#!/usr/bin/env python
# (C) 2022 Cadence Design Systems, Inc. (Cadence)
# All rights reserved.
# TERMS FOR USE OF SAMPLE CODE The software below ("Sample Code") is
# provided to current licensees or subscribers of Cadence products or
# SaaS offerings (each a "Customer").
# Customer is hereby permitted to use, copy, and modify the Sample Code,
# subject to these terms. Cadence claims no rights to Customer's
# modifications. Modification of Sample Code is at Customer's sole and
# exclusive risk. Sample Code may require Customer to have a then
# current license or subscription to the applicable Cadence offering.
# THE SAMPLE CODE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
# EXPRESS OR IMPLIED. OPENEYE DISCLAIMS ALL WARRANTIES, INCLUDING, BUT
# NOT LIMITED TO, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
# PARTICULAR PURPOSE AND NONINFRINGEMENT. In no event shall Cadence be
# liable for any damages or liability in connection with the Sample Code
# or its use.
#############################################################################
# Depicts shape and color overlap between a 3D reference structure and
# a sets of 3D fit molecules. The molecules have to be pre-aligned.
# The first molecule is expected be the reference.
#############################################################################
import sys
from openeye import oechem
from openeye import oedepict
from openeye import oegrapheme
from openeye import oeshape
def main(argv=[__name__]):
itf = oechem.OEInterface(InterfaceData)
if not oechem.OEParseCommandLine(itf, argv):
return 1
iname = itf.GetString("-in")
oname = itf.GetString("-out")
maxhits = itf.GetInt("-maxhits")
ext = oechem.OEGetFileExtension(oname)
if not oedepict.OEIsRegisteredMultiPageImageFile(ext):
oechem.OEThrow.Fatal("Unknown multipage image type!")
ifs = oechem.oemolistream()
if not ifs.open(iname):
oechem.OEThrow.Fatal("Cannot open input molecule file!")
refmol = oechem.OEGraphMol()
if not oechem.OEReadMolecule(ifs, refmol):
oechem.OEThrow.Fatal("Cannot read reference molecule!")
ropts = oedepict.OEReportOptions(3, 1)
ropts.SetHeaderHeight(40.0)
ropts.SetFooterHeight(20.0)
report = oedepict.OEReport(ropts)
cff = oeshape.OEColorForceField()
cff.Init(oeshape.OEColorFFType_ImplicitMillsDean)
cffdisplay = oegrapheme.OEColorForceFieldDisplay(cff)
qopts = GetShapeQueryDisplayOptions()
sopts = GetShapeOverlapDisplayOptions()
copts = GetColorOverlapDisplayOptions()
refdisp = oegrapheme.OEShapeQueryDisplay(refmol, cff, qopts)
dots = oechem.OEDots(100, 10, "shape overlaps")
for fitmol in ifs.GetOEGraphMols():
if maxhits > 0 and dots.GetCounts() >= maxhits:
break
dots.Update()
maincell = report.NewCell()
grid = oedepict.OEImageGrid(maincell, 1, 3)
grid.SetMargins(5.0)
grid.SetCellGap(5.0)
# TITLE + SCORE GRAPH + QUERY
cell = grid.GetCell(1, 1)
cellw, cellh = cell.GetWidth(), cell.GetHeight()
font = oedepict.OEFont(oedepict.OEFontFamily_Default, oedepict.OEFontStyle_Bold, 10,
oedepict.OEAlignment_Left, oechem.OEBlack)
pos = oedepict.OE2DPoint(10.0, 10.0)
cell.DrawText(pos, fitmol.GetTitle(), font, cell.GetWidth())
rframe = oedepict.OEImageFrame(cell, cellw, cellh * 0.35,
oedepict.OE2DPoint(0.0, cellh * 0.10))
mframe = oedepict.OEImageFrame(cell, cellw, cellh * 0.50,
oedepict.OE2DPoint(0.0, cellh * 0.50))
RenderScoreRadial(rframe, fitmol)
oegrapheme.OERenderShapeQuery(mframe, refdisp)
font = oedepict.OEFont(oedepict.OEFontFamily_Default, oedepict.OEFontStyle_Bold, 8,
oedepict.OEAlignment_Center, oechem.OEGrey)
pos = oedepict.OE2DPoint(20.0, 10.0)
mframe.DrawText(pos, "query", font)
oedepict.OEDrawCurvedBorder(mframe, oedepict.OELightGreyPen, 10.0)
odisp = oegrapheme.OEShapeOverlapDisplay(refdisp, fitmol, sopts, copts)
# SHAPE OVERLAP
cell = grid.GetCell(1, 2)
oegrapheme.OERenderShapeOverlap(cell, odisp)
RenderScore(cell, fitmol, "ROCS_ShapeTanimoto", "Shape Tanimoto")
# COLOR OVERLAP
cell = grid.GetCell(1, 3)
oegrapheme.OERenderColorOverlap(cell, odisp)
RenderScore(cell, fitmol, "ROCS_ColorTanimoto", "Color Tanimoto")
oedepict.OEDrawCurvedBorder(maincell, oedepict.OELightGreyPen, 10.0)
dots.Total()
cffopts = oegrapheme.OEColorForceFieldLegendDisplayOptions(1, 6)
for header in report.GetHeaders():
oegrapheme.OEDrawColorForceFieldLegend(header, cffdisplay, cffopts)
oedepict.OEDrawCurvedBorder(header, oedepict.OELightGreyPen, 10.0)
font = oedepict.OEFont(oedepict.OEFontFamily_Default, oedepict.OEFontStyle_Default, 12,
oedepict.OEAlignment_Center, oechem.OEBlack)
for idx, footer in enumerate(report.GetFooters()):
oedepict.OEDrawTextToCenter(footer, "-" + str(idx + 1) + "-", font)
oedepict.OEWriteReport(oname, report)
return 0
def AddCommonDisplayOptions(opts):
opts.SetTitleLocation(oedepict.OETitleLocation_Hidden)
opts.SetAtomLabelFontScale(1.5)
pen = oedepict.OEPen(oechem.OEBlack, oechem.OEBlack, oedepict.OEFill_Off, 1.5)
opts.SetDefaultBondPen(pen)
def GetShapeQueryDisplayOptions():
qopts = oegrapheme.OEShapeQueryDisplayOptions()
AddCommonDisplayOptions(qopts)
arcpen = oedepict.OEPen(oedepict.OELightGreyPen)
qopts.SetSurfaceArcFxn(oegrapheme.OEDefaultArcFxn(arcpen))
qopts.SetDepictOrientation(oedepict.OEDepictOrientation_Square)
return qopts
def GetShapeOverlapDisplayOptions():
sopts = oegrapheme.OEShapeOverlapDisplayOptions()
AddCommonDisplayOptions(sopts)
arcpen = oedepict.OEPen(oechem.OEGrey, oechem.OEGrey, oedepict.OEFill_Off, 1.0, 0x1111)
sopts.SetQuerySurfaceArcFxn(oegrapheme.OEDefaultArcFxn(arcpen))
sopts.SetOverlapColor(oechem.OEColor(110, 110, 190))
return sopts
def GetColorOverlapDisplayOptions():
copts = oegrapheme.OEColorOverlapDisplayOptions()
AddCommonDisplayOptions(copts)
arcpen = oedepict.OEPen(oechem.OEGrey, oechem.OEGrey, oedepict.OEFill_Off, 1.0, 0x1111)
copts.SetQuerySurfaceArcFxn(oegrapheme.OEDefaultArcFxn(arcpen))
return copts
def GetScore(mol, sdtag):
if oechem.OEHasSDData(mol, sdtag):
return float(oechem.OEGetSDData(mol, sdtag))
return 0.0
def RenderScoreRadial(image, mol):
sscore = max(min(GetScore(mol, "ROCS_ShapeTanimoto"), 1.0), 0.00)
cscore = max(min(GetScore(mol, "ROCS_ColorTanimoto"), 1.0), 0.00)
if sscore > 0.0 or cscore > 0.0:
scores = oechem.OEDoubleVector([sscore, cscore])
oegrapheme.OEDrawROCSScores(image, scores)
def RenderScore(image, mol, sdtag, label):
score = GetScore(mol, sdtag)
if score == 0.0:
return
w, h = image.GetWidth(), image.GetHeight()
frame = oedepict.OEImageFrame(image, w, h * 0.10, oedepict.OE2DPoint(0.0, h * 0.90))
font = oedepict.OEFont(oedepict.OEFontFamily_Default, oedepict.OEFontStyle_Default, 9,
oedepict.OEAlignment_Center, oechem.OEBlack)
oedepict.OEDrawTextToCenter(frame, label + " = " + str(score), font)
#############################################################################
# INTERFACE
#############################################################################
InterfaceData = '''
!BRIEF [-in] [-out]