def from_snapshot(snapshot, scale=1.0):
"""Convert a Snapshot to a Compound.
Snapshot can be a hoomd.data.Snapshot or a gsd.hoomd.Snapshot.
Parameters
----------
snapshot : hoomd._hoomd.SnapshotSystemData_float or gsd.hoomd.Snapshot
Snapshot from which to build the mbuild Compound.
scale : float, optional, default 1.0
Value by which to scale the length values
Returns
-------
comp : Compound
Note
----
GSD and HOOMD snapshots center their boxes on the origin (0,0,0), so the
compound is shifted by half the box lengths
"""
comp = Compound()
bond_array = snapshot.bonds.group
n_atoms = snapshot.particles.N
if "SnapshotSystemData_float" in dir(hoomd._hoomd) and isinstance(
snapshot, hoomd._hoomd.SnapshotSystemData_float
):
# hoomd v2
box = snapshot.box
comp.box = Box.from_lengths_tilt_factors(
lengths=np.array([box.Lx, box.Ly, box.Lz]) * scale,
tilt_factors=np.array([box.xy, box.xz, box.yz]),
)
else:
# gsd / hoomd v3
box = snapshot.configuration.box
comp.box = Box.from_lengths_tilt_factors(
lengths=box[:3] * scale, tilt_factors=box[3:]
)
# GSD and HOOMD snapshots center their boxes on the origin (0,0,0)
shift = np.array(comp.box.lengths) / 2
# Add particles
for i in range(n_atoms):
name = snapshot.particles.types[snapshot.particles.typeid[i]]
xyz = snapshot.particles.position[i] * scale + shift
charge = snapshot.particles.charge[i]
atom = Particle(name=name, pos=xyz, charge=charge)
comp.add(atom, label=str(i))
# Add bonds
particle_dict = {idx: p for idx, p in enumerate(comp.particles())}
for i in range(bond_array.shape[0]):
atom1 = int(bond_array[i][0])
atom2 = int(bond_array[i][1])
comp.add_bond([particle_dict[atom1], particle_dict[atom2]])
return comp
def reverse_map_molecule(molecule, target, mapping_moieties):
print('unique')
cg_molecule = clone(molecule) # CG molecule
aa_template = target[molecule.name] # full aa Compound for molecule
aa_moieties = mapping_moieties[
molecule.name] # list of lists of indices for each bead
aa_molecule = Compound() # this will have the final aa molecule
cg_to_aa = [] # list of tuples containing (real index, aa atom)
# now cycle through beads
for index, bead in enumerate(cg_molecule.particles()):
aa_atoms = Compound() # placeholder for molecule atoms
[
aa_atoms.add(clone(aa_template.children[i]))
for i in aa_moieties[index]
]
aa_atoms.translate_to(bead.pos) # shift to cg_bead position
cg_to_aa += list(zip(aa_moieties[index], aa_atoms.children))
# sort atoms in cg_to_aa and add them to the aa_molecule
cg_to_aa = sorted(cg_to_aa)
for atom in cg_to_aa:
aa_molecule.add(clone(atom[1]))
# add bonds from the template
aa_template = aa_template.to_trajectory()
for i, j in aa_template.top.bonds:
aa_molecule.add_bond([aa_molecule[i.index], aa_molecule[j.index]])
# equilibrate molecule and shift back to center
# if the atom names match OpenBabel forcefield naming convention:
try:
aa_molecule.energy_minimization(steps=2500)
# otherwise rename with just element names:
except:
atomnames = [i.name for i in aa_molecule] # get the atomnames
for atom in aa_molecule: # make the atomnames elements
atom.name = atom.name[0]
aa_molecule.energy_minimization(steps=2500)
for i, atom in enumerate(atomnames):
aa_molecule[i].name = atomnames[i]
#aa_molecule.translate(center)
aa_molecule.name = molecule.name
return aa_molecule