def setup_conformation_restraints(template,
targets,
windows,
attach_fractions,
structure,
resname,
fc=6.0):
conformational_restraints = []
host_residues = len(structure[":{}".format(resname.upper())].residues)
first_host_residue = structure[":{}".format(
resname.upper())].residues[0].number + 1
for n in range(first_host_residue, host_residues + first_host_residue):
if n + 1 < host_residues + first_host_residue:
next_residue = n + 1
else:
next_residue = first_host_residue
for (index, atoms), target in zip(enumerate(template), targets):
conformational_restraint_atoms = []
if index == 0:
conformational_restraint_atoms.append(f":{n}@{atoms[0]}")
conformational_restraint_atoms.append(f":{n}@{atoms[1]}")
conformational_restraint_atoms.append(f":{n}@{atoms[2]}")
conformational_restraint_atoms.append(
f":{next_residue}@{atoms[3]}")
else:
conformational_restraint_atoms.append(f":{n}@{atoms[0]}")
conformational_restraint_atoms.append(f":{n}@{atoms[1]}")
conformational_restraint_atoms.append(
f":{next_residue}@{atoms[2]}")
conformational_restraint_atoms.append(
f":{next_residue}@{atoms[3]}")
this = DAT_restraint()
this.auto_apr = True
this.amber_index = True
this.topology = structure
this.mask1 = conformational_restraint_atoms[0]
this.mask2 = conformational_restraint_atoms[1]
this.mask3 = conformational_restraint_atoms[2]
this.mask4 = conformational_restraint_atoms[3]
this.attach["fraction_list"] = attach_fractions
this.attach["target"] = target
this.attach["fc_final"] = fc
this.pull["target_final"] = target
this.pull["num_windows"] = windows[1]
this.release["fraction_list"] = attach_fractions[::-1]
this.release["target"] = target
this.release["fc_final"] = fc
this.initialize()
conformational_restraints.append(this)
return conformational_restraints
def build_guest_restraints(
cls,
coordinate_path: str,
attach_lambdas: List[float],
n_pull_windows: Optional[int],
restraint_schemas: List[Dict[str, Any]],
use_amber_indices: bool = False,
) -> List[DAT_restraint]:
"""A method to convert a set of guest restraints defined by their 'schemas'
into corresponding ``DAT_restraint``objects.
Each 'schema' should be a dictionary with:
* an ``atoms`` entry with a value of the atom selection make which specifies
which atoms the restraint will apply to
and additionally a nested ``attach`` and ``pull`` dictionary with
* a ``force_constant`` entry which specifies the force constant of the
restraint.
* a ``target`` entry which specifies the target value of the restraint.
These 'schemas` map directly to the 'restraints -> guest -> restraint'
dictionaries specified in the `taproom` guest YAML files.
Parameters
----------
coordinate_path
The path to the coordinate file which the restraints will be applied to.
This should contain either the host or the complex, the dummy atoms and
and solvent.
attach_lambdas
The values 'lambda' being used during the attach phase of the APR
calculation.
n_pull_windows
The total number of pull windows being used in the APR calculation.
restraint_schemas
The list of dictionaries which provide the settings to use for each
wall restraint to add.
use_amber_indices
Whether to use amber based (i.e. starting from 1) restraint indices or
OpenMM based (i.e. starting from 0) indices.
Returns
-------
The constructed wall restraint objects.
"""
restraints = []
for restraint_schema in restraint_schemas:
mask = restraint_schema["atoms"].split()
guest_restraint = DAT_restraint()
guest_restraint.auto_apr = True
guest_restraint.continuous_apr = False
guest_restraint.amber_index = use_amber_indices
guest_restraint.topology = coordinate_path
guest_restraint.mask1 = mask[0]
guest_restraint.mask2 = mask[1]
guest_restraint.mask3 = mask[2] if len(mask) > 2 else None
guest_restraint.mask4 = mask[3] if len(mask) > 3 else None
guest_restraint.attach["target"] = restraint_schema["attach"]["target"]
guest_restraint.attach["fc_final"] = restraint_schema["attach"][
"force_constant"
]
guest_restraint.attach["fraction_list"] = attach_lambdas
if n_pull_windows:
guest_restraint.pull["target_final"] = restraint_schema["pull"][
"target"
]
guest_restraint.pull["num_windows"] = n_pull_windows
guest_restraint.initialize()
restraints.append(guest_restraint)
return restraints
def initialize_restraints(self, structure="output.pdb"):
if self.guest != "release":
windows = [
self.host_yaml["calculation"]["windows"]["attach"],
self.host_yaml["calculation"]["windows"]["pull"],
None,
]
else:
windows = [
None, None, self.host_yaml["calculation"]["windows"]["release"]
]
static_restraints = []
for restraint in self.host_yaml["restraints"]["static"]:
static = static_DAT_restraint(
restraint_mask_list=restraint["restraint"]["atoms"].split(),
num_window_list=windows,
ref_structure=str(structure),
force_constant=restraint["restraint"]["force_constant"],
amber_index=False if self.backend == "openmm" else True,
)
static_restraints.append(static)
conformational_restraints = []
if self.host_yaml["restraints"]["conformational"]:
for conformational in self.host_yaml["restraints"][
"conformational"]:
mask = conformational["restraint"]["atoms"].split()
conformational_restraint = DAT_restraint()
conformational_restraint.auto_apr = True
conformational_restraint.continuous_apr = True
conformational_restraint.amber_index = False if self.backend == "openmm" else True
conformational_restraint.topology = str(structure)
conformational_restraint.mask1 = mask[0]
conformational_restraint.mask2 = mask[1]
conformational_restraint.mask3 = mask[2] if len(
mask) > 2 else None
conformational_restraint.mask4 = mask[3] if len(
mask) > 3 else None
if self.guest != "release":
conformational_restraint.attach["target"] = conformational[
"restraint"]["target"]
conformational_restraint.attach[
"fc_final"] = conformational["restraint"][
"force_constant"]
conformational_restraint.attach[
"fraction_list"] = self.host_yaml["calculation"][
"lambda"]["attach"]
conformational_restraint.pull[
"target_final"] = conformational["restraint"]["target"]
conformational_restraint.pull["num_windows"] = windows[1]
else:
conformational_restraint.auto_apr = False
conformational_restraint.continuous_apr = False
conformational_restraint.release[
"target"] = conformational["restraint"]["target"]
conformational_restraint.release[
"fc_final"] = conformational["restraint"][
"force_constant"]
conformational_restraint.release[
"fraction_list"] = self.host_yaml["calculation"][
"lambda"]["release"]
conformational_restraint.initialize()
conformational_restraints.append(conformational_restraint)
else:
logger.debug("Skipping conformational restraints...")
symmetry_restraints = []
if self.guest != "release" and "symmetry_correction" in self.guest_yaml:
for symmetry in self.guest_yaml["symmetry_correction"][
"restraints"]:
symmetry_restraint = DAT_restraint()
symmetry_restraint.auto_apr = True
symmetry_restraint.continuous_apr = True
symmetry_restraint.amber_index = False if self.backend == "openmm" else True
symmetry_restraint.topology = str(structure)
symmetry_restraint.mask1 = symmetry["atoms"].split()[0]
symmetry_restraint.mask2 = symmetry["atoms"].split()[1]
symmetry_restraint.mask3 = symmetry["atoms"].split()[2]
symmetry_restraint.attach["fc_final"] = symmetry[
"force_constant"]
symmetry_restraint.attach["fraction_list"] = [1.0] * len(
self.host_yaml["calculation"]["lambda"]["attach"])
# This target should be overridden by the custom values.
symmetry_restraint.attach["target"] = 999.99
symmetry_restraint.custom_restraint_values["r2"] = 91
symmetry_restraint.custom_restraint_values["r3"] = 91
# 0 force constant between 91 degrees and 180 degrees.
symmetry_restraint.custom_restraint_values["rk3"] = 0.0
symmetry_restraint.initialize()
symmetry_restraints.append(symmetry_restraint)
else:
logger.debug("Skipping symmetry restraints...")
wall_restraints = []
if self.guest != "release" and "wall_restraints" in self.guest_yaml[
'restraints']:
for wall in self.guest_yaml["restraints"]["wall_restraints"]:
wall_restraint = DAT_restraint()
wall_restraint.auto_apr = True
wall_restraint.continuous_apr = True
wall_restraint.amber_index = False if self.backend == "openmm" else True
wall_restraint.topology = str(structure)
wall_restraint.mask1 = wall["restraint"]["atoms"].split()[0]
wall_restraint.mask2 = wall["restraint"]["atoms"].split()[1]
wall_restraint.attach["fc_final"] = wall["restraint"][
"force_constant"]
wall_restraint.attach["fraction_list"] = [1.0] * len(
self.host_yaml["calculation"]["lambda"]["attach"])
wall_restraint.attach["target"] = wall["restraint"]["target"]
# Minimum distance is 0 Angstrom
wall_restraint.custom_restraint_values["r1"] = 0
wall_restraint.custom_restraint_values["r2"] = 0
# Harmonic force constant beyond target distance.
wall_restraint.custom_restraint_values["rk2"] = wall[
"restraint"]["force_constant"]
wall_restraint.custom_restraint_values["rk3"] = wall[
"restraint"]["force_constant"]
wall_restraint.initialize()
wall_restraints.append(wall_restraint)
else:
logger.debug("Skipping wall restraints...")
guest_restraints = []
for restraint in [] if not hasattr(
self,
'guest_yaml') else self.guest_yaml["restraints"]["guest"]:
mask = restraint["restraint"]["atoms"].split()
guest_restraint = DAT_restraint()
guest_restraint.auto_apr = True
guest_restraint.continuous_apr = True
guest_restraint.amber_index = False if self.backend == "openmm" else True
guest_restraint.topology = str(structure)
guest_restraint.mask1 = mask[0]
guest_restraint.mask2 = mask[1]
guest_restraint.mask3 = mask[2] if len(mask) > 2 else None
guest_restraint.mask4 = mask[3] if len(mask) > 3 else None
guest_restraint.attach["target"] = restraint["restraint"][
"attach"]["target"]
guest_restraint.attach["fc_final"] = restraint["restraint"][
"attach"]["force_constant"]
guest_restraint.attach["fraction_list"] = self.host_yaml[
"calculation"]["lambda"]["attach"]
guest_restraint.pull["target_final"] = restraint["restraint"][
"pull"]["target"]
guest_restraint.pull["num_windows"] = windows[1]
guest_restraint.initialize()
guest_restraints.append(guest_restraint)
return (
static_restraints,
conformational_restraints,
symmetry_restraints,
wall_restraints,
guest_restraints,
)