def MolToQPixmap(mol, size=(300,300), kekulize=True, wedgeBonds=True,
fitImage=False, options=None, **kwargs):
""" Generates a drawing of a molecule on a Qt QPixmap
"""
if not mol:
raise ValueError('Null molecule provided')
from rdkit.Chem.Draw.qtCanvas import Canvas
canvas = Canvas(size)
if options is None:
options = DrawingOptions()
options.bgColor = None
if fitImage:
options.dotsPerAngstrom = int(min(size) / 10)
options.wedgeDashedBonds=wedgeBonds
if kekulize:
from rdkit import Chem
mol = Chem.Mol(mol.ToBinary())
Chem.Kekulize(mol)
if not mol.GetNumConformers():
from rdkit.Chem import AllChem
AllChem.Compute2DCoords(mol)
drawer = MolDrawing(canvas=canvas, drawingOptions=options)
drawer.AddMol(mol, **kwargs)
canvas.flush()
return canvas.pixmap
def MolToMPL(mol,size=(300,300),kekulize=True, wedgeBonds=True,
imageType=None, fitImage=False, options=None, **kwargs):
""" Generates a drawing of a molecule on a matplotlib canvas
"""
if not mol:
raise ValueError('Null molecule provided')
from rdkit.Chem.Draw.mplCanvas import Canvas
canvas = Canvas(size)
if options is None:
options = DrawingOptions()
options.bgColor=None
if fitImage:
drawingOptions.dotsPerAngstrom = int(min(size) / 10)
options.wedgeDashedBonds=wedgeBonds
drawer = MolDrawing(canvas=canvas, drawingOptions=options)
omol=mol
if kekulize:
from rdkit import Chem
mol = Chem.Mol(mol.ToBinary())
Chem.Kekulize(mol)
if not mol.GetNumConformers():
from rdkit.Chem import AllChem
AllChem.Compute2DCoords(mol)
drawer.AddMol(mol,**kwargs)
omol._atomPs=drawer.atomPs[mol]
for k,v in iteritems(omol._atomPs):
omol._atomPs[k]=canvas.rescalePt(v)
canvas._figure.set_size_inches(float(size[0])/100,float(size[1])/100)
return canvas._figure
def draw_mol_to_svg(mol, filename):
"""
Draw a single molecule to an SVG file with transparent BG.
"""
# change BG to transperent
# (https://sourceforge.net/p/rdkit/mailman/message/31637105/)
o = DrawingOptions()
o.bgColor = None
# Use copy of molecule to avoid changing instance of mol.
new_mol = rdkit.MolFromMolBlock(rdkit.MolToMolBlock(mol))
rdkit.Compute2DCoords(new_mol)
Draw.MolToFile(new_mol,
filename,
fitImage=True,
imageType='svg',
options=o)
def draw_smiles_to_svg(smiles, filename):
"""
Draw a single molecule to an SVG file with transparent BG.
"""
mol = Chem.MolFromSmiles(smiles)
# change BG to transperent
# (https://sourceforge.net/p/rdkit/mailman/message/31637105/)
o = DrawingOptions()
o.bgColor = None
Chem.Compute2DCoords(mol)
Draw.MolToFile(
mol,
filename,
fitImage=True,
imageType='svg',
options=o
)
def MolToMPL(mol,
size=(300, 300),
kekulize=True,
wedgeBonds=True,
imageType=None,
fitImage=False,
options=None,
**kwargs):
""" Generates a drawing of a molecule on a matplotlib canvas
"""
if not mol:
raise ValueError('Null molecule provided')
from rdkit.Chem.Draw.mplCanvas import Canvas
canvas = Canvas(size)
if options is None:
options = DrawingOptions()
options.bgColor = None
if fitImage:
options.dotsPerAngstrom = int(min(size) / 10)
options.wedgeDashedBonds = wedgeBonds
drawer = MolDrawing(canvas=canvas, drawingOptions=options)
omol = mol
if kekulize:
from rdkit import Chem
mol = Chem.Mol(mol.ToBinary())
Chem.Kekulize(mol)
if not mol.GetNumConformers():
from rdkit.Chem import AllChem
AllChem.Compute2DCoords(mol)
drawer.AddMol(mol, **kwargs)
omol._atomPs = drawer.atomPs[mol]
for k, v in omol._atomPs.items():
omol._atomPs[k] = canvas.rescalePt(v)
canvas._figure.set_size_inches(float(size[0]) / 100, float(size[1]) / 100)
return canvas._figure
def generate_fragemnts(self):
# Clear class level list
del self.molecule[:]
# Get text input from LineEdit widget
self.smile = str(self.NTPS_smiles_entry.text())
# Append cStructure mol to class level list
self.molecule.append(
cStructure('precursor', self.smile, 'precursor.png'))
# SMARTS string for bond disconnection
self.patt = Chem.MolFromSmarts(
'[!$([NH]!@C(=O))&!D1&!$(*#*)]-&!@[!$([NH]!@C(=O))&!D1&!$(*#*)]')
# Init parent mol object
self.mol = Chem.MolFromSmiles(self.smile)
# find the rotatable bonds
self.bonds = self.mol.GetSubstructMatches(self.patt)
# create an editable molecule, break the bonds, and add dummies:
self.all_smis = [self.smile]
# disconnect rotatable bonds
for a, b in self.bonds:
self.em = Chem.EditableMol(self.mol)
self.nAts = self.mol.GetNumAtoms()
self.em.RemoveBond(a, b)
self.em.AddAtom(Chem.Atom(0))
self.em.AddBond(a, self.nAts, Chem.BondType.SINGLE)
self.em.AddAtom(Chem.Atom(0))
self.em.AddBond(b, self.nAts + 1, Chem.BondType.SINGLE)
self.nAts += 2
self.p = self.em.GetMol()
Chem.SanitizeMol(self.p)
self.smis = [
Chem.MolToSmiles(x, True)
for x in Chem.GetMolFrags(self.p, asMols=True)
]
for self.smi in self.smis:
self.all_smis.append(self.smi)
# draw molecules and save png images for display in structure viewer widget
# --> there's probably a better way to do this...
self.draw = 0
for i, self.smi in enumerate(self.all_smis):
if i == 0:
struct_type = 'precursor'
img_path = 'precursor.png'
else:
struct_type, img_path = 'fragment', 'fragment_%s.png' % self.draw
self.molecule.append(cStructure(struct_type, self.smi, img_path))
self.template = Chem.MolFromSmiles(self.smi)
drawOptions = DrawingOptions()
drawOptions.bgColor = (0, 0, 0)
Draw.MolToFile(self.template, img_path, options=drawOptions)
# append to class level list
self.structures.append(img_path)
# append to GUI fragments listbox - file name only
self.NTPS_frag_list.addItem(
QtGui.QListWidgetItem(
img_path.split('/')[-1].strip().split('.')[0]))
self.draw += 1
self.autocomplete_mod_properties()
# add image of first structure to graphicsview
scene = QtGui.QGraphicsScene()
scene.addPixmap(QtGui.QPixmap(self.structures[0]))
self.NTPS_structure_view.setScene(scene)
self.NTPS_structure_view.show()
return
