Beispiel #1
0
    def test_write_list(self):
        """Test the lib.software.sparky.write_list() function."""

        # The data.
        res_names = ['LEU', 'GLY', 'SER', 'MET', 'TRP', 'TRP', 'ASN']
        res_nums = [3, 4, 5, 6, 40, 40, 55]
        atom1_names = ['N', 'N', 'N', 'N', 'N', 'NE1', 'N']
        atom2_names = ['HN', 'HN', 'HN', 'HN', 'HN', 'HE1', 'HN']
        w1 = [122.454, 111.978, 115.069, 120.910, 123.335, 130.204, 116.896]
        w2 = [8.397, 8.720, 8.177, 8.813, 8.005, 10.294, 7.468]
        heights = [2535, 5050, 51643, 53663, -65111, -181131, -105322]

        # The result.
        file_data = [
            '      Assignment         w1         w2   Data Height\n',
            '\n',
            '         LEU3N-HN    122.454      8.397         2535\n',
            '         GLY4N-HN    111.978      8.720         5050\n',
            '         SER5N-HN    115.069      8.177        51643\n',
            '         MET6N-HN    120.910      8.813        53663\n',
            '        TRP40N-HN    123.335      8.005       -65111\n',
            '     TRP40NE1-HE1    130.204     10.294      -181131\n',
            '        ASN55N-HN    116.896      7.468      -105322\n'
        ]

        # Write the data out.
        file = DummyFileObject()
        write_list(file_prefix=file, res_names=res_names, res_nums=res_nums, atom1_names=atom1_names, atom2_names=atom2_names, w1=w1, w2=w2, data_height=heights)

        # Check the file data.
        lines = file.readlines()
        self.assertEqual(len(lines), len(file_data))
        for i in range(len(lines)):
            self.assertEqual(lines[i], file_data[i])
Beispiel #2
0
    def test_write_list(self):
        """Test the lib.software.sparky.write_list() function."""

        # The data.
        res_names = ['LEU', 'GLY', 'SER', 'MET', 'TRP', 'TRP', 'ASN']
        res_nums = [3, 4, 5, 6, 40, 40, 55]
        atom1_names = ['N', 'N', 'N', 'N', 'N', 'NE1', 'N']
        atom2_names = ['HN', 'HN', 'HN', 'HN', 'HN', 'HE1', 'HN']
        w1 = [122.454, 111.978, 115.069, 120.910, 123.335, 130.204, 116.896]
        w2 = [8.397, 8.720, 8.177, 8.813, 8.005, 10.294, 7.468]
        heights = [2535, 5050, 51643, 53663, -65111, -181131, -105322]

        # The result.
        file_data = [
            '      Assignment         w1         w2   Data Height\n', '\n',
            '         LEU3N-HN    122.454      8.397         2535\n',
            '         GLY4N-HN    111.978      8.720         5050\n',
            '         SER5N-HN    115.069      8.177        51643\n',
            '         MET6N-HN    120.910      8.813        53663\n',
            '        TRP40N-HN    123.335      8.005       -65111\n',
            '     TRP40NE1-HE1    130.204     10.294      -181131\n',
            '        ASN55N-HN    116.896      7.468      -105322\n'
        ]

        # Write the data out.
        file = DummyFileObject()
        write_list(file_prefix=file,
                   res_names=res_names,
                   res_nums=res_nums,
                   atom1_names=atom1_names,
                   atom2_names=atom2_names,
                   w1=w1,
                   w2=w2,
                   data_height=heights)

        # Check the file data.
        lines = file.readlines()
        self.assertEqual(len(lines), len(file_data))
        for i in range(len(lines)):
            self.assertEqual(lines[i], file_data[i])
Beispiel #3
0
                # The rate.
                nomen = pA * pB * dw[spin_index]**2 * kex
                denom = omega_aeff2[spin_index] * omega_beff2[
                    spin_index] / omega_eff2[spin_index] + kex**2
                rx = r1[spin_index, frq_index] * cos_theta2 + sin_theta2 * (
                    r1rho_prime[spin_index, frq_index] + nomen / denom)

                # The peak intensity.
                intensities.append(i0[spin_index, frq_index] *
                                   exp(-rx * times[time_index]))

            # Create a Sparky .list file.
            if time_index == 0 and spin_lock_index == 0:
                name = 'ref_%s' % frq_label[frq_index]
            elif time_index == 0:
                name = None
            else:
                name = 'nu_%s_%s' % (spin_lock[spin_lock_index],
                                     frq_label[frq_index])
            if name:
                write_list(file_prefix=name,
                           dir=None,
                           res_names=res_names,
                           res_nums=res_nums,
                           atom1_names=atomN_names,
                           atom2_names=atomH_names,
                           w1=wN,
                           w2=wH,
                           data_height=intensities)
Beispiel #4
0
        omega_beff2 = omega1**2 + delta_b**2
        omega_eff2 = omega1**2 + delta_ave**2

        # Loop over the relaxation times.
        for time_index in range(len(times)):
            # Loop over the spins.
            intensities = []
            for spin_index in range(len(r1rho_prime)):
                # Spin dependent parameters.
                theta = atan(omega1 / delta_ave[spin_index])
                sin_theta2 = sin(theta)**2
                cos_theta2 = cos(theta)**2

                # The rate.
                nomen = pA * pB * dw[spin_index]**2 * kex
                denom = omega_aeff2[spin_index] * omega_beff2[spin_index] / omega_eff2[spin_index] + kex**2
                rx = r1[spin_index, frq_index] * cos_theta2 + sin_theta2 * (r1rho_prime[spin_index, frq_index] + nomen / denom)
    
                # The peak intensity.
                intensities.append(i0[spin_index, frq_index] * exp(-rx*times[time_index]))

            # Create a Sparky .list file.
            if time_index == 0 and spin_lock_index == 0:
                name = 'ref_%s' % frq_label[frq_index]
            elif time_index == 0:
                name = None
            else:
                name = 'nu_%s_%s' % (spin_lock[spin_lock_index], frq_label[frq_index])
            if name:
                write_list(file_prefix=name, dir=None, res_names=res_names, res_nums=res_nums, atom1_names=atomN_names, atom2_names=atomH_names, w1=wN, w2=wH, data_height=intensities)