def cg_by_index(trj,
atom_indices_list,
bead_label_list,
chain_list=None,
segment_id_list=None,
resSeq_list=None,
inplace=False,
bonds=None,
split_shared_atoms=False,
mod_weights_list=None,
mapping_function="com",
charge_tol=1e-5,
center_postwrap=False):
"""Create a coarse grained (CG) trajectory from subsets of atoms by
computing centers of mass of selected sets of atoms.
Parameters
----------
atom_indices_list :
list of array-like, dtype=int, shape=(n_beads,n_atoms)
List of indices of atoms to combine into CG sites
bead_label_list :
list of maximum 4-letter strings to label CG sites
chain_list :
optional list of chain id's to split resulting beads into separate
chains
resSeq_list :
optional list of residue sequence id's to assign cg residues
segment_id_list :
optional list of segment id's to assign cg residues
inplace :
bool, default=False
If ``True``, the operation is done inplace, modifying ``trj``.
Otherwise, a copy is returned with the sliced atoms, and
``trj`` is not modified.
bonds : array-like,dtype=int, shape=(n_bonds,2), default=None
If specified, sets these bonds in new topology
split_shared_atoms: boolean
If specified, check to see if atoms are shared per molecule in beads. If
so, equally divide their weight accordingly for each bead.
mapping_function: string, default='com': how to map xyz coordinates
options: %s
center_postwrap: Boolean
Whether to wrap the CG system after it is mapped. Assumes that box is
centered at 0, and only has effect if periodic information is present.
Note - If repeated resSeq values are used, as for a repeated motiff
in a CG polymer, those sections most be broken into separate
chains or an incorrect topology will result
Returns
-------
traj : md.Trajectory
The return value is either ``trj``, or the new trajectory,
depending on the value of ``inplace``.
""" % mapping_options.keys()
if not len(atom_indices_list) == len(bead_label_list):
raise ValueError("Must supply a list of bead labels of the "
"same length as a list of selected atom indices")
for bead_label in bead_label_list:
if not (type(bead_label) is
str) or len(bead_label) > 4 or len(bead_label) < 1:
raise ValueError("Specified bead label '%s' is not valid, \
must be a string between 1 and 4 characters" %
bead_label)
bead_label_list = [bead_label.upper() for bead_label in bead_label_list]
if mapping_function not in mapping_options:
raise ValueError("Must select a mapping function from: %s"\
%mapping_options.keys())
if chain_list is None:
chain_list = np.ones(len(atom_indices_list), dtype=int)
elif len(chain_list) != len(atom_indices_list):
raise ValueError("Supplied chain_list must be of the same length "
"as a list of selected atom indices")
if segment_id_list is not None and len(segment_id_list) != len(
atom_indices_list):
raise ValueError("Supplied segment_id_list must be of the same "
"length as a list of selected atom indices")
if resSeq_list is not None and len(resSeq_list) != len(atom_indices_list):
raise ValueError("Supplied resSeq_list must be of the same "
"length as a list of selected atom indices")
n_beads = len(atom_indices_list)
xyz = np.zeros((trj.xyz.shape[0], n_beads, trj.xyz.shape[2]),
dtype=trj.xyz.dtype,
order='C')
forces = np.zeros((trj.xyz.shape[0], n_beads, trj.xyz.shape[2]),
dtype=np.double,
order='C')
columns = ["serial", "name", "element", "resSeq", "resName", "chainID"]
#total masse for each cg bead.
masses = np.zeros((n_beads), dtype=np.float64)
#list of masses for elements in cg bead.
masses_i = []
#masses
for ii in range(n_beads):
#atoms in curent cg bead.
atom_indices = atom_indices_list[ii]
#first, construct lists of masses in current cg bead.
temp_masses = np.array([])
for jj in atom_indices:
temp_masses = np.append(temp_masses, trj.top.atom(jj).element.mass)
masses_i.append(temp_masses)
masses[ii] = masses_i[ii].sum()
if hasattr(trj.top.atom(1), 'charge'):
#total charge for each cg bead.
charges = np.zeros((n_beads), dtype=np.float64)
#lists of charges for in current cg bead
charges_i = []
#charges
for ii in range(n_beads):
#atoms in curent cg bead.
atom_indices = atom_indices_list[ii]
#first, construct lists of masses in current cg bead.
temp_charges = np.array([])
for jj in atom_indices:
temp_charges = np.append(temp_charges, trj.top.atom(jj).charge)
charges_i.append(temp_charges)
charges[ii] = charges_i[ii].sum()
forcenorm_i = []
if mapping_function == 'cof' or mapping_function == 'center_of_force':
for ii in range(n_beads):
atom_indices = atom_indices_list[ii]
forcenorm_i.append(get_forcenorms(trj, atom_indices))
if mapping_function == 'coc' or mapping_function == 'center_of_charge':
for charge in charges:
if np.absolute(charge) < charge_tol:
raise ValueError("Total charge on site %i is near zero" % ii)
topology_labels = []
element_label_dict = {}
if (split_shared_atoms):
mod_weights_list = gen_unique_overlap_mod_weights(atom_indices_list)
has_forces = False
try:
trj.__dict__['forces']
test_forces = map_forces(trj, (0, ))
has_forces = True
except TypeError:
print("WARNING: Invalid Forces\nNo Map applied to forces")
except KeyError:
pass
except:
print("Unknown error, check your forces\nexiting...")
raise
for i in range(n_beads):
atom_indices = atom_indices_list[i]
bead_label = bead_label_list[i]
xyz_i = xyz[:, i, :]
if mapping_function == 'coc' or mapping_function == 'center_of_charge':
weights = charges_i[i]
elif mapping_function == 'com' or mapping_function == 'center_of_mass':
weights = masses_i[i]
elif mapping_function == 'cof' or mapping_function == 'center_of_force':
weights = forcenorm_i[i]
elif mapping_function == 'center':
weights = np.ones(len(atom_indices))
if (mod_weights_list is not None):
weights[:] = np.multiply(weights, mod_weights_list[i])
compute_center_weighted(xyz_i,
trj.xyz,
atom_indices,
weights,
unitcell_lengths=trj.unitcell_lengths,
center_postwrap=center_postwrap)
if has_forces:
forces_i = map_forces(trj, atom_indices)
forces[:, i, :] = forces_i
if resSeq_list is not None:
resSeq = resSeq_list[i]
else:
resSeq = i + 1
#element_label='%4s'%('B%i'%(resSeq))
if not bead_label in element_label_dict:
element_label = '%2s' % ('B%i' % (len(element_label_dict) % 10))
element_label_dict[bead_label] = element_label
else:
element_label = element_label_dict[bead_label]
if element_label.strip().upper(
) not in element.Element._elements_by_symbol:
element.Element(1000 + resSeq, element_label, element_label,
masses[i], 1.0)
topology_labels.append([
i, bead_label, element_label, resSeq,
'%3s' % bead_label, chain_list[i]
])
df = pd.DataFrame(topology_labels, columns=columns)
topology = Topology.from_dataframe(df, bonds=bonds)
if segment_id_list is not None:
for beadidx, bead in enumerate(topology.atoms):
bead.residue.segment_id = segment_id_list[beadidx]
if inplace:
if trj._topology is not None:
trj._topology = topology
trj._xyz = xyz
return trj
unitcell_lengths = unitcell_angles = None
if trj._have_unitcell:
unitcell_lengths = trj._unitcell_lengths.copy()
unitcell_angles = trj._unitcell_angles.copy()
time = trj._time.copy()
new_trj = Trajectory(xyz=xyz,
topology=topology,
time=time,
unitcell_lengths=unitcell_lengths,
unitcell_angles=unitcell_angles)
new_trj.forces = forces
return new_trj
def cg_by_index(trj,
atom_indices_list,
bead_label_list,
chain_list=None,
segment_id_list=None,
resSeq_list=None,
inplace=False,
bonds=None,
mapping_function="com"):
"""Create a coarse grained (CG) trajectory from subsets of atoms by
computing centers of mass of selected sets of atoms.
Parameters
----------
atom_indices_list : list of array-like, dtype=int, shape=(n_beads,n_atoms)
List of indices of atoms to combine into CG sites
bead_label_list : list of maximum 4-letter strings to label CG sites
chain_list : optional list of chain id's to split resulting beads into separate chains
resSeq_list : optional list of residue sequence id's to assign cg residues
segment_id_list : optional list of segment id's to assign cg residues
inplace : bool, default=False
If ``True``, the operation is done inplace, modifying ``trj``.
Otherwise, a copy is returned with the sliced atoms, and
``trj`` is not modified.
bonds : array-like,dtype=int, shape=(n_bonds,2), default=None
If specified, sets these bonds in new topology
mapping_function: string, default='com': how to map xyz coordinates
options: %s
Note - If repeated resSeq values are used, as for a repeated motiff in a CG polymer,
those sections most be broken into separate chains or an incorrect topology will result
Returns
-------
traj : md.Trajectory
The return value is either ``trj``, or the new trajectory,
depending on the value of ``inplace``.
""" % mapping_options.keys()
if not len(atom_indices_list) == len(bead_label_list):
raise ValueError(
"Must supply a list of bead labels of the same length as a list of selected atom indices"
)
for bead_label in bead_label_list:
if not (type(bead_label) is
str) or len(bead_label) > 4 or len(bead_label) < 1:
raise ValueError(
"Specified bead label '%s' is not valid, must be a string between 1 and 4 characters"
% bead_label)
bead_label_list = [bead_label.upper() for bead_label in bead_label_list]
if mapping_function not in mapping_options:
raise ValueError("Must select a mapping function from: %s" %
mapping_options.keys())
map_coords = mapping_options[mapping_function]
if chain_list is None:
chain_list = np.ones(len(atom_indices_list), dtype=int)
elif len(chain_list) != len(atom_indices_list):
raise ValueError(
"Supplied chain_list must be of the same length as a list of selected atom indices"
)
if segment_id_list is not None and len(segment_id_list) != len(
atom_indices_list):
raise ValueError(
"Supplied segment_id_list must be of the same length as a list of selected atom indices"
)
if resSeq_list is not None and len(resSeq_list) != len(atom_indices_list):
raise ValueError(
"Supplied resSeq_list must be of the same length as a list of selected atom indices"
)
n_beads = len(atom_indices_list)
xyz = np.zeros((trj.xyz.shape[0], n_beads, trj.xyz.shape[2]),
dtype=trj.xyz.dtype,
order='C')
forces = np.zeros((trj.xyz.shape[0], n_beads, trj.xyz.shape[2]),
dtype=np.double,
order='C')
columns = ["serial", "name", "element", "resSeq", "resName", "chainID"]
masses = np.array([
np.sum([a.mass for a in trj.top.atoms if a.index in atom_indices])
for atom_indices in atom_indices_list
],
dtype=np.float64)
charges = np.array([
np.sum([a.charge for a in trj.top.atoms if a.index in atom_indices])
for atom_indices in atom_indices_list
],
dtype=np.float64)
topology_labels = []
element_label_dict = {}
xyz_i = np.zeros((trj.xyz.shape[0], trj.xyz.shape[2]),
dtype=trj.xyz.dtype,
order='C')
for i in range(n_beads):
atom_indices = atom_indices_list[i]
bead_label = bead_label_list[i]
#xyz_i = map_coords(trj,atom_indices)
masses_i = np.array(
[a.mass for a in trj.top.atoms if a.index in atom_indices_list[i]],
dtype=np.float64)
map_coords(xyz_i,
trj.xyz,
atom_indices,
masses_i,
unitcell_lengths=trj.unitcell_lengths)
xyz[:, i, :] = xyz_i
if "forces" in trj.__dict__ and len(trj.forces) > 0:
forces_i = map_forces(trj, atom_indices)
forces[:, i, :] = forces_i
if resSeq_list is not None:
resSeq = resSeq_list[i]
else:
resSeq = i + 1
#element_label='%4s'%('B%i'%(resSeq))
if not bead_label in element_label_dict:
element_label = '%2s' % ('B%i' % (len(element_label_dict) % 10))
element_label_dict[bead_label] = element_label
else:
element_label = element_label_dict[bead_label]
if element_label.strip().upper(
) not in element.Element._elements_by_symbol:
element.Element(1000 + resSeq, element_label, element_label,
masses[i], 1.0)
topology_labels.append([
i, bead_label, element_label, resSeq,
'%3s' % bead_label, chain_list[i]
])
df = pd.DataFrame(topology_labels, columns=columns)
topology = Topology.from_dataframe(df, bonds=bonds)
if segment_id_list is not None:
for beadidx, bead in enumerate(topology.atoms):
bead.residue.segment_id = segment_id_list[beadidx]
if inplace:
if trj._topology is not None:
trj._topology = topology
trj._xyz = xyz
return trj
unitcell_lengths = unitcell_angles = None
if trj._have_unitcell:
unitcell_lengths = trj._unitcell_lengths.copy()
unitcell_angles = trj._unitcell_angles.copy()
time = trj._time.copy()
new_trj = Trajectory(xyz=xyz,
topology=topology,
time=time,
unitcell_lengths=unitcell_lengths,
unitcell_angles=unitcell_angles)
new_trj.forces = forces
return new_trj
def cg_by_index(trj, atom_indices_list, bead_label_list, chain_list=None, segment_id_list=None, resSeq_list=None, inplace=False, bonds=None, mapping_function="com"):
"""Create a coarse grained (CG) trajectory from subsets of atoms by
computing centers of mass of selected sets of atoms.
Parameters
----------
atom_indices_list : list of array-like, dtype=int, shape=(n_beads,n_atoms)
List of indices of atoms to combine into CG sites
bead_label_list : list of maximum 4-letter strings to label CG sites
chain_list : optional list of chain id's to split resulting beads into separate chains
resSeq_list : optional list of residue sequence id's to assign cg residues
segment_id_list : optional list of segment id's to assign cg residues
inplace : bool, default=False
If ``True``, the operation is done inplace, modifying ``trj``.
Otherwise, a copy is returned with the sliced atoms, and
``trj`` is not modified.
bonds : array-like,dtype=int, shape=(n_bonds,2), default=None
If specified, sets these bonds in new topology
mapping_function: string, default='com': how to map xyz coordinates
options: %s
Note - If repeated resSeq values are used, as for a repeated motiff in a CG polymer,
those sections most be broken into separate chains or an incorrect topology will result
Returns
-------
traj : md.Trajectory
The return value is either ``trj``, or the new trajectory,
depending on the value of ``inplace``.
"""%mapping_options.keys()
if not len(atom_indices_list)==len(bead_label_list):
raise ValueError("Must supply a list of bead labels of the same length as a list of selected atom indices")
for bead_label in bead_label_list:
if not (type(bead_label) is str) or len(bead_label)>4 or len(bead_label)<1:
raise ValueError("Specified bead label '%s' is not valid, must be a string between 1 and 4 characters"%bead_label)
bead_label_list = [ bead_label.upper() for bead_label in bead_label_list ]
if mapping_function not in mapping_options:
raise ValueError("Must select a mapping function from: %s"%mapping_options.keys())
map_coords = mapping_options[mapping_function]
if chain_list is None:
chain_list = np.ones(len(atom_indices_list),dtype=int)
elif len(chain_list)!=len(atom_indices_list):
raise ValueError("Supplied chain_list must be of the same length as a list of selected atom indices")
if segment_id_list is not None and len(segment_id_list)!=len(atom_indices_list):
raise ValueError("Supplied segment_id_list must be of the same length as a list of selected atom indices")
if resSeq_list is not None and len(resSeq_list)!=len(atom_indices_list):
raise ValueError("Supplied resSeq_list must be of the same length as a list of selected atom indices")
n_beads = len(atom_indices_list)
xyz = np.zeros((trj.xyz.shape[0],n_beads,trj.xyz.shape[2]),dtype=trj.xyz.dtype,order='C')
forces = np.zeros((trj.xyz.shape[0],n_beads,trj.xyz.shape[2]),dtype=np.double,order='C')
columns = ["serial","name","element","resSeq","resName","chainID"]
masses = np.array([ np.sum([a.mass for a in trj.top.atoms if a.index in atom_indices]) for atom_indices in atom_indices_list],dtype=np.float64)
charges = np.array([ np.sum([a.charge for a in trj.top.atoms if a.index in atom_indices]) for atom_indices in atom_indices_list],dtype=np.float64)
topology_labels = []
element_label_dict = {}
xyz_i = np.zeros((trj.xyz.shape[0],trj.xyz.shape[2]),dtype=trj.xyz.dtype,order='C')
for i in range(n_beads):
atom_indices = atom_indices_list[i]
bead_label = bead_label_list[i]
#xyz_i = map_coords(trj,atom_indices)
masses_i = np.array([a.mass for a in trj.top.atoms if a.index in atom_indices_list[i]],dtype=np.float64)
map_coords(xyz_i,trj.xyz,atom_indices,masses_i,unitcell_lengths=trj.unitcell_lengths)
xyz[:,i,:] = xyz_i
if "forces" in trj.__dict__ and len(trj.forces)>0:
forces_i = map_forces(trj,atom_indices)
forces[:,i,:] = forces_i
if resSeq_list is not None:
resSeq = resSeq_list[i]
else:
resSeq = i + 1
#element_label='%4s'%('B%i'%(resSeq))
if not bead_label in element_label_dict:
element_label='%2s'%('B%i'%(len(element_label_dict)%10))
element_label_dict[bead_label] = element_label
else:
element_label = element_label_dict[bead_label]
if element_label.strip().upper() not in element.Element._elements_by_symbol:
element.Element(1000+resSeq, element_label, element_label, masses[i], 1.0)
topology_labels.append( [i,bead_label,element_label,resSeq,'%3s'%bead_label,chain_list[i]] )
df = pd.DataFrame(topology_labels,columns=columns)
topology = Topology.from_dataframe(df,bonds=bonds)
if segment_id_list is not None:
for beadidx,bead in enumerate(topology.atoms):
bead.residue.segment_id = segment_id_list[beadidx]
if inplace:
if trj._topology is not None:
trj._topology = topology
trj._xyz = xyz
return trj
unitcell_lengths = unitcell_angles = None
if trj._have_unitcell:
unitcell_lengths = trj._unitcell_lengths.copy()
unitcell_angles = trj._unitcell_angles.copy()
time = trj._time.copy()
new_trj = Trajectory(xyz=xyz, topology=topology, time=time,
unitcell_lengths=unitcell_lengths,
unitcell_angles=unitcell_angles)
new_trj.forces = forces
return new_trj
