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Fix code formatting in docstrings for a few functions #6848

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Fix code formatting in docstrings for a few functions #6848

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36 changes: 18 additions & 18 deletions rdkit/Chem/AtomPairs/Pairs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -74,32 +74,32 @@ def pyScorePair(at1, at2, dist, atomCodes=None, includeChirality=False):

def ExplainPairScore(score, includeChirality=False):
"""
>>> from rdkit import Chem
>>> m = Chem.MolFromSmiles('C=CC')
>>> score = pyScorePair(m.GetAtomWithIdx(0), m.GetAtomWithIdx(1), 1)
>>> ExplainPairScore(score)
>>> from rdkit import Chem
>>> m = Chem.MolFromSmiles('C=CC')
>>> score = pyScorePair(m.GetAtomWithIdx(0), m.GetAtomWithIdx(1), 1)
>>> ExplainPairScore(score)
(('C', 1, 1), 1, ('C', 2, 1))
>>> score = pyScorePair(m.GetAtomWithIdx(0), m.GetAtomWithIdx(2), 2)
>>> ExplainPairScore(score)
>>> score = pyScorePair(m.GetAtomWithIdx(0), m.GetAtomWithIdx(2), 2)
>>> ExplainPairScore(score)
(('C', 1, 0), 2, ('C', 1, 1))
>>> score = pyScorePair(m.GetAtomWithIdx(1), m.GetAtomWithIdx(2), 1)
>>> ExplainPairScore(score)
>>> score = pyScorePair(m.GetAtomWithIdx(1), m.GetAtomWithIdx(2), 1)
>>> ExplainPairScore(score)
(('C', 1, 0), 1, ('C', 2, 1))
>>> score = pyScorePair(m.GetAtomWithIdx(2), m.GetAtomWithIdx(1), 1)
>>> ExplainPairScore(score)
>>> score = pyScorePair(m.GetAtomWithIdx(2), m.GetAtomWithIdx(1), 1)
>>> ExplainPairScore(score)
(('C', 1, 0), 1, ('C', 2, 1))

We can optionally deal with chirality too
>>> m = Chem.MolFromSmiles('C[C@H](F)Cl')
>>> score = pyScorePair(m.GetAtomWithIdx(0), m.GetAtomWithIdx(1), 1)
>>> ExplainPairScore(score)
>>> m = Chem.MolFromSmiles('C[C@H](F)Cl')
>>> score = pyScorePair(m.GetAtomWithIdx(0), m.GetAtomWithIdx(1), 1)
>>> ExplainPairScore(score)
(('C', 1, 0), 1, ('C', 3, 0))
>>> score = pyScorePair(m.GetAtomWithIdx(0), m.GetAtomWithIdx(1), 1, includeChirality=True)
>>> ExplainPairScore(score, includeChirality=True)
>>> score = pyScorePair(m.GetAtomWithIdx(0), m.GetAtomWithIdx(1), 1, includeChirality=True)
>>> ExplainPairScore(score, includeChirality=True)
(('C', 1, 0, ''), 1, ('C', 3, 0, 'R'))
>>> m = Chem.MolFromSmiles('F[C@@H](Cl)[C@H](F)Cl')
>>> score = pyScorePair(m.GetAtomWithIdx(1), m.GetAtomWithIdx(3), 1, includeChirality=True)
>>> ExplainPairScore(score, includeChirality=True)
>>> m = Chem.MolFromSmiles('F[C@@H](Cl)[C@H](F)Cl')
>>> score = pyScorePair(m.GetAtomWithIdx(1), m.GetAtomWithIdx(3), 1, includeChirality=True)
>>> ExplainPairScore(score, includeChirality=True)
(('C', 3, 0, 'R'), 1, ('C', 3, 0, 'S'))

"""
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72 changes: 35 additions & 37 deletions rdkit/Chem/Draw/__init__.py
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Expand Up @@ -94,9 +94,9 @@ def _legacyMolToImage(mol, size, kekulize, wedgeBonds, fitImage, options, canvas
use 'matplotlib.colors.to_rgb()' to convert string and
HTML color codes into the RGB tuple representation, eg.

from matplotlib.colors import ColorConverter
img = Draw.MolToImage(m, highlightAtoms=[1,2], highlightColor=ColorConverter().to_rgb('aqua'))
img.save("molecule.png")
>>> from matplotlib.colors import ColorConverter
>>> img = Draw.MolToImage(m, highlightAtoms=[1,2], highlightColor=ColorConverter().to_rgb('aqua'))
>>> img.save("molecule.png")

RETURNS:

Expand Down Expand Up @@ -729,40 +729,38 @@ def MolsMatrixToGridImage(molsMatrix, subImgSize=(200, 200), legendsMatrix=None,

EXAMPLES:

from rdkit import Chem
from rdkit.Chem.Draw import MolsMatrixToGridImage, rdMolDraw2D
FCl = Chem.MolFromSmiles("FCl")
molsMatrix = [[FCl, FCl], [FCl, None, FCl]]

# Minimal example: Only molsMatrix is supplied,
# result will be a drawing containing (where each row contains molecules):
# F-Cl F-Cl
# F-Cl F-Cl
img = MolsMatrixToGridImage(molsMatrix)
img.save("MolsMatrixToGridImageMinimal.png")
# img is a PIL object for a PNG image file like:
# <PIL.PngImagePlugin.PngImageFile image mode=RGB size=600x200 at 0x1648CC390>
# Drawing will be saved as PNG file MolsMatrixToGridImageMinimal.png

# Exhaustive example: All parameters are supplied,
# result will be a drawing containing (where each row of molecules is followed by a row of legends):
# 1 F-Cl 0 1 F-Cl 0
# no highlighting bond highlighted
# 1 F-Cl 0 1 F-Cl 0
# sodium highlighted chloride and bond highlighted
legendsMatrix = [["no highlighting", "bond highlighted"],
["F highlighted", "", "Cl and bond highlighted"]]
highlightAtomListsMatrix = [[[],[]], [[0], None, [1]]]
highlightBondListsMatrix = [[[],[0]], [[], None, [0]]]

dopts = rdMolDraw2D.MolDrawOptions()
dopts.addAtomIndices = True

img_binary = MolsMatrixToGridImage(molsMatrix=molsMatrix, subImgSize=(300, 400),
legendsMatrix=legendsMatrix, highlightAtomListsMatrix=highlightAtomListsMatrix,
highlightBondListsMatrix=highlightBondListsMatrix, useSVG=False, returnPNG=True, drawOptions=dopts)
print(img_binary[:20])
# Prints a binary string: b'\x89PNG\r\n\x1a\n\x00\x00\x00\rIHDR\x00\x00\x03\x84'
>>> from rdkit import Chem
>>> from rdkit.Chem.Draw import MolsMatrixToGridImage, rdMolDraw2D
>>> FCl = Chem.MolFromSmiles("FCl")
>>> molsMatrix = [[FCl, FCl], [FCl, None, FCl]]

>>> # Minimal example: Only molsMatrix is supplied,
>>> # result will be a drawing containing (where each row contains molecules):
>>> # F-Cl F-Cl
>>> # F-Cl F-Cl
>>> img = MolsMatrixToGridImage(molsMatrix)
>>> img.save("MolsMatrixToGridImageMinimal.png")
>>> # img is a PIL object for a PNG image file like:
>>> # <PIL.PngImagePlugin.PngImageFile image mode=RGB size=600x200 at 0x1648CC390>
>>> # Drawing will be saved as PNG file MolsMatrixToGridImageMinimal.png

>>> # Exhaustive example: All parameters are supplied,
>>> # result will be a drawing containing (where each row of molecules is followed by a row of legends):
>>> # 1 F-Cl 0 1 F-Cl 0
>>> # no highlighting bond highlighted
>>> # 1 F-Cl 0 1 F-Cl 0
>>> # sodium highlighted chloride and bond highlighted
>>> legendsMatrix = [["no highlighting", "bond highlighted"],
>>> ["F highlighted", "", "Cl and bond highlighted"]]
>>> highlightAtomListsMatrix = [[[],[]], [[0], None, [1]]]
>>> highlightBondListsMatrix = [[[],[0]], [[], None, [0]]]

>>> dopts = rdMolDraw2D.MolDrawOptions()
>>> dopts.addAtomIndices = True

>>> img_exhaustive = MolsMatrixToGridImage(molsMatrix=molsMatrix, subImgSize=(300, 400), legendsMatrix=legendsMatrix, highlightAtomListsMatrix=highlightAtomListsMatrix, highlightBondListsMatrix=highlightBondListsMatrix, useSVG=False, returnPNG=False, drawOptions=dopts)
>>> img.save("MolsMatrixToGridImageExhaustive.png")
>>> # Drawing will be saved as PNG file MolsMatrixToGridImageExhaustive.png
"""
mols, molsPerRow, legends, highlightAtomLists, highlightBondLists = _MolsNestedToLinear(
molsMatrix, legendsMatrix, highlightAtomListsMatrix, highlightBondListsMatrix)
Expand Down