In [1]:
from rdkit import Chem
from rdkit.Chem.Draw import IPythonConsole
from rdkit.Chem.Draw import MolsToGridImage
from rdkit.Chem.Draw.MolDrawing import MolDrawing, DrawingOptions
IPythonConsole.ipython_useSVG = False
DrawingOptions.includeAtomNumbers = False
def show_mol_grid(mols):
return MolsToGridImage(
[x.asRDMol() for x in mols]
, subImgSize=(250,200)
, legends=[x.parent_operator for x in mols]
)
In [2]:
import molpher
from molpher.core.operations import *
from molpher.core import MolpherMol, ExplorationTree as ETree
class MyFilterMorphs(TreeOperation):
"""
A custom tree operation that accepts
only the first ten morphs after
the list of candidates is sorted.
"""
def __call__(self):
"""
This method is called automatically by the tree.
The tree this operation is being run on is accessible
from the 'tree' member of the class.
"""
self.tree.candidates_mask = [
True if idx < 10 and self.tree.candidates[idx].sascore < 6
else False
for idx, x in enumerate(self.tree.candidates_mask)
]
cocaine = MolpherMol('CN1[CH]2CC[CH]1[CH](C(OC)=O)[CH](OC(C3=CC=CC=C3)=O)C2')
procaine = MolpherMol('O=C(OCCN(CC)CC)c1ccc(N)cc1')
tree = ETree.create(source=cocaine, target=procaine) # create the tree
# list of tree operations, defines one iteration
iteration = [
GenerateMorphsOper()
, SortMorphsOper()
, MyFilterMorphs() # our custom filtering procedure
, ExtendTreeOper()
, PruneTreeOper()
]
# apply the operations in the list one by one
for oper in iteration:
tree.runOperation(oper)
# observe the results
print(tree.generation_count)
print(len(tree.leaves))
show_mol_grid(tree.leaves)
Out[2]:
In [3]:
from molpher.core.operations.callbacks import TraverseCallback
class MyCallback(TraverseCallback):
"""
This callback just prints some information
about the molecules in the tree.
"""
def __call__(self, morph):
"""
Method called on each morph in the tree
-- starting from the root to leaves.
"""
if not morph.getParentSMILES():
print("# Root #")
else:
print('# Morph #')
print('Parent:', morph.getParentSMILES())
print('SMILES: ', morph.getSMILES())
print('Descendents: ', morph.getDescendants())
callback = MyCallback() # initialize a callback
traverse = TraverseOper(callback=callback) # attach it to a tree traversal operation
tree.runOperation(traverse) # run the operation
In [4]:
def process(morph):
"""
Prints some information
about the molecules in the tree.
"""
if not morph.getParentSMILES():
print("# Root #")
else:
print('# Morph #')
print('Parent:', morph.getParentSMILES())
print('SMILES: ', morph.getSMILES())
print('Descendents: ', morph.getDescendants())
tree.traverse(process) # use the traverse method to run the callback function
In [5]:
template_file = 'cocaine-procaine-template.xml'
tree = ETree.create(template_file)
print(tree.params)
# apply the tree operations
for oper in iteration:
tree.runOperation(oper)
print(
sorted( # grab the new leaves as a list sorted according to their distance from target
[
(x.getSMILES(), x.getDistToTarget())
for x in tree.leaves
], key=lambda x : x[1]
)
)
# save the tree in a snapshot file
tree.save('snapshot.xml')
In [6]:
new_tree = ETree.create('snapshot.xml') # create a new tree from the saved snapshot
print(new_tree.params)
sorted( # grab the leaves in the created tree (these should be the same as those in the original tree)
[
(x.getSMILES(), x.getDistToTarget())
for x in new_tree.leaves
], key=lambda x : x[1]
)
Out[6]:
In [7]:
iteration = [
GenerateMorphsOper()
, SortMorphsOper()
, MyFilterMorphs()
, ExtendTreeOper()
, PruneTreeOper()
]
tree = ETree.create(source=cocaine, target=procaine)
counter = 0
while not tree.path_found:
for oper in iteration:
tree.runOperation(oper)
counter+=1
print("Iteration", counter)
print(
sorted(
[
(x.getSMILES(), x.getDistToTarget())
for x in tree.leaves
], key=lambda x : x[1]
)[0]
)
show_mol_grid(tree.fetchPathTo(tree.params['target']))
Out[7]:
