OEDepict Examples Summary

The following table lists the currently available OEDepict TK examples:

Program Description
depict generating 2D coordinates
match2img depicting substructure search match
mcsalign2D aligning molecules based on MCS
mdlquery2img depicting MDL query
mdlreaction2img depicting MDL reaction
mol2img depicting a single molecule
mols2pdf depicting molecules in a multi-page image
mols2img depicting molecules in a grid
ringdict2pdf generating 2D ring dictionary report
smartsalign2D aligning molecules based on substructure search
viewmdlsearch depicting MDL query substructure search hits

Generating 2D coordinates

A program that assigns 2D coordinates to molecule(s).

Command Line Interface

A description of the command line interface can be obtained by executing the program with the –help argument.

prompt> depict --help

will generate the following output:

Simple parameter list
input/output options :
   -in : Input filename
   -out : Output filename
   -ringdict : User-defined 2D ring dictionary

 prepare depiction options :
   -orientation : Set the preferred orientation of 2D coordinates
   -suppressH : Suppress explicit hydrogens of molecule(s)

Example

prompt> depict .ism .mol

C(=O)N

will generate the following output:

  -OEChem-07031123462D

  3  2  0     0  0  0  0  0  0999 V2000
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5000   -0.8660    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  1  3  1  0  0  0  0
M  END

Note

The above program can generate 2D coordinates with user-defined 2D ring layouts when using the -ringdict parameter.

See also the 2D coordinate generation utilities section of the OEChem TK manual that shows examples about how to generate and utilize user-defined ring dictionaries.

Depicting Substructure Search Match

A program that performs a substructure search initialized with the given SMARTS pattern and highlights the identified matches on the depicted molecule.

Command Line Interface

A description of the command line interface can be obtained by executing the program with the –help argument.

prompt> match2img --help

will generate the following output:

Simple parameter list
 highlight options :
   -highlightcolor : Highlighting color
   -highlightstyle : Highlighting style

 image options :
   -height : Height of output image
   -width : Width of output image

 input/output options :
   -in : Input filename
   -out : Output filename
   -smarts : SMARTS pattern

 molecule display options :
   -aromstyle : Aromatic ring display style
   -atomcolor : Atom coloring style
   -atomlabelfontscale : Atom label font scale
   -atomprop : Atom property display
   -atomstereostyle : Atom stereo display style
   -bondcolor : Bond coloring style
   -bondprop : Bond property display
   -bondstereostyle : Bond stereo display style
   -hydrstyle : Hydrogen display style
   -linewidth : Default bond line width
   -scale : Scaling of the depicted molecule
   -superdisp : Super atom display style
   -titleloc : Location of the molecule title

 prepare depiction options :
   -clearcoords : Clear and regenerate 2D coordinates of molecule(s)
   -orientation : Set the preferred orientation of 2D coordinates
   -suppressH : Suppress explicit hydrogens of molecule(s)

Examples

prompt> match2img -in indole.ism -out image.png -smarts "c1ccccc1"

will generate the image shown in Figure: Example of using the program with default highlighting

../_images/match2img-01.png

Example of using the program with default highlighting

prompt> match2img -in indole.ism -out image.png -smarts "c1ccccc1" -highlightcolor green

will generate the image shown in Figure: Example of using the program with green highlighting

../_images/match2img-02.png

Example of using the program with green highlighting

prompt> match2img -in indole.ism -out image.png -smarts "c1ccccc1" -highlightstyle BallAndStick

will generate the image shown in Figure: Example of using the program with ball and stick

../_images/match2img-03.png

Example of using the program with ball and stick highlighting

See also

Aligning Molecule Based on MCS

A program that aligns molecules based on their maximum common substructure.

Command Line Interface

A description of the command line interface can be obtained by executing the program with the –help argument.

prompt> mcsalign2D --help

will generate the following output:

Simple parameter list
 input/output options :
   -fit : Align filename
   -out : Output filename
   -ref : Ref filename

Example

prompt> mcsalign2D -ref ace1.ism -fit ace2.ism -out out.mol

taking the output coordinates and generating the images with the mol2img program will produce the images shown in Table: Example of using the program to align two molecules based on MCS.

Example of using the program to align two molecules based on MCS
reference molecule aligned molecule
../_images/mcsalign2D-out-ref.png ../_images/mcsalign2D-out-fit.png

See also

Depicting MDL Query

A program that converts an MDL query structure into an image file.

Command Line Interface

A description of the command line interface can be obtained by executing the program with the –help argument.

prompt> mdlquery2img --help

will generate the following output:

Simple parameter list
 image options :
   -height : Height of output image
   -width : Width of output image

 input/output options :
   -in : Input filename
   -out : Output filename

 molecule display options :
   -aromstyle : Aromatic ring display style
   -atomcolor : Atom coloring style
   -atomlabelfontscale : Atom label font scale
   -atomprop : Atom property display
   -atomstereostyle : Atom stereo display style
   -bondcolor : Bond coloring style
   -bondprop : Bond property display
   -bondstereostyle : Bond stereo display style
   -hydrstyle : Hydrogen display style
   -linewidth : Default bond line width
   -scale : Scaling of the depicted molecule
   -superdisp : Super atom display style
   -titleloc : Location of the molecule title

Example

prompt> mdlquery2img -in mdlquery.mol -out image.png
prompt> MDLQuery2Img -in mdlquery.mol -out image.png

will generate the image shown in Figure: Example of depicting an MDL query

../_images/mdlquery2img-01.png

Example of depicting an MDL query

See also

Depicting MDL Reaction

A program that converts an MDL reaction into an image file.

Command Line Interface

A description of the command line interface can be obtained by executing the program with the –help argument.

prompt> mdlreaction2img --help

will generate the following output:

Simple parameter list

 image options :
   -height : Height of output image
   -width : Width of output image

 input/output options :
   -in : Input filename
   -out : Output filename

 molecule display options :
   -aromstyle : Aromatic ring display style
   -atomcolor : Atom coloring style
   -atomlabelfontscale : Atom label font scale
   -atomprop : Atom property display
   -atomstereostyle : Atom stereo display style
   -bondcolor : Bond coloring style
   -bondprop : Bond property display
   -bondstereostyle : Bond stereo display style
   -hydrstyle : Hydrogen display style
   -linewidth : Default bond line width
   -scale : Scaling of the depicted molecule
   -superdisp : Super atom display style
   -titleloc : Location of the molecule title

Example

prompt> mdlreaction2img -in mdlreaction.sdf -out image.png

will generate the following image: Figure: Example of depicting an MDL reaction

../_images/mdlreaction2img-01.png

Example of depicting an MDL reaction

prompt> mdlreaction2img -in mdlreaction.sdf -out image.png -atomprop MapIdx
prompt> MDLReaction2Img -in mdlreaction.sdf -out image.png -atomprop MapIdx

will generate the following image: Figure: Example of depicting an MDL reaction with atom map indices

../_images/mdlreaction2img-02.png

Example of depicting an MDL reaction with atom map indices

See also

Depicting a Single Molecule

A program that converts a molecular structure into an image file.

Command Line Interface

A description of the command line interface can be obtained by executing the program with the –help argument.

prompt> mol2img --help

will generate the following output:

Simple parameter list
 image options :
   -height : Height of output image
   -width : Width of output image

 input/output options :
   -in : Input filename
   -out : Output filename
   -ringdict : User-defined 2D ring dictionary

 molecule display options :
   -aromstyle : Aromatic ring display style
   -atomcolor : Atom coloring style
   -atomlabelfontscale : Atom label font scale
   -atomprop : Atom property display
   -atomstereostyle : Atom stereo display style
   -bondcolor : Bond coloring style
   -bondprop : Bond property display
   -bondstereostyle : Bond stereo display style
   -hydrstyle : Hydrogen display style
   -linewidth : Default bond line width
   -scale : Scaling of the depicted molecule
   -superdisp : Super atom display style
   -titleloc : Location of the molecule title

 prepare depiction options :
   -clearcoords : Clear and regenerate 2D coordinates of molecule(s)
   -orientation : Set the preferred orientation of 2D coordinates
   -suppressH : Suppress explicit hydrogens of molecule(s)

Example

prompt> mol2img -in nexium.ism -out image.png
prompt> Mol2img -in nexium.ism -out image.png

will generate the image shown in Figure: Example of using the program with default parameters.

../_images/mol2img-01.png

Example of using the program with default parameters

prompt> mol2img -in nexium.ism -out image.png -atomcolor WhiteMonochrome
prompt> Mol2Img -in nexium.ism -out image.png -atomcolor WhiteMonochrome

will generate the image shown in Figure: Example of using the program with the white monochrome atom coloring style.

../_images/mol2img-02.png

Example of using the program with the white monochrome atom coloring style

prompt> mol2img -in nexium.ism -out image.png -aromstyle Circle

will generate the image shown in Figure: Example of using the program with aromaticity style ‘Circle’.

../_images/mol2img-03.png

Example of using the program with aromaticity style ‘Circle’

prompt> mol2img -in nexium.ism -out image.png -atomstereostyle "AtomStereo|CIPAtomStereo"

will generate the image shown in Figure: Example of the mol2img program with CIP atom stereo option.

../_images/mol2img-04.png

Example of using the program with CIP atom stereo option

prompt> mol2img -in nexium.ism -out image.png -linewidth 4

will generate the image shown in Figure: Example of using the program with user-defined line width.

../_images/mol2img-05.png

Example of using the program with user-defined line width

prompt> mol2img -in nexium.ism -out image.png -superdisp All

will generate the image shown in Figure: Example of using the program with superatom style.

../_images/mol2img-06.png

Example of using the program with superatom style

Note

The above program can generate 2D coordinates with user-defined 2D ring layouts when using the -ringdict parameter.

See also the 2D coordinate generation utilities section of the OEChem TK manual that shows examples about how to generate and utilize user-defined ring dictionaries.

See also

Depicting Molecules in Multi-Page

A program that converts molecular structures into a multi-page PDF image.

Command Line Interface

A description of the command line interface can be obtained by executing the program with the –help argument.

prompt> mols2pdf --help

will generate the following output:

Simple parameter list
input/output options :
  -in : Input filename
  -out : Output filename
  -ringdict : User-defined 2D ring dictionary

molecule display options :
  -aromstyle : Aromatic ring display style
  -atomcolor : Atom coloring style
  -atomlabelfontscale : Atom label font scale
  -atomprop : Atom property display
  -atomstereostyle : Atom stereo display style
  -bondcolor : Bond coloring style
  -bondprop : Bond property display
  -bondstereostyle : Bond stereo display style
  -hydrstyle : Hydrogen display style
  -linewidth : Default bond line width
  -scale : Scaling of the depicted molecule
  -superdisp : Super atom display style
  -titleloc : Location of the molecule title

prepare depiction options :
  -clearcoords : Clear and regenerate 2D coordinates of molecule(s)
  -orientation : Set the preferred orientation of 2D coordinates
  -suppressH : Suppress explicit hydrogens of molecule(s)

report options :
  -colsperpage : Number of columns per page
  -pageheight : Page height
  -pageorientation : Page orientation
  -pagesize : Page size
  -pagewidth : Page width
  -rowsperpage : Number of rows per page

See also

Note

The above program can generate 2D coordinates with user-defined 2D ring layouts when using the -ringdict parameter.

See also the 2D coordinate generation utilities section of the OEChem TK manual that shows examples about how to generate and utilize user-defined ring dictionaries.

Depicting Molecules In a Grid

A program that converts molecular structures into an image with a grid layout. By default the input molecules are depicted in a 3x2 grid.

Command Line Interface

A description of the command line interface can be obtained by executing the program with the –help argument.

prompt> mols2img --help

will generate the following output:

Simple parameter list
 -height : Height of output image
 -width : Width of output image

 image grid options :
   -cols : Number of columns
   -rows : Number of rows

 input/output options :
   -in : Input filename(s)
   -out : Output filename

 molecule display options :
   -aromstyle : Aromatic ring display style
   -atomcolor : Atom coloring style
   -atomlabelfontscale : Atom label font scale
   -atomprop : Atom property display
   -atomstereostyle : Atom stereo display style
   -bondcolor : Bond coloring style
   -bondprop : Bond property display
   -bondstereostyle : Bond stereo display style
   -hydrstyle : Hydrogen display style
   -linewidth : Default bond line width
   -scale : Scaling of the depicted molecule
   -superdisp : Super atom display style
   -titleloc : Location of the molecule title

 prepare depiction options :
   -clearcoords : Clear and regenerate 2D coordinates of molecule(s)
   -orientation : Set the preferred orientation of 2D coordinates
   -suppressH : Suppress explicit hydrogens of molecule(s)

Examples

prompt> mols2img -in amino.ism -out image.png

will generate the image shown in Figure: Example of using the program with default parameters.

../_images/mols2img-01.png

Example of using the program with default parameters

Note

By default the program depicts molecules in a 3x2 grid

prompt> mols2img -in amino.ism -out image.png -rows 2 -cols 3

will generate the image shown in Figure: Example of using the program with user-defined number of rows and columns.

../_images/mols2img-02.png

Example of using the program with user-defined number of rows and columns

prompt> mols2img -in amino.ism -out image.png  -rows 2 -cols 2 -titleloc Bottom

will generate the image shown in Figure: Example of using the program with molecule titles displayed at the bottom.

../_images/mols2img-03.png

Example of using the program with molecule titles displayed at the bottom

See also

Generating 2D Ring Dictionary Report

A program that generate a multi-page PDF report of the 2D ring dictionary.

Command Line Interface

A description of the command line interface can be obtained by executing the program with the –help argument.

prompt> ringdict2pdf --help

Will generate the following output:

Simple parameter list
    input/output options :
      -out : Output filename
      -ringdict : Input ring dictionary filename

    report options :
      -colsperpage : Number of columns per page
      -pageheight : Page height
      -pageorientation : Page orientation
      -pagesize : Page size
      -pagewidth : Page width
      -rowsperpage : Number of rows per page

Example

prompt> ringdict2pdf -ringdict rtd.oeb -out rtd.pdf

will generate a multi-page PDF report similar to the one shown in Table: Example of ring dictionary report.

Example of ring dictionary report (The pages are reduced here for visualization convenience)
cover page page 1 page 2
../_images/rtd-example-report-1.png ../_images/rtd-example-report-2.png ../_images/rtd-example-report-3.png

See also

Depicting MDL Query Substructure Search Hits

A program that performs substructure search on a molecule using an MDL query and generates an image file one match per molecule.

Command Line Interface

A description of the command line interface can be obtained by executing the program with the –help argument.

prompt> viewmdlsearch --help

Will generate the following output:

Simple parameter list
 general options :
   -align : Align hits to query

 highlight options :
   -highlightcolor : Highlighting color
   -highlightstyle : Highlighting style

 input/output options :
   -out : Output image filename
   -query : Input query filename
   -target : Input target filename

 molecule display options :
   -aromstyle : Aromatic ring display style
   -atomcolor : Atom coloring style
   -atomlabelfontscale : Atom label font scale
   -atomprop : Atom property display
   -atomstereostyle : Atom stereo display style
   -bondcolor : Bond coloring style
   -bondprop : Bond property display
   -bondstereostyle : Bond stereo display style
   -hydrstyle : Hydrogen display style
   -linewidth : Default bond line width
   -scale : Scaling of the depicted molecule
   -superdisp : Super atom display style
   -titleloc : Location of the molecule title

 report options :
   -colsperpage : Number of columns per page
   -pageheight : Page height
   -pageorientation : Page orientation
   -pagesize : Page size
   -pagewidth : Page width
   -rowsperpage : Number of rows per page

See also