def testUpdateTcoordFromModel(self):
ligand = Ligand()
ligand.read_pdbqt("./Inputs/ind.pdbqt")
ligand.update_tcoord_model("./Results/ind_1.model")
exp = ['Axis3: 0.2650, 6.2150, -11.8050',
'Axis3: 1.6440, 6.5520, -11.3580',
'Axis3: 2.5770, 5.4910, -10.8120',
'Axis3: 3.8610, 6.1570, -10.3960',
'Axis3: 3.8790, 6.9140, -9.4330',
'Axis3: 4.9330, 5.8950, -11.1170',
'Axis3: 1.7850, 4.9560, -9.6490',
'Axis3: 0.3230, 4.7560, -9.8090',
'Axis3: -0.4250, 5.7310, -10.6940',
'Axis3: 2.3400, 3.8350, -8.9190',
'Axis3: 2.3890, 4.0350, -7.4040',
'Axis3: 3.5380, 4.7410, -6.6620',
'Axis3: 3.4900, 4.9260, -5.1390',
'Axis3: 4.7390, 5.6420, -4.5980',
'Axis3: 2.2500, 5.6920, -4.6940',
'Axis3: 1.9290, 6.7510, -5.2540',
'Axis3: 1.6390, 5.2110, -3.6150',
'Axis3: 0.6620, 5.9970, -2.8790',
'Axis3: 0.7240, 5.7290, -1.3860',
'Axis3: -0.6400, 6.1130, -0.8570',
'Axis3: -1.7010, 5.8730, -1.9010',
'Axis3: -3.0650, 5.7010, -1.9350',
'Axis3: -3.6710, 5.4540, -3.1710',
'Axis3: -2.9080, 5.3860, -4.3470',
'Axis3: -1.5290, 5.5470, -4.3420',
'Axis3: -0.8420, 5.7860, -3.1940',
'Axis3: 4.7660, 5.2960, -11.9390',
'Axis3: 1.8650, 4.2600, -3.2920',
'Axis3: 2.4490, 2.6750, -7.0990',
'Axis3: 2.0460, 2.1300, -7.8750',
'Axis3: 4.6930, 5.8290, -3.1250',
'Axis3: 4.9250, 7.0630, -2.5180',
'Axis3: 4.9090, 7.1840, -1.1350',
'Axis3: 4.6580, 6.0480, -0.3630',
'Axis3: 4.4170, 4.8090, -0.9700',
'Axis3: 4.4350, 4.7040, -2.3620',
'Axis3: -0.4560, 7.2290, -12.5830',
'Axis3: 0.1500, 7.8440, -13.8500',
'Axis3: 0.7060, 9.1300, -13.8860',
'Axis3: 1.2960, 9.7510, -14.9980',
'Axis3: 1.2650, 8.9090, -16.1080',
'Axis3: 0.7270, 7.6180, -16.1420',
'Axis3: 0.1600, 7.0740, -14.9930',
'Axis3: 6.2880, 6.3080, -10.9420',
'Axis3: 6.6440, 6.0580, -9.4640',
'Axis3: 6.5040, 7.6350, -11.2720',
'Axis3: 7.2500, 5.4970, -11.6940',
'Axis3: 1.0740, 4.3740, -1.1440',
'Axis3: 0.2230, 3.7950, -1.1340']
for i, atom in enumerate(ligand.atoms):
self.assertEquals(str(atom.tcoord), exp[i])
def create_ligands(self):
base_r_list = np.full(self.number_of_ligands, self.nanoparticle_radius)
base_theta_list = np.random.uniform(low=0,
high=(2 * np.pi),
size=self.number_of_ligands)
base_phi_list = np.random.uniform(low=0,
high=np.pi,
size=self.number_of_ligands)
bases = [
np.array([r, theta, phi]) for r, theta, phi in np.nditer(
[base_r_list, base_theta_list, base_phi_list])
] #reshape into one vector
tip_r_list = np.random.uniform(low=0,
high=self.ligand_length,
size=self.number_of_ligands)
tip_theta_list = np.random.uniform(low=0,
high=(2 * np.pi),
size=self.number_of_ligands)
tip_phi_list = np.random.uniform(low=0,
high=(0.5 * np.pi),
size=self.number_of_ligands)
tips = [
np.array([r, theta, phi]) for r, theta, phi in np.nditer(
[tip_r_list, tip_theta_list, tip_phi_list])
]
for i in range(self.number_of_ligands):
ligand = Ligand(i, self.agent_id, self.position,
self.nanoparticle_radius, self.ligand_length,
bases.pop(), tips.pop(), self.binding_energy,
self.ligand_radius, self.time_unit)
self.ligands.append(ligand)
def testUpdateTcoordFromModel(self):
ligand = Ligand()
ligand.read_pdbqt("./Inputs/ind.pdbqt")
ligand.update_tcoord_model("./Results/ind_1.model")
exp = [
'Axis3: 0.2650, 6.2150, -11.8050',
'Axis3: 1.6440, 6.5520, -11.3580',
'Axis3: 2.5770, 5.4910, -10.8120',
'Axis3: 3.8610, 6.1570, -10.3960',
'Axis3: 3.8790, 6.9140, -9.4330',
'Axis3: 4.9330, 5.8950, -11.1170',
'Axis3: 1.7850, 4.9560, -9.6490', 'Axis3: 0.3230, 4.7560, -9.8090',
'Axis3: -0.4250, 5.7310, -10.6940',
'Axis3: 2.3400, 3.8350, -8.9190', 'Axis3: 2.3890, 4.0350, -7.4040',
'Axis3: 3.5380, 4.7410, -6.6620', 'Axis3: 3.4900, 4.9260, -5.1390',
'Axis3: 4.7390, 5.6420, -4.5980', 'Axis3: 2.2500, 5.6920, -4.6940',
'Axis3: 1.9290, 6.7510, -5.2540', 'Axis3: 1.6390, 5.2110, -3.6150',
'Axis3: 0.6620, 5.9970, -2.8790', 'Axis3: 0.7240, 5.7290, -1.3860',
'Axis3: -0.6400, 6.1130, -0.8570',
'Axis3: -1.7010, 5.8730, -1.9010',
'Axis3: -3.0650, 5.7010, -1.9350',
'Axis3: -3.6710, 5.4540, -3.1710',
'Axis3: -2.9080, 5.3860, -4.3470',
'Axis3: -1.5290, 5.5470, -4.3420',
'Axis3: -0.8420, 5.7860, -3.1940',
'Axis3: 4.7660, 5.2960, -11.9390',
'Axis3: 1.8650, 4.2600, -3.2920', 'Axis3: 2.4490, 2.6750, -7.0990',
'Axis3: 2.0460, 2.1300, -7.8750', 'Axis3: 4.6930, 5.8290, -3.1250',
'Axis3: 4.9250, 7.0630, -2.5180', 'Axis3: 4.9090, 7.1840, -1.1350',
'Axis3: 4.6580, 6.0480, -0.3630', 'Axis3: 4.4170, 4.8090, -0.9700',
'Axis3: 4.4350, 4.7040, -2.3620',
'Axis3: -0.4560, 7.2290, -12.5830',
'Axis3: 0.1500, 7.8440, -13.8500',
'Axis3: 0.7060, 9.1300, -13.8860',
'Axis3: 1.2960, 9.7510, -14.9980',
'Axis3: 1.2650, 8.9090, -16.1080',
'Axis3: 0.7270, 7.6180, -16.1420',
'Axis3: 0.1600, 7.0740, -14.9930',
'Axis3: 6.2880, 6.3080, -10.9420',
'Axis3: 6.6440, 6.0580, -9.4640',
'Axis3: 6.5040, 7.6350, -11.2720',
'Axis3: 7.2500, 5.4970, -11.6940',
'Axis3: 1.0740, 4.3740, -1.1440', 'Axis3: 0.2230, 3.7950, -1.1340'
]
for i, atom in enumerate(ligand.atoms):
self.assertEquals(str(atom.tcoord), exp[i])
def rmsd_pdbqts(pdbqt_file1, pdbqt_file2):
ligand1 = Ligand()
ligand1.read_pdbqt(pdbqt_file1)
ligand2 = Ligand()
ligand2.read_pdbqt(pdbqt_file2)
return Analysis.rmsd_ligands(ligand1, ligand2)
def rmsd_pdbqts(pdbqt_file1, pdbqt_file2):
ligand1 = Ligand()
ligand1.read_pdbqt(pdbqt_file1)
ligand2 = Ligand()
ligand2.read_pdbqt(pdbqt_file2)
return Analysis.rmsd_ligands(ligand1, ligand2)
def testRead(self):
ligand = Ligand()
ligand.read_pdbqt("./Inputs/ind.pdbqt")
exp = ['N',
'C',
'C',
'C',
'OA',
'N',
'N',
'C',
'C',
'C',
'C',
'C',
'C',
'C',
'C',
'OA',
'N',
'C',
'C',
'C',
'A',
'A',
'A',
'A',
'A',
'A',
'HD',
'HD',
'OA',
'HD',
'A',
'A',
'A',
'A',
'A',
'A',
'C',
'A',
'A',
'NA',
'A',
'A',
'A',
'C',
'C',
'C',
'C',
'OA',
'HD']
for i, atom in enumerate(ligand.atoms):
self.assertEquals(atom.type, exp[i])
exp = ['Axis3: -3.8840, -2.4210, -3.9000',
'Axis3: -3.6460, -0.9580, -4.0310',
'Axis3: -3.2320, -0.3420, -5.3520',
'Axis3: -3.0130, 1.1320, -5.1400',
'Axis3: -2.0700, 1.5250, -4.4640',
'Axis3: -3.8810, 1.9530, -5.6980',
'Axis3: -1.9620, -1.0900, -5.6540',
'Axis3: -1.9050, -2.5470, -5.3780',
'Axis3: -2.6800, -3.0650, -4.1840',
'Axis3: -1.3110, -0.8220, -6.9200',
'Axis3: 0.1790, -0.4990, -6.8030',
'Axis3: 0.7400, 0.9070, -6.5230',
'Axis3: 2.2520, 1.1350, -6.3910',
'Axis3: 2.5990, 2.6090, -6.1250',
'Axis3: 2.8660, 0.2770, -5.2910',
'Axis3: 2.3500, 0.2330, -4.1640',
'Axis3: 4.0270, -0.2960, -5.5960',
'Axis3: 4.8900, -0.8600, -4.5710',
'Axis3: 6.3610, -0.6770, -4.9020',
'Axis3: 7.0790, -1.7600, -4.1290',
'Axis3: 6.2030, -2.9780, -3.9830',
'Axis3: 6.3700, -4.3170, -3.7160',
'Axis3: 5.2370, -5.1380, -3.7120',
'Axis3: 3.9630, -4.6090, -3.9720',
'Axis3: 3.7660, -3.2640, -4.2540',
'Axis3: 4.8000, -2.3820, -4.2870',
'Axis3: -4.6640, 1.4910, -6.1820',
'Axis3: 4.3220, -0.3400, -6.5820',
'Axis3: 0.4840, -0.8300, -8.1240',
'Axis3: 0.5170, 0.0270, -8.6940',
'Axis3: 4.0610, 2.8330, -5.9890',
'Axis3: 4.9780, 2.4140, -6.9530',
'Axis3: 6.3390, 2.6110, -6.7670',
'Axis3: 6.7740, 3.2360, -5.5960',
'Axis3: 5.8560, 3.6650, -4.6300',
'Axis3: 4.4900, 3.4600, -4.8320',
'Axis3: -4.5580, -2.8860, -2.6820',
'Axis3: -5.9930, -2.4600, -2.3510',
'Axis3: -7.1180, -2.9970, -2.9930',
'Axis3: -8.4590, -2.6730, -2.7310',
'Axis3: -8.5480, -1.7190, -1.7190',
'Axis3: -7.4700, -1.1430, -1.0390',
'Axis3: -6.1680, -1.5200, -1.3590',
'Axis3: -3.9080, 3.3800, -5.7390',
'Axis3: -5.2730, 3.7850, -6.3260',
'Axis3: -2.8790, 3.9270, -6.4870',
'Axis3: -3.8780, 4.0050, -4.4130',
'Axis3: 6.5610, -0.7430, -6.3060',
'Axis3: 6.5100, 0.2050, -6.7060']
for i, atom in enumerate(ligand.atoms):
self.assertEquals(str(atom.tcoord), exp[i])
exp = [0.096,
0.307,
0.2,
0.242,
-0.271,
-0.351,
-0.395,
0.148,
0.292,
0.149,
0.136,
0.047,
0.084,
0.052,
0.222,
-0.273,
-0.35,
0.147,
0.149,
0.073,
-0.047,
0.008,
0.001,
0.001,
0.01,
-0.027,
0.163,
0.163,
-0.394,
0.21,
-0.057,
0.007,
0.001,
0.0,
0.001,
0.007,
0.312,
-0.013,
0.125,
-0.273,
0.116,
0.02,
0.012,
0.022,
0.037,
0.037,
0.037,
-0.393,
0.21]
for i, atom in enumerate(ligand.atoms):
self.assertEquals(atom.charge, exp[i])
exp = [0.096,
0.307,
0.2,
0.242,
0.271,
0.351,
0.395,
0.148,
0.292,
0.149,
0.136,
0.047,
0.084,
0.052,
0.222,
0.273,
0.35,
0.147,
0.149,
0.073,
0.047,
0.008,
0.001,
0.001,
0.01,
0.027,
0.163,
0.163,
0.394,
0.21,
0.057,
0.007,
0.001,
0.0,
0.001,
0.007,
0.312,
0.013,
0.125,
0.273,
0.116,
0.02,
0.012,
0.022,
0.037,
0.037,
0.037,
0.393,
0.21]
for i, atom in enumerate(ligand.atoms):
self.assertEquals(abs(atom.charge), exp[i])
def testRead(self):
ligand = Ligand()
ligand.read_pdbqt("./Inputs/ind.pdbqt")
exp = [
'N', 'C', 'C', 'C', 'OA', 'N', 'N', 'C', 'C', 'C', 'C', 'C', 'C',
'C', 'C', 'OA', 'N', 'C', 'C', 'C', 'A', 'A', 'A', 'A', 'A', 'A',
'HD', 'HD', 'OA', 'HD', 'A', 'A', 'A', 'A', 'A', 'A', 'C', 'A',
'A', 'NA', 'A', 'A', 'A', 'C', 'C', 'C', 'C', 'OA', 'HD'
]
for i, atom in enumerate(ligand.atoms):
self.assertEquals(atom.type, exp[i])
exp = [
'Axis3: -3.8840, -2.4210, -3.9000',
'Axis3: -3.6460, -0.9580, -4.0310',
'Axis3: -3.2320, -0.3420, -5.3520',
'Axis3: -3.0130, 1.1320, -5.1400',
'Axis3: -2.0700, 1.5250, -4.4640',
'Axis3: -3.8810, 1.9530, -5.6980',
'Axis3: -1.9620, -1.0900, -5.6540',
'Axis3: -1.9050, -2.5470, -5.3780',
'Axis3: -2.6800, -3.0650, -4.1840',
'Axis3: -1.3110, -0.8220, -6.9200',
'Axis3: 0.1790, -0.4990, -6.8030',
'Axis3: 0.7400, 0.9070, -6.5230', 'Axis3: 2.2520, 1.1350, -6.3910',
'Axis3: 2.5990, 2.6090, -6.1250', 'Axis3: 2.8660, 0.2770, -5.2910',
'Axis3: 2.3500, 0.2330, -4.1640',
'Axis3: 4.0270, -0.2960, -5.5960',
'Axis3: 4.8900, -0.8600, -4.5710',
'Axis3: 6.3610, -0.6770, -4.9020',
'Axis3: 7.0790, -1.7600, -4.1290',
'Axis3: 6.2030, -2.9780, -3.9830',
'Axis3: 6.3700, -4.3170, -3.7160',
'Axis3: 5.2370, -5.1380, -3.7120',
'Axis3: 3.9630, -4.6090, -3.9720',
'Axis3: 3.7660, -3.2640, -4.2540',
'Axis3: 4.8000, -2.3820, -4.2870',
'Axis3: -4.6640, 1.4910, -6.1820',
'Axis3: 4.3220, -0.3400, -6.5820',
'Axis3: 0.4840, -0.8300, -8.1240',
'Axis3: 0.5170, 0.0270, -8.6940', 'Axis3: 4.0610, 2.8330, -5.9890',
'Axis3: 4.9780, 2.4140, -6.9530', 'Axis3: 6.3390, 2.6110, -6.7670',
'Axis3: 6.7740, 3.2360, -5.5960', 'Axis3: 5.8560, 3.6650, -4.6300',
'Axis3: 4.4900, 3.4600, -4.8320',
'Axis3: -4.5580, -2.8860, -2.6820',
'Axis3: -5.9930, -2.4600, -2.3510',
'Axis3: -7.1180, -2.9970, -2.9930',
'Axis3: -8.4590, -2.6730, -2.7310',
'Axis3: -8.5480, -1.7190, -1.7190',
'Axis3: -7.4700, -1.1430, -1.0390',
'Axis3: -6.1680, -1.5200, -1.3590',
'Axis3: -3.9080, 3.3800, -5.7390',
'Axis3: -5.2730, 3.7850, -6.3260',
'Axis3: -2.8790, 3.9270, -6.4870',
'Axis3: -3.8780, 4.0050, -4.4130',
'Axis3: 6.5610, -0.7430, -6.3060', 'Axis3: 6.5100, 0.2050, -6.7060'
]
for i, atom in enumerate(ligand.atoms):
self.assertEquals(str(atom.tcoord), exp[i])
exp = [
0.096, 0.307, 0.2, 0.242, -0.271, -0.351, -0.395, 0.148, 0.292,
0.149, 0.136, 0.047, 0.084, 0.052, 0.222, -0.273, -0.35, 0.147,
0.149, 0.073, -0.047, 0.008, 0.001, 0.001, 0.01, -0.027, 0.163,
0.163, -0.394, 0.21, -0.057, 0.007, 0.001, 0.0, 0.001, 0.007,
0.312, -0.013, 0.125, -0.273, 0.116, 0.02, 0.012, 0.022, 0.037,
0.037, 0.037, -0.393, 0.21
]
for i, atom in enumerate(ligand.atoms):
self.assertEquals(atom.charge, exp[i])
exp = [
0.096, 0.307, 0.2, 0.242, 0.271, 0.351, 0.395, 0.148, 0.292, 0.149,
0.136, 0.047, 0.084, 0.052, 0.222, 0.273, 0.35, 0.147, 0.149,
0.073, 0.047, 0.008, 0.001, 0.001, 0.01, 0.027, 0.163, 0.163,
0.394, 0.21, 0.057, 0.007, 0.001, 0.0, 0.001, 0.007, 0.312, 0.013,
0.125, 0.273, 0.116, 0.02, 0.012, 0.022, 0.037, 0.037, 0.037,
0.393, 0.21
]
for i, atom in enumerate(ligand.atoms):
self.assertEquals(abs(atom.charge), exp[i])
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the
# Free Software Foundation, Inc.,
# 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
# References:
# - AutoDock 4.2.3 Source Code
# http://autodock.scripps.edu
from Ligand import Ligand
from Grid import Grid
from Parameters import Field
from Map import ElectrostaticMap, DesolvationMap, AtomTypeMap
from Dock import Dock
ligand = Ligand()
ligand.read_pdbqt("./Inputs/ind.pdbqt")
ligand.update_tcoord_model("./Results/ind.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(grid, ligand)
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)
def testCalcLinInterp3(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
protein = Protein()
u0, v0, w0, u1, v1, w1, \
p000, p001, p010, p011, p100, p101, p110, p111 = \
Dock.calc_linInterp3(grid, ligand, protein)
exp_u0 = [24, 27, 30, 33, 33, 36, 28, 24, 22, 29, 29, 32, 32, 35, 29, \
28, 27, 25, 25, 21, 18, 15, 13, 15, 19, 21, 36, 28, 29, 28, \
35, 36, 36, 35, 35, 35, 22, 23, 25, 26, 26, 25, 23, 40, 41, \
40, 42, 26, 23]
self.assertEquals(u0, exp_u0)
exp_v0 = [29, 30, 27, 29, 31, 28, 25, 25, 27, 22, 23, 25, 25, 27, 27, \
30, 26, 28, 27, 28, 28, 27, 27, 27, 27, 28, 26, 24, 19, 18, \
28, 31, 31, 28, 25, 25, 31, 33, 37, 38, 36, 32, 31, 29, 28, \
33, 27, 24, 22]
self.assertEquals(v0, exp_v0)
exp_w0 = [18, 19, 21, 22, 24, 20, 24, 23, 21, 26, 30, 32, 36, 37, 37, \
35, 40, 42, 46, 47, 44, 44, 41, 38, 38, 41, 18, 41, 31, 29, \
41, 43, 46, 49, 47, 43, 16, 13, 12, 10, 7, 6, 10, 20, 24, \
19, 18, 46, 46]
self.assertEquals(w0, exp_w0)
exp_u1 = [25, 28, 31, 34, 34, 37, 29, 25, 23, 30, 30, 33, 33, 36, 30, \
29, 28, 26, 26, 22, 19, 16, 14, 16, 20, 22, 37, 29, 30, 29, \
36, 37, 37, 36, 36, 36, 23, 24, 26, 27, 27, 26, 24, 41, 42, \
41, 43, 27, 24]
self.assertEquals(u1, exp_u1)
exp_v1 = [30, 31, 28, 30, 32, 29, 26, 26, 28, 23, 24, 26, 26, 28, 28, \
31, 27, 29, 28, 29, 29, 28, 28, 28, 28, 29, 27, 25, 20, 19, \
29, 32, 32, 29, 26, 26, 32, 34, 38, 39, 37, 33, 32, 30, 29, \
34, 28, 25, 23]
self.assertEquals(v1, exp_v1)
exp_w1 = [19, 20, 22, 23, 25, 21, 25, 24, 22, 27, 31, 33, 37, 38, 38, \
36, 41, 43, 47, 48, 45, 45, 42, 39, 39, 42, 19, 42, 32, 30, \
42, 44, 47, 50, 48, 44, 17, 14, 13, 11, 8, 7, 11, 21, 25, \
20, 19, 47, 47]
self.assertEquals(w1, exp_w1)
exp_p000 = [0.0049920000000003, 0.07082279822222158, \
0.010670762666666705, 0.014893662814814962, \
0.05954753422222141, 0.06692323555555484, \
0.02218827851851877, 0.05730432948148176, \
0.09164231111110999, 0.11063039999999903, \
0.07689557333333293, 0.05574929066666695, \
0.15205717333333324, 0.510503367111111, \
0.13600474074074018, 0.3160871632592622, \
0.14260223999999969, 0.020969604740741634, \
0.07576166400000024, 0.43352632888888754, \
0.24339291022222376, 0.11683840000000191, \
0.06234385066666788, 0.0069254826666658295, \
0.049472398222222956, 0.004077568000000049, \
0.005478324148148441, 0.001810014814814871, \
0.04792319999999972, 0.0, 0.11909688888888928, \
0.06675531851851867, 0.34005930666666545, \
0.019190670222224544, 0.022714595555556102, \
0.02363960888888848, 0.04932630755555612, \
0.028551111111111964, 0.0027955200000004095, \
0.002817744592593219, 0.013583075555555114, \
0.2548221724444463, 0.007528391111110991, \
0.04061548088888999, 0.031737780148146724, \
0.017002571851849876, 0.1769813333333323, \
0.061945476740739906, 0.7125060266666654]
self.assertEquals(p000, exp_p000)
exp_p001 = [0.0046080000000002855, 0.028647423999999776, \
0.052845681777776904, 0.038809448296297094, \
0.010895132444444356, 0.12177009777777835, \
0.06019394370370367, 0.010699226074073875, \
0.0982243555555557, 0.40154737777778016, \
0.22347775999999855, 0.18181870933333166, \
0.3616494933333342, 0.1806112995555552, \
0.14577303703703634, 0.0034079478518515044, \
0.2535150933333334, 0.04401883970370486, \
0.17345433599999888, 0.17308700444444436, \
0.018132423111111077, 0.022254933333333133, \
0.052258816000000166, 0.010048739555554584, \
0.06794626844444453, 0.004370432000000051, \
0.02819989807407561, 0.006367762962963142, \
0.6432768000000015, 0.2736355555555557, \
0.05954844444444527, 0.16720023703703696, \
0.009316693333334796, 0.5805177742222254, \
0.032240071111111795, 0.01006705777777773, \
0.06143635911111165, 0.3997155555555576, \
8.448000000000805e-05, 0.5255093665185175, \
0.28604359111111133, 0.012100494222221909, \
0.3957782755555553, 0.008835185777778117, \
0.009876442074073755, 0.0010596503703702597, \
0.039907555555555606, 0.0033060788148146308, \
0.01752064000000065]
self.assertEquals(p001, exp_p001)
exp_p010 = [0.01580800000000109, 0.43991853511111095, \
0.02382523733333365, 0.1596414482962953, \
0.5130249102222195, 0.10615409777777662, \
0.002949499259259329, 0.10673478162962986, \
0.004891022222222317, 0.013209599999999733, \
0.10332842666666649, 0.1244747093333352, \
0.03738282666666654, 0.2064957440000002, \
0.024884148148148186, 0.15615461451851684, \
0.11083775999999886, 0.010866839703704239, \
0.004494336000000094, 0.014331448888888855, \
0.4986586453333299, 0.017561600000000257, \
0.23359214933333552, 0.22917051733333157, \
0.05838893511111133, 0.0383970986666671, \
0.001462120296296389, 0.06606554074074122, \
0.011980799999999877, 0.0, 0.4462364444444414, \
0.0664002370370377, 0.0726340266666656, \
0.004958663111111672, 0.02357873777777808, \
0.08857372444444203, 0.0029261368888889743, \
0.020337777777778118, 0.20686847999999752, \
0.0013920331851854889, 0.018452479999999438, \
0.00484716088888932, 0.006658275555555493, \
0.04261296355555679, 0.006903997629629396, \
0.6205938725925908, 0.36701866666666505, \
0.1253896343703712, 0.19322197333333457]
self.assertEquals(p010, exp_p010)
exp_p011 = [0.01459200000000103, 0.17794457600000016, \
0.11799165155555476, 0.41598877392592776, \
0.09386575644444448, 0.19315256888888976, \
0.008001611851851947, 0.019928329481481058, \
0.005242311111111285, 0.04794595555555529, \
0.3002982399999991, 0.4059572906666669, \
0.08891050666666664, 0.07305625599999993, \
0.026671407407407432, 0.001683607703703498, \
0.19704490666666513, 0.02281138251851927, \
0.010289664000000117, 0.0057218844444444465, \
0.0371493546666661, 0.003345066666666631, \
0.19580518399999866, 0.3325219271111166, \
0.08019239822222142, 0.04115490133333377, \
0.007526324148148633, 0.2324233481481492, \
0.16081919999999966, 0.5156977777777759, \
0.22311822222222305, 0.16631087407407527, \
0.0019899733333336236, 0.14999955911111074, \
0.033466595555555895, 0.03771960888888834, \
0.0036445297777778743, 0.2847288888888866, \
0.006251519999999605, 0.2596141890370355, \
0.38858752000000113, 0.0002301724444444573, \
0.3500350577777798, 0.009269703111111484, \
0.002148446814814769, 0.03867723851851886, \
0.08275911111111132, 0.00669214340740717, \
0.004751360000000215]
self.assertEquals(p011, exp_p011)
exp_p100 = [0.11980799999999879, 0.027907868444444307, \
0.04129723733333381, 0.008772114962962983, \
0.028367132444444516, 0.0702145422222216, \
0.21554327703703846, 0.23706722607407538, \
0.36656924444444156, 0.082329599999999, \
0.03233109333333362, 0.016840931555555577, \
0.08553215999999973, 0.015427299555555727, \
0.2720094814814818, 0.34610661451852076, \
0.059957760000000714, 0.19156017303703798, \
0.21121433600000142, 0.2582710044444453, \
0.061865756444445814, 0.6134016000000012, \
0.05225881600000055, 0.005042517333332682, \
0.1437791573333353, 0.042258432000000005, \
0.12291989807407339, 0.004092207407407501, \
0.007543466666666573, 0.0, 0.021347555555555793, \
0.07629179259259218, 0.4619673599999994, \
0.006238663111111675, 0.18009429333333427, \
0.12410794666666769, 0.37106835911111075, \
0.010382222222222482, 0.010146702222223856, \
0.0007520331851853598, 0.005638257777777585, \
0.6820240497777759, 0.002377386666666608, \
0.36019518577777554, 0.5946657754074057, \
0.008099650370369561, 0.0884906666666671, \
0.2519674121481454, 0.05528063999999922]
self.assertEquals(p100, exp_p100)
exp_p101 = [0.11059199999999907, 0.011288575999999958, \
0.2045196515555538, 0.022858107259259554, \
0.005190200888888931, 0.12775879111111194, \
0.5847411674074044, 0.044262551703702906, \
0.3928974222222245, 0.2988259555555563, \
0.09396224000000072, 0.05492440177777706, \
0.20342783999999997, 0.0054580337777778275, \
0.29154607407407424, 0.0037316077037033123, \
0.10659157333333487, 0.4021180491851807, \
0.48356966399999857, 0.10311566222222283, \
0.0046089102222222865, 0.11683839999999726, \
0.04380518399999974, 0.00731659377777701, \
0.19746884266666664, 0.045293567999999985, \
0.6327352130370342, 0.014396681481481769, \
0.10125653333333291, 0.07303111111111188, \
0.010673777777778011, 0.19108598518518363, \
0.012656640000002016, 0.18871955911110633, \
0.2556177066666673, 0.05285205333333443, \
0.46216897422222053, 0.14535111111111115, \
0.00030663111111114483, 0.14025418903703818, \
0.11873507555555546, 0.03238661688888772, \
0.12498261333333217, 0.07835414755555593, \
0.18505333570370552, 0.0005047940740740295, \
0.019953777777778015, 0.01344769896296225, \
0.0013593600000000336]
self.assertEquals(p101, exp_p101)
exp_p110 = [0.3793919999999994, 0.1733507982222229, \
0.09220676266666863, 0.09402610725925796, \
0.24439375644444714, 0.11137479111111008, \
0.028652278518519068, 0.4415603294814827, \
0.019564088888889355, 0.009830399999999769, \
0.0434449066666672, 0.03760173511111153, \
0.021027839999999878, 0.006240256000000077, \
0.04976829629629663, 0.1709849410370347, \
0.04660224000000018, 0.09927004918518634, \
0.012529664000000305, 0.00853788444444448, \
0.12674935466666779, 0.09219840000000003, \
0.19580518400000008, 0.16686148266666403, \
0.1696928426666671, 0.3979335679999997, \
0.0328063241481483, 0.14936557037037024, \
0.0018858666666666348, 0.0, 0.07998577777777786, \
0.07588598518518534, 0.09867263999999876, \
0.0016120035555556883, 0.18694570666666555, \
0.4650120533333325, 0.022012529777778147, \
0.007395555555555644, 0.7508559644444464, \
0.0003715223703704551, 0.007659519999999756, \
0.012973283555556579, 0.0021026133333332956, \
0.3779097031111094, 0.12935911348148255, \
0.29563723851852247, 0.18350933333333447, \
0.5100308100740788, 0.01499135999999991]
self.assertEquals(p110, exp_p110)
exp_p111 = [0.3502080000000001, 0.07011942400000036, \
0.45664301511111166, 0.2450103371851844, \
0.04471557688888963, 0.2026518755555568, \
0.07772994370370429, 0.08244322607407237, \
0.020969244444445232, 0.03568071111111079, \
0.1262617600000014, 0.12263293155555516, \
0.05001215999999986, 0.002207744000000023, \
0.05334281481481515, 0.0018435034074071772, \
0.08284842666666718, 0.20838506192592499, \
0.02868633600000042, 0.0034087822222222453, \
0.009442645333333338, 0.01756159999999956, \
0.1641308159999974, 0.2421127395555576, \
0.23305915733333074, 0.4265144319999994, \
0.16887189807407502, 0.5254788740740721, \
0.025314133333333114, 0.13763555555555645, \
0.039992888888889355, 0.19006957037037026, \
0.0027033600000004004, 0.048763107555553936, \
0.26534229333333104, 0.19802794666666879, \
0.02741680355555594, 0.10353777777777645, \
0.02269070222222112, 0.06928892207407435, \
0.16130048000000022, 0.0006160497777778058, \
0.11053738666666636, 0.08220763022222277, \
0.040255108740741584, 0.018424983703704163, \
0.041379555555556106, 0.027220745481480586, \
0.0003686400000000121]
self.assertEquals(p111, exp_p111)
