def test8():
"""
Build a composite of more than 2 atoms.
Repeat 100:
Get a composite c that is stable
Add it to a list composites
Get an atom a
for each composite in composites:
for each atom in composite:
try to bond a to atom (which uses the composite's attractor)
"""
composites = []
for i in range(100):
a, sitea, b, siteb = getbondingpair()
assert reaction.sitescanbond(sitea, siteb)
reaction.do_edge_swaps(sitea, siteb)
c = particle.Composite([a] + [b])
sitea.bondedto, siteb.bondedto = siteb, sitea
stable = reaction.sitescanbond(sitea, siteb)
if not stable:
print(f'{i} Failed stability')
else:
composites.append(c)
a = particle.Atom.new(12, 2)
for composite in composites:
for atom in composite.atoms:
sitea, siteb = reaction.getbondablesites(a, atom)
if sitea and siteb:
reaction.do_edge_swaps(sitea, siteb)
sitea.bondedto, siteb.bondedto = siteb, sitea
c = particle.Composite([a] + composite.atoms)
print(c.atoms)
break
else:
print("No bonding possible between composite and atom.")
def break_bond(site1, site2):
assert site1.bondedto is site2 and site2.bondedto is site1, "Trying to break bond between unbonded Atoms."
do_edge_swaps(site1, site1)
site1.bondedto, site2.bondedto = None, None
# Need to set new parent composites here otherwise wrong attractor will be calculated.
# Create composite from each atom by traversing.
# Then return two composites.
return particle.Composite(particle.Composite.traverse(
site1.parent_atom)), particle.Composite(
particle.Composite.traverse(site2.parent_atom))
def test9():
# ! Problems here. The number of atoms in self.atoms disagrees with the atoms returned
# ! by the Atom traversal. The traversal is correct, so bonds are happening where
# ! they shouldn't be.
# * The problem was that I kept going through the 2-composites over and over and the
# * the second and subsequent times through some of them were already bonded.
# Build some larger molecules to test the traversal defined in Composite.
composites = []
for i in range(10000):
a, sitea, b, siteb = getbondingpair()
assert reaction.sitescanbond(sitea, siteb)
reaction.do_edge_swaps(sitea, siteb)
c = particle.Composite([a] + [b])
sitea.bondedto, siteb.bondedto = siteb, sitea
stable = reaction.sitescanbond(sitea, siteb)
if stable:
composites.append(c)
print(len(composites))
composites3 = []
a = particle.Atom.new(12, 2)
for composite in composites:
if len(composite.atoms) != len(particle.Composite.traverse(composite.atoms[0])):
print("error")
for atom in composite.atoms:
sitea, siteb = reaction.getbondablesites(a, atom)
if sitea and siteb:
reaction.do_edge_swaps(sitea, siteb)
sitea.bondedto, siteb.bondedto = siteb, sitea
c = particle.Composite([a] + composite.atoms)
composites3.append(c)
a = particle.Atom.new(12, 2)
break
# for composite in composites3:
# print([atom.id for atom in particle.Composite.traverse(composite.atoms[0])])
# print([atom.id for atom in particle.Composite.traverse(composite.atoms[1])])
# print([atom.id for atom in particle.Composite.traverse(composite.atoms[2])])
# print()
print(len(composites3))
composites4 = []
a = particle.Atom.new(12, 2)
for composite in composites3:
if len(composite.atoms) != len(particle.Composite.traverse(composite.atoms[0])):
print("error")
for atom in composite.atoms:
sitea, siteb = reaction.getbondablesites(a, atom)
if sitea and siteb:
reaction.do_edge_swaps(sitea, siteb)
sitea.bondedto, siteb.bondedto = siteb, sitea
c = particle.Composite([a] + composite.atoms)
composites4.append(c)
a = particle.Atom.new(12, 2)
break
print(len(composites4))
def test6():
# This checks that interaction sites are the same after bonding and unbonding.
for i in range(1000):
a, sitea, b, siteb = getbondingpair()
# Get spikes before
typea1 = sitea.spike_type()
vala1 = sitea.spike_value()
typeb1 = siteb.spike_type()
valb1 = siteb.spike_value()
# print(f'{typea1}, {vala1}, {typeb1}, {valb1}')
# Now bond
reaction.do_edge_swaps(sitea, siteb)
c = particle.Composite([a] + [b])
# Now unbond
reaction.do_edge_swaps(sitea, siteb)
sitea.parent_atom.parent_composite = None
siteb.parent_atom.parent_composite = None
# Get spikes after
typea2 = sitea.spike_type()
vala2 = sitea.spike_value()
typeb2 = siteb.spike_type()
valb2 = siteb.spike_value()
# print(f'{typea2}, {vala2}, {typeb2}, {valb2}')
# Check
if typea1 != typea2 or vala1 != vala2 or typeb1 != typeb2 or valb1 != valb2:
print("Error")
break
def test7():
# Get two Atoms that meeting the bonding criteria but fail the stability criteria.
for i in range(100):
a, sitea, b, siteb = getbondingpair()
assert reaction.sitescanbond(sitea, siteb)
reaction.do_edge_swaps(sitea, siteb)
c = particle.Composite([a] + [b])
stable = reaction.sitescanbond(sitea, siteb)
if not stable:
print(f'{i} Failed stability')
break
def test10():
# Create 100 2-atom composites and check that their len(self.atoms) agrees with
# the number of atoms returned by the traversal.
composites = []
for i in range(1000):
a, sitea, b, siteb = getbondingpair()
assert reaction.sitescanbond(sitea, siteb)
reaction.do_edge_swaps(sitea, siteb)
c = particle.Composite([a] + [b])
sitea.bondedto, siteb.bondedto = siteb, sitea
stable = reaction.sitescanbond(sitea, siteb)
print([atom.id for atom in c.atoms])
print([atom.id for atom in particle.Composite.traverse(c.atoms[0])])
print([atom.id for atom in particle.Composite.traverse(c.atoms[1])])
if len(c.atoms) != len(particle.Composite.traverse(c.atoms[0])) or len(c.atoms) != len(particle.Composite.traverse(c.atoms[1])):
print("error")
print('done')
def bond(site1, site2):
assert site1.bondedto is None and site2.bondedto is None, "Trying to bonded sites that are already bonded."
do_edge_swaps(site1, site1)
site1.bondedto, site2.bondedto = site2, site1
return particle.Composite(particle.Composite.traverse(site1.parent_atom))
def test5():
# Bond two Atoms and then unbond them to check the algorithm works.
# When I first did this test it occasionally gave a different attractor for an atom
# after it had been unbonded from the attractor before it was bonded. I found that
# RBN.get_cycle() was zeroing the values of the nodes properly. Test 6 tries to check
# that this bug no longer exists.
a, sitea, b, siteb = getbondingpair()
# print('Before')
print(f'Site A: {sitea}')
# for strnode in [f'{str(node)}' for node in sitea.nodes]:
# print(strnode)
# _, attractor = rbn.RBN.get_cycle(sitea.parent_atom.rbn.nodes)
# print(attractor)
# print()
print(f'Site B: {siteb}')
# for strnode in [f'{str(node)}' for node in siteb.nodes]:
# print(strnode)
# _, attractor = rbn.RBN.get_cycle(siteb.parent_atom.rbn.nodes)
# print(attractor)
# print(f'Sites can bond: {reaction.sitescanbond(sitea, siteb)}')
typea1 = sitea.spike_type()
vala1 = sitea.spike_value()
typeb1 = siteb.spike_type()
valb1 = siteb.spike_value()
print(f'{typea1}, {vala1}, {typeb1}, {valb1}')
# print()
reaction.do_edge_swaps(sitea, siteb)
c = particle.Composite([a] + [b])
# print('After')
print(f'Site A: {sitea}')
# for strnode in [f'{str(node)}' for node in sitea.nodes]:
# print(strnode)
# print()
print(f'Site B: {siteb}')
# for strnode in [f'{str(node)}' for node in siteb.nodes]:
# print(strnode)
# print(f'Sites can bond: {reaction.sitescanbond(sitea, siteb)}')
# print()
reaction.do_edge_swaps(sitea, siteb)
sitea.parent_atom.parent_composite = None
siteb.parent_atom.parent_composite = None
# print('And back again...')
print(f'Site A: {sitea}') # ! This was the cause of the error but the zeroing of the nodes states fixes it.
# for strnode in [f'{str(node)}' for node in sitea.nodes]:
# print(strnode)
# _, attractor = rbn.RBN.get_cycle(sitea.parent_atom.rbn.nodes)
# print(attractor)
# print()
print(f'Site B: {siteb}')
# for strnode in [f'{str(node)}' for node in siteb.nodes]:
# print(strnode)
# _, attractor = rbn.RBN.get_cycle(siteb.parent_atom.rbn.nodes)
# print(attractor)
# print(f'Sites can bond: {reaction.sitescanbond(sitea, siteb)}')
typea2 = sitea.spike_type()
vala2 = sitea.spike_value()
typeb2 = siteb.spike_type()
valb2 = siteb.spike_value()
print(f'{typea2}, {vala2}, {typeb2}, {valb2}')
# Check
if typea1 != typea2 or vala1 != vala2 or typeb1 != typeb2 or valb1 != valb2:
print("Error")