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Adds SVG reaction depiction #993

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Adds SVG reaction depiction #993

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52bbb34
Adds SVG reaction depiction
Jul 26, 2016
868fe1e
Cleans up code, scales relative fontsizes
Jul 27, 2016
382ba23
Render at a larger scale, fix extra +, make saner choice of relativeS…
Jul 27, 2016
2849fe5
Fixes clipping
Jul 27, 2016
bef16ca
Remove rendering at higher resolutions
Jul 27, 2016
94ba5fe
Finish remove rendering at higher resolutions
Jul 27, 2016
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57 changes: 32 additions & 25 deletions rdkit/Chem/Draw/__init__.py
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Expand Up @@ -439,9 +439,7 @@ def is2D(conf):
allZeroes = False
return not allZeroes

def _cleanupRXN(rxn):
"""Cleanup reactions so the computed coords are sane for depiction"""
for mol in rxn.GetReactants():
def _prepareRxnMol(mol):
compute2D=False
for conf in mol.GetConformers():
compute2D = not is2D(conf)
Expand All @@ -454,19 +452,11 @@ def _cleanupRXN(rxn):
pass
if compute2D:
AllChem.Compute2DCoords(mol)

for mol in rxn.GetProducts():
compute2D=False
for conf in mol.GetConformers():
compute2D = not is2D(conf)
try:
AllChem.SanitizeMol(mol,
sanitizeOps=(AllChem.SanitizeFlags.SANITIZE_ALL^
AllChem.SanitizeFlags.SANITIZE_KEKULIZE))
except:
pass
if compute2D:
AllChem.Compute2DCoords(mol)

def _cleanupRXN(rxn):
"""Cleanup reactions so the computed coords are sane for depiction"""
map(_prepareRxnMol, rxn.GetReactants())
map(_prepareRxnMol, rxn.GetProducts())
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(An aside, not important): I'm wondering about style here. Is using map idiomatic Python?

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Well, regardless of whether it is idomatic or not, this doesn't work with python3, where map just returns an iterator. A direct loop or list comprehension is needed

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I really have to make the switch I think.

return rxn

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I would rather do a _prepareRXNMol function here and call it for each of the molecules in your molecule list below instead of duplicating the code for reactants and products.

#source https://commons.wikimedia.org/wiki/File:Tab_plus.svg
Expand All @@ -486,6 +476,7 @@ def _cleanupRXN(rxn):
from xml.dom import minidom
fontSizePattern = re.compile(".*font[-]size[:](.*)px")
def getBBox(svg, width, height):
"""svg, width, height -> minx, maxx, miny, maxy"""
doc = minidom.parseString(svg) # parseString also exists
# get all vector paths
path_strings = [path.getAttribute('d') for path
Expand Down Expand Up @@ -557,7 +548,7 @@ def makeRect(minx, maxx, miny, maxy):


def ReactionToSVG(rxn, subImgSize=(200,200), stripSVGNamespace=True,
scaleRelative=False,
scaleRelative=True,
debugRender=False,
**kwargs):
"""
Expand All @@ -572,15 +563,10 @@ def ReactionToSVG(rxn, subImgSize=(200,200), stripSVGNamespace=True,
mols = list(rxn.GetReactants()) + list(rxn.GetProducts())

# get the relative sizes of the molecules
relativeSizes = [float(m.GetNumAtoms()) for m in mols]
largest = max(relativeSizes)
if scaleRelative:
relativeSizes = [x/largest for x in relativeSizes]
else:
relativeSizes = [1.0] * len(relativeSizes)
relativeSizes = [1.0] * len(mols)

num_mols = len(mols)
svg_size = fullSize = (subImgSize[0] * num_mols + 20*num_reactants + 25, subImgSize[1])
svg_size = fullSize = (subImgSize[0] * num_mols + 20*num_reactants + 25 + 20*num_products, subImgSize[1])

blocks = [''] * num_mols
hdr = ''
Expand All @@ -591,6 +577,27 @@ def ReactionToSVG(rxn, subImgSize=(200,200), stripSVGNamespace=True,
xOffset = 0
xdelta = subImgSize[0]

if scaleRelative:
fontSizes = []
for col,mol in enumerate(mols):
scale = relativeSizes[col]
img_width = int(subImgSize[0] * scale)
img_height = int(subImgSize[1] * scale)
nmol = rdMolDraw2D.PrepareMolForDrawing(mol,kekulize=kwargs.get('kekulize',False))
d2d = rdMolDraw2D.MolDraw2DSVG(img_width, img_height)
d2d.DrawMolecule(nmol)
d2d.FinishDrawing()
txt = d2d.GetDrawingText()
fontSizes.append(max( list(map(float, fontSizePattern.findall(txt))) + [0] ))

median = fontSizes[:]
median.sort()
print median
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this won't run with python3 (I expect the travis tests will fail)

relFont = median[int(len(median)/2)]
print fontSizes
relativeSizes = [relFont/fn*0.75 for fn in fontSizes]
print relativeSizes

# for each molecule make an svg and scale place it in the appropriate
# position
top_layer = []
Expand Down Expand Up @@ -632,7 +639,7 @@ def ReactionToSVG(rxn, subImgSize=(200,200), stripSVGNamespace=True,
xOffset += xdelta*scale

# add the plus signs
if col < num_reactants - 1:
if col < num_reactants - 1 or col >= num_reactants:
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you end up with an extra + in the products.

start,end = rect_matcher.match(rect.replace("opacity:1.0", "opacity:0.0")).groups()
elem = start + repr(20) + end + svg_plus
top_layer.append('<g transform="translate(%d,%d)" >%s</g>'%(
Expand Down