molwitch-renderer

NCATS custom Molecule Renderer that uses Molwitch Chemical objects into image files.

This project is used by the GSRS Project

Customizable by JSON Configuration

The RendererOptions class has many configuration options to change how the renderer displays. An instance can either be created by making a new RendererOptions instance and then call the appriopriate setter methods or you can use JSON and create an instance using Jackson

 RendererOptions expected = RendererOptions.createUSPLike();

String json = mapper.writer().writeValueAsString(map);


RendererOptions renderOptions = mapper.readValue(json, RendererOptions.class);

Example JSON

{
  "options" : {
    "DEF_FONT_GAP_PERCENT" : 1.02,
    "DEF_WEDGE_ANG" : 0.1156106096521044,
    "PROP_KEY_DRAW_GREYSCALE" : true,
    "PROP_KEY_DRAW_WEDGE_AS_POINT" : false,
    "SUBSCRIPT_Y_DISPLACEMENT_FRACTION" : 0.17,
    "DEF_FONT_PERCENT" : 0.47918,
    "DEF_STROKE_PERCENT" : 0.032,
    "DEF_DBL_BOND_GAP" : 0.19949999999999998,
    "PROP_KEY_DRAW_STEREO_LAST_DASH_ON_NON_SYMBOLS" : false,
    "PROP_KEY_DRAW_STEREO_WEDGE_JOIN" : true,
    "DEF_NUM_DASH" : 8.0
  },
  "add-shadow" : true,
  "add-border" : true,
  "color-bg" : "0",
  "color-border" : "ff000000"
}

and you can be even more creative like you can change the colors for each atom like this:

{
  "options" : {
    "DEF_FONT_GAP_PERCENT" : 1.02,
    "DEF_WEDGE_ANG" : 0.1156106096521044,
    "PROP_KEY_DRAW_GREYSCALE" : true,
    "PROP_KEY_DRAW_WEDGE_AS_POINT" : false,
    "SUBSCRIPT_Y_DISPLACEMENT_FRACTION" : 0.17,
    "DEF_FONT_PERCENT" : 0.47918,
    "DEF_STROKE_PERCENT" : 0.032,
    "DEF_DBL_BOND_GAP" : 0.19949999999999998,
    "PROP_KEY_DRAW_STEREO_LAST_DASH_ON_NON_SYMBOLS" : false,
    "PROP_KEY_DRAW_STEREO_WEDGE_JOIN" : true,
    "colorPalette" : {
      "atomColors" : {
        "P" : "ffe6db45",
        "Br" : "ff735423",
        "S" : "ff2d2d43",
        "C" : "ff3a3a3a",
        "Na" : "ff308fa0",
        "F" : "ff36b449",
        "H" : "ff3a3a3a",
        "Cl" : "ff36b449",
        "I" : "ffe645cd",
        "N" : "ff5d45e6",
        "O" : "ffe65d45"
      }
    },
    "DEF_NUM_DASH" : 8.0
  },
  "add-shadow" : false,
  "add-border" : false,
  "color-bg" : "ffff0000",
  "color-border" : "ff000000"
}

Once you have your RenderOptions you can create your ChemicalRenderer instance:

RendererOptions renderOptions = ...

ChemicalRenderer renderer = new ChemicalRender( renderOptions);

 Chemical c = Chemical.parseMol(mol);
 int imageSize=500;
 ImageIO.write(renderer.createImage(c, imageSize), "PNG", new File("myRenderedImage.png"));