def to_element(x):
if isinstance(x, (list, tuple)):
assert len(x) == 1
x = x[0]
if '.' in x: # orbital-hybridizations in SYBL
return x.split('.')[0]
try:
# check if we can convert the whole str to an Element,
# if not, we only pass the first letter.
from mdtraj.core.element import Element
Element.getBySymbol(x)
except KeyError:
return to_element(x[0])
return x
def convert_Traj_RDF():
"""Convert the trajectory and structure files into the rdf"""
## add parameters to function calls - maybe add other functions
## other potential functions:
## - check_file_overwrite()
## - check_g_r_dropoff() - integrate with plot function
## - manage_filetypes() - read in files (maybe for mdtraj flexibility)
traj_filename = os.path.join(os.getcwd(), 'data/traj_unwrapped.dcd')
struct_filename = os.path.join(os.getcwd(), 'data/start_aa.hoomdxml')
search_mapping_filename = os.path.join(os.getcwd(),
'data/propane_search_mapping.xml')
user_mapping_filename = os.path.join(os.getcwd(),
'data/propane_user_mapping.xml')
t = md.load(traj_filename, top=struct_filename)
print("Loaded struct & traj files")
molecules = t.top.find_molecules()
first_mol_indices = [atom.index for atom in list(molecules[0])]
first_molecule = t.top.subset(
first_mol_indices) # topology for first molecule
for atom in first_molecule.atoms: #possible other function
atom.element = Element.getBySymbol(atom.name)
topology = first_molecule.to_openmm(
traj=None) # openmm topology accepted by foyer
# import pdb; pdb.set_trace()
read_search_mapping(search_mapping_filename, user_mapping_filename,
topology)
def create_system_mapping(element_names, n_beads_TOTAL, t):
"""Create a system mapping
Parameters
----------
element_names : (???)
(???)
n_beads_TOTAL : int
Number of beads in the system
t : mdTraj.Trajectory
Initial trajectory object generated from structure and trajectory files
"""
# SLOWEST PART OF CODE IS THIS FUNCTION
# Initialize atoms with elements
## for loop to traverse element_names array for elements
## need to expand from just carbon to more/different elements
## maybe use elements from periodic package
for atom in t.top.atoms: #possible other function
atom.element = Element.getBySymbol(atom.name) # check element
#need for the xml file to have element symbol as type
# Map the beads accordingly
cg_idx = 0
start_idx = 0
propane_map = {0: [0, 1, 2]} ## mapping definition needs to be created
# from search and user files
## TEST CODE
######################################################################
######################################################################
## TEST CODE
system_mapping = {}
for n in range(n_beads_TOTAL
): # what does sections mean in this particular context
for bead, atoms in propane_map.items():
system_mapping[cg_idx] = [x + start_idx for x in atoms]
start_idx += len(atoms) # understand this part
cg_idx += 1
# Apply mapping for XYZ coordinates
cg_xyz = np.empty((t.n_frames, len(system_mapping), 3))
for cg_bead, aa_indices in system_mapping.items():
cg_xyz[:, cg_bead, :] = md.compute_center_of_mass(
t.atom_slice(aa_indices))
# Apply mapping for Topology object
cg_top = md.Topology()
for cg_bead in system_mapping.keys(): #i got the keys keys keys
cg_top.add_atom('carbon', element.virtual_site,
cg_top.add_residue('A', cg_top.add_chain()))
## Check element and name for items 'A'
## Possible interface with mbuild for better UI and aesthetics
return cg_xyz, cg_top
def get_form_factor(element_name=None, water=None):
if water:
return get_form_factor_water(element_name=element_name)
if element_name is not None:
elem = Element.getBySymbol(element_name)
warnings.warn('Estimating atomic form factor as atomic number')
form_factor = elem.atomic_number
return form_factor
def get_form_factor(element_name=None, water=None):
if water:
return get_form_factor_water(element_name=element_name)
if element_name is not None:
elem = Element.getBySymbol(element_name)
warnings.warn('Estimating atomic form factor as atomic number')
form_factor = elem.atomic_number
return form_factor if form_factor > 0 else 1
def get_form_factor_water(element_name=None):
if element_name is not None:
elem = Element.getBySymbol(element_name)
else:
raise ValueError('Need an element')
if elem.atomic_number not in [1, 8]:
raise ValueError('')
if elem.atomic_number == 1:
form_factor = float(1/3)
elif elem.atomic_number == 8:
form_factor = float(9 + 1/3)
else:
raise ValueError('Found an element not in water')
form_factor = None
return form_factor
def get_form_factor_water(element_name=None):
if element_name is not None:
elem = Element.getBySymbol(element_name)
else:
raise ValueError('Need an element')
if elem.atomic_number not in [1, 8]:
raise ValueError('')
if elem.atomic_number == 1:
form_factor = float(1 / 3)
elif elem.atomic_number == 8:
form_factor = float(9 + 1 / 3)
else:
raise ValueError('Found an element not in water')
form_factor = None
return form_factor
def get_form_factor(element_name=None, q=None, method="atomic", water=None):
"""Get form factor for elements"""
if method == "cromer-mann" and q is None:
raise ValueError(
"q must be a non-null value when method='cromer-mann'")
if water:
return get_form_factor_water(element_name=element_name)
if element_name is not None:
elem = Element.getBySymbol(element_name)
if method == "atomic":
warnings.warn('Estimating atomic form factor as atomic number')
form_factor = elem.atomic_number
elif method == "cromer-mann":
form_factor = cromermann.fxrayatq(elem.symbol, q)
else:
raise ValueError(
f"Invalid method {method}. Use `atomic` or `cromer-mann`.")
return form_factor if form_factor > 0 else 1
def _traj_from_xyza(xyz, atomic_numbers, units='nm'):
"""
Parameters
----------
xyz : np.array, float, shape( num_atom, 3)
array of x,y,z,a
atomic_numbers : np.array, int, shape( num_atom, 1 )
the atomic numbers of each of the atoms.
Optional Parameters
-------------------
units : str
if units == 'nm' then nothing happens. if units == 'ang' then
we convert them to nm.
Returns
-------
structure : mdtraj.trajectory
A meta-data minimal mdtraj instance
"""
if units == 'ang':
xyz /= 10.
top = Topology()
chain = top.add_chain()
residue = top.add_residue('XXX', chain)
for i in range(xyz.shape[0]):
element_symb = periodic_table[atomic_numbers[i]][1] # should give symbol
element = Element.getBySymbol(element_symb)
name = '%s' % element_symb
top.add_atom(name, element, residue)
structure = Trajectory(xyz=xyz, topology=top)
return structure
def _read(self):
"Read a single frame"
from mdtraj.core.topology import Topology
from mdtraj.core.element import Element, virtual
# Read in the number of atoms.
line = self._fh.readline()
if line == '':
raise _EOF()
self._n_atoms = int(line.split()[0])
self._line_counter += 1
coords = np.empty((self._n_atoms, 3), dtype=np.float32)
bond_partners = [[] for i in xrange(self._n_atoms)]
atom_names = ['' for i in xrange(self._n_atoms)]
line = self._fh.readline()
s = line.split()
self._line_counter += 1
# See if we have box info on this line or not
cell_lengths = cell_angles = None
if len(s) == 6:
try:
cell_lengths = np.asarray(
[float(s[0]), float(s[1]), float(s[2])]
)
cell_angles = np.asarray(
[float(s[3]), float(s[4]), float(s[5])]
)
line = self._fh.readline()
self._line_counter += 1
except ValueError:
pass
i = 0
while i < self._n_atoms - 1:
atom_names[i] = s[1]
bond_partners[i] = [int(x) for x in s[6:]]
coords[i,:] = [float(s[pos]) for pos in [2, 3, 4]]
i += 1
line = self._fh.readline()
s = line.split()
self._line_counter += 1
# Now do the last atom
atom_names[i] = s[1]
bond_partners[i] = [int(x) for x in s[6:]]
coords[i,:] = [float(s[pos]) for pos in [2, 3, 4]]
# Now see if we have to build a topology
if self.topology is None:
self.topology = top = Topology()
chain = top.add_chain() # only 1 chain
res = top.add_residue('RES', chain, 1) # only 1 residue
for at in atom_names:
# First get the element. Try for common 2-letter elements, then
# use the first letter only (default to None if I can't find it)
if at[:2].upper() in ('NA', 'CL', 'MG'):
elem = Element.getBySymbol(at[:2])
else:
try:
elem = Element.getBySymbol(at[0])
except KeyError:
elem = virtual
top.add_atom(at, elem, res)
# Now add the bonds
atoms = list(top.atoms)
for i, bonds in enumerate(bond_partners):
me = atoms[i]
for b in bonds:
b -= 1
if b < i: continue
it = atoms[b]
top.add_bond(me, it)
self._frame_index += 1
return coords, cell_lengths, cell_angles
def _read(self):
"Read a single frame"
from mdtraj.core.topology import Topology
from mdtraj.core.element import Element, virtual
# Read in the number of atoms.
line = self._fh.readline()
if line == '':
raise _EOF()
self._n_atoms = int(line.split()[0])
self._line_counter += 1
coords = np.empty((self._n_atoms, 3), dtype=np.float32)
bond_partners = [[] for i in xrange(self._n_atoms)]
atom_names = ['' for i in xrange(self._n_atoms)]
line = self._fh.readline()
s = line.split()
self._line_counter += 1
# See if we have box info on this line or not
cell_lengths = cell_angles = None
if len(s) == 6:
try:
cell_lengths = np.asarray(
[float(s[0]), float(s[1]),
float(s[2])])
cell_angles = np.asarray(
[float(s[3]), float(s[4]),
float(s[5])])
line = self._fh.readline()
self._line_counter += 1
except ValueError:
pass
i = 0
while i < self._n_atoms - 1:
atom_names[i] = s[1]
bond_partners[i] = [int(x) for x in s[6:]]
coords[i, :] = [float(s[pos]) for pos in [2, 3, 4]]
i += 1
line = self._fh.readline()
s = line.split()
self._line_counter += 1
# Now do the last atom
atom_names[i] = s[1]
bond_partners[i] = [int(x) for x in s[6:]]
coords[i, :] = [float(s[pos]) for pos in [2, 3, 4]]
# Now see if we have to build a topology
if self.topology is None:
self.topology = top = Topology()
chain = top.add_chain() # only 1 chain
res = top.add_residue('RES', chain, 1) # only 1 residue
for at in atom_names:
# First get the element. Try for common 2-letter elements, then
# use the first letter only (default to None if I can't find it)
if at[:2].upper() in ('NA', 'CL', 'MG'):
elem = Element.getBySymbol(at[:2])
else:
try:
elem = Element.getBySymbol(at[0])
except KeyError:
elem = virtual
top.add_atom(at, elem, res)
# Now add the bonds
atoms = list(top.atoms)
for i, bonds in enumerate(bond_partners):
me = atoms[i]
for b in bonds:
b -= 1
if b < i: continue
it = atoms[b]
top.add_bond(me, it)
self._frame_index += 1
return coords, cell_lengths, cell_angles
molecule_types = molecule_types,
mapping_function = 'center')
cg_trj.save(output_dir + output_traj_native)
cg_trj[0].save(output_dir + output_top_native)
############################### run null mass ############################
### pull in trajectories
trj = md.load(input_dir + input_traj,top=input_dir + input_top)
#the types of each molecule in the trajectory.
molecule_types = [lipid_types.index(r.name) for r in trj.top.residues]
#preprocess trajectory content by adding new parts
for a in trj.top.atoms: a.element = Element.getBySymbol('H')
#actual map command
cg_trj = cg.map_molecules( trj = trj,
selection_list = [ name_lists ],
bead_label_list = [ label_lists ],
molecule_types = molecule_types,
mapping_function = 'com')
cg_trj.save(output_dir + output_traj_null_mass)
cg_trj[0].save(output_dir + output_top_null_mass)
############################### check results ###############################
# reloading results from disk.
cg_traj_null_mass = cg_trj.load(output_dir + output_traj_null_mass,
