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molecule.py
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molecule.py
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# -*- coding: utf-8 -*-
"""
Molecule structure matching based on inter-atomic distances,
using the algorithm described in:
Gardiner, Eleanor J., Peter J. Artymiuk, and Peter Willett.
"Clique-detection algorithms for matching three-dimensional molecular
structures." Journal of Molecular Graphics and Modelling 15.4 (1997):
245-253.
The bzr_3d.sd dataset was obtained from:
Sutherland, Jeffrey J., Lee A. O'brien, and Donald F. Weaver.
"Spline-fitting with a genetic algorithm: A method for developing
classification structure− activity relationships." Journal of chemical
information and computer sciences 43.6 (2003): 1906-1915.
"""
import numpy as np
import cliquematch
from rdkit.Chem import PandasTools, Draw
from matplotlib import pyplot as plt
class MolData(object):
def __init__(self, mol):
self._mol = mol
self._mol.Compute2DCoords()
self.positions = np.array(self._mol.GetConformer().GetPositions())
def condition_closure(M1, M2):
def condition(P, i1, j1, Q, i2, j2):
b1 = M1.GetBondBetweenAtoms(i1, j1)
b2 = M2.GetBondBetweenAtoms(i2, j2)
if b1 is None and b2 is None:
return True
elif b1 is not None and b2 is not None:
return ~(b1.IsInRing() ^ b2.IsInRing())
else:
return False
return condition
def main():
mols = PandasTools.LoadSDF("./bzr_3d.sd")
data = [MolData(x) for x in mols["ROMol"]]
plot(data[0], data[1], "comp_0_1.png")
def plot(d1, d2, filename=None):
G = cliquematch.A2AGraph(d1.positions, d2.positions)
cfunc = condition_closure(d1._mol, d2._mol)
G.epsilon = 1e-6
G.build_edges_with_condition(cfunc, False)
sub1, sub2 = G.get_correspondence(
use_heuristic=True, use_dfs=True, return_indices=True
)
fig = plt.figure(figsize=(12.1, 6.1))
axs = fig.subplots(1, 2)
mdraw = Draw.rdMolDraw2D.MolDraw2DCairo(600, 600)
mdraw.drawOptions().fillHighlights = False
Draw.rdMolDraw2D.PrepareAndDrawMolecule(
mdraw,
d1._mol,
highlightAtoms=sub1,
highlightAtomColors={
int(x): (0.05 * i, 1.0 - 0.05 * i, 0.0) for i, x in enumerate(sub1)
},
)
mdraw.WriteDrawingText("./mol1.png")
img0 = plt.imread("./mol1.png")
mdraw.ClearDrawing()
axs[0].imshow(np.array(img0))
axs[0].set_xticks([])
axs[0].set_yticks([])
Draw.rdMolDraw2D.PrepareAndDrawMolecule(
mdraw,
d2._mol,
highlightAtoms=sub2,
highlightAtomColors={
int(x): (0.05 * i, 1.0 - 0.05 * i, 0.0) for i, x in enumerate(sub2)
},
)
mdraw.WriteDrawingText("./mol2.png")
mdraw.ClearDrawing()
img1 = plt.imread("./mol2.png")
axs[1].imshow(np.array(img1))
axs[1].set_xticks([])
axs[1].set_yticks([])
fig.subplots_adjust(left=0.05, right=0.95, top=0.95, bottom=0.05)
fig.savefig(filename)
plt.close()
print(
len(d1.positions),
len(d2.positions),
G.n_edges,
len(G.get_max_clique(use_heuristic=True, use_dfs=True)),
)
if __name__ == "__main__":
main()