Better Depictions with Ogham

CUP XI. Santa Fe 

Bob Tolbert 

VP, Development 

April 19, 2010

• Current version 

– Single pixel lines with BMP output 

– Poor fonts 

– Decent coordinate generation 

– Core API in ints not floats 

• Ogham 2.0 plans 

• Using native graphics in Python, Java, .Net 


Ogham 

April 19, 2010

• Replace OEDepictView with OEMolView 

– More straightforward access to atom and bond properties 

• Replace OEDepictBase with OEImageBase 

– Replace int with float API 

• OEPen for user-defined line properties 

– Including width 

Ogham 2.0 

• Older classes will stay around for backward compatibility 


April 19, 2010

• Much work on layout algorithm to remove clashes 

– Send us your clashing structure 

• Many new built-in ring templates 

• Working “aligned” depictions 

– Current version has severe limitations 

– Can’t align to part of a ring system 

• User-defined templates 


Ogham 2.0 

April 19, 2010

• C++ - Qt 

– Depictions in VIDA 

• Python – PyCairo 

– mol2png web service 

• Java – Graphics2D 

– Mol2Img.java 

• .Net – System.Drawing.Drawing2D 


Using Native Graphics 

April 19, 2010

• Cairo – LGPL library for low-level 2D graphics 

– Part of GTK/GNOME project 

• PyCairo – Python wrapper for Cairo 

– Usually installable via yum or apt-get on Linux 

– Installation a bit of a pain on Windows 


PyCairo 

April 19, 2010

import cairo 

from openeye.oechem import * 

from openeye.oedepict import * 

class OECairoImage(OEDepictBase): 

def __init__(self, ctx, w, h): 


OEDepictBase.__init__(self) 

self.context = ctx 

Derive new class from OEDepictBase 

self.context.set_line_cap(cairo.LINE_CAP_ROUND) 

self.context.select_font_face("monospace", 

cairo.FONT_SLANT_NORMAL, 

cairo.FONT_WEIGHT_BOLD) 

ctx is a PyCairo context 

Set some default style information 

April 19, 2010

def DrawLine(self, x1, y1, x2, y2, c): 

self.SetColor(c) 

self.context.move_to(x1, y1) 

self.context.line_to(x2, y2) 

self.context.stroke() 

def DrawString(self, x, y, str, c): 

self.SetFont() 

self.SetColor(c) 

self.context.move_to(x,y-self.offset) 

self.context.show_text(str) 

Overload as many methods as you can for the best native performance 


Add some overloads 

April 19, 2010

import cairo 

from openeye.oechem import * 

from openeye.oedepict import * 

from OECairoImage import OECairoImage 

. . . 

def main(args, interfaceData): 

. . . 

WIDTH = itf.GetInt("-w") 

HEIGHT = itf.GetInt("-h") 

surface = cairo.ImageSurface(cairo.FORMAT_ARGB32,WIDTH,HEIGHT) 

ctx = cairo.Context (surface) 

img = OECairoImage(ctx, WIDTH, HEIGHT) 


mol2png.py 

Declare a PyCairo image and then pass to OECairoImage ctor 

April 19, 2010

view = OEDepictView() 

…set up OEDepictView options 

# set some atoms to be selected by SMARTS 

setSelected(mol, SMARTS) 

view.SetMolecule(mol) 

# render the image 

view.RenderImage(img) 

# draw transparent selection on top 

drawSelected(view, ctx, (0.0,1.0,0.0,0.3)) 


mol2png.py (part 2) 

RGBA color 

To draw directly to the context 

To access molecule information and view coordinates 

April 19, 2010

def setSelected(mol, smarts): 

if smarts: 

pat=OESubSearch() 

selectedAtoms=set() 

bondedAtoms=set() 

if not pat.Init(smarts): 


print "Invalid smarts: \"%s\""%smarts 

return 

for match in pat.Match(mol): 

for a in match.GetTargetAtoms(): 

selectedAtoms.add(a) 

a.SetBoolData("atom_selected", True) 

for match in pat.Match(mol): 

for b in match.GetTargetBonds(): 

b.SetBoolData("selected",True) 

bondedAtoms.add(b.GetBgn()) 

bondedAtoms.add(b.GetEnd()) 

selectedAtoms -= bondedAtoms 

for a in selectedAtoms: 

a.SetBoolData("selected", True) 

setSelected 

April 19, 2010

def drawSelected(view, ctx, rgb): 

ctx.push_group() 

ctx.set_source_rgba(rgb[0], rgb[1], rgb[2], 1.0) 

for bond in view.GetMolecule().GetBonds(): 

if bond.HasData("selected"): 

a1 = bond.GetBgn() 

astyle1 = view.AStyle(a1.GetIdx()) 

a2 = bond.GetEnd() 

astyle2 = view.AStyle(a2.GetIdx()) 

if astyle1.hidden or astyle2.hidden: 

continue 

xyz1 = view.GetViewCoords(view.GetMolecule(), a1) 

drawSelected 

xyz2 = view.GetViewCoords(view.GetMolecule(), a2) 

ctx.set_line_width(view.GetFontSize()*SELECTION_WIDTH_SCALE) 

ctx.move_to(xyz1[0], xyz1[1]) 

ctx.line_to(xyz2[0], xyz2[1]) 

ctx.stroke() 

ctx.pop_group_to_source() 

ctx.paint_with_alpha(rgb[3]) 

Draw transparent – alpha < 1.0 


Loop over the selected bonds 

Draw a wide line 

April 19, 2010

class Root(object): 

def depict(self, *args, **kwargs): 

cherrypy.response.headers['Content-Type'] = "image/png" 

return depictWeb(kwargs) 

depict.exposed=True 

def main(): 

root=Root() 

cherrypy.quickstart(root) 

Uses CherryPy web service 

Start a server and expose “depict” as a REST URL. 


mol2png_server.py 

April 19, 2010

def depictWeb(query): 

. . . . 

import cStringIO 

buffer = cStringIO.StringIO() 

surface.write_to_png(buffer) 

png_string=buffer.getvalue() 

buffer.close() 

return [png_string] 

mol2png_server.py (part 2) 

Draw to PyCairo surface, write to buffer in memory, return as PNG. 


April 19, 2010


mol2png_server demo 

April 19, 2010

public class OEJavaMolDepiction extends OEDepictBase { 

protected Graphics2D g2; 

public OEJavaMolDepiction(Graphics g, int w, int h) { 

g2 = (Graphics2D) g; 

} 


width = w; 

height = h; 

Java2DMolDepiction - 

derives from OEDepictBase 

contains Java Graphics2D object 

OEJavaMolDepiction.java 

April 19, 2010

BufferedImage bi = new BufferedImage(w, h, 

BufferedImage.TYPE_INT_RGB); 

Graphics2D g2 = bi.createGraphics(); 

OEJavaMolDepiction img = new OEJavaMolDepiction(g2, w, h); 

Draw(img, w, h); 

WriteImage(outputfile, bi); 


Mol2Img.java 

April 19, 2010

For more information, please contact us. 

business@eyesopen.com 

support@eyesopen.com 

www.eyesopen.com 

505-473-7385 


April 19, 2010

Better Depictions with Ogham

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