def get_params(options):
mol = get_mol_from_file(options.ligand_path, options.ftype)
# get rdkit conformer and compute x,y,z of top and bottom corner of confounding cuboid
conf = mol.GetConformer()
params = rdShapeHelpers.ComputeConfBox(conf)
# change tuples to arrays
coords1 = np.array(params[0])
coords2 = np.array(params[1])
# get the centre of the box
center = np.mean((coords1, coords2), axis=0)
# calculate box dimensions
dims = np.abs(coords1 - coords2)
# optionally add buffers in each direction - expansion
box_dims = [
dims[0] + options.bufx, dims[1] + options.bufy, dims[2] + options.bufz
]
optionalvals = ""
if options.seed is not None:
optionalvals += "seed = " + str(options.seed) + "\n"
if options.exhaustiveness is not None:
optionalvals += "exhaustiveness = " + str(
options.exhaustiveness) + "\n"
with open(options.output, "w") as f:
f.write("""
size_x = {}
size_y = {}
size_z = {}
center_x = {}
center_y = {}
center_z = {}
{}""".format(
box_dims[0],
box_dims[1],
box_dims[2],
center[0],
center[1],
center[2],
optionalvals,
))
def get_params(options):
# make sure we have a mol file by initiating rdkit mol object from input
mol = Chem.MolFromMolFile(options.ligand_path)
if not mol:
raise IOError
# get rdkit conformer and compute x,y,z of top and bottom corner of confounding cuboid
conf = mol.GetConformer()
params = rdShapeHelpers.ComputeConfBox(conf)
# change tuples to arrays
coords1 = np.array(params[0])
coords2 = np.array(params[1])
# get the centre of the box
center = np.mean((coords1, coords2), axis=0)
# calculate box dimensions
dims = np.abs(coords1 - coords2)
# optionally add buffers in each direction - expansion
box_dims = [
dims[0] + options.bufx, dims[1] + options.bufy, dims[2] + options.bufz
]
# if no seed set, then randomly generate one between 0 and 2**31
if options.seed == None:
options.seed = randint(0, 2147483647)
with open(options.output, 'w') as f:
f.write("""
size_x = {}
size_y = {}
size_z = {}
center_x = {}
center_y = {}
center_z = {}
num_modes = 9999
energy_range = 9999
exhaustiveness = {}
cpu = 4
seed = {}
""".format(box_dims[0], box_dims[1], box_dims[2], center[0],
center[1], center[2], options.exhaustiveness,
options.seed))
def get_params(options):
# make sure we have a mol file by initiating rdkit mol object from input
mol = Chem.MolFromMolFile(options.ligand_path)
if not mol:
raise IOError
# get rdkit conformer and compute x,y,z of top and bottom corner of confounding cuboid
conf = mol.GetConformer()
params = rdShapeHelpers.ComputeConfBox(conf)
# change tuples to arrays
coords1 = np.array(params[0])
coords2 = np.array(params[1])
# get the centre of the box
center = np.mean((coords1, coords2), axis=0)
# calculate box dimensions
dims = np.abs(coords1 - coords2)
# optionally add buffers in each direction - expansion
box_dims = [
dims[0] + options.bufx, dims[1] + options.bufy, dims[2] + options.bufz
]
optionalvals = ""
if options.seed != None:
optionalvals += "seed = " + str(options.seed) + "\n"
if options.exhaustiveness != None:
optionalvals += "exhaustiveness = " + str(
options.exhaustiveness) + "\n"
with open(options.output, 'w') as f:
f.write("""
size_x = {}
size_y = {}
size_z = {}
center_x = {}
center_y = {}
center_z = {}
{}""".format(box_dims[0], box_dims[1], box_dims[2], center[0], center[1],
center[2], optionalvals))
def test1Shape(self):
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol',
'ShapeHelpers', 'test_data', '1oir.mol')
m = Chem.MolFromMolFile(fileN)
rdmt.CanonicalizeMol(m)
dims1, offset1 = rdshp.ComputeConfDimsAndOffset(m.GetConformer())
grd = geom.UniformGrid3D(30.0, 16.0, 10.0)
rdshp.EncodeShape(m, grd, 0)
ovect = grd.GetOccupancyVect()
self.failUnless(ovect.GetTotalVal() == 9250)
m = Chem.MolFromMolFile(fileN)
trans = rdmt.ComputeCanonicalTransform(m.GetConformer())
dims, offset = rdshp.ComputeConfDimsAndOffset(m.GetConformer(),
trans=trans)
dims -= dims1
offset -= offset1
self.failUnless(feq(dims.Length(), 0.0))
self.failUnless(feq(offset.Length(), 0.0))
grd1 = geom.UniformGrid3D(30.0, 16.0, 10.0)
rdshp.EncodeShape(m, grd1, 0, trans)
ovect = grd1.GetOccupancyVect()
self.failUnless(ovect.GetTotalVal() == 9250)
grd2 = geom.UniformGrid3D(30.0, 16.0, 10.0)
rdshp.EncodeShape(m, grd2, 0)
fileN2 = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol',
'ShapeHelpers', 'test_data', '1oir_conf.mol')
m2 = Chem.MolFromMolFile(fileN2)
rmsd = rdMolAlign.AlignMol(m, m2)
self.failUnless(feq(rdshp.ShapeTanimotoDist(m, m2), 0.2813))
dist = rdshp.ShapeTanimotoDist(mol1=m,
mol2=m2,
confId1=0,
confId2=0,
gridSpacing=0.25,
stepSize=0.125)
self.failUnless(feq(dist, 0.3021))
m = Chem.MolFromMolFile(fileN)
cpt = rdmt.ComputeCentroid(m.GetConformer())
dims, offset = rdshp.ComputeConfDimsAndOffset(m.GetConformer())
grd = geom.UniformGrid3D(dims.x, dims.y, dims.z, 0.5,
DataStructs.DiscreteValueType.TWOBITVALUE,
offset)
dims -= geom.Point3D(13.927, 16.97, 9.775)
offset -= geom.Point3D(-4.353, 16.829, 2.782)
self.failUnless(feq(dims.Length(), 0.0))
self.failUnless(feq(offset.Length(), 0.0))
rdshp.EncodeShape(m, grd, 0)
ovect = grd.GetOccupancyVect()
self.failUnless(ovect.GetTotalVal() == 9275)
geom.WriteGridToFile(grd, '1oir_shape.grd')
m = Chem.MolFromMolFile(fileN)
lc, uc = rdshp.ComputeConfBox(m.GetConformer())
rdmt.CanonicalizeMol(m)
lc1, uc1 = rdshp.ComputeConfBox(m.GetConformer())
lc2, uc2 = rdshp.ComputeUnionBox((lc, uc), (lc1, uc1))
lc -= geom.Point3D(-4.353, 16.829, 2.782)
uc -= geom.Point3D(9.574, 33.799, 12.557)
self.failUnless(feq(lc.Length(), 0.0))
self.failUnless(feq(uc.Length(), 0.0))
lc1 -= geom.Point3D(-10.7519, -6.0778, -3.0123)
uc1 -= geom.Point3D(8.7163, 5.3279, 3.1621)
self.failUnless(feq(lc1.Length(), 0.0))
self.failUnless(feq(uc1.Length(), 0.0))
lc2 -= geom.Point3D(-10.7519, -6.0778, -3.01226)
uc2 -= geom.Point3D(9.574, 33.799, 12.557)
self.failUnless(feq(lc2.Length(), 0.0))
self.failUnless(feq(uc2.Length(), 0.0))