コード例 #1
0
ファイル: test_points.py プロジェクト: mtrellet/disvis
    def test_dilate_points(self):
        shape = (9, 8, 7)
        vol = volume.zeros(shape, voxelspacing=1, origin=(1,0,0))

        dilate_points(np.asarray([[1, 0, 0]]), np.asarray([1]), vol)

        answer = volume.zeros(shape, voxelspacing=1, origin=(1,0,0))
        answer.array[0, 0, 0] = 1
        answer.array[0, 0, 1] = 1
        answer.array[0, 0, -1] = 1
        answer.array[0, 1, 0] = 1
        answer.array[0, -1, 0] = 1
        answer.array[1, 0, 0] = 1
        answer.array[-1, 0, 0] = 1

        self.assertTrue(np.allclose(answer.array, vol.array))
コード例 #2
0
ファイル: fullsaxs.py プロジェクト: latrocinia/saxstools
def rsurface(points, radius, shape, voxelspacing):

    dimensions = [x*voxelspacing for x in shape]
    origin = volume_origin(points, dimensions)
    rsurf = volume.zeros(shape, voxelspacing, origin)

    rsurf = dilate_points(points, radius, rsurf)

    return rsurf
コード例 #3
0
    print(pdbs[2 * n + 1], pdbs[2 * n])
    try:
        p1 = PDB.fromfile(pdbs[2 * n + 1])
        p2 = PDB.fromfile(pdbs[2 * n])

        shape = grid_shape(p1.coor, p2.coor, VOXELSPACING)

        vdw_radii = p1.vdw_radius
        radii = vdw_radii + 3.0

        rsurf = rsurface(p1.coor, radii, shape, VOXELSPACING)
        rcore = rsurface(p1.coor, vdw_radii, shape, VOXELSPACING)

        lsurf = rsurf.duplicate()
        lsurf._array.fill(0)
        lsurf = dilate_points(p2.coor, p2.vdw_radius, lsurf)

        #rsurf.tofile('rsurf.mrc')
        #rcore.tofile('rcore.mrc')
        #lsurf.tofile('lsurf.mrc')

        overlap = (rsurf.array * lsurf.array).sum()
        clash = (rcore.array * lsurf.array).sum()
        overlaps.append(overlap)
        cores.append(clash)

        print(pdbs[2 * n][:4])
        print('overlap: ', overlap)
        print('clash: ', clash)
        print()
    except:
コード例 #4
0
ファイル: analyze.py プロジェクト: latrocinia/disvis
    print(pdbs[2 * n + 1], pdbs[2 * n])
    try:
        p1 = PDB.fromfile(pdbs[2 * n + 1])
        p2 = PDB.fromfile(pdbs[2 * n])

        shape = grid_shape(p1.coor, p2.coor, VOXELSPACING)

        vdw_radii = p1.vdw_radius
        radii = vdw_radii + 3.0

        rsurf = rsurface(p1.coor, radii, shape, VOXELSPACING)
        rcore = rsurface(p1.coor, vdw_radii, shape, VOXELSPACING)

        lsurf = rsurf.duplicate()
        lsurf._array.fill(0)
        lsurf = dilate_points(p2.coor, p2.vdw_radius, lsurf)

        # rsurf.tofile('rsurf.mrc')
        # rcore.tofile('rcore.mrc')
        # lsurf.tofile('lsurf.mrc')

        overlap = (rsurf.array * lsurf.array).sum()
        clash = (rcore.array * lsurf.array).sum()
        overlaps.append(overlap)
        cores.append(clash)

        print(pdbs[2 * n][:4])
        print("overlap: ", overlap)
        print("clash: ", clash)
        print()
    except:
コード例 #5
0
ファイル: fullsaxs.py プロジェクト: latrocinia/saxstools
    def _initialize(self):

        # check if requirements are set
        if any(x is None for x in (self.receptor, self.ligand)):
            raise ValueError("Not all requirements are met for a search")

        if self.weights is None:
            self.weights = np.ones(self.rotations.shape[0], dtype=np.float64)

        if len(self.weights) != len(self.rotations):
            raise ValueError("")

        d = self.data

        # determine size for grid
        shape = grid_shape(self.receptor.coor, self.ligand.coor, self.voxelspacing)

        # calculate the interaction surface and core of the receptor
        vdw_radii = self.receptor.vdw_radius
        radii = vdw_radii + self.interaction_radius
        d['rsurf'] = rsurface(self.receptor.coor, radii, 
                shape, self.voxelspacing)
        d['rcore'] = rsurface(self.receptor.coor, vdw_radii, 
                shape, self.voxelspacing)

        # keep track of some data for later calculations
        d['origin'] = np.asarray(d['rcore'].origin, dtype=np.float64)
        d['shape'] = d['rcore'].shape
        d['start'] = d['rcore'].start
        d['nrot'] = self.rotations.shape[0]

        # set ligand center to the origin of the receptor map
        # and make a grid of the ligand
        radii = self.ligand.vdw_radius
        d['lsurf'] = dilate_points((self.ligand.coor - self.ligand.center \
                + self.receptor.center), radii, volume.zeros_like(d['rcore']))
        d['im_center'] = np.asarray((self.receptor.center - d['rcore'].origin)/self.voxelspacing, dtype=np.float64)

        d['max_clash'] = self.max_clash/self.voxelspacing**3
        d['min_interaction'] = self.min_interaction/self.voxelspacing**3

        # SAXS data
	d['q'] = self._q
        d['targetIq'] = self._Iq
	d['sq'] = self._sq

        if self.coarse_grain:
            e1, xyz1 = coarse_grain(self.receptor, bpr=self.beads_per_residue)
            e2, xyz2 = coarse_grain(self.ligand, bpr=self.beads_per_residue)

        else:
            e1, xyz1 = self.receptor.elements, self.receptor.coor
            e2, xyz2 = self.ligand.elements, self.ligand.coor

        d['base_Iq'] = scattering_curve(self._q, e1, xyz1, bpr=self.beads_per_residue)
        d['base_Iq'] += scattering_curve(self._q, e2, xyz2, bpr=self.beads_per_residue)

        d['fifj'], d['rind'], d['lind'] = create_fifj_lookup_table(d['q'], e1, e2, bpr=self.beads_per_residue)
        d['rxyz'] = xyz1
        d['lxyz'] = xyz2 - self.ligand.center

        d['chi2'] = np.zeros(d['rcore'].shape, dtype=np.float64)
        d['best_chi2'] = np.zeros_like(d['chi2'])