ZBH - Center for Bioinformatics

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With the view tool you can visualize a SMARTS pattern. Here is how to use it:

Type in your SMARTS expression. If a syntax error occurs, please inspect the error message which should direct you to the wrong element of your expression.
Once a visualization is created, you can click on it to get a highresolution image for download.
Feel free to use the graphics in publications or other material. The license is granted provided that the SMARTSview web service and the corresponding publication is properly cited and the graphic is not manually modified.

Under 'more options' you can control:

  • Visualization Mode: 'Complete Visualization' is our standard. You can use 'Element Symbols' if you want to print B/W or have problems in detecting colors. ID-Mapping and Structure Diagram-Like help to understand the SMARTS pattern. Just give it a try.
  • Visualization of Default Bonds: A default bond is formally interpreted as 'single or aromatic bond', which is somehow disturbing in SMARTSview. You can switch between the standard mode (show a single bond only) or the formally correct 'single or aromatic' mode.
  • More Options: SMARTS-Trim is an algorithm which detects redundant elements in your SMARTS expression and removes them automatically. Show atom labels integrates the atom IDs (the order in which they appear in the string or the manually defined order (i.e. [O:2])) into the graphical representation.
  • Legend Options: Allows you to customize the legend shown below the SMARTSview graphic and to print the input SMARTS pattern into the picture header.

With the compare tool you can calculate and visualize the similarity of two SMARTS patterns. Here is how to use it:

Type in your SMARTS expressions. If a syntax error occurs, please inspect the error message which should direct you to the wrong element of your expression. Once a visualization is created, you can click on it to get a high resolution image for download.
Feel free to use the graphics in publications or other material. The license is granted provided that the SMARTSview web service and the corresponding publication is properly cited and the graphic is not manually modified.

Most of the 'More Options' you find here are already explained in the view section of this tutorial. The two new ones are as follows:

  • Compare Options: This option lets you choose whether you want to get a similarity value between 0 (no similarities) to 1 (identical) or a message if pattern 1 (2) is more specific than pattern 2 (1) or a message if both pattern are identical. Changing the compare option has no impact on the image generated but only on the message displayed.
  • Aromaticity Handling: There are two different options available. In SMARTS aromaticity has to be modeled into the patterns explicitly. Here you can choose whether you want small rings consisting entirely of aromatic nodes to be handled as aromatic, including its bonds and whether a SMILES like aromaticity detection should be included to identify and adjust potential aromatic rings.

With the search tool you can calculate and visualize the similarity of a SMARTS pattern to SMARTS from established filter sets. Here is how to use it:

Type in your SMARTS expressions. If a syntax error occurs, please inspect the error message which should direct you to the wrong element of your expression.
If there are no errors with your, input you will be redirected to the result page where you see your query at the top. At this point you will not see a result because there is some extensive computation going on. This will take about 5 to 10 seconds.
Once the calculation completes you get a interactive table where you can e.g. search for filter sets. In the second column is the computed similarity value of your input SMARTS pattern and the pattern in the corresponding row of that similarity value. You can find this SMARTS pattern in the third column. Right below the SMARTS pattern you will find an annotation and the filter set the SMARTS pattern derives from. In the last column you see a picture of the SMARTS pattern in that row. You can click on it to enlarge it. If you click on the SMARTS pattern in the third column you will get a popup of an image visualizing the similarity of your input SMARTS pattern and the SMARTS pattern you just clicked on. In the popup you will also find a download button to download the image. You can also right click on the SMARTS pattern and select 'open in new tab' (or click on it with your middle mouse button) to open the image in our compare tool where you e.g. can make small adjustments to the SMARTS patterns.
Feel free to use the graphics in publications or other material. The license is granted provided that the SMARTSview web service and the corresponding publication is properly cited and the graphic is not manually modified.

Under 'More Options' the options 'Visualization Mode' and 'Visualization of Default Bonds' are already explained in the view section of this tutorial and 'Aromaticity Handling' is already explained in the compare section of this tutorial. Note that due to pregenerated images this options do not affect the images in the fourth column of the table.
With the other 'More Options' you can control:

  • Number of Entries: How many entries do you want at max in the resulting table? Default is 100. You can use -1 for no limitations. If you pick a number x, the table shows the first x entries with largest similarity values. Keep in mind that more entries mean more computing time.
  • Compare Options: 'Similarity Search' lists all found SMARTS patterns. 'Search for More Specific Patterns' only includes SMARTS patterns in the result table which are more specific (only includes SMARTS patterns that your SMARTS pattern is a part of). 'Search for More Generic Patterns' only includes SMARTS patterns in the result table which are more generic (only includes SMARTS patterns that are part of your SMARTS pattern). 'Identical Patterns' only includes patterns in the table that are identical to your SMARTS pattern.
  • Compare Filter Sets: You can choose the filter sets to compare you smarts pattern with. Keep in mind that more filter sets mean more computing time.

With the create tool you can create SMARTS patterns differentiating two compound sets from another. Here is how to use it:

Upload two molecule files (smiles, sdf and mol2-files are supported). One set contains the positive molecules to be matched, the other one contains the negative structures not to be matched.
After uploading the files, you will be redirected to the result page. First, your input files are preprocessed. The result page contains visual depictions of your compounds and a result table with SMARTS patterns differentiating the sets. For each set (positive and negative) up to 180 compounds are visualized. After that, the SMARTS pattern generation will be run asynchronously. Once the result table is initialized, you can manually refresh it if new patterns are available. Typically, it takes 15 to 30 seconds until the first patterns are generated and visualized. Pattern generation will run at most 3 minutes.
Once there are patterns in the table available, you can apply filters on them using various properties and modify the table sorting. Each row of the table represents a pattern. If you click on the pattern depiction in the leftmost column, a popup window will open showing a large image of the pattern. The remaining columns contain the SMARTS string, the number of nodes of the pattern, the number of rings, the overall score and the support values. Finally, in the rightmost column you can open an expandable menu showing the matches of the SMARTS in both compound sets.
If you perform several different calculations using the same input files, an additional overview of your jobs on the same input is shown. It allows you to inspect the results without recalculating them.
Feel free to use the graphics in publications or other material. The license is granted provided that the SMARTSview web service and the corresponding publication is properly cited and the graphic is not manually modified.

For the pattern generation you have the following options:

  • Positive Support: Percentage p% of the compounds in the positive set that must be matched by each pattern generated. Keep in mind that smaller numbers mean more results.
  • Negative Support: Percentage n% of the compounds in the negative set that are allowed to be matched by each pattern generated. Keep in mind that higher numbers mean more results.
  • Filter Method:
    • Balanced: Use default search strategy. Try to find small and large patterns with unique match sets on the positive and negative compounds.
    • Small Patterns: Modified search strategy. Enumerate patterns by 'Number of Nodes' and 'Positive Support'. Ensure that each match set on the positive and negative compounds is unique.
    • No Filter: Enumerate patterns by their positive support value.