searching algorithm will ignore any chiral properties of a molecule.
Models which contain CO2 groups with resonant bonds cannot be parsed into SMILES strings. To avoid this, change the CO2 groups to Kekulé representation.
Import/Export libraries from MDL RG files
Import RG files
You can also build a combinatorial library by importing the library definition (scaffold model, R group positions, and R group substituents) from an RG file generated, for example, by MDL's Project Library. To do this, go to the LIBRARY CONSTRUCTION card and select the Import Library menu item. This opens the Import Library control panel, which contains a file browser that allows you to select and read in an RG file:
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Select the desired RG file and click the IMPORT button (or double-click the RG filename) to read in the library definition. This displays the library scaffold model, with its defined R group positions, in the Cerius2 Models window. Clicking IMPORT also creates a directory containing all the fragments defined in the RG file and makes the directory accessible to the Analog Builder control panel. The fragments corresponding to each R group position are automatically selected and listed in the R Group list box of the Analog Builder control panel.
At this point, you can generate the entire library by clicking the GENERATE ANALOGS button in the Analog Builder control panel. Alternatively, you can generate a partial set from the library by editing the lists of fragments selected for each R group position, adding or removing fragments, and then clicking the GENERATE ANALOGS button.
The Preferences... button in the Import Library control panel allows you to turn on or off options to minimize the R group fragments read from the RG file (this is especially recommended for RG files that contain only 2D structures) and to delete the fragments from the Cerius2 Models window after you import the library.
Export RG files
Libraries defined in the Analog Builder can be exported in MDL RG file format using the panel shown below. This functionality can be accessed by selecting the Export Library command in the Library Construction card (COMBI-CHEM I deck).
Importing data from Oracle tables
Data can be imported directly from Oracle databases into Cerius2 Study Tables. The interface for accessing Oracle is accessible in several ways: through the Import Oracle... item on the ORACLE READ card in the QSAR deck, the Import Oracle... item in the LIBRARY MANAGEMENT card in the COMBI-CHEM I deck, and the File/Import Oracle... item in the menu bar of the Study Table control panel.
Logging in to the Oracle server (Oracle Logon)
The Import Oracle option guides you through the Oracle panels.
Enter the login name (the default is your UNIX login name) and password required to access the Oracle server. The name of the Oracle server is optional. If it is left empty the value of the ORACLE_SID environment variable is used. Click the NEXT > pushbutton to continue. This panel comes up automatically only when you need to log in.
Setting up the import process (Column Selection)
Select the column from the Study Table to retrieve primary key values; the entire column must be selected. If the desired values are from the row's title column, then select the check box. Click NEXT > to continue. If you click the < BACK button you return to the previous panel and have to re-log in to Oracle as a new user or as the same user. The < BACK button always takes you to the previous panel.
Specification of Oracle Table (Available Tables)
Select the Oracle table to load the data. When a value for Schemas is selected, the tables within that schema are listed in the Table Names list box. Select the appropriate table and then click the NEXT > button to continue.
Specification of Oracle Columns (Table Columns)
Select the database table column in the list box on the left side of the panel to use as the primary key for accessing data values. This column is mapped to the values selected with the Column Selection panel. Select any number of columns from the list box, which are then loaded into the study table. Click DONE to load the data.
Last updated May 19, 2000 at 01:51PM Pacific Daylight Time.
Copyright © 2000, Molecular Simulations Inc. All rights
reserved.