def create_directory():
work_dir = 'amber_test'
if os.path.exists(work_dir):
shutil.rmtree(work_dir)
os.makedirs(work_dir)
path = './'+work_dir+'/'
guest_restraints = setup_restraints()
window_list = restraints.create_window_list(guest_restraints)
for window in window_list:
os.makedirs(path+window)
struct_dir = "cb6-but"
topology_file = "cb6-but-dum.prmtop"
coordinate_file = "cb6-but-dum.rst7"
pull_distances = [0.0,5.0,18.0]
for index, window in enumerate(window_list):
open(path+window+'/no_restraints.in', 'a').close()
shutil.copyfile(struct_dir+'/'+topology_file,
path+window+'/'+topology_file)
if window[0] == 'a':
shutil.copyfile(struct_dir+'/'+coordinate_file,
path+window+'/'+coordinate_file)
elif window[0] == 'p':
structure = pmd.load_file(struct_dir+'/'+topology_file,
struct_dir+'/'+coordinate_file)
target_difference = pull_distances[index]
for atom in structure.atoms:
if atom.residue.name == 'BUT':
atom.xz += target_difference
structure.save(path+window+'/'+coordinate_file)
with open(path+window+'/restraints.in', 'w') as f:
#problem using amber_restraint_line
for rest in guest_restraints:
string = restraints.amber_restraint_line(rest,window)
if string is not None:
f.write(string)
guest_rests[-1].amber_index = True
guest_rests[-1].topology = pmd_parm
guest_rests[-1].mask1 = dummy_anch[0]
guest_rests[-1].mask2 = guest_anch[0]
guest_rests[-1].mask3 = guest_anch[1]
guest_rests[-1].attach['target'] = attach_ang_target
guest_rests[-1].attach['fraction_list'] = attach_fractions
guest_rests[-1].attach['fc_final'] = attach_ang_fc
guest_rests[-1].pull['fc'] = attach_ang_fc
guest_rests[-1].pull['target_initial'] = pull_ang_target
guest_rests[-1].pull['target_final'] = pull_ang_target
guest_rests[-1].pull['num_windows'] = num_pull_windows
guest_rests[-1].initialize()
# Make window list
window_list = restraints.create_window_list(guest_rests)
# Collect Data
data = np.zeros((2, len(fractions), 10))
for fraction_index, fraction in enumerate(fractions):
fecalc = analysis.fe_calc()
fecalc.prmtop = 'vac.prmtop'
# fecalc.trajectory = [
# 'prod.001.nc', 'prod.002.nc', 'prod.003.nc', 'prod.004.nc',
# 'prod.005.nc', 'prod.006.nc', 'prod.007.nc', 'prod.008.nc',
# 'prod.009.nc', 'prod.010.nc',
# ]
fecalc.trajectory = 'prod.*.nc'
fecalc.path = os.path.join(conf_name, 'windows')
fecalc.restraint_list = guest_rests
rest3.topology = inputpdb
rest3.mask1 = ":CB6@O11"
rest3.mask2 = ":CB6@O1"
rest3.mask3 = ":CB6@O"
rest3.mask4 = ":BUT@C1"
rest3.attach["target"] = -60.0
rest3.attach["fraction_list"] = [0.00, 0.04, 0.181, 0.496, 1.000]
rest3.attach["fc_final"] = 50.0
rest3.pull["fc"] = rest3.attach["fc_final"]
rest3.pull["target_initial"] = rest3.attach["target"]
rest3.pull["target_final"] = rest3.attach["target"]
rest3.pull["num_windows"] = 19
rest3.initialize()
# Create window directories
window_list = restraints.create_window_list([rest1, rest2, rest3])
# Phase abbreviations
phase_dict = {"a": "attach", "p": "pull", "r": "release"}
np.random.seed(12345)
# fecalc = analysis.fe_calc()
# fecalc.prmtop = 'cb6_but_gb_apr_ref_data/vac.prmtop'
# fecalc.trajectory = '*.nc'
# fecalc.path = 'cb6_but_gb_apr_ref_data/'
# fecalc.restraint_list = [rest1, rest2, rest3]
# fecalc.methods = ['mbar-block']
# fecalc.bootcycles = 100
# fecalc.quick_ti_matrix = True
# fecalc.collect_data(single_prmtop=True)
guest_wall_targets = [11.3, 13.3, 80.0]
guest_wall_restraints = setup_guest_wall_restraints(
guest_wall_template,
guest_wall_targets,
structure,
windows,
resname="MGO",
angle_fc=500.0,
distance_fc=50.0,
)
restraints = (static_restraints + conformational_restraints +
guest_restraints + guest_wall_restraints)
window_list = create_window_list(restraints)
for window in window_list:
if not os.path.isdir(
os.path.join("systems", f"{cyclodextrin}-release", "smirnoff",
window)):
print(
f"""Creating {os.path.join("systems", f'{cyclodextrin}-release', "smirnoff", window)}"""
)
os.makedirs(
os.path.join("systems", f"{cyclodextrin}-release", "smirnoff",
window))
for window in window_list:
with open(
os.path.join("systems", f"{cyclodextrin}-release", "smirnoff",
def test_fe_calc():
inputpdb = pmd.load_file('cb6_but_gb_apr_ref_data/vac.pdb')
# Distance restraint
rest1 = restraints.DAT_restraint()
rest1.continuous_apr = True
rest1.amber_index = True
rest1.topology = inputpdb
rest1.mask1 = ':CB6@O'
rest1.mask2 = ':BUT@C1'
rest1.attach['target'] = 4.5
rest1.attach['fraction_list'] = [0.00, 0.04, 0.181, 0.496, 1.000]
rest1.attach['fc_final'] = 5.0
rest1.pull['fc'] = rest1.attach['fc_final']
rest1.pull['target_initial'] = rest1.attach['target']
rest1.pull['target_final'] = 18.5
rest1.pull['num_windows'] = 19
rest1.initialize()
# Angle restraint
rest2 = restraints.DAT_restraint()
rest2.continuous_apr = True
rest2.amber_index = True
rest2.topology = inputpdb
rest2.mask1 = ':CB6@O1'
rest2.mask2 = ':CB6@O'
rest2.mask3 = ':BUT@C1'
rest2.attach['target'] = 8.0
rest2.attach['fraction_list'] = [0.00, 0.04, 0.181, 0.496, 1.000]
rest2.attach['fc_final'] = 50.0
rest2.pull['fc'] = rest2.attach['fc_final']
rest2.pull['target_initial'] = rest2.attach['target']
rest2.pull['target_final'] = rest2.attach['target']
rest2.pull['num_windows'] = 19
rest2.initialize()
# Dihedral restraint
rest3 = restraints.DAT_restraint()
rest3.continuous_apr = True
rest3.amber_index = True
rest3.topology = inputpdb
rest3.mask1 = ':CB6@O11'
rest3.mask2 = ':CB6@O1'
rest3.mask3 = ':CB6@O'
rest3.mask4 = ':BUT@C1'
rest3.attach['target'] = -60.0
rest3.attach['fraction_list'] = [0.00, 0.04, 0.181, 0.496, 1.000]
rest3.attach['fc_final'] = 50.0
rest3.pull['fc'] = rest3.attach['fc_final']
rest3.pull['target_initial'] = rest3.attach['target']
rest3.pull['target_final'] = rest3.attach['target']
rest3.pull['num_windows'] = 19
rest3.initialize()
# Create window directories
restraints.create_window_list([rest1, rest2, rest3])
# Phase abbreviations
phase_dict = {'a': 'attach', 'p': 'pull', 'r': 'release'}
np.random.seed(12345)
fecalc = analysis.fe_calc()
fecalc.prmtop = 'cb6_but_gb_apr_ref_data/vac.prmtop'
fecalc.trajectory = '*.nc'
fecalc.path = 'cb6_but_gb_apr_ref_data/'
fecalc.restraint_list = [rest1, rest2, rest3]
fecalc.methods = ['mbar-block', 'ti-block']
fecalc.bootcycles = 100
fecalc.ti_matrix = 'diagonal'
fecalc.compute_largest_neighbor = True
fecalc.compute_roi = True
#fecalc.fractions = [0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0]
fecalc.collect_data(single_prmtop=True)
fecalc.compute_free_energy()
##################
# Test mbar-block
##################
method = 'mbar-block'
# Test mbar-block free energies and uncertainties
test_vals = [
fecalc.results['attach'][method]['fe'],
fecalc.results['attach'][method]['sem'],
fecalc.results['pull'][method]['fe'],
fecalc.results['pull'][method]['sem']
]
ref_vals = [13.267731176, 0.16892084090, -2.1791430735, 0.93638948302]
for i in range(len(test_vals)):
assert np.isclose(ref_vals[i], test_vals[i], rtol=0.0, atol=0.00001)
# Test attach mbar-block largest_neighbor values
test_vals = fecalc.results['attach'][method]['largest_neighbor']
ref_vals = np.array(
[0.0198918, 0.0451676, 0.0564517, 0.1079282, 0.1079282])
for i in range(len(test_vals)):
assert np.isclose(ref_vals[i], test_vals[i], rtol=0.0, atol=0.00001)
# Test pull mbar-block largest_neighbor values
test_vals = fecalc.results['pull'][method]['largest_neighbor']
ref_vals = np.array([
0.2053769, 0.2053769, 0.1617423, 0.1747668, 0.5255023, 0.5255023,
0.1149945, 0.1707901, 0.2129136, 0.2129136, 0.1942189, 0.1768906,
0.1997338, 0.1997338, 0.2014766, 0.2014766, 0.1470727, 0.1442517,
0.1434395
])
for i in range(len(test_vals)):
assert np.isclose(ref_vals[i], test_vals[i], rtol=0.0, atol=0.00001)
##################
# Test ti-block
##################
method = 'ti-block'
# Test ti-block free energies and uncertainties
test_vals = [
fecalc.results['attach'][method]['fe'],
fecalc.results['attach'][method]['sem'],
fecalc.results['pull'][method]['fe'],
fecalc.results['pull'][method]['sem']
]
ref_vals = np.array([13.35823327, 0.25563407, -1.77873259, 0.95162741])
for i in range(len(test_vals)):
assert np.isclose(ref_vals[i], test_vals[i])
# Test attach roi values
test_vals = fecalc.results['attach'][method]['roi']
ref_vals = np.array(
[-0.00027503, -0.00020536, 0.00000691, -0.00062548, -0.00029785])
for i in range(len(test_vals)):
assert np.isclose(ref_vals[i], test_vals[i])
# Test pull roi values
test_vals = fecalc.results['pull'][method]['roi']
ref_vals = np.array([
-0.00191275, -0.00047460, -0.00284036, -0.00144093, -0.00199245,
-0.00160141, -0.00071836, -0.00188979, -0.00162371, -0.00108091,
-0.00197727, -0.00223339, -0.00144556, -0.00272537, -0.00098154,
-0.00071218, -0.00073691, -0.00195884, -0.00155617
])
for i in range(len(test_vals)):
assert np.isclose(ref_vals[i], test_vals[i])
# Test attach ti-block largest_neighbor values
test_vals = fecalc.results['attach'][method]['largest_neighbor']
ref_vals = np.array(
[0.02809982, 0.07439878, 0.09719278, 0.16782417, 0.16782417])
for i in range(len(test_vals)):
assert np.isclose(ref_vals[i], test_vals[i])
# Test pull ti-block largest_neighbor values
test_vals = fecalc.results['pull'][method]['largest_neighbor']
ref_vals = np.array([
0.31296449, 0.31296449, 0.23297017, 0.24211187, 0.24211187, 0.13217678,
0.11879266, 0.15423428, 0.15423428, 0.12861334, 0.11276903, 0.11276903,
0.11150722, 0.13483801, 0.17510575, 0.17510575, 0.14725404, 0.12972769,
0.11803089
])
for i in range(len(test_vals)):
assert np.isclose(ref_vals[i], test_vals[i])
#######################
# Test ref_state_work
#######################
# Test reference state calculation
fecalc.compute_ref_state_work([rest1, rest2, rest3, None, None, None])
assert np.isclose(-4.34372240, fecalc.results['ref_state_work'])