ZBH - Center for Bioinformatics

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SMARTSviewer and SMARTScompareViewer automatic visualization retrieving

Visualizations of the SMARTSviewer and the SMARTScompareViewer can be downloaded automatically as images via the SMARTSviewer URL. For this purpose, a special syntax needs to be followed:

https://smarts.plus/smartsview/download_rest?<option_1>=<value_1>;<option_2>=<value_2>;...;<option_n>=<value_n>

The options do not have to be in a specific order. You will find further explanation of the options at our Tutorial.

Options and Parameters

Option Description
smarts The SMARTS pattern for you want to visualize. This is the only option that has to be specified in the URL, all other options are optional.
The Following characters have to be escaped, see example 3:
% ↦ %25
& ↦ %26
+ ↦ %2B
# ↦ %23
; ↦ %3B
comparesmarts The SMARTS pattern to compare with. If you specify this you will get a compare image. If you do not specify this you will get a normal visualization of your smarts.
The Following characters have to be escaped, see example 3:
% ↦ %25
& ↦ %26
+ ↦ %2B
# ↦ %23
; ↦ %3B
vmode Visualization Mode:
0 = Complete visualization (default)
1 = ID-Mapping
2 = Element symbols
3 = Structure Diagram-Like
vbonds Visualization of Default Bonds:
0 or 1 (0 = Single Bonds (default), 1 = Single or Aromatic Bonds
textdesc Legend Option 1: Textual desciption
0 or 1 (0 = No, 1 = Yes (default))
depsymbols Legend Option 2: Depiction of SMARTS symbols
0 or 1 (0 = No, 1 = Yes (default))
smartsheading Legend Option 3: Write SMARTS as picture heading
0 or 1 (0 = No, 1 = Yes (default))
trim SMARTS trim active:
0 or 1 (0 = No, 1 = Yes (default))
labels Show Atom Labels:
0 or 1 (0 = No (default), 1 = Yes)
cmode Compare Mode: This only affects compare images
1 = Search for Identical Patterns
2 = Subset search from smarts
3 = subset search from comparesmarts
4 = Similarity Search (default)
detectarom Detect Aromatic Bonds:
0 or 1 (0 = No, 1 = Yes (default))
smileslikearom SMILES-Like Aromaticity Detection:
0 or 1 (0 = No, 1 = Yes (default))
filetype Output File Type:
png (default), svg or pdf

Examples of Usage

  • SMARTS:[CX3](=[OX1])[OX2][CX3](=[OX1])
    Image in png-format, as Complete Visualization and without a legend:

    https://smarts.plus/smartsview/download_rest?smarts=[CX3](=[OX1])[OX2][CX3](=[OX1]);filetype=png;vmode=0;textdesc=0;depsymbols=0;smartsheading=0

    Note that this is the same request as
    https://smarts.plus/smartsview/download_rest?smarts=[CX3](=[OX1])[OX2][CX3](=[OX1]);textdesc=0;depsymbols=0;smartsheading=0
    because of the default values for file type and visualization mode

  • SMARTS: [$([nr5]:[nr5,or5,sr5]),$([nr5]:[cr5]:[nr5,or5,sr5])]
    Image in pdf-format, visualization with element symbols:

    https://smarts.plus/smartsview/download_rest?smarts=[$([nr5]:[nr5,or5,sr5]),$([nr5]:[cr5]:[nr5,or5,sr5])];filetype=pdf;vmode=2

  • SMARTS: [#6][$([NX2]=O),$(N=C=O),$(OC#N),$(SC#N)]
    Compare SMARTS: N(C)=C=[#8]
    Cave: The '#'-Symbol has a special meaning in urls, therefore it has to be escaped with a %23, leading to the strings [%236][$([NX2]=O),$(N=C=O),$(OC%23N),$(SC%23N)] and N(C)=C=[%238].

    https://smarts.plus/smartsview/download_rest?smarts=[%236][$([NX2]=O),$(N=C=O),$(OC%23N),$(SC%23N)];comparesmarts=N(C)=C=[%238]

Warning: If your SMARTS contains syntax-errors or the image generation fails, you get only an empty image. In that case you should visit the smarts.plus homepage and use the error messages there to fix your SMARTS expression.

Copyright: Be sure to mention the origin of the visualization as „SMARTSviewer smartsview.zbh.uni-hamburg.de, ZBH Center for Bioinformatics, University of Hamburg“

Search for SMARTS in Filter Sets

A Request for the comparison of a SMARTS with the SMARTS from filter sets can be send via URL. For this purpose, a special syntax needs to be followed:

https://smarts.plus/smartssearch/search_rest?<option_1>=<value_1>;<option_2>=<value_2>;...;<option_n>=<value_n>

The options do not have to be in a specific order.

Options and Parameters

Option Description
smarts The SMARTS pattern to compare. This is the only option that has to be specified in the URL, there is no default value. The Following characters have to be escaped, see example 3:
% ↦ %25
& ↦ %26
+ ↦ %2B
# ↦ %23
; ↦ %3B
fsets Filter sets to compare with, comma-separated and not case-sensitive. If not specified, will be compared with each filter set. Choose from one or more of the following filter sets:
BMS
Dundee
Glaxo
Inpharmatica
LINT
MLSMR
PAINS
SMARTCyp
SureChEMBL
vmode Visualization Mode:
0 or 2 (0 = Complete Visualization (default), 2 = Element Symbols)
vbonds Visualization of Default Bonds:
0 or 1 (0 = Single Bonds (default), 1 = Single or Aromatic Bonds
detectarom Detect Aromatic Bonds:
0 or 1 (0 = No, 1 = Yes (default))
smileslikearom SMILES-Like Aromaticity Detection:
0 or 1 (0 = No, 1 = Yes (default))
cmode Compare Mode:
1 = Search for Identical Patterns
2 = Subset of Pattern in Filter Set(s)
3 = Superset of Pattern in Filter Set(s)
4 = Similarity Search (default)

Examples of Usage

  • SMARTS:[CX3](=[OX1])[OX2][CX3](=[OX1])
    Search in filter set BMS and use default values for the other options:

    https://smarts.plus/smartssearch/search_rest?smarts=[CX3](=[OX1])[OX2][CX3](=[OX1]);fsets=BMS

  • SMARTS: [$([nr5]:[nr5,or5,sr5]),$([nr5]:[cr5]:[nr5,or5,sr5])]
    Search in filter sets PAINS, Glaxo and SureChEMBL with element symbols as visualization mode:

    https://smarts.plus/smartssearch/search_rest?smarts=[$([nr5]:[nr5,or5,sr5]),$([nr5]:[cr5]:[nr5,or5,sr5]);fsets=pains,glaxo,surechembl;vmode=2

  • SMARTS: [$([#16&D3]),$([#16D4])]=,:[#6+]
    Cave: The '#', '&' and '+'-Symbol have special meanings in urls, therefore they have to be escaped, leading to the string [$([%2316%26D3]),$([%2316D4])]=,:[%236%2B]
    Search in filter set Dundee:

    https://smarts.plus/smartssearch/search_rest?smarts=[$([%2316%26D3]),$([%2316D4])]=,:[%236%2B];fsets=dundee