def run(self):
with open(self.docking_parameter_file, 'r') as p_file:
for line in p_file:
if line.startswith("intelec"):
self.dock.dps.calc_inter_elec_e = True
# Atomic bonding parameter file
if line.startswith("b_prm"):
self.dock.bond.read(line.split()[1])
if line.startswith("ligand_types"):
for type in line.split('#')[0].split()[1:]:
self.dock.ligand.atom_types.append(type)
self.atom_type_map_files[type] = ""
self.dock.bond.calc_internal_energy_tables(
self.dock.ligand)
if line.startswith("fld"):
self.grid_field_file = "./Parameters/" + line.split()[1]
self.dock.grid.field = Field(self.grid_field_file)
if line.startswith("map"):
filename = line.split()[1]
type = filename.split('.')[1]
self.atom_type_map_files[type] = "./Maps/" + filename
self.dock.grid.maps[type] = AtomTypeMap(
self.atom_type_map_files[type],
self.dock.grid.field).map
if line.startswith("elecmap"):
self.electrostatic_map_file = "./Maps/" + line.split()[1]
self.dock.grid.maps['e'] = ElectrostaticMap(
self.electrostatic_map_file, self.dock.grid.field).map
if line.startswith("desolvmap"):
self.desolvation_map_file = "./Maps/" + line.split()[1]
self.dock.grid.maps['d'] = DesolvationMap(
self.desolvation_map_file, self.dock.grid.field).map
# Set movable molecule (ligand)
if line.startswith("move"):
self.ligand_file = "./Inputs/" + line.split()[1]
self.dock.ligand.read_pdbqt(self.ligand_file)
# Set flexible portion of molecule (normally protein receptor)
if line.startswith("flexres"):
self.protein_file = "./Inputs/" + line.split()[1]
self.dock.protein.read_flex_pdbqt(self.protein_file)
if line.startswith("about"):
about = Axis3(0.0, 0.0, 0.0)
about.xyz = [float(axis) for axis in line.split()[1:4]]
self.dock.ligand.about = about
# Zero-out central point. Applicable only for all ligand
# atoms (not protein atoms)
for i in xrange(len(self.dock.ligand.ori_atoms)):
self.dock.ligand.ori_atoms[i].tcoord -= about
self.dock.ligand.reset_atoms()
# Pre-energy calculation
if line.startswith("pre_energy_calc"):
# Get atomic non-bond lists
self.dock.get_non_bond_list()
# Calculate binding torsional free energy
self.dock.torsional_energy = self.dock.bond.torsional_dof * \
self.dock.bond.fec_tors
# --------------------------------------- Empirical Settings ---
# 1-4 interactions
if line.startswith("include_1_4_interactions"):
# By default, 1-4 interactions is disabled. Only 1-1, 1-2,
# and 1-3 interactions are considered.
self.dock.bond.include_1_4_interactions = True
# Torsional degrees of freedom (DoF)
if line.startswith("torsdof"):
self.dock.bond.torsional_dof = int(line.split()[1])
#---------------------------------------------- Optimization ---
# Define optimization type to use
if line.startswith("opt_type"):
type = line.split()[1]
if type == "ga":
if self.accelerator == "sequential":
self.optimization = \
Optimization.GeneticAlgorithm(self.dock)
if self.accelerator == "opencl":
self.optimization = \
Optimization.GeneticAlgorithmOpenCL(self.dock, \
self.cl_device_type)
# Run optimization
if line.startswith("opt_run"):
self.optimization.run()
#------------------------------------ Opt: Genetic Algorithm ---
if line.startswith("opt_ga"):
words = line.split()
type = words[1]
value = words[2]
if type == "community_size":
self.optimization.community_size = int(value)
if type == "pop_size":
self.optimization.population_size = int(value)
if type == "num_generations":
self.optimization.num_gen = int(value)
#----------------------------------------------- Accelerator ---
# Define parallel processing accelerator
if line.startswith("accelerator"):
self.accelerator = line.split()[1]
if self.accelerator == "sequential":
self.dock = Dock()
if self.accelerator == "opencl":
self.dock = DockOpenCL()
# Define OpenCL device types
if line.startswith("ocl_device_type"):
self.cl_device_type = line.split()[1]
def testCalcEnergy(self):
ligand = Ligand()
ligand.read_pdbqt("./Inputs/ind.pdbqt")
ligand.update_tcoord_model("./Results/ind_1.model")
grid = Grid()
grid.field = Field("./Parameters/hsg1_rigid.maps.fld")
grid.maps['e'] = ElectrostaticMap("./Maps/hsg1_rigid.e.map", grid.field).map
grid.maps['d'] = DesolvationMap("./Maps/hsg1_rigid.d.map", grid.field).map
grid.maps['A'] = AtomTypeMap("./Maps/hsg1_rigid.A.map", grid.field).map
grid.maps['C'] = AtomTypeMap("./Maps/hsg1_rigid.C.map", grid.field).map
grid.maps['HD'] = AtomTypeMap("./Maps/hsg1_rigid.HD.map", grid.field).map
grid.maps['N'] = AtomTypeMap("./Maps/hsg1_rigid.N.map", grid.field).map
grid.maps['NA'] = AtomTypeMap("./Maps/hsg1_rigid.NA.map", grid.field).map
grid.maps['OA'] = AtomTypeMap("./Maps/hsg1_rigid.OA.map", grid.field).map
dock = Dock()
dock.ligand = ligand
dock.grid = grid
dock.calc_energy()
exp_elecs = [-0.037623435264000013, -0.11408866126250672, \
-0.13002690236871114, -0.11316478799697538, \
0.079400682425344024, 0.16382104147968005, \
0.35572237014565938, -0.13983584352051195, \
-0.14455922704497778, -0.2437679729095111, \
-0.2233031453627734, -0.057756149112888927, \
-0.079042238535680001, -0.032257681663999997, \
-0.14416303698488891, 0.10750629826486036, \
0.24778700799999992, -0.084038775587896894, \
-0.106404338719744, -0.052751354779306661, \
0.024654531648227552, -0.0042321141760000005, \
-0.00035986557866666673, -0.00033659216281599992, \
-0.0041046807466666672, 0.012465198300672001, \
-0.090822509727725043, -0.17177248957202962, \
1.1082351947605333, -0.89707293013333311, \
0.026757765866666665, -0.0020757145903407409, \
-0.00025216804266666674, -0, -0.00048987137962666649, \
-0.0041342845067377787, -0.077292167626752006, \
0.0028771771022222214, -0.035468487893333331, \
0.061588514183964438, -0.025041379570346665, \
-0.0055949960533333357, -0.0031704985600000007, \
-0.0069595652002702214, -0.012058230703198818, \
-0.0079140675343170441, -0.012375409536000002, \
0.3866265132258988, -0.20299363642879997]
self.assertEquals(dock.elecs, exp_elecs)
exp_elec_total = -0.689862915434
self.assertLessEqual(dock.elec_total - exp_elec_total, 0.000000000001)
self.assertGreaterEqual(dock.elec_total - exp_elec_total, -0.000000000001)
exp_emaps = [-0.27127903027200001, -0.16588333043273959, \
-0.20299416690915556, -0.21193308408991288, \
-0.22342833248403907, -0.10887097308672009, \
-0.069412406582518515, -0.32392036196890539, \
-0.22020219191751092, -0.35971221242311113, \
-0.36151369650175996, -0.33589534698001067, \
-0.31399731050837326, -0.37602125178402135, \
-0.18051097352533335, -0.17621873305273847, \
-0.092143525887999983, -0.2309628750124183, \
-0.24049173290393594, -0.30815793025564453, \
-0.39344854528779372, -0.50645809636693317, \
-0.53159663755332287, -0.49475817361601443, \
-0.34577077998990213, -0.31340080937233067, \
0.083165888601903395, -0.37009113352391104, \
-0.26495262599680025, -0.35829845333333321, \
-0.27628956787200004, -0.36140396483508141, \
-0.31815226712832012, -0.2094688831146666, \
-0.23815943764081771, -0.24906767845688918, \
-0.22192987677536707, -0.25745685461333312, \
-0.19937555381333344, -0.2350488774924894, \
-0.19400907040085333, -0.14228789478968887, \
-0.23528794258204436, -0.4346495467977386, \
-0.44998934942632773, -0.52384750919471401, \
-0.51774914410666673, -0.26729886470788744, \
0.052065064174933465]
self.assertEquals(dock.emaps, exp_emaps)
exp_emap_total = -13.5485660526
self.assertLessEqual(dock.emap_total - exp_emap_total, 0.0000000001)
self.assertGreaterEqual(dock.emap_total - exp_emap_total, -0.0000000001)
