Grapheme Example Summary

The following table lists the currently available Grapheme TK example:

Program Description
BFactor2Img depicting BFactor
Complex2Img depicting active site interactions
ShapeOverlap2PDF depicting shape and color atom overlaps

Depicting BFactor

A program that depicts the BFactor of a ligand and its environment.

Command Line Interface

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

prompt> BFactor2Img --help

will generate the following output:

[-complex] <input> [-out] <output pdf>

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

    SplitMolComplex options :
      -ligandname : Ligand name

    input/output options
      -complex : Input filename of the protein complex
      -out : Output filename

    molecule display options
      -aromstyle : Aromatic ring display style

Examples

prompt> BFactor2Img -complex 1MEH.pdb -ligandname MOA -out MOA.png

will generate the following output:

Average BFactor of the complex = +32.721
Minimum BFactor of the ligand and its environment = +21.500
Maximum BFactor of the ligand and its environment = +72.060

and the image shown in Figure: Example of depicting the BFactor of MOA and its environment.

../_images/bfactor2img_MOA.png

Example of depicting the BFactor of MOA and its environment

prompt> BFactor2Img -complex 1LEE.pdb -ligandname R36 -out MOA.R36

will generate the following output:

Average BFactor of the complex = +23.754
Minimum BFactor of the ligand and its environment = +6.040
Maximum BFactor of the ligand and its environment = +32.050

and the image shown in Figure: Example of depicting the BFactor of R36 and its environment.

../_images/bfactor2img_R36.png

Example of depicting the BFactor of R36 and its environment

Depicting Active Site Interactions

A program that depicts receptor-ligand interactions.

Command Line Interface

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

prompt> Complex2Img --help

will generate the following output:

[-complex] <input> [-out] <output image>

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

    SplitMolComplex options :
      -ligandname : Ligand name

    input/output options
      -complex : Input filename of the protein complex
      -out : Output filename

    molecule display options
      -aromstyle : Aromatic ring display style

Examples

prompt> Complex2Img complex2img.py -complex pdb1br6.ent -out 1br6-PT1.png

will generate the image shown in Figure: Example of depicting the receptor-ligand interaction (PDB: 1br6).

../_images/complex2img-1br6-PT1.png

Example of depicting the receptor-ligand interactions (PDB: 1br6)

prompt> Complex2Img.py -complex pdb1eoc.ent -out 1eoc-4NC.png

will generate the image shown in Figure: Example of depicting the receptor-ligand interaction (PDB: 1eoc).

../_images/complex2img-1eoc-4NC.png

Example of depicting the receptor-ligand interactions (PDB: 1eoc)

Depicting Shape and Color Atom Overlaps

A program that depicts the shape and the color overlap between a 3D reference structure and a sets of pre-aligned 3D fit molecules. It is implemented to visualize the output of ROCS but can be used to visualize the shape and color similarities of any molecules that have been pre-aligned with other applications.

Note

OEShape TK license is not required to run this example.

Command Line Interface

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

prompt> ShapeOverlap2PDF --help

will generate the following output:

[-in] <input> [-out] <output pdf>

 Simple parameter list
     input/output options:
       -in : Input molecule filename
       -out : Output image filename

     general options:
       -maxhits : Maximum number of hits depicted

Examples

prompt> ShapeOverlap2PDF -in rocs.sdf -out overlaps.pdf
Example of depicting the shape and color atom overlaps (The pages are reduced here for visualization convenience)
page 1 page 2 page 3
../_images/shapeoverlap2pdf-page-1.png ../_images/shapeoverlap2pdf-page-2.png ../_images/shapeoverlap2pdf-page-3.png