def test_box_vectors():
box_vector_q = unit.Quantity(
[[64.0, 0.0, 0.0], [-21.0, 61.0, 0.0], [-21.0, -30.0, 53.0]],
unit=unit.angstrom)
box_vector = base.Box_vectors()
box_vector.from_quantity(box_vector_q)
assert np.isclose(box_vector.ax, 6.4)
assert np.isclose(box_vector.ay, 0.0)
assert np.isclose(box_vector.az, 0.0)
assert np.isclose(box_vector.bx, -2.1)
assert np.isclose(box_vector.by, 6.1)
assert np.isclose(box_vector.bz, 0.0)
assert np.isclose(box_vector.cx, -2.1)
assert np.isclose(box_vector.cy, -3.0)
assert np.isclose(box_vector.cz, 5.3)
box_vector_q2 = box_vector.to_quantity()
assert np.isclose(box_vector_q2.value_in_unit(unit.nanometers)[0][0], 6.4)
assert np.isclose(box_vector_q2.value_in_unit(unit.nanometers)[0][1], 0.0)
assert np.isclose(box_vector_q2.value_in_unit(unit.nanometers)[0][2], 0.0)
assert np.isclose(box_vector_q2.value_in_unit(unit.nanometers)[1][0], -2.1)
assert np.isclose(box_vector_q2.value_in_unit(unit.nanometers)[1][1], 6.1)
assert np.isclose(box_vector_q2.value_in_unit(unit.nanometers)[1][2], 0.0)
assert np.isclose(box_vector_q2.value_in_unit(unit.nanometers)[2][0], -2.1)
assert np.isclose(box_vector_q2.value_in_unit(unit.nanometers)[2][1], -3.0)
assert np.isclose(box_vector_q2.value_in_unit(unit.nanometers)[2][2], 5.3)
def make_amber_params(anchor, building_dir, engine="openmm"):
anchor.amber_params = base.Amber_params()
this_dir = os.path.dirname(os.path.realpath(__file__))
if engine == "openmm":
prmtop_src = os.path.join(this_dir,
"../data/hostguest_files/hostguest.parm7")
elif engine == "namd":
prmtop_src = os.path.join(
this_dir, "../data/hostguest_files/hostguest_for_NAMD.parm7")
else:
raise Exception("Engine not implemented: %s" % engine)
inpcrd_src = os.path.join(this_dir,
"../data/hostguest_files/hostguest.rst7")
pdb_coord_src = os.path.join(
this_dir, "../data/hostguest_files/hostguest_at1.5.pdb")
prmtop_dest = os.path.join(building_dir, "hostguest.parm7")
#inpcrd_dest = os.path.join(building_dir, "hostguest.rst7")
pdb_coord_dest = os.path.join(building_dir, "hostguest_at1.5.pdb")
copyfile(prmtop_src, prmtop_dest)
#copyfile(inpcrd_src, inpcrd_dest)
copyfile(pdb_coord_src, pdb_coord_dest)
anchor.amber_params.prmtop_filename = "hostguest.parm7"
#anchor.amber_params.inpcrd_filename = "hostguest.rst7"
anchor.amber_params.pdb_coordinates_filename = "hostguest_at1.5.pdb"
anchor.amber_params.box_vectors = base.Box_vectors()
anchor.amber_params.box_vectors.from_quantity(
parmed.load_file(pdb_coord_src).box_vectors)
return
def check_pre_sim_MD_and_BD_salt_concentration(model):
"""
Users might inadvertently define different salt concentrations
between the MD and BD stages.
Examine BD settings and count the numbers of ions in MD starting
structures to ensure that ion concentrations are relatively
consistent to avoid situations where different salt concentrations
exist between the various anchors and scales.
"""
RELATIVE_TOLERANCE = 0.25
ABSOLUTE_TOLERANCE = 0.1
if model.k_on_info:
bd_ionic_strength = 0.0
for ion in model.k_on_info.ions:
bd_ionic_strength += 0.5 * ion.conc * ion.charge**2
else:
# No BD to check
return True
for anchor in model.anchors:
md_ionic_strength = 0.0
structure = load_structure_with_parmed(model, anchor)
if structure is None:
continue
box_6_vector = structure.get_box()
assert box_6_vector is not None, "Unable to compute box volume for "\
"structures in anchor {}".format(anchor.index)
box_vectors = base.Box_vectors()
box_vectors.from_6_vector(box_6_vector[0])
box_volume = box_vectors.get_volume()
particle_concentration = 1.0e24 / (AVOGADROS_NUMBER * box_volume)
for index, atom in enumerate(structure.atoms):
if is_ion(atom):
found_ion = False
for key in ION_CHARGE_DICT:
if atom.name.lower().startswith(key):
charge = ION_CHARGE_DICT[key]
md_ionic_strength += particle_concentration * charge**2
found_ion = True
if not found_ion:
print("Found unbonded atom with index: "\
"{} and name: {}.".format(index, atom.name)\
+"Charge is uncertain, assuming zero.")
if not np.isclose(md_ionic_strength,
bd_ionic_strength,
rtol=RELATIVE_TOLERANCE,
atol=ABSOLUTE_TOLERANCE):
print("""CHECK FAILURE: BD simulation has significantly different
ionic strength of {} M*e^2 than MD simulation ionic strength of
{} M*e^2 for anchor {}. Please check the ion concentrations in the
BD simulation settings, and also count the number of ions
in the MD simulations.""".format(bd_ionic_strength, md_ionic_strength,
anchor.index))
return False
return True
def make_forcefield_params(anchor, building_dir):
anchor.forcefield_params = base.Forcefield_params()
this_dir = os.path.dirname(os.path.realpath(__file__))
xml_src = os.path.join(this_dir, "../data/hostguest_files/hostguest.xml")
pdb_coord_src = os.path.join(
this_dir, "../data/hostguest_files/hostguest_for_xml.pdb")
xml_dest = os.path.join(building_dir, "hostguest.xml")
pdb_coord_dest = os.path.join(building_dir, "hostguest_for_xml.pdb")
copyfile(xml_src, xml_dest)
copyfile(pdb_coord_src, pdb_coord_dest)
anchor.forcefield_params.built_in_forcefield_filenames = \
["amber14/tip3pfb.xml"]
anchor.forcefield_params.custom_forcefield_filenames = ["hostguest.xml"]
anchor.forcefield_params.pdb_filename = "hostguest_for_xml.pdb"
anchor.forcefield_params.box_vectors = base.Box_vectors()
anchor.forcefield_params.box_vectors.from_quantity(
parmed.load_file(pdb_coord_src).box_vectors)
return
def copy_building_files_by_anchor(anchor, input_anchor, rootdir):
"""
For each of the anchors and other directories, copy the necessary
initial simulation (building) files for the simulations into those
directories.
Parameters:
-----------
anchor : Anchor
the Anchor to copy the building files into.
input_anchor : Input_anchor
Input_model's Input_anchor() objects which contain the input
files to copy.
rootdir : str
A path to the model's root directory.
"""
if not anchor.md:
return
if anchor.__class__.__name__ in ["MMVT_toy_anchor", "Elber_toy_anchor"]:
anchor.starting_positions = input_anchor.starting_positions
return
anchor_building_dir = os.path.join(rootdir, anchor.directory,
anchor.building_directory)
assert os.path.exists(anchor_building_dir)
amber = input_anchor.starting_amber_params
new_prmtop_filename = None
if amber is not None:
anchor.amber_params = base.Amber_params()
if amber.prmtop_filename is not None and \
amber.prmtop_filename != "":
amber.prmtop_filename = os.path.expanduser(
amber.prmtop_filename)
assert os.path.exists(amber.prmtop_filename), \
"Provided file does not exist: {}".format(
amber.prmtop_filename)
prmtop_filename = os.path.basename(amber.prmtop_filename)
new_prmtop_filename = os.path.join(anchor_building_dir,
prmtop_filename)
copyfile(amber.prmtop_filename, new_prmtop_filename)
anchor.amber_params.prmtop_filename = prmtop_filename
if amber.pdb_coordinates_filename is not None and \
amber.pdb_coordinates_filename != "":
pdb_filename = os.path.basename(amber.pdb_coordinates_filename)
new_pdb_filename = os.path.join(anchor_building_dir,
pdb_filename)
copyfile(os.path.expanduser(amber.pdb_coordinates_filename),
new_pdb_filename)
anchor.amber_params.pdb_coordinates_filename = pdb_filename
anchor.amber_params.box_vectors = amber.box_vectors
if anchor.amber_params.box_vectors is None:
anchor.amber_params.box_vectors = base.Box_vectors()
box_vectors = base.get_box_vectors_from_pdb(new_pdb_filename)
anchor.amber_params.box_vectors.from_quantity(
box_vectors)
forcefield = input_anchor.starting_forcefield_params
if forcefield is not None:
assert amber is None, "Parameters may not be included for both "\
"Amber and Forcefield inputs."
anchor.forcefield_params = base.Forcefield_params()
if forcefield.built_in_forcefield_filenames is not None and \
len(forcefield.built_in_forcefield_filenames) > 0:
for filename in forcefield.built_in_forcefield_filenames:
anchor.forcefield_params.built_in_forcefield_filenames.\
append(os.path.expanduser(filename))
if forcefield.custom_forcefield_filenames is not None and \
len(forcefield.custom_forcefield_filenames) > 0:
for filename in forcefield.custom_forcefield_filenames:
ff_filename = os.path.basename(filename)
new_ff_filename = os.path.join(anchor_building_dir,
ff_filename)
copyfile(filename, new_ff_filename)
anchor.forcefield_params.custom_forcefield_filenames.\
append(os.path.expanduser(ff_filename))
if forcefield.pdb_coordinates_filename is not None and \
forcefield.pdb_coordinates_filename != "":
forcefield.pdb_coordinates_filename = os.path.expanduser(
forcefield.pdb_coordinates_filename)
assert os.path.exists(forcefield.pdb_coordinates_filename), \
"Provided file does not exist: {}".format(
forcefield.pdb_coordinates_filename)
pdb_filename = os.path.basename(forcefield.pdb_coordinates_filename)
new_pdb_filename = os.path.join(anchor_building_dir,
pdb_filename)
copyfile(forcefield.pdb_coordinates_filename, new_pdb_filename)
anchor.forcefield_params.pdb_coordinates_filename = pdb_filename
anchor.forcefield_params.box_vectors = forcefield.box_vectors
if anchor.forcefield_params.box_vectors is None:
anchor.forcefield_params.box_vectors = base.Box_vectors()
box_vectors = base.get_box_vectors_from_pdb(new_pdb_filename)
anchor.forcefield_params.box_vectors.from_quantity(
box_vectors)
return
def copy_building_files(model, input_model, rootdir):
"""
For each of the anchors and other directories, copy the necessary
files for the simulations into those directories.
Parameters:
-----------
model : list
the Model to prepare files for
input_anchors : list
An equivalent list of the Input_model's Input_anchor() objects.
Which contain the input files to copy.
rootdir : str
A path to the model's root directory.
"""
input_anchors = input_model.cv_inputs[0].input_anchors
for anchor, input_anchor in zip(model.anchors, input_anchors):
if not anchor.md:
continue
anchor_building_dir = os.path.join(rootdir, anchor.directory,
anchor.building_directory)
print(anchor_building_dir)
assert os.path.exists(anchor_building_dir)
try: # TODO: fix simple XML parser so this isn't necessary
amber = input_anchor.starting_amber_params
except AttributeError:
amber = None
if amber is not None:
anchor.amber_params = base.Amber_params()
#assert amber.prmtop_filename is not None, \
# "Amber PRMTOP file must be provided for anchor {}".format(
# anchor.index)
#assert amber.prmtop_filename != "", \
# "Amber PRMTOP file must be provided for anchor {}".format(
# anchor.index)
if amber.prmtop_filename is not None and \
amber.prmtop_filename != "":
assert os.path.exists(amber.prmtop_filename)
prmtop_filename = os.path.basename(amber.prmtop_filename)
new_prmtop_filename = os.path.join(anchor_building_dir,
prmtop_filename)
copyfile(amber.prmtop_filename, new_prmtop_filename)
anchor.amber_params.prmtop_filename = prmtop_filename
"""# TODO: remove
if amber.inpcrd_filename is not None and \
amber.inpcrd_filename != "":
assert os.path.exists(amber.inpcrd_filename)
inpcrd_filename = os.path.basename(amber.inpcrd_filename)
new_inpcrd_filename = os.path.join(anchor_building_dir,
inpcrd_filename)
copyfile(amber.inpcrd_filename, new_inpcrd_filename)
anchor.amber_params.inpcrd_filename = inpcrd_filename
if anchor.amber_params.box_vectors is None:
assert new_prmtop_filename is not None
anchor.amber_params.box_vectors = base.Box_vectors()
inpcrd_structure = parmed.load_file(new_prmtop_filename,
xyz=new_inpcrd_filename)
anchor.amber_params.box_vectors.from_quantity(
inpcrd_structure.box_vectors)
"""
#assert amber.pdb_coordinates_filename is not None and \
# amber.pdb_coordinates_filename != "", \
# "PDB file must be provided for anchor {}".format(
# anchor.index)
#amber.pdb_coordinates_filename = os.path.expanduser(
# amber.pdb_coordinates_filename)
#assert os.path.exists(amber.pdb_coordinates_filename), \
# "Provided file does not exist: {}".format(
# amber.pdb_coordinates_filename)
if amber.pdb_coordinates_filename is not None and \
amber.pdb_coordinates_filename != "":
pdb_filename = os.path.basename(amber.pdb_coordinates_filename)
new_pdb_filename = os.path.join(anchor_building_dir,
pdb_filename)
copyfile(amber.pdb_coordinates_filename, new_pdb_filename)
anchor.amber_params.pdb_coordinates_filename = pdb_filename
if amber.box_vectors is not None:
if not isinstance(amber.box_vectors, base.Box_vectors):
flattened_box_vectors = np.array(
[val for row in amber.box_vectors for val in row])
box_vectors = base.Box_vectors()
box_vectors.ax, box_vectors.ay, box_vectors.az, \
box_vectors.bx, box_vectors.by, box_vectors.bz, \
box_vectors.cx, box_vectors.cy, box_vectors.cz = \
flattened_box_vectors
amber.box_vectors = box_vectors
anchor.amber_params.box_vectors = amber.box_vectors
elif anchor.amber_params.box_vectors is None:
anchor.amber_params.box_vectors = base.Box_vectors()
pdb_structure = parmed.load_file(new_pdb_filename)
anchor.amber_params.box_vectors.from_quantity(
pdb_structure.box_vectors)
try: # TODO: fix simple XML parser so this isn't necessary
forcefield = input_anchor.starting_forcefield_params
except AttributeError:
forcefield = None
if forcefield is not None:
assert amber is None, "Parameters may not be included for both "\
"Amber and Forcefield inputs."
anchor.forcefield_params = base.Forcefield_params()
if forcefield.built_in_forcefield_filenames is not None and \
len(forcefield.built_in_forcefield_filenames) > 0:
for filename in forcefield.built_in_forcefield_filenames:
anchor.forcefield_params.built_in_forcefield_filenames.\
append(filename)
if forcefield.custom_forcefield_filenames is not None and \
len(forcefield.custom_forcefield_filenames) > 0:
for filename in forcefield.custom_forcefield_filenames:
ff_filename = os.path.basename(filename)
new_ff_filename = os.path.join(anchor_building_dir,
ff_filename)
copyfile(filename, new_ff_filename)
anchor.forcefield_params.custom_forcefield_filenames.\
append(ff_filename)
if forcefield.pdb_filename is not None and \
forcefield.pdb_filename != "":
assert os.path.exists(forcefield.pdb_filename)
pdb_filename = os.path.basename(forcefield.pdb_filename)
new_pdb_filename = os.path.join(anchor_building_dir,
pdb_filename)
copyfile(forcefield.pdb_filename, new_pdb_filename)
anchor.forcefield_params.pdb_filename = pdb_filename
anchor.forcefield_params.box_vectors = forcefield.box_vectors
if anchor.forcefield_params.box_vectors is None:
pdb_structure = parmed.load_file(new_pdb_filename)
anchor.forcefield_params.box_vectors.from_quantity(
pdb_structure.box_vectors)
if model.k_on_info is not None:
bd_settings = model.browndye_settings
bd_input_settings = input_model.browndye_settings_input
k_on_info = model.k_on_info
b_surface_dir = os.path.join(rootdir, k_on_info.b_surface_directory)
ligand_pqr_filename = os.path.basename(bd_settings.ligand_pqr_filename)
ligand_pqr_dest_filename = os.path.join(b_surface_dir,
ligand_pqr_filename)
copyfile(bd_input_settings.ligand_pqr_filename,
ligand_pqr_dest_filename)
receptor_pqr_filename = os.path.basename(
bd_settings.receptor_pqr_filename)
receptor_pqr_dest_filename = os.path.join(b_surface_dir,
receptor_pqr_filename)
copyfile(bd_input_settings.receptor_pqr_filename,
receptor_pqr_dest_filename)
return