Esempio n. 1
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    def test_molecule_loop(self):
        """Test the proper operation of the molecule loop with molecule selection.

        The function tested is pipe_control.mol_res_spin.molecule_loop().
        """

        # Loop over the molecules.
        for mol in mol_res_spin.molecule_loop('#RNA'):
            # Test the molecule name.
            self.assertEqual(mol.name, 'RNA')

        # Test loop length.
        self.assertEqual(len(list(mol_res_spin.molecule_loop('#RNA'))), 1)
Esempio n. 2
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    def test_molecule_loop(self):
        """Test the proper operation of the molecule loop with molecule selection.

        The function tested is pipe_control.mol_res_spin.molecule_loop().
        """

        # Loop over the molecules.
        for mol in mol_res_spin.molecule_loop('#RNA'):
            # Test the molecule name.
            self.assertEqual(mol.name, 'RNA')

        # Test loop length.
        self.assertEqual(len(list(mol_res_spin.molecule_loop('#RNA'))), 1)
Esempio n. 3
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    def update(self, pipe_name=None):
        """Update the tree view using the given data pipe."""

        # Acquire the pipe and spin locks.
        status.pipe_lock.acquire('spin viewer window')
        status.spin_lock.acquire('spin viewer window')
        try:
            # The data pipe.
            if not pipe_name:
                pipe = cdp
            else:
                pipe = get_pipe(pipe_name)

            # No data pipe, so delete everything and return.
            if not pipe:
                self.tree.DeleteChildren(self.root)
                return

            # Update the molecules.
            for mol, mol_id in molecule_loop(return_id=True):
                self.update_mol(mol, mol_id)

            # Remove any deleted molecules.
            self.prune_mol()

        # Release the locks.
        finally:
            status.pipe_lock.release('spin viewer window')
            status.spin_lock.release('spin viewer window')
Esempio n. 4
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    def update(self, pipe_name=None):
        """Update the tree view using the given data pipe."""

        # Acquire the pipe and spin locks.
        status.pipe_lock.acquire('spin viewer window')
        status.spin_lock.acquire('spin viewer window')
        try:
            # The data pipe.
            if not pipe_name:
                pipe = cdp
            else:
                pipe = get_pipe(pipe_name)

            # No data pipe, so delete everything and return.
            if not pipe:
                self.tree.DeleteChildren(self.root)
                return

            # Update the molecules.
            for mol, mol_id in molecule_loop(return_id=True):
                self.update_mol(mol, mol_id)

            # Remove any deleted molecules.
            self.prune_mol()

        # Release the locks.
        finally:
            status.pipe_lock.release('spin viewer window')
            status.spin_lock.release('spin viewer window')
Esempio n. 5
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    def update_data(self):
        """Method called from self.build_element_safe() to update the list data."""

        # Expand the number of rows to match the number of molecules, and add the data.
        i = 0
        for mol, mol_id in molecule_loop(return_id=True):
            # Set the index.
            self.element.InsertStringItem(i, str_to_gui(mol_id))

            # Set the molecule name.
            if mol.name != None:
                self.element.SetStringItem(i, 1, str_to_gui(mol.name))

            # Set the molecule type.
            if hasattr(mol, 'type'):
                self.element.SetStringItem(i, 2, str_to_gui(mol.type))

            # Set the thiol state.
            if hasattr(cdp, 'exp_info') and hasattr(cdp.exp_info,
                                                    'thiol_state'):
                self.element.SetStringItem(
                    i, 3, str_to_gui(cdp.exp_info.thiol_state))

            # Increment the counter.
            i += 1
Esempio n. 6
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    def is_complete(self):
        """Determine if the data input is complete.

        @return:    A list of all the missing components.
        @rtype:     list of str
        """

        # Initialise.
        missing = []

        # Relaxation data metadata.
        if hasattr(cdp, 'ri_ids'):
            # Loop over the data.
            for i in range(len(cdp.ri_ids)):
                # Check the peak intensity types.
                if not hasattr(cdp, 'exp_info') or not hasattr(
                        cdp.exp_info, 'peak_intensity_type'
                ) or not cdp.ri_ids[i] in cdp.exp_info.peak_intensity_type:
                    missing.append(
                        "The peak intensity type for the relaxation data ID '%s'."
                        % cdp.ri_ids[i])

                # Check the temperature calibration methods.
                if not hasattr(cdp, 'exp_info') or not hasattr(
                        cdp.exp_info, 'temp_calibration'
                ) or not cdp.ri_ids[i] in cdp.exp_info.temp_calibration:
                    missing.append(
                        "The temperature calibration method for the relaxation data ID '%s'."
                        % cdp.ri_ids[i])

                # Check the temperature control methods.
                if not hasattr(cdp, 'exp_info') or not hasattr(
                        cdp.exp_info, 'temp_control'
                ) or not cdp.ri_ids[i] in cdp.exp_info.temp_control:
                    missing.append(
                        "The temperature control method for the relaxation data ID '%s'."
                        % cdp.ri_ids[i])

        # Loop over the molecules.
        for mol, mol_id in molecule_loop(return_id=True):
            # No name.
            if mol.name == None:
                missing.append("The name of the molecule for %s." % mol_id)
                continue

            # No molecule type.
            if not hasattr(mol, 'type') or mol.type == None:
                missing.append("The type of the molecule %s." % mol_id)

            # No thiol state.
            if not hasattr(cdp, 'exp_info') or not hasattr(
                    cdp.exp_info, 'thiol_state'):
                missing.append("The thiol state of the molecule %s." % mol_id)

        # Return the list of missing data.
        return missing
Esempio n. 7
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    def test_molecule_loop_no_selection(self):
        """Test the proper operation of the molecule loop when no selection is present.

        The function tested is pipe_control.mol_res_spin.molecule_loop().
        """

        # Molecule data.
        name = ['Ap4Aase', 'RNA']

        # Loop over the molecules.
        i = 0
        for mol in mol_res_spin.molecule_loop():
            # Test the molecule names.
            self.assertEqual(mol.name, name[i])

            # Increment i.
            i = i + 1

        # Test loop length.
        self.assertEqual(len(list(mol_res_spin.molecule_loop())), 2)
Esempio n. 8
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    def test_molecule_loop_no_selection(self):
        """Test the proper operation of the molecule loop when no selection is present.

        The function tested is pipe_control.mol_res_spin.molecule_loop().
        """

        # Molecule data.
        name = ['Ap4Aase', 'RNA']

        # Loop over the molecules.
        i = 0
        for mol in mol_res_spin.molecule_loop():
            # Test the molecule names.
            self.assertEqual(mol.name, name[i])

            # Increment i.
            i = i + 1

        # Test loop length.
        self.assertEqual(len(list(mol_res_spin.molecule_loop())), 2)
Esempio n. 9
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    def is_complete(self):
        """Determine if the data input is complete.

        @return:    A list of all the missing components.
        @rtype:     list of str
        """

        # Initialise.
        missing = []

        # Relaxation data metadata.
        if hasattr(cdp, 'ri_ids'):
            # Loop over the data.
            for i in range(len(cdp.ri_ids)):
                # Check the peak intensity types.
                if not hasattr(cdp, 'exp_info') or not hasattr(cdp.exp_info, 'peak_intensity_type') or not cdp.ri_ids[i] in cdp.exp_info.peak_intensity_type.keys():
                    missing.append("The peak intensity type for the relaxation data ID '%s'." % cdp.ri_ids[i])

                # Check the temperature calibration methods.
                if not hasattr(cdp, 'exp_info') or not hasattr(cdp.exp_info, 'temp_calibration') or not cdp.ri_ids[i] in cdp.exp_info.temp_calibration.keys():
                    missing.append("The temperature calibration method for the relaxation data ID '%s'." % cdp.ri_ids[i])

                # Check the temperature control methods.
                if not hasattr(cdp, 'exp_info') or not hasattr(cdp.exp_info, 'temp_control') or not cdp.ri_ids[i] in cdp.exp_info.temp_control.keys():
                    missing.append("The temperature control method for the relaxation data ID '%s'." % cdp.ri_ids[i])


        # Loop over the molecules.
        for mol, mol_id in molecule_loop(return_id=True):
            # No name.
            if mol.name == None:
                missing.append("The name of the molecule for %s." % mol_id)
                continue

            # No molecule type.
            if not hasattr(mol, 'type') or mol.type == None:
                missing.append("The type of the molecule %s." % mol_id)

            # No thiol state.
            if not hasattr(cdp, 'exp_info') or not hasattr(cdp.exp_info, 'thiol_state'):
                missing.append("The thiol state of the molecule %s." % mol_id)

        # Return the list of missing data.
        return missing
Esempio n. 10
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    def test_molecule_loop_no_data(self):
        """Test the proper operation of the molecule loop when no data is present.

        The function tested is pipe_control.mol_res_spin.molecule_loop().
        """

        # Reset relax.
        reset()

        # Add a data pipe to the data store.
        ds.add(pipe_name='orig', pipe_type='mf')

        # Loop over the molecules.
        i = 0
        for molecule in mol_res_spin.molecule_loop():
            i = i + 1

        # Test loop length.
        self.assertEqual(i, 0)
Esempio n. 11
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    def test_molecule_loop_no_data(self):
        """Test the proper operation of the molecule loop when no data is present.

        The function tested is pipe_control.mol_res_spin.molecule_loop().
        """

        # Reset relax.
        reset()

        # Add a data pipe to the data store.
        ds.add(pipe_name='orig', pipe_type='mf')

        # Loop over the molecules.
        i = 0
        for molecule in mol_res_spin.molecule_loop():
            i = i + 1

        # Test loop length.
        self.assertEqual(i, 0)
Esempio n. 12
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    def update_data(self):
        """Method called from self.build_element_safe() to update the list data."""

        # Expand the number of rows to match the number of molecules, and add the data.
        i = 0
        for mol, mol_id in molecule_loop(return_id=True):
            # Set the index.
            self.element.InsertStringItem(i, str_to_gui(mol_id))

            # Set the molecule name.
            if mol.name != None:
                self.element.SetStringItem(i, 1, str_to_gui(mol.name))

            # Set the molecule type.
            if hasattr(mol, 'type'):
                self.element.SetStringItem(i, 2, str_to_gui(mol.type))

            # Set the thiol state.
            if hasattr(cdp, 'exp_info') and hasattr(cdp.exp_info, 'thiol_state'):
                self.element.SetStringItem(i, 3, str_to_gui(cdp.exp_info.thiol_state))

            # Increment the counter.
            i += 1
Esempio n. 13
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    def is_complete(self):
        """Determine if the data input is complete.

        @return:    The answer to the question.
        @rtype:     bool
        """

        # Loop over the molecules.
        for mol in molecule_loop():
            # No name.
            if mol.name == None:
                return False

            # No molecule type.
            if not hasattr(mol, 'type') or mol.type == None:
                return False

            # No thiol state.
            if not hasattr(cdp, 'exp_info') or not hasattr(cdp.exp_info, 'thiol_state'):
                return False

        # Data input is complete.
        return True
Esempio n. 14
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    def is_complete(self):
        """Determine if the data input is complete.

        @return:    The answer to the question.
        @rtype:     bool
        """

        # Loop over the molecules.
        for mol in molecule_loop():
            # No name.
            if mol.name == None:
                return False

            # No molecule type.
            if not hasattr(mol, 'type') or mol.type == None:
                return False

            # No thiol state.
            if not hasattr(cdp, 'exp_info') or not hasattr(
                    cdp.exp_info, 'thiol_state'):
                return False

        # Data input is complete.
        return True
Esempio n. 15
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 def fail_test():
     for molecule in mol_res_spin.molecule_loop():
         pass
Esempio n. 16
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 def fail_test():
     for molecule in mol_res_spin.molecule_loop():
         pass