def bonds():
return [
mch.Bond(0, 0, 1),
mch.Bond(1, 0, 2),
mch.Bond(2, 0, 3),
mch.Bond(3, 3, 4),
mch.Bond(4, 3, 5)
]
def get_mch_bonds(state):
"""
Yield the bonds of the :mod:`MCHammer` molecule.
Parameters
----------
state : :class:`.ConstructionState`
The state of the molecule under construction.
Yields
-------
:class:`MCHammer.Bond`
A bond in the molecule.
"""
for i, bond_infos in enumerate(state.get_bond_infos()):
ba1 = bond_infos.get_bond().get_atom1().get_id()
ba2 = bond_infos.get_bond().get_atom2().get_id()
# Must ensure bond atom id ordering is the same here as in
# line 30. Therefore, sort here.
ba1, ba2 = sorted((ba1, ba2))
yield mch.Bond(id=i, atom_ids=(ba1, ba2))
import mchammer as mch
benzene = stk.BuildingBlock.init_from_file('benzene.mol')
benzene_atoms = [(atom.get_id(), atom.__class__.__name__)
for atom in benzene.get_atoms()]
benzene_bonds = []
for i, bond in enumerate(benzene.get_bonds()):
# Must ensure that bond atom ids are ordered by atom id.
b_ids = ((bond.get_atom1().get_id(), bond.get_atom2().get_id())
if bond.get_atom1().get_id() < bond.get_atom2().get_id() else
(bond.get_atom2().get_id(), bond.get_atom1().get_id()))
benzene_bonds.append((i, b_ids))
mch_mol = mch.Molecule(
atoms=(mch.Atom(id=i[0], element_string=i[1]) for i in benzene_atoms),
bonds=(mch.Bond(id=i[0], atom1_id=i[1][0], atom2_id=i[1][1])
for i in benzene_bonds),
position_matrix=benzene.get_position_matrix(),
)
target_bond_length = 1.2
optimizer = mch.Optimizer(
step_size=0.25,
target_bond_length=target_bond_length,
num_steps=100,
)
subunits = mch_mol.get_subunits(bond_pair_ids=((2, 3), (1, 5)), )
# Get all steps.
mch_result = optimizer.get_trajectory(
mol=mch_mol,
bond_pair_ids=((2, 3), (1, 5)),
},
),
)
cage.write('poc.mol')
stk_long_bond_ids = get_long_bond_ids(cage)
mch_mol = mch.Molecule(
atoms=(
mch.Atom(
id=atom.get_id(),
element_string=atom.__class__.__name__,
) for atom in cage.get_atoms()
),
bonds=(
mch.Bond(
id=i,
atom1_id=bond.get_atom1().get_id(),
atom2_id=bond.get_atom2().get_id()
) for i, bond in enumerate(cage.get_bonds())
),
position_matrix=cage.get_position_matrix(),
)
mch_mol_nci = deepcopy(mch_mol)
optimizer = mch.Optimizer(
step_size=0.25,
target_bond_length=1.2,
num_steps=500,
)
subunits = mch_mol.get_subunits(
bond_pair_ids=stk_long_bond_ids,
)
def bonds():
return [
mch.Bond(0, (0, 1)), mch.Bond(1, (0, 2)), mch.Bond(2, (0, 3)),
mch.Bond(3, (3, 4)), mch.Bond(4, (3, 5))
]
@pytest.fixture(
params=(
(mch.Atom(id=0, element_string='N'), 0, 'N'),
(mch.Atom(id=65, element_string='P'), 65, 'P'),
(mch.Atom(id=2, element_string='C'), 2, 'C'),
)
)
def atom_info(request):
return request.param
@pytest.fixture(
params=(
(mch.Bond(id=0, atom_ids=(0, 1)), 0, 0, 1),
(mch.Bond(id=65, atom_ids=(2, 3)), 65, 2, 3),
(mch.Bond(id=2, atom_ids=(3, 4)), 2, 3, 4),
(mch.Bond(id=3, atom_ids=(0, 9)), 3, 0, 9),
)
)
def bond_info(request):
return request.param
@pytest.fixture
def atoms():
return [
mch.Atom(0, 'C'), mch.Atom(1, 'C'), mch.Atom(2, 'C'),
mch.Atom(3, 'C'), mch.Atom(4, 'C'), mch.Atom(5, 'C'),
]
import matplotlib.pyplot as plt
import os
import stk
import mchammer as mch
benzene = stk.BuildingBlock.init_from_file('benzene.mol')
benzene_atoms = [(atom.get_id(), atom.__class__.__name__)
for atom in benzene.get_atoms()]
benzene_bonds = []
for i, bond in enumerate(benzene.get_bonds()):
b_ids = (bond.get_atom1().get_id(), bond.get_atom2().get_id())
benzene_bonds.append((i, b_ids))
mch_mol = mch.Molecule(
atoms=(mch.Atom(id=i[0], element_string=i[1]) for i in benzene_atoms),
bonds=(mch.Bond(id=i[0], atom_ids=i[1]) for i in benzene_bonds),
position_matrix=benzene.get_position_matrix(),
)
target_bond_length = 1.2
optimizer = mch.Optimizer(
step_size=0.25,
target_bond_length=target_bond_length,
num_steps=100,
)
subunits = mch_mol.get_subunits(bond_pair_ids=((2, 3), (1, 5)), )
# Get all steps.
mch_mol, mch_result = optimizer.get_trajectory(
mol=mch_mol,
bond_pair_ids=((2, 3), (1, 5)),
subunits=subunits,
import pytest
import numpy as np
import mchammer as mch
@pytest.fixture(params=(
(mch.Atom(id=0, element_string='N'), 0, 'N'),
(mch.Atom(id=65, element_string='P'), 65, 'P'),
(mch.Atom(id=2, element_string='C'), 2, 'C'),
))
def atom_info(request):
return request.param
@pytest.fixture(params=(
(mch.Bond(id=0, atom1_id=0, atom2_id=1), 0, 0, 1),
(mch.Bond(id=65, atom1_id=2, atom2_id=3), 65, 2, 3),
(mch.Bond(id=2, atom1_id=3, atom2_id=4), 2, 3, 4),
(mch.Bond(id=3, atom1_id=0, atom2_id=9), 3, 0, 9),
))
def bond_info(request):
return request.param
@pytest.fixture
def atoms():
return [
mch.Atom(0, 'C'),
mch.Atom(1, 'C'),
mch.Atom(2, 'C'),
mch.Atom(3, 'C'),
bb1: range(2),
bb2: (2, 3),
bb3: 4,
bb4: 5,
bb5: range(6, 10),
}, ), )
cage.write('poc.mol')
stk_long_bond_ids = get_long_bond_ids(cage)
mch_mol = mch.Molecule(
atoms=(mch.Atom(
id=atom.get_id(),
element_string=atom.__class__.__name__,
) for atom in cage.get_atoms()),
bonds=(mch.Bond(id=i,
atom_ids=(
bond.get_atom1().get_id(),
bond.get_atom2().get_id(),
)) for i, bond in enumerate(cage.get_bonds())),
position_matrix=cage.get_position_matrix(),
)
optimizer = mch.Collapser(
step_size=0.05,
distance_threshold=1.2,
scale_steps=True,
)
subunits = get_subunits(mol=cage)
# Get all steps.
mch_mol, mch_result = optimizer.get_trajectory(
mol=mch_mol,
bond_pair_ids=stk_long_bond_ids,