In [1]:

%%time
from IPython.core.display import HTML
from retropaths.molecules.molecule import Molecule

HTML('<script src="//d3js.org/d3.v3.min.js"></script>')

%%time from IPython.core.display import HTML from retropaths.molecules.molecule import Molecule HTML('')

CPU times: user 343 ms, sys: 129 ms, total: 472 ms
Wall time: 577 ms

Out[1]:

MOLECULE¶

Creation and drawing:¶

In [2]:

# a molecule can be created from a smiles string
# mol = Molecule.from_smiles('Cn1cnc2n(C)c(=O)n(C)c(=O)c12')
mol = Molecule.from_smiles('CCCCCC')
mol.draw()  # <- it draws the molecule

# a molecule can be created from a smiles string # mol = Molecule.from_smiles('Cn1cnc2n(C)c(=O)n(C)c(=O)c12') mol = Molecule.from_smiles('CCCCCC') mol.draw() # <- it draws the molecule

Out[2]:

In [3]:

# different drawing method, so you can see the internal graph representation.
print(mol)  # <- printing the molecule shows the nodes and edges with the various attributes.
mol.draw(mode='d3')

# different drawing method, so you can see the internal graph representation. print(mol) # <- printing the molecule shows the nodes and edges with the various attributes. mol.draw(mode='d3')

nodes = [(0, {'neighbors': 4, 'element': 'C', 'charge': 0}), (1, {'neighbors': 4, 'element': 'C', 'charge': 0}), (2, {'neighbors': 4, 'element': 'C', 'charge': 0}), (3, {'neighbors': 4, 'element': 'C', 'charge': 0}), (4, {'neighbors': 4, 'element': 'C', 'charge': 0}), (5, {'neighbors': 4, 'element': 'C', 'charge': 0}), (6, {'neighbors': 1, 'element': 'H', 'charge': 0}), (7, {'neighbors': 1, 'element': 'H', 'charge': 0}), (8, {'neighbors': 1, 'element': 'H', 'charge': 0}), (9, {'neighbors': 1, 'element': 'H', 'charge': 0}), (10, {'neighbors': 1, 'element': 'H', 'charge': 0}), (11, {'neighbors': 1, 'element': 'H', 'charge': 0}), (12, {'neighbors': 1, 'element': 'H', 'charge': 0}), (13, {'neighbors': 1, 'element': 'H', 'charge': 0}), (14, {'neighbors': 1, 'element': 'H', 'charge': 0}), (15, {'neighbors': 1, 'element': 'H', 'charge': 0}), (16, {'neighbors': 1, 'element': 'H', 'charge': 0}), (17, {'neighbors': 1, 'element': 'H', 'charge': 0}), (18, {'neighbors': 1, 'element': 'H', 'charge': 0}), (19, {'neighbors': 1, 'element': 'H', 'charge': 0})]
edges = [(0, 1, {'bond_order': 'single'}), (0, 6, {'bond_order': 'single'}), (0, 7, {'bond_order': 'single'}), (0, 8, {'bond_order': 'single'}), (1, 2, {'bond_order': 'single'}), (1, 9, {'bond_order': 'single'}), (1, 10, {'bond_order': 'single'}), (2, 3, {'bond_order': 'single'}), (2, 11, {'bond_order': 'single'}), (2, 12, {'bond_order': 'single'}), (3, 4, {'bond_order': 'single'}), (3, 13, {'bond_order': 'single'}), (3, 14, {'bond_order': 'single'}), (4, 5, {'bond_order': 'single'}), (4, 15, {'bond_order': 'single'}), (4, 16, {'bond_order': 'single'}), (5, 17, {'bond_order': 'single'}), (5, 18, {'bond_order': 'single'}), (5, 19, {'bond_order': 'single'})]

Out[3]:

In [4]:

# molecules can be added together
mol2 = mol + mol
mol2.draw(mode='d3', percentage=0.6)

# molecules can be added together mol2 = mol + mol mol2.draw(mode='d3', percentage=0.6)

Out[4]:

In [5]:

# multiplication also works
mol10 = mol * 10
mol10.draw(mode='d3', size=(1200, 1200), percentage=1)  # we increase the canvas size so 10 molecules fit better

# multiplication also works mol10 = mol * 10 mol10.draw(mode='d3', size=(1200, 1200), percentage=1) # we increase the canvas size so 10 molecules fit better

Out[5]:

List of molecules. Separation, Deduplication, Addition¶

In [6]:

# this creates a single molecule object from a list of smiles
mol_from_list = Molecule.from_list_of_smiles_to_single_graph(['C', 'CC', 'CCC', 'C'])
mol_from_list.draw()

# this creates a single molecule object from a list of smiles mol_from_list = Molecule.from_list_of_smiles_to_single_graph(['C', 'CC', 'CCC', 'C']) mol_from_list.draw()

Out[6]:

In [7]:

list_of_molecules = mol_from_list.separate_graph_in_pieces()  # <- You can separate the molecule back in a list of molecules
Molecule.draw_list(list_of_molecules)  # <- this staticmethod draws a list of molecules in a HTML table.

list_of_molecules = mol_from_list.separate_graph_in_pieces() # <- You can separate the molecule back in a list of molecules Molecule.draw_list(list_of_molecules) # <- this staticmethod draws a list of molecules in a HTML table.

Out[7]:

In [8]:

dedup_molecules = Molecule.delete_duplicates(list_of_molecules)  # <- this eliminates duplicates from the list, giving unique molecules.
Molecule.draw_list(dedup_molecules)  # <- draw deduplicated list

dedup_molecules = Molecule.delete_duplicates(list_of_molecules) # <- this eliminates duplicates from the list, giving unique molecules. Molecule.draw_list(dedup_molecules) # <- draw deduplicated list

Out[8]:

In [9]:

back_in_a_single_graph = Molecule.add_list_of_molecules(dedup_molecules)  # <- this adds a list of molecule into a single graph
print(f'smiles = {back_in_a_single_graph.smiles}')  # <- the smiles method works with multiple molecule graphs, too!!
back_in_a_single_graph.draw()

back_in_a_single_graph = Molecule.add_list_of_molecules(dedup_molecules) # <- this adds a list of molecule into a single graph print(f'smiles = {back_in_a_single_graph.smiles}') # <- the smiles method works with multiple molecule graphs, too!! back_in_a_single_graph.draw()

smiles = C.CC.CCC

Out[9]:

Molecule properties¶

In [10]:

mol.molecular_formula

mol.molecular_formula

Out[10]:

C₆H₁₄

In [11]:

# take a look at other various properties of the molecule object!
print(f'{mol.weight=}\n{mol.charge=}\n{mol.num_heavy_atoms=}\n{mol.bond_order=}\n{mol.atom_types=}\n{mol.neighbors_number=}\n{mol.is_template=}\n')

# take a look at other various properties of the molecule object! print(f'{mol.weight=}\n{mol.charge=}\n{mol.num_heavy_atoms=}\n{mol.bond_order=}\n{mol.atom_types=}\n{mol.neighbors_number=}\n{mol.is_template=}\n')

mol.weight=50
mol.charge=0
mol.num_heavy_atoms=6
mol.bond_order={(0, 1): 'single', (0, 6): 'single', (0, 7): 'single', (0, 8): 'single', (1, 2): 'single', (1, 9): 'single', (1, 10): 'single', (2, 3): 'single', (2, 11): 'single', (2, 12): 'single', (3, 4): 'single', (3, 13): 'single', (3, 14): 'single', (4, 5): 'single', (4, 15): 'single', (4, 16): 'single', (5, 17): 'single', (5, 18): 'single', (5, 19): 'single'}
mol.atom_types={0: 'C', 1: 'C', 2: 'C', 3: 'C', 4: 'C', 5: 'C', 6: 'H', 7: 'H', 8: 'H', 9: 'H', 10: 'H', 11: 'H', 12: 'H', 13: 'H', 14: 'H', 15: 'H', 16: 'H', 17: 'H', 18: 'H', 19: 'H'}
mol.neighbors_number={0: 4, 1: 4, 2: 4, 3: 4, 4: 4, 5: 4, 6: 1, 7: 1, 8: 1, 9: 1, 10: 1, 11: 1, 12: 1, 13: 1, 14: 1, 15: 1, 16: 1, 17: 1, 18: 1, 19: 1}
mol.is_template=False

In [12]:

# properties functional form
print(f'{mol.which_atoms_are_in()=}\n{mol.list_of_elements()=}\n{mol.force_smiles()=}\n{mol.is_empty()=}\n')

# properties functional form print(f'{mol.which_atoms_are_in()=}\n{mol.list_of_elements()=}\n{mol.force_smiles()=}\n{mol.is_empty()=}\n')

mol.which_atoms_are_in()={'H', 'C'}
mol.list_of_elements()=['C', 'C', 'C', 'C', 'C', 'C', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
mol.force_smiles()='CCCCCC'
mol.is_empty()=False

Debug¶

In [13]:

# printing a molecule will give you graph internals
print(mol)

# printing a molecule will give you graph internals print(mol)

nodes = [(0, {'neighbors': 4, 'element': 'C', 'charge': 0}), (1, {'neighbors': 4, 'element': 'C', 'charge': 0}), (2, {'neighbors': 4, 'element': 'C', 'charge': 0}), (3, {'neighbors': 4, 'element': 'C', 'charge': 0}), (4, {'neighbors': 4, 'element': 'C', 'charge': 0}), (5, {'neighbors': 4, 'element': 'C', 'charge': 0}), (6, {'neighbors': 1, 'element': 'H', 'charge': 0}), (7, {'neighbors': 1, 'element': 'H', 'charge': 0}), (8, {'neighbors': 1, 'element': 'H', 'charge': 0}), (9, {'neighbors': 1, 'element': 'H', 'charge': 0}), (10, {'neighbors': 1, 'element': 'H', 'charge': 0}), (11, {'neighbors': 1, 'element': 'H', 'charge': 0}), (12, {'neighbors': 1, 'element': 'H', 'charge': 0}), (13, {'neighbors': 1, 'element': 'H', 'charge': 0}), (14, {'neighbors': 1, 'element': 'H', 'charge': 0}), (15, {'neighbors': 1, 'element': 'H', 'charge': 0}), (16, {'neighbors': 1, 'element': 'H', 'charge': 0}), (17, {'neighbors': 1, 'element': 'H', 'charge': 0}), (18, {'neighbors': 1, 'element': 'H', 'charge': 0}), (19, {'neighbors': 1, 'element': 'H', 'charge': 0})]
edges = [(0, 1, {'bond_order': 'single'}), (0, 6, {'bond_order': 'single'}), (0, 7, {'bond_order': 'single'}), (0, 8, {'bond_order': 'single'}), (1, 2, {'bond_order': 'single'}), (1, 9, {'bond_order': 'single'}), (1, 10, {'bond_order': 'single'}), (2, 3, {'bond_order': 'single'}), (2, 11, {'bond_order': 'single'}), (2, 12, {'bond_order': 'single'}), (3, 4, {'bond_order': 'single'}), (3, 13, {'bond_order': 'single'}), (3, 14, {'bond_order': 'single'}), (4, 5, {'bond_order': 'single'}), (4, 15, {'bond_order': 'single'}), (4, 16, {'bond_order': 'single'}), (5, 17, {'bond_order': 'single'}), (5, 18, {'bond_order': 'single'}), (5, 19, {'bond_order': 'single'})]

In [14]:

# you can create the molecule object back from the printed output (copy paste here the new string if you changed smiles above)
nodes = [(0, {'neighbors': 4, 'element': 'C', 'charge': 0}), (1, {'neighbors': 1, 'element': 'H', 'charge': 0}), (2, {'neighbors': 1, 'element': 'H', 'charge': 0}), (3, {'neighbors': 1, 'element': 'H', 'charge': 0}), (4, {'neighbors': 1, 'element': 'H', 'charge': 0})]
edges = [(0, 1, {'bond_order': 'single'}), (0, 2, {'bond_order': 'single'}), (0, 3, {'bond_order': 'single'}), (0, 4, {'bond_order': 'single'})]
molx = Molecule.from_debug_string(nodes, edges)
molx.draw()

# you can create the molecule object back from the printed output (copy paste here the new string if you changed smiles above) nodes = [(0, {'neighbors': 4, 'element': 'C', 'charge': 0}), (1, {'neighbors': 1, 'element': 'H', 'charge': 0}), (2, {'neighbors': 1, 'element': 'H', 'charge': 0}), (3, {'neighbors': 1, 'element': 'H', 'charge': 0}), (4, {'neighbors': 1, 'element': 'H', 'charge': 0})] edges = [(0, 1, {'bond_order': 'single'}), (0, 2, {'bond_order': 'single'}), (0, 3, {'bond_order': 'single'}), (0, 4, {'bond_order': 'single'})] molx = Molecule.from_debug_string(nodes, edges) molx.draw()

Out[14]:

Serialization¶

In [15]:

# This will create a SMILES.svg file in the folder
mol.to_svg()

# This will create a SMILES.svg file in the folder mol.to_svg()