import random
import re
import unittest
from os import environ

import numpy as np

from rdkit import Chem, Geometry, RDConfig
from rdkit.Chem import AllChem, Draw, rdDepictor
from rdkit.Chem.Draw import rdMolDraw2D


class TestCase(unittest.TestCase):

    def setUp(self):
        pass

    def test1(self):
        m = Chem.MolFromSmiles('c1ccc(C)c(C)c1C')
        AllChem.Compute2DCoords(m)
        d = Draw.MolDraw2DSVG(300, 300)
        d.DrawMolecule(m)
        d.FinishDrawing()
        txt = d.GetDrawingText()
        self.assertTrue(txt.find("<svg") != -1)
        self.assertTrue(txt.find("</svg>") != -1)

    def test2(self):
        m = Chem.MolFromSmiles('c1ccc(C)c(C)c1C')
        AllChem.Compute2DCoords(m)
        d = Draw.MolDraw2DSVG(300, 300, -1, -1, True)
        do = d.drawOptions()
        do.atomLabels[3] = 'foolabel'
        d.DrawMolecule(m)
        d.FinishDrawing()
        txt = d.GetDrawingText()
        self.assertTrue(txt.find(">f</text>") != -1)
        self.assertTrue(txt.find(">o</text>") != -1)
        self.assertTrue(txt.find(">l</text>") != -1)
        self.assertTrue(txt.find(">a</text>") != -1)

    @unittest.skipUnless(hasattr(Draw, 'MolDraw2DCairo'), 'Cairo support not enabled')
    def testGithubIssue571(self):
        m = Chem.MolFromSmiles('c1ccc(C)c(C)c1C')
        AllChem.Compute2DCoords(m)
        d = Draw.MolDraw2DCairo(300, 300)
        d.DrawMolecule(m)
        d.FinishDrawing()
        txt = d.GetDrawingText()

    def testPrepareForDrawing(self):
        m = Chem.MolFromSmiles('c1ccccc1[C@H](F)Cl')
        nm = rdMolDraw2D.PrepareMolForDrawing(m)
        self.assertEqual(nm.GetNumAtoms(), 9)
        self.assertEqual(nm.GetNumConformers(), 1)
        m = Chem.MolFromSmiles('C1CC[C@H]2NCCCC2C1')
        nm = rdMolDraw2D.PrepareMolForDrawing(m)
        self.assertEqual(nm.GetNumAtoms(), 11)
        self.assertEqual(nm.GetNumConformers(), 1)
        nm = rdMolDraw2D.PrepareMolForDrawing(m, addChiralHs=False)
        self.assertEqual(nm.GetNumAtoms(), 10)
        self.assertEqual(nm.GetNumConformers(), 1)

        m = Chem.MolFromSmiles('CC=CC')
        m.GetBondWithIdx(1).SetStereo(Chem.BondStereo.STEREOANY)
        nm = rdMolDraw2D.PrepareMolForDrawing(m)
        self.assertEqual(nm.GetBondWithIdx(1).GetStereo(), Chem.BondStereo.STEREOANY)
        self.assertEqual(nm.GetBondWithIdx(0).GetBondDir(), Chem.BondDir.NONE)
        nm = rdMolDraw2D.PrepareMolForDrawing(m, wavyBonds=True)
        self.assertEqual(nm.GetBondWithIdx(1).GetStereo(), Chem.BondStereo.STEREONONE)
        self.assertEqual(nm.GetBondWithIdx(0).GetBondDir(), Chem.BondDir.UNKNOWN)

    def testRepeatedPrepareForDrawingCalls(self):
        m = Chem.MolFromMolBlock("""
          11280715312D 1   1.00000     0.00000     0

 33 36  0     1  0            999 V2000
    7.6125   -5.7917    0.0000 C   0  0  0  0  0  0           0  0  0
    7.0917   -6.0917    0.0000 C   0  0  1  0  0  0           0  0  0
    6.4792   -6.8917    0.0000 C   0  0  2  0  0  0           0  0  0
    8.1292   -6.0792    0.0000 N   0  0  0  0  0  0           0  0  0
    5.5042   -6.8917    0.0000 C   0  0  3  0  0  0           0  0  0
   11.2375   -4.8542    0.0000 N   0  0  0  0  0  0           0  0  0
    9.6792   -5.1667    0.0000 N   0  0  3  0  0  0           0  0  0
    5.9917   -6.5417    0.0000 C   0  0  0  0  0  0           0  0  0
    7.6042   -5.1917    0.0000 O   0  0  0  0  0  0           0  0  0
   10.7167   -5.1625    0.0000 C   0  0  0  0  0  0           0  0  0
    6.2917   -7.4667    0.0000 C   0  0  0  0  0  0           0  0  0
    6.5750   -5.7917    0.0000 C   0  0  0  0  0  0           0  0  0
   10.2000   -4.8667    0.0000 C   0  0  0  0  0  0           0  0  0
    8.6500   -5.7792    0.0000 C   0  0  3  0  0  0           0  0  0
    8.6417   -5.1792    0.0000 C   0  0  0  0  0  0           0  0  0
    9.1667   -6.0750    0.0000 C   0  0  0  0  0  0           0  0  0
    9.6875   -5.7667    0.0000 C   0  0  0  0  0  0           0  0  0
    9.1542   -4.8750    0.0000 C   0  0  0  0  0  0           0  0  0
    5.6917   -7.4667    0.0000 C   0  0  0  0  0  0           0  0  0
    5.2042   -7.4042    0.0000 F   0  0  0  0  0  0           0  0  0
    4.9875   -6.5917    0.0000 F   0  0  0  0  0  0           0  0  0
    7.5167   -6.5167    0.0000 O   0  0  0  0  0  0           0  0  0
   11.7542   -5.1500    0.0000 C   0  0  0  0  0  0           0  0  0
   11.2417   -6.0542    0.0000 C   0  0  0  0  0  0           0  0  0
   10.7250   -5.7625    0.0000 C   0  0  0  0  0  0           0  0  0
    6.5750   -5.1917    0.0000 C   0  0  0  0  0  0           0  0  0
    6.0542   -6.0917    0.0000 C   0  0  0  0  0  0           0  0  0
   11.7667   -5.7542    0.0000 C   0  0  0  0  0  0           0  0  0
   12.2750   -4.8417    0.0000 C   0  0  0  0  0  0           0  0  0
    6.0542   -4.8917    0.0000 C   0  0  0  0  0  0           0  0  0
    5.5375   -5.7917    0.0000 C   0  0  0  0  0  0           0  0  0
    5.5375   -5.1917    0.0000 C   0  0  0  0  0  0           0  0  0
    6.3167   -6.3042    0.0000 H   0  0  0  0  0  0           0  0  0
  2  1  1  0     0  0
  3  2  1  0     0  0
  4  1  1  0     0  0
  5  8  1  0     0  0
  6 10  1  0     0  0
  7 17  1  0     0  0
  8  3  1  0     0  0
  9  1  2  0     0  0
 10 13  1  0     0  0
 11  3  1  0     0  0
 12  2  1  0     0  0
 13  7  1  0     0  0
 14  4  1  0     0  0
 15 14  1  0     0  0
 16 14  1  0     0  0
 17 16  1  0     0  0
 18 15  1  0     0  0
 19 11  1  0     0  0
 20  5  1  0     0  0
 21  5  1  0     0  0
  2 22  1  6     0  0
 23  6  2  0     0  0
 24 25  1  0     0  0
 25 10  2  0     0  0
 26 12  1  0     0  0
 27 12  2  0     0  0
 28 24  2  0     0  0
 29 23  1  0     0  0
 30 26  2  0     0  0
 31 27  1  0     0  0
 32 31  2  0     0  0
  3 33  1  6     0  0
  7 18  1  0     0  0
 19  5  1  0     0  0
 32 30  1  0     0  0
 28 23  1  0     0  0
M  END""")
        nm = Draw.PrepareMolForDrawing(m)
        self.assertEqual(nm.GetBondBetweenAtoms(2, 1).GetBondType(), Chem.BondType.SINGLE)
        self.assertEqual(nm.GetBondBetweenAtoms(2, 1).GetBondDir(), Chem.BondDir.NONE)
        self.assertEqual(nm.GetBondBetweenAtoms(2, 7).GetBondType(), Chem.BondType.SINGLE)
        self.assertEqual(nm.GetBondBetweenAtoms(2, 7).GetBondDir(), Chem.BondDir.BEGINWEDGE)
        nm = Draw.PrepareMolForDrawing(nm)
        self.assertEqual(nm.GetBondBetweenAtoms(2, 1).GetBondType(), Chem.BondType.SINGLE)
        self.assertEqual(nm.GetBondBetweenAtoms(2, 1).GetBondDir(), Chem.BondDir.NONE)
        self.assertEqual(nm.GetBondBetweenAtoms(2, 7).GetBondType(), Chem.BondType.SINGLE)
        self.assertEqual(nm.GetBondBetweenAtoms(2, 7).GetBondDir(), Chem.BondDir.BEGINWEDGE)

    def testDrawMoleculesArgs(self):
        smis = [
            'O=C1c2cccc3c(N4CCCCC4)ccc(c23)C(=O)N1c1ccccn1', 'Cc1ccc[n+](C2=Nc3ccccc3[N-]C2=C(C#N)C#N)c1',
            'CC(=O)NC1=NN(C(C)=O)C(c2ccccn2)S1', 'COc1cc(Cc2nccc3cc(OC)c(OC)cc23)c(S(=O)(=O)O)cc1OC'
        ]
        tms = [Chem.MolFromSmiles(x) for x in smis]
        [rdMolDraw2D.PrepareMolForDrawing(x) for x in tms]
        drawer = rdMolDraw2D.MolDraw2DSVG(600, 600, 300, 300)
        p = Chem.MolFromSmarts('c1ccccn1')
        matches = [x.GetSubstructMatch(p) for x in tms]
        acolors = []
        for mv in matches:
            clrs = {}
            random.seed(0xf00d)
            for idx in mv:
                clrs[idx] = (random.random(), random.random(), random.random())
            acolors.append(clrs)
        # the bonds between the matching atoms too
        bnds = []
        for mol, mv in zip(tms, matches):
            tmp = []
            for bnd in p.GetBonds():
                tmp.append(
                    mol.GetBondBetweenAtoms(mv[bnd.GetBeginAtomIdx()], mv[bnd.GetEndAtomIdx()]).GetIdx())
            bnds.append(tmp)
        drawer.DrawMolecules(tms, highlightAtoms=matches, highlightBonds=bnds,
                             highlightAtomColors=acolors)
        drawer.FinishDrawing()
        svg = drawer.GetDrawingText()
        # 4 molecules, 6 bonds each:
        re_str = r"path class='bond-\d+ atom-\d+ atom-\d+' d='M \d+.\d+,\d+.\d+ L \d+.\d+,\d+.\d+ L \d+.\d+,\d+.\d+ L \d+.\d+,\d+.\d+ Z' style='fill:"
        patt = re.compile(re_str)
        self.assertEqual(len(patt.findall(svg)), 24)
        # 4 molecules, one atom each:
        self.assertEqual(svg.count('fill:#DB2D2B;fill-rule:evenodd;stroke:#DB2D2B'), 4)

    def testGetDrawCoords(self):
        m = Chem.MolFromSmiles('c1ccc(C)c(C)c1C')
        AllChem.Compute2DCoords(m)
        d = Draw.MolDraw2DSVG(300, 300)
        d.DrawMolecule(m)
        conf = m.GetConformer()
        for idx in range(m.GetNumAtoms()):
            pos = conf.GetAtomPosition(idx)
            pos = Geometry.Point2D(pos.x, pos.y)
            dpos1 = d.GetDrawCoords(idx)
            dpos2 = d.GetDrawCoords(pos)
            self.assertAlmostEqual(dpos1.x, dpos2.x, 6)
            self.assertAlmostEqual(dpos1.y, dpos2.y, 6)

    def testReaction1(self):
        rxn = AllChem.ReactionFromSmarts(
            '[CH3:1][C:2](=[O:3])[OH:4].[CH3:5][NH2:6]>CC(O)C.[Pt]>[CH3:1][C:2](=[O:3])[NH:6][CH3:5].[OH2:4]',
            useSmiles=True)
        d = Draw.MolDraw2DSVG(900, 300)
        d.DrawReaction(rxn)
        d.FinishDrawing()
        txt = d.GetDrawingText()
        self.assertTrue(txt.find("<svg") != -1)
        self.assertTrue(txt.find("</svg>") != -1)
        # print(txt,file=open('blah1.svg','w+'))

    def testReaction2(self):
        rxn = AllChem.ReactionFromSmarts(
            '[CH3:1][C:2](=[O:3])[OH:4].[CH3:5][NH2:6]>CC(O)C.[Pt]>[CH3:1][C:2](=[O:3])[NH:6][CH3:5].[OH2:4]',
            useSmiles=True)
        d = Draw.MolDraw2DSVG(900, 300)
        d.DrawReaction(rxn, highlightByReactant=True)
        d.FinishDrawing()
        txt = d.GetDrawingText()
        self.assertTrue(txt.find("<svg") != -1)
        self.assertTrue(txt.find("</svg>") != -1)
        # print(txt,file=open('blah2.svg','w+'))

    def testReaction3(self):
        rxn = AllChem.ReactionFromSmarts(
            '[CH3:1][C:2](=[O:3])[OH:4].[CH3:5][NH2:6]>CC(O)C.[Pt]>[CH3:1][C:2](=[O:3])[NH:6][CH3:5].[OH2:4]',
            useSmiles=True)
        colors = [(0.3, 0.7, 0.9), (0.9, 0.7, 0.9), (0.6, 0.9, 0.3), (0.9, 0.9, 0.1)]
        d = Draw.MolDraw2DSVG(900, 300)
        d.DrawReaction(rxn, highlightByReactant=True, highlightColorsReactants=colors)
        d.FinishDrawing()
        txt = d.GetDrawingText()
        self.assertTrue(txt.find("<svg") != -1)
        self.assertTrue(txt.find("</svg>") != -1)

    def testReaction4(self):
        rxn = AllChem.ReactionFromSmarts(
            '[CH3:1][C:2](=[O:3])[OH:4].[CH3:5][NH2:6]>CC(O)C.[Pt]>[CH3:1][C:2](=[O:3])[NH:6][CH3:5].[OH2:4]',
            useSmiles=True)
        colors = [(100, 155, 245), (0, 45, 155)]
        d = Draw.MolDraw2DSVG(900, 300)
        self.assertRaises(ValueError, d.DrawReaction, rxn, True, colors)

    def testBWDrawing(self):
        m = Chem.MolFromSmiles('CCOCNCCl')
        dm = Draw.PrepareMolForDrawing(m)
        d = Draw.MolDraw2DSVG(300, 300)
        d.DrawMolecule(dm)
        d.FinishDrawing()
        txt = d.GetDrawingText()
        self.assertTrue(txt.find("stroke:#000000") >= 0)
        self.assertTrue(txt.find("stroke:#00CC00") >= 0)

        d = Draw.MolDraw2DSVG(300, 300)
        d.drawOptions().useBWAtomPalette()
        d.DrawMolecule(dm)
        d.FinishDrawing()
        txt = d.GetDrawingText()
        self.assertTrue(txt.find("stroke:#000000") >= 0)
        self.assertTrue(txt.find("stroke:#00CC00") == -1)

    def testUpdatePalette(self):
        m = Chem.MolFromSmiles('CCOCNCCl')
        dm = Draw.PrepareMolForDrawing(m)
        d = Draw.MolDraw2DSVG(300, 300)
        d.DrawMolecule(dm)
        d.FinishDrawing()
        txt = d.GetDrawingText()
        self.assertTrue(txt.find("stroke:#000000") >= 0)
        self.assertTrue(txt.find("stroke:#00CC00") >= 0)

        d = Draw.MolDraw2DSVG(300, 300)
        d.drawOptions().updateAtomPalette({6: (1, 1, 0)})
        d.DrawMolecule(dm)
        d.FinishDrawing()
        txt = d.GetDrawingText()
        self.assertTrue(txt.find("stroke:#000000") == -1)
        self.assertTrue(txt.find("stroke:#00CC00") >= 0)
        self.assertTrue(txt.find("stroke:#FFFF00") >= 0)

    def testSetPalette(self):
        m = Chem.MolFromSmiles('CCOCNCCl')
        dm = Draw.PrepareMolForDrawing(m)
        d = Draw.MolDraw2DSVG(300, 300)
        d.DrawMolecule(dm)
        d.FinishDrawing()
        txt = d.GetDrawingText()
        self.assertTrue(txt.find("stroke:#000000") >= 0)
        self.assertTrue(txt.find("stroke:#00CC00") >= 0)

        d = Draw.MolDraw2DSVG(300, 300)
        d.drawOptions().setAtomPalette({-1: (1, 1, 0)})
        d.DrawMolecule(dm)
        d.FinishDrawing()
        txt = d.GetDrawingText()
        self.assertTrue(txt.find("stroke:#000000") == -1)
        self.assertTrue(txt.find("stroke:#00CC00") == -1)
        self.assertTrue(txt.find("stroke:#FFFF00") >= 0)

        # try a palette that doesn't have a default:
        d = Draw.MolDraw2DSVG(300, 300)
        d.drawOptions().setAtomPalette({0: (1, 1, 0)})
        d.DrawMolecule(dm)
        d.FinishDrawing()
        txt = d.GetDrawingText()
        self.assertTrue(txt.find("stroke:#000000") >= 0)
        self.assertTrue(txt.find("stroke:#00CC00") == -1)
        self.assertTrue(txt.find("stroke:#FFFF00") == -1)

    def testGithub1829(self):
        d = Draw.MolDraw2DSVG(300, 300, 100, 100)
        d.DrawMolecules(tuple())
        d.FinishDrawing()
        d.GetDrawingText()

    def testSetLineWidth(self):
        " this was github #2149 "
        m = Chem.MolFromSmiles('CC')
        dm = Draw.PrepareMolForDrawing(m)
        d = Draw.MolDraw2DSVG(300, 300)
        d.DrawMolecule(dm)
        d.FinishDrawing()
        txt = d.GetDrawingText()
        self.assertTrue(txt.find("stroke-width:2.0px") >= 0)
        self.assertTrue(txt.find("stroke-width:4.0px") == -1)
        d = Draw.MolDraw2DSVG(300, 300)
        d.SetLineWidth(4)
        d.DrawMolecule(dm)
        d.FinishDrawing()
        txt = d.GetDrawingText()
        self.assertTrue(txt.find("stroke-width:2.0px") == -1)
        self.assertTrue(txt.find("stroke-width:4.0px") >= 0)

    def testPrepareAndDrawMolecule(self):
        m = Chem.MolFromSmiles("C1N[C@@H]2OCC12")
        d = Draw.MolDraw2DSVG(300, 300, -1, -1, True)
        rdMolDraw2D.PrepareAndDrawMolecule(d, m)
        d.FinishDrawing()
        txt = d.GetDrawingText()
        self.assertTrue(txt.find(">H</text>") > 0)

        m = Chem.MolFromSmiles("c1ccccc1")
        d = Draw.MolDraw2DSVG(300, 300, -1, -1, True)
        rdMolDraw2D.PrepareAndDrawMolecule(d, m)
        d.FinishDrawing()
        txt = d.GetDrawingText()
        self.assertLess(txt.find("stroke-dasharray"), 0)
        d = Draw.MolDraw2DSVG(300, 300, -1, -1, True)
        rdMolDraw2D.PrepareAndDrawMolecule(d, m, kekulize=False)
        d.FinishDrawing()
        txt = d.GetDrawingText()
        self.assertGreater(txt.find("stroke-dasharray"), 0)

    def testAtomTagging(self):
        m = Chem.MolFromSmiles("C1N[C@@H]2OCC12")
        d = Draw.MolDraw2DSVG(300, 300)
        dm = Draw.PrepareMolForDrawing(m)
        rdMolDraw2D.PrepareAndDrawMolecule(d, dm)
        d.TagAtoms(dm, events={'onclick': 'alert'})
        d.FinishDrawing()
        txt = d.GetDrawingText()
        self.assertTrue(txt.find("<circle") > 0)
        self.assertTrue(txt.find("onclick=") > 0)

    def testMolContours(self):
        m = Chem.MolFromSmiles("C1N[C@@H]2OCC12")
        dm = Draw.PrepareMolForDrawing(m)

        conf = dm.GetConformer()
        gs = []
        ws = []
        hs = []
        for i in range(conf.GetNumAtoms()):
            p = conf.GetAtomPosition(i)
            p2 = Geometry.Point2D(p.x, p.y)
            gs.append(p2)
            hs.append(0.4)
            if not i % 2:
                ws.append(-0.5)
            else:
                ws.append(1)

        d = Draw.MolDraw2DSVG(300, 300)
        d.ClearDrawing()
        Draw.ContourAndDrawGaussians(d, gs, hs, ws, mol=dm)
        d.drawOptions().clearBackground = False
        d.DrawMolecule(dm)
        d.FinishDrawing()
        txt = d.GetDrawingText()
        with open("contour_from_py_1.svg", 'w+') as outf:
            print(txt, file=outf)

        d = Draw.MolDraw2DSVG(300, 300)
        d.ClearDrawing()
        ps = Draw.ContourParams()
        ps.fillGrid = True
        Draw.ContourAndDrawGaussians(d, gs, hs, ws, params=ps, mol=dm)
        d.drawOptions().clearBackground = False
        d.DrawMolecule(dm)
        d.FinishDrawing()
        txt = d.GetDrawingText()
        with open("contour_from_py_2.svg", 'w+') as outf:
            print(txt, file=outf)

    def testGridContours(self):
        grid = np.zeros((50, 100), np.double)
        ycoords = list(np.arange(0, 5, 0.1))
        xcoords = list(np.arange(0, 10, 0.1))
        for i in range(grid.shape[1]):
            gxp = xcoords[i]
            for j in range(grid.shape[0]):
                gyp = ycoords[j]
                for v in range(1, 4):
                    dvx = 2 * v - gxp
                    dvy = v - gyp
                    d2 = dvx * dvx + dvy * dvy
                    if d2 > 0:
                        grid[j, i] += 1 / np.sqrt(d2)

        # sg = 255 * grid / np.max(grid)
        # from PIL import Image
        # img = Image.fromarray(sg.astype(np.uint8))
        # img.save('img.png')

        d = Draw.MolDraw2DSVG(300, 300)
        d.ClearDrawing()
        Draw.ContourAndDrawGrid(d, np.transpose(grid), xcoords, ycoords)
        d.drawOptions().clearBackground = False
        d.FinishDrawing()
        txt = d.GetDrawingText()
        with open("contour_from_py_3.svg", 'w+') as outf:
            print(txt, file=outf)

    def testExtraDrawingCommands(self):
        " this is another test just to make sure that things work "
        m = Chem.MolFromMolBlock("""
  Mrv1810 07271915232D          

  6  6  0  0  0  0            999 V2000
   -1.5      -1.5       0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5       0.0       0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0       0.0       0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0      -1.5       0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5       1.5       0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5      -1.5       0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  1  1  0  0  0  0
  2  5  1  0  0  0  0
  4  6  1  0  0  0  0
M  END
""")
        d = Draw.MolDraw2DSVG(300, 300)
        dm = Draw.PrepareMolForDrawing(m)
        d.DrawMolecule(dm)
        conf = dm.GetConformer()
        ps3 = (
          conf.GetAtomPosition(0),
          conf.GetAtomPosition(1),
          conf.GetAtomPosition(3),
        )
        ps = [Geometry.Point2D(p.x, p.y) for p in ps3]
        d.DrawPolygon(ps)
        d.DrawArrow(Geometry.Point2D(0, 0), Geometry.Point2D(0, 1.5))
        d.DrawAttachmentLine(Geometry.Point2D(0, 0), Geometry.Point2D(1.5, 0), (0.5, 0.5, 0.5), len=0.5)
        d.DrawLine(Geometry.Point2D(0, 0), Geometry.Point2D(1.5, 0))
        d.DrawWavyLine(Geometry.Point2D(0, 0), Geometry.Point2D(1.5, 1.5), (0, 0, 0), (1, 0.2, 0.2))
        d.FinishDrawing()
        txt = d.GetDrawingText()
        with open("extras_1.svg", "w+") as outf:
          outf.write(txt)

    def testSetDrawOptions(self):
      m = Chem.MolFromSmiles('CCNC(=O)O')
      d = rdMolDraw2D.MolDraw2DSVG(250, 200, -1, -1, True)
      rdMolDraw2D.PrepareAndDrawMolecule(d, m)
      d.FinishDrawing()
      txt = d.GetDrawingText()
      self.assertNotEqual(txt.find("fill:#0000FF' >N</text>"), -1)
      self.assertEqual(txt.find("fill:#000000' >N</text>"), -1)

      d = rdMolDraw2D.MolDraw2DSVG(250, 200, -1, -1, True)
      do = rdMolDraw2D.MolDrawOptions()
      do.useBWAtomPalette()
      d.SetDrawOptions(do)
      rdMolDraw2D.PrepareAndDrawMolecule(d, m)
      d.FinishDrawing()
      txt = d.GetDrawingText()
      self.assertEqual(txt.find("fill:#0000FF' >N</text>"), -1)
      self.assertNotEqual(txt.find("fill:#000000' >N</text>"), -1)

    def testAlternativeFreetypeFont(self):
      # this one, you have to look at the pictures
      m = Chem.MolFromSmiles('S(=O)(=O)(O)c1c(Cl)c(Br)c(I)c(F)c(N)1')
      d = rdMolDraw2D.MolDraw2DSVG(250, 200)
      rdMolDraw2D.PrepareAndDrawMolecule(d, m)
      d.FinishDrawing()
      txt = d.GetDrawingText()
      with open('test_ff.svg', 'w') as f:
        f.write(txt)

      d = rdMolDraw2D.MolDraw2DSVG(250, 200)
      do = rdMolDraw2D.MolDrawOptions()
      rdbase = environ['RDBASE']
      if rdbase:
        do.fontFile = '{}/Code/GraphMol/MolDraw2D/Amadeus.ttf'.format(rdbase)
        d.SetDrawOptions(do)
        rdMolDraw2D.PrepareAndDrawMolecule(d, m)
        d.FinishDrawing()
        txt = d.GetDrawingText()
        with open('test_aff.svg', 'w') as f:
          f.write(txt)
      else:
        pass

    def testExplictMethyl(self):
      m = Chem.MolFromSmiles('CC')
      d = rdMolDraw2D.MolDraw2DSVG(250, 200)
      rdMolDraw2D.PrepareAndDrawMolecule(d, m)
      d.FinishDrawing()
      txt = d.GetDrawingText()
      self.assertEqual(txt.find("class='atom-"), -1)

      d = rdMolDraw2D.MolDraw2DSVG(250, 200)
      do = rdMolDraw2D.MolDrawOptions()
      do.explicitMethyl = True
      d.SetDrawOptions(do)
      rdMolDraw2D.PrepareAndDrawMolecule(d, m)
      d.FinishDrawing()
      txt = d.GetDrawingText()
      self.assertNotEqual(txt.find("class='atom-"), -1)

    def testDrawMoleculeWithHighlights(self):
      COLS = [(1.0, 0.0, 0.0), (0.0, 1.0, 0.0), (0.0, 0.0, 1.0), (1.0, 0.55, 0.0)]

      def get_hit_atoms_and_bonds(mol, smt):
        alist = []
        blist = []
        q = Chem.MolFromSmarts(smt)
        for match in mol.GetSubstructMatches(q):
          alist.extend(match)

        for ha1 in alist:
          for ha2 in alist:
            if ha1 > ha2:
              b = mol.GetBondBetweenAtoms(ha1, ha2)
              if b:
                blist.append(b.GetIdx())

        return alist, blist

      def add_colours_to_map(els, cols, col_num):
        for el in els:
          if el not in cols:
            cols[el] = []
          if COLS[col_num] not in cols[el]:
            cols[el].append(COLS[col_num])

      def do_a_picture(smi, smarts, label, lasso=None):

        rdDepictor.SetPreferCoordGen(False)
        mol = Chem.MolFromSmiles(smi)
        mol = Draw.PrepareMolForDrawing(mol)

        acols = {}
        bcols = {}
        h_rads = {}
        h_lw_mult = {}

        for i, smt in enumerate(smarts):
          alist, blist = get_hit_atoms_and_bonds(mol, smt)
          h_rads[alist[0]] = 0.4
          h_lw_mult[blist[0]] = 2
          col = i % 4
          add_colours_to_map(alist, acols, col)
          add_colours_to_map(blist, bcols, col)

        d = rdMolDraw2D.MolDraw2DSVG(500, 500)
        d.drawOptions().fillHighlights = False
        if lasso is not None:
          if lasso == "Direct":
            d.drawOptions().multiColourHighlightStyle = Draw.MultiColourHighlightStyle.Lasso
          elif lasso == "ViaJSON":
            print('json lasso')
            Draw.UpdateDrawerParamsFromJSON(d, '{"multiColourHighlightStyle": "Lasso"}')
        d.DrawMoleculeWithHighlights(mol, label, acols, bcols, h_rads, h_lw_mult, -1)

        d.FinishDrawing()
        return d.GetDrawingText()

      smi = 'CO[C@@H](O)C1=C(O[C@H](F)Cl)C(C#N)=C1ONNC[NH3+]'
      smarts = ['CONN', 'N#CC~CO', 'C=CON', 'CONNCN']
      txt = do_a_picture(smi, smarts, 'pyTest2')
      self.assertGreater(txt.find('stroke:#FF8C00;stroke-width:8.0'), -1)
      self.assertEqual(
        txt.find("ellipse cx='244.253' cy='386.518'"
                " rx='11.9872' ry='12.8346'"
                " style='fill:none;stroke:#00FF00'"), -1)
      txt = do_a_picture(smi, smarts, 'pyTest4', lasso="Direct")
      # the lasso mode puts paths, not ellipses.
      self.assertGreater(txt.find("<path class='atom-5'"), -1)
      self.assertEqual(txt.find("ellipse"), -1)

      txt = do_a_picture(smi, smarts, 'pyTest4', lasso="ViaJSON")
      # the lasso mode puts paths, not ellipses.
      self.assertGreater(txt.find("<path class='atom-5'"), -1)
      self.assertEqual(txt.find("ellipse"), -1)

      # test for no-longer-mysterious OSX crash.
      smi = 'c1ccccc1Cl'
      smarts = []
      do_a_picture(smi, smarts, 'pyTest3')

    @unittest.skipUnless(hasattr(Draw, 'MolDraw2DCairo'), 'Cairo support not enabled')
    @unittest.skipUnless(hasattr(Chem,'MolFromPNGString'),
                     "RDKit not built with iostreams support")
    def testPNGMetadata(self):
        m = Chem.MolFromMolBlock('''
  Mrv2014 08172015242D          

  0  0  0     0  0            999 V3000
M  V30 BEGIN CTAB
M  V30 COUNTS 3 2 0 0 0
M  V30 BEGIN ATOM
M  V30 1 C 2.31 -1.3337 0 0
M  V30 2 C 3.6437 -2.1037 0 0
M  V30 3 O 4.9774 -1.3337 0 0
M  V30 END ATOM
M  V30 BEGIN BOND
M  V30 1 1 1 2
M  V30 2 1 2 3
M  V30 END BOND
M  V30 END CTAB
M  END''')
        d = Draw.MolDraw2DCairo(200, 200)
        d.DrawMolecule(m)
        txt = d.GetDrawingText()
        nm = Chem.MolFromPNGString(txt)
        self.assertEqual(Chem.MolToSmiles(m), Chem.MolToSmiles(nm))

    def testUpdateMolDrawOptionsAndDrawerParamsFromJSON(self):
        m = Chem.MolFromSmiles('c1ccccc1NC(=O)C1COC1')
        d2d = Draw.MolDraw2DSVG(250, 200, -1, -1, True)
        d2d.DrawMolecule(m)
        d2d.FinishDrawing()
        txt = d2d.GetDrawingText()
        self.assertFalse('>8</text>' in txt)

        drawOptions = rdMolDraw2D.MolDrawOptions()
        Draw.UpdateMolDrawOptionsFromJSON(drawOptions, '{"addAtomIndices": 1}')
        self.assertTrue(drawOptions.addAtomIndices)
        d2d = Draw.MolDraw2DSVG(250, 200, -1, -1, True)
        d2d.SetDrawOptions(drawOptions)
        d2d.DrawMolecule(m)
        d2d.FinishDrawing()
        txt = d2d.GetDrawingText()
        self.assertTrue('>8</text>' in txt)

        d2d = Draw.MolDraw2DSVG(250, 200, -1, -1, True)
        Draw.UpdateDrawerParamsFromJSON(d2d, '{"addAtomIndices": 1}')
        d2d.DrawMolecule(m)
        d2d.FinishDrawing()
        txt = d2d.GetDrawingText()
        self.assertTrue('>8</text>' in txt)

    def testIsotopeLabels(self):
        m = Chem.MolFromSmiles("[1*]c1cc([2*])c([3*])c[14c]1")
        regex = re.compile(r"<text\s+.*>\d</text>")
        self.assertIsNotNone(m)

        d2d = Draw.MolDraw2DSVG(300, 300, -1, -1, True)
        d2d.DrawMolecule(m)
        d2d.FinishDrawing()
        textIsoDummyIso = d2d.GetDrawingText()
        nIsoDummyIso = len(regex.findall(textIsoDummyIso))
        self.assertEqual(nIsoDummyIso, 5)

        d2d = Draw.MolDraw2DSVG(300, 300, -1, -1, True)
        d2d.drawOptions().isotopeLabels = False
        d2d.DrawMolecule(m)
        d2d.FinishDrawing()
        textNoIsoDummyIso = d2d.GetDrawingText()
        nNoIsoDummyIso = len(regex.findall(textNoIsoDummyIso))
        self.assertEqual(nNoIsoDummyIso, 3)

        d2d = Draw.MolDraw2DSVG(300, 300, -1, -1, True)
        d2d.drawOptions().dummyIsotopeLabels = False
        d2d.DrawMolecule(m)
        d2d.FinishDrawing()
        textIsoNoDummyIso = d2d.GetDrawingText()
        nIsoNoDummyIso = len(regex.findall(textIsoNoDummyIso))
        self.assertEqual(nIsoNoDummyIso, 2)

        d2d = Draw.MolDraw2DSVG(300, 300, -1, -1, True)
        d2d.drawOptions().isotopeLabels = False
        d2d.drawOptions().dummyIsotopeLabels = False
        d2d.DrawMolecule(m)
        d2d.FinishDrawing()
        textNoIsoNoDummyIso = d2d.GetDrawingText()
        nNoIsoNoDummyIso = len(regex.findall(textNoIsoNoDummyIso))
        self.assertEqual(nNoIsoNoDummyIso, 0)

        m = Chem.MolFromSmiles("C([1H])([2H])([3H])[H]")
        deuteriumTritiumRegex = re.compile(r"<text\s+.*>[DT]</text>")
        d2d = Draw.MolDraw2DSVG(300, 300, -1, -1, True)
        d2d.drawOptions().isotopeLabels = False
        d2d.drawOptions().dummyIsotopeLabels = False
        d2d.drawOptions().atomLabelDeuteriumTritium = True
        d2d.DrawMolecule(m)
        d2d.FinishDrawing()
        textDeuteriumTritium = d2d.GetDrawingText()
        nDeuteriumTritium = len(deuteriumTritiumRegex.findall(textDeuteriumTritium))
        self.assertEqual(nDeuteriumTritium, 2)

    def testNewDrawingModes(self):
        m = Chem.MolFromSmiles("CS(=O)(=O)COC(=N)c1cc(Cl)cnc1[NH3+] |SgD:7:note:some extra text:=:::|")

        d2d = Draw.MolDraw2DSVG(300, 300)
        rdMolDraw2D.SetDarkMode(d2d)
        d2d.DrawMolecule(m)
        d2d.FinishDrawing()
        text = d2d.GetDrawingText()
        self.assertIn("<rect style='opacity:1.0;fill:#000000;stroke:none'", text)

        d2d = Draw.MolDraw2DSVG(300, 300)
        rdMolDraw2D.SetMonochromeMode(d2d, (1, 1, 1), (.5, .5, .5))
        d2d.DrawMolecule(m)
        d2d.FinishDrawing()
        text = d2d.GetDrawingText()
        self.assertIn("<rect style='opacity:1.0;fill:#7F7F7F;stroke:none'", text)
        self.assertIn("stroke:#FFFFFF;stroke-width:2", text)

        d2d = Draw.MolDraw2DSVG(300, 300)
        d2d.drawOptions().useAvalonAtomPalette()
        d2d.DrawMolecule(m)
        d2d.FinishDrawing()
        text = d2d.GetDrawingText()
        self.assertIn("<rect style='opacity:1.0;fill:#FFFFFF;stroke:none'", text)
        self.assertIn("stroke:#007E00;stroke-width:2", text)

        d2d = Draw.MolDraw2DSVG(300, 300)
        d2d.drawOptions().useCDKAtomPalette()
        d2d.DrawMolecule(m)
        d2d.FinishDrawing()
        text = d2d.GetDrawingText()
        self.assertIn("<rect style='opacity:1.0;fill:#FFFFFF;stroke:none'", text)
        self.assertIn("stroke:#2F50F7;stroke-width:2", text)

    def testGithub4838(self):
        m = Chem.MolFromSmiles("CCCC")
        d2d = Draw.MolDraw2DSVG(300, 300)
        d2d.DrawMolecule(m)
        d2d.DrawString("foo1", Geometry.Point2D(1, 0))
        d2d.DrawString("foo0", Geometry.Point2D(1, 1), 0)
        d2d.DrawString("foo2", Geometry.Point2D(1, 2), 1)
        d2d.DrawString("foo3", Geometry.Point2D(1, 3), 2)
        with self.assertRaises(ValueError):
            d2d.DrawString("fail", Geometry.Point2D(1, 4), 3)

    def testGithub5298(self):
        with self.assertRaises(RuntimeError):
            rdMolDraw2D.PrepareMolForDrawing(None)

    def testACS1996Mode(self):
        m = Chem.MolFromSmiles("CS(=O)(=O)COC(=N)c1cc(Cl)cnc1[NH3+]")
        AllChem.Compute2DCoords(m)
        rdMolDraw2D.PrepareMolForDrawing(m)
        svg = rdMolDraw2D.MolToACS1996SVG(m, "ACS Mode")
        with open("testACSMode_1.svg", 'w') as f:
            f.write(svg)

        highlight_atoms = [0, 2, 4, 6, 8]
        highlight_bonds = [1, 3, 5, 7, 9]
        highlight_atom_cols = {
            0: (1.0, 1.0, 0.0),
            8: (1.0, 0.0, 1.0),
        }
        highlight_bond_cols = {
            0: (0.0, 1.0, 1.0),
            8: (0.0, 0.0, 1.0),
        }

        svg = rdMolDraw2D.MolToACS1996SVG(m, "Highlights", highlight_atoms, highlight_bonds,
                                          highlight_atom_cols, highlight_bond_cols)
        with open("testACSMode_2.svg", 'w') as f:
            f.write(svg)
        if hasattr(Draw, 'MolDraw2DCairo'):
            drawer = rdMolDraw2D.MolDraw2DCairo(-1, -1)
            rdMolDraw2D.DrawMoleculeACS1996(drawer, m)
            drawer.FinishDrawing()
            drawer.WriteDrawingText('testACSMode_1.png')

    def testMolSize(self):
        m = Chem.MolFromSmiles("CS(=O)(=O)COC(=N)c1cc(Cl)cnc1[NH3+]")
        AllChem.Compute2DCoords(m)
        rdMolDraw2D.PrepareMolForDrawing(m)
        d2d = rdMolDraw2D.MolDraw2DSVG(-1, -1)
        d2d.DrawMolecule(m)
        sz = d2d.Width(), d2d.Height()

        d2d = rdMolDraw2D.MolDraw2DSVG(-1, -1)
        sz2 = d2d.GetMolSize(m)
        self.assertEqual(sz, sz2)

    def testQueryColour(self):
        m = Chem.MolFromSmarts("c1ccc2nc([*:1])nc([*:2])c2c1")
        self.assertIsNotNone(m)
        # Check that default queryColour is #7F7F7F.
        d2d = rdMolDraw2D.MolDraw2DSVG(-1, -1)
        d2d.DrawMolecule(m)
        d2d.FinishDrawing()
        text = d2d.GetDrawingText()
        self.assertTrue("#7F7F7F" in text)

        # Check that queryColour can be set to black.
        query_colour = (0.0, 0.0, 0.0)
        d2d = rdMolDraw2D.MolDraw2DSVG(-1, -1)
        d2d.drawOptions().setQueryColour(query_colour)
        d2d.DrawMolecule(m)
        d2d.FinishDrawing()
        text = d2d.GetDrawingText()
        self.assertTrue("#7F7F7F" not in text)

    @unittest.skipUnless(hasattr(Draw, 'MolDraw2DCairo'), 'Cairo support not enabled')
    def testGithub7409(self):
        m = Chem.MolFromSmiles('CC |(-0.75,0,;0.75,0,)|')
        m.GetConformer().SetId(5)
        d2d = rdMolDraw2D.MolDraw2DCairo(200, 200)
        # it's enough to check that this doesn't throw an exception
        d2d.DrawMolecule(m)


if __name__ == "__main__":
    unittest.main()