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Published 20 hours ago • verified publisher icon MolecularAI

No module named 'ccdc'

Open Evert-Homan opened this issue 3 years ago • 4 comments

I believe I successfully installed the normal (not Full) DockStream package as per your instructions on the github site, and then tried to run the unit test, but this fails with a complaint regarding the ccdc module missing (see below). But I want to use Glide so wouldn’t need (nor have) ccdc. I am doing this on Ubuntu 18.04.

Dockstream/python ./unit_tests.py Traceback (most recent call last): File "./unit_tests.py", line 10, in from tests.Gold import * File "/media/data/evehom/Projects/CompChem/DockStream/tests/Gold/init.py", line 1, in from tests.Gold.test_Gold_target_preparation import * File "/media/data/evehom/Projects/CompChem/DockStream/tests/Gold/test_Gold_target_preparation.py", line 11, in from dockstream.core.Gold.Gold_target_preparator import GoldTargetPreparator File "/media/data/evehom/Projects/CompChem/DockStream/dockstream/core/Gold/Gold_target_preparator.py", line 3, in import ccdc ModuleNotFoundError: No module named 'ccdc'

Evert-Homan avatar Feb 02 '22 15:02 Evert-Homan

Hi Evert,

Thanks for using our tools. This is indeed not something that should happen if you are using the normal environment. I see that you are trying to execute the unit tests and for GOLD ones, CCDC is required (there should be a safeguard in place, though).

Can you try to comment out this line in the unit_tests.py: from tests.Gold import *

As for how to execute Glide, that depends on your installation. Do you use a module? Or do you call it from the command-line?

Best, Christian

CMargreitter avatar Feb 02 '22 15:02 CMargreitter

I made the unit_test.py file look like this but I get a lot of error messages when running it:

#!/usr/bin/env python

coding=utf-8

import unittest

from tests import *

from tests.ligand import *

from tests.AutodockVina import *

from tests.RDkit import *

from tests.rDock import *

from tests.Gold import *

from tests.Schrodinger import *

from tests.OpenEye_Hybrid import *

from tests.Corina import *

from tests.TautEnum import *

if name == 'main': unittest.main()

This produces a lot of garbage but maybe it looks OK?

EEEEEEE[17:13:04] SMILES Parse Error: syntax error while parsing: CXXC [17:13:04] SMILES Parse Error: Failed parsing SMILES 'CXXC' for input: 'CXXC' EEEEEEEEEEEEEE.

ERROR: test_aligning_discard (tests.Schrodinger.test_ligprep_ligand_preparation.Test_Ligprep_ligand_preparation)

Traceback (most recent call last): File "/media/data/evehom/Projects/CompChem/DockStream/tests/Schrodinger/test_ligprep_ligand_preparation.py", line 354, in test_aligning_discard prep = LigprepLigandPreparator(ligands=lig_parser.get_ligands(), **conf) File "/media/data/evehom/Projects/CompChem/DockStream/dockstream/core/Schrodinger/Ligprep_ligand_preparator.py", line 108, in init raise LigandPreparationFailed("Cannot initialize Ligprep backend - abort.") dockstream.utils.dockstream_exceptions.LigandPreparationFailed: Cannot initialize Ligprep backend - abort.

====================================================================== ERROR: test_aligning_keep (tests.Schrodinger.test_ligprep_ligand_preparation.Test_Ligprep_ligand_preparation)

Traceback (most recent call last): File "/media/data/evehom/Projects/CompChem/DockStream/tests/Schrodinger/test_ligprep_ligand_preparation.py", line 313, in test_aligning_keep prep = LigprepLigandPreparator(ligands=lig_parser.get_ligands(), **conf) File "/media/data/evehom/Projects/CompChem/DockStream/dockstream/core/Schrodinger/Ligprep_ligand_preparator.py", line 108, in init raise LigandPreparationFailed("Cannot initialize Ligprep backend - abort.") dockstream.utils.dockstream_exceptions.LigandPreparationFailed: Cannot initialize Ligprep backend - abort.

====================================================================== ERROR: test_coordinate_generation (tests.Schrodinger.test_ligprep_ligand_preparation.Test_Ligprep_ligand_preparation)

Traceback (most recent call last): File "/media/data/evehom/Projects/CompChem/DockStream/tests/Schrodinger/test_ligprep_ligand_preparation.py", line 40, in test_coordinate_generation prep = LigprepLigandPreparator(ligands=lig_parser.get_ligands(), **conf) File "/media/data/evehom/Projects/CompChem/DockStream/dockstream/core/Schrodinger/Ligprep_ligand_preparator.py", line 108, in init raise LigandPreparationFailed("Cannot initialize Ligprep backend - abort.") dockstream.utils.dockstream_exceptions.LigandPreparationFailed: Cannot initialize Ligprep backend - abort.

====================================================================== ERROR: test_coordinate_generation_AWS (tests.Schrodinger.test_ligprep_ligand_preparation.Test_Ligprep_ligand_preparation)

Traceback (most recent call last): File "/media/data/evehom/Projects/CompChem/DockStream/tests/Schrodinger/test_ligprep_ligand_preparation.py", line 67, in test_coordinate_generation_AWS prep = LigprepLigandPreparator(ligands=lig_parser.get_ligands(), **conf) File "/media/data/evehom/Projects/CompChem/DockStream/dockstream/core/Schrodinger/Ligprep_ligand_preparator.py", line 108, in init raise LigandPreparationFailed("Cannot initialize Ligprep backend - abort.") dockstream.utils.dockstream_exceptions.LigandPreparationFailed: Cannot initialize Ligprep backend - abort.

====================================================================== ERROR: test_coordinate_generation_parallelized (tests.Schrodinger.test_ligprep_ligand_preparation.Test_Ligprep_ligand_preparation)

Traceback (most recent call last): File "/media/data/evehom/Projects/CompChem/DockStream/tests/Schrodinger/test_ligprep_ligand_preparation.py", line 112, in test_coordinate_generation_parallelized prep = LigprepLigandPreparator(ligands=lig_parser.get_ligands(), **conf) File "/media/data/evehom/Projects/CompChem/DockStream/dockstream/core/Schrodinger/Ligprep_ligand_preparator.py", line 108, in init raise LigandPreparationFailed("Cannot initialize Ligprep backend - abort.") dockstream.utils.dockstream_exceptions.LigandPreparationFailed: Cannot initialize Ligprep backend - abort.

====================================================================== ERROR: test_coordinate_generation_with_Ligprep_stereo (tests.Schrodinger.test_ligprep_ligand_preparation.Test_Ligprep_ligand_preparation)

Traceback (most recent call last): File "/media/data/evehom/Projects/CompChem/DockStream/tests/Schrodinger/test_ligprep_ligand_preparation.py", line 231, in test_coordinate_generation_with_Ligprep_stereo prep = LigprepLigandPreparator(ligands=lig_parser.get_ligands(), **conf) File "/media/data/evehom/Projects/CompChem/DockStream/dockstream/core/Schrodinger/Ligprep_ligand_preparator.py", line 108, in init raise LigandPreparationFailed("Cannot initialize Ligprep backend - abort.") dockstream.utils.dockstream_exceptions.LigandPreparationFailed: Cannot initialize Ligprep backend - abort.

====================================================================== ERROR: test_coordinate_generation_with_Ligprep_stereo_command_line_parameters (tests.Schrodinger.test_ligprep_ligand_preparation.Test_Ligprep_ligand_preparation)

Traceback (most recent call last): File "/media/data/evehom/Projects/CompChem/DockStream/tests/Schrodinger/test_ligprep_ligand_preparation.py", line 255, in test_coordinate_generation_with_Ligprep_stereo_command_line_parameters prep = LigprepLigandPreparator(ligands=lig_parser.get_ligands(), **conf) File "/media/data/evehom/Projects/CompChem/DockStream/dockstream/core/Schrodinger/Ligprep_ligand_preparator.py", line 108, in init raise LigandPreparationFailed("Cannot initialize Ligprep backend - abort.") dockstream.utils.dockstream_exceptions.LigandPreparationFailed: Cannot initialize Ligprep backend - abort.

====================================================================== ERROR: test_coordinate_generation_with_RDkit_stereo (tests.Schrodinger.test_ligprep_ligand_preparation.Test_Ligprep_ligand_preparation)

Traceback (most recent call last): File "/media/data/evehom/Projects/CompChem/DockStream/tests/Schrodinger/test_ligprep_ligand_preparation.py", line 280, in test_coordinate_generation_with_RDkit_stereo prep = LigprepLigandPreparator(ligands=lig_parser.get_ligands(), **conf) File "/media/data/evehom/Projects/CompChem/DockStream/dockstream/core/Schrodinger/Ligprep_ligand_preparator.py", line 108, in init raise LigandPreparationFailed("Cannot initialize Ligprep backend - abort.") dockstream.utils.dockstream_exceptions.LigandPreparationFailed: Cannot initialize Ligprep backend - abort.

====================================================================== ERROR: test_coordinate_generation_with_epik (tests.Schrodinger.test_ligprep_ligand_preparation.Test_Ligprep_ligand_preparation)

Traceback (most recent call last): File "/media/data/evehom/Projects/CompChem/DockStream/tests/Schrodinger/test_ligprep_ligand_preparation.py", line 139, in test_coordinate_generation_with_epik prep = LigprepLigandPreparator(ligands=lig_parser.get_ligands(), **conf) File "/media/data/evehom/Projects/CompChem/DockStream/dockstream/core/Schrodinger/Ligprep_ligand_preparator.py", line 108, in init raise LigandPreparationFailed("Cannot initialize Ligprep backend - abort.") dockstream.utils.dockstream_exceptions.LigandPreparationFailed: Cannot initialize Ligprep backend - abort.

====================================================================== ERROR: test_coordinate_generation_with_epik_and_filtering (tests.Schrodinger.test_ligprep_ligand_preparation.Test_Ligprep_ligand_preparation)

Traceback (most recent call last): File "/media/data/evehom/Projects/CompChem/DockStream/tests/Schrodinger/test_ligprep_ligand_preparation.py", line 189, in test_coordinate_generation_with_epik_and_filtering prep = LigprepLigandPreparator(ligands=lig_parser.get_ligands(), **conf) File "/media/data/evehom/Projects/CompChem/DockStream/dockstream/core/Schrodinger/Ligprep_ligand_preparator.py", line 108, in init raise LigandPreparationFailed("Cannot initialize Ligprep backend - abort.") dockstream.utils.dockstream_exceptions.LigandPreparationFailed: Cannot initialize Ligprep backend - abort.

====================================================================== ERROR: test_coordinate_generation_with_epik_parameters_set (tests.Schrodinger.test_ligprep_ligand_preparation.Test_Ligprep_ligand_preparation)

Traceback (most recent call last): File "/media/data/evehom/Projects/CompChem/DockStream/tests/Schrodinger/test_ligprep_ligand_preparation.py", line 166, in test_coordinate_generation_with_epik_parameters_set prep = LigprepLigandPreparator(ligands=lig_parser.get_ligands(), **conf) File "/media/data/evehom/Projects/CompChem/DockStream/dockstream/core/Schrodinger/Ligprep_ligand_preparator.py", line 108, in init raise LigandPreparationFailed("Cannot initialize Ligprep backend - abort.") dockstream.utils.dockstream_exceptions.LigandPreparationFailed: Cannot initialize Ligprep backend - abort.

====================================================================== ERROR: test_failed_generation (tests.Schrodinger.test_ligprep_ligand_preparation.Test_Ligprep_ligand_preparation)

Traceback (most recent call last): File "/media/data/evehom/Projects/CompChem/DockStream/tests/Schrodinger/test_ligprep_ligand_preparation.py", line 94, in test_failed_generation prep = LigprepLigandPreparator(ligands=lig_parser.get_ligands(), **conf) File "/media/data/evehom/Projects/CompChem/DockStream/dockstream/core/Schrodinger/Ligprep_ligand_preparator.py", line 108, in init raise LigandPreparationFailed("Cannot initialize Ligprep backend - abort.") dockstream.utils.dockstream_exceptions.LigandPreparationFailed: Cannot initialize Ligprep backend - abort.

====================================================================== ERROR: test_Glide_docking_and_result_parsing (tests.Schrodinger.test_Schrodinger_backend.Test_Schrodinger_backend)

Traceback (most recent call last): File "/media/data/evehom/Projects/CompChem/DockStream/tests/Schrodinger/test_Schrodinger_backend.py", line 147, in test_Glide_docking_and_result_parsing docker = Glide(**run_parameters) File "/media/data/evehom/Projects/CompChem/DockStream/dockstream/core/Schrodinger/Glide_docker.py", line 203, in init raise DockingRunFailed("Cannot initialize Glide docker, as Schrodinger backend is not available - abort.") dockstream.utils.dockstream_exceptions.DockingRunFailed: Cannot initialize Glide docker, as Schrodinger backend is not available - abort.

====================================================================== ERROR: test_Glide_docking_and_result_parsing_parallelized (tests.Schrodinger.test_Schrodinger_backend.Test_Schrodinger_backend)

Traceback (most recent call last): File "/media/data/evehom/Projects/CompChem/DockStream/tests/Schrodinger/test_Schrodinger_backend.py", line 207, in test_Glide_docking_and_result_parsing_parallelized docker = Glide(**run_parameters) File "/media/data/evehom/Projects/CompChem/DockStream/dockstream/core/Schrodinger/Glide_docker.py", line 203, in init raise DockingRunFailed("Cannot initialize Glide docker, as Schrodinger backend is not available - abort.") dockstream.utils.dockstream_exceptions.DockingRunFailed: Cannot initialize Glide docker, as Schrodinger backend is not available - abort.

====================================================================== ERROR: test_Glide_docking_and_result_parsing_parallelized_constraints (tests.Schrodinger.test_Schrodinger_backend.Test_Schrodinger_backend)

Traceback (most recent call last): File "/media/data/evehom/Projects/CompChem/DockStream/tests/Schrodinger/test_Schrodinger_backend.py", line 364, in test_Glide_docking_and_result_parsing_parallelized_constraints docker = Glide(**run_parameters) File "/media/data/evehom/Projects/CompChem/DockStream/dockstream/core/Schrodinger/Glide_docker.py", line 203, in init raise DockingRunFailed("Cannot initialize Glide docker, as Schrodinger backend is not available - abort.") dockstream.utils.dockstream_exceptions.DockingRunFailed: Cannot initialize Glide docker, as Schrodinger backend is not available - abort.

====================================================================== ERROR: test_Glide_docking_and_result_parsing_parallelized_enumerated_ligands (tests.Schrodinger.test_Schrodinger_backend.Test_Schrodinger_backend)

Traceback (most recent call last): File "/media/data/evehom/Projects/CompChem/DockStream/tests/Schrodinger/test_Schrodinger_backend.py", line 294, in test_Glide_docking_and_result_parsing_parallelized_enumerated_ligands docker = Glide(**run_parameters) File "/media/data/evehom/Projects/CompChem/DockStream/dockstream/core/Schrodinger/Glide_docker.py", line 203, in init raise DockingRunFailed("Cannot initialize Glide docker, as Schrodinger backend is not available - abort.") dockstream.utils.dockstream_exceptions.DockingRunFailed: Cannot initialize Glide docker, as Schrodinger backend is not available - abort.

====================================================================== ERROR: test_Glide_docking_and_result_parsing_parallelized_subjob_restriction (tests.Schrodinger.test_Schrodinger_backend.Test_Schrodinger_backend)

Traceback (most recent call last): File "/media/data/evehom/Projects/CompChem/DockStream/tests/Schrodinger/test_Schrodinger_backend.py", line 251, in test_Glide_docking_and_result_parsing_parallelized_subjob_restriction docker = Glide(**run_parameters) File "/media/data/evehom/Projects/CompChem/DockStream/dockstream/core/Schrodinger/Glide_docker.py", line 203, in init raise DockingRunFailed("Cannot initialize Glide docker, as Schrodinger backend is not available - abort.") dockstream.utils.dockstream_exceptions.DockingRunFailed: Cannot initialize Glide docker, as Schrodinger backend is not available - abort.

====================================================================== ERROR: test_Glide_docking_with_token_guard (tests.Schrodinger.test_Schrodinger_backend.Test_Schrodinger_backend)

Traceback (most recent call last): File "/media/data/evehom/Projects/CompChem/DockStream/tests/Schrodinger/test_Schrodinger_backend.py", line 416, in test_Glide_docking_with_token_guard docker = Glide(**run_parameters) File "/media/data/evehom/Projects/CompChem/DockStream/dockstream/core/Schrodinger/Glide_docker.py", line 203, in init raise DockingRunFailed("Cannot initialize Glide docker, as Schrodinger backend is not available - abort.") dockstream.utils.dockstream_exceptions.DockingRunFailed: Cannot initialize Glide docker, as Schrodinger backend is not available - abort.

====================================================================== ERROR: test_Glide_input_file_preparation_constraint (tests.Schrodinger.test_Schrodinger_backend.Test_Schrodinger_backend)

Traceback (most recent call last): File "/media/data/evehom/Projects/CompChem/DockStream/tests/Schrodinger/test_Schrodinger_backend.py", line 129, in test_Glide_input_file_preparation_constraint docker = Glide(**run_parameters) File "/media/data/evehom/Projects/CompChem/DockStream/dockstream/core/Schrodinger/Glide_docker.py", line 203, in init raise DockingRunFailed("Cannot initialize Glide docker, as Schrodinger backend is not available - abort.") dockstream.utils.dockstream_exceptions.DockingRunFailed: Cannot initialize Glide docker, as Schrodinger backend is not available - abort.

====================================================================== ERROR: test_Glide_input_file_preparation_simple (tests.Schrodinger.test_Schrodinger_backend.Test_Schrodinger_backend)

Traceback (most recent call last): File "/media/data/evehom/Projects/CompChem/DockStream/tests/Schrodinger/test_Schrodinger_backend.py", line 98, in test_Glide_input_file_preparation_simple docker = Glide(**run_parameters) File "/media/data/evehom/Projects/CompChem/DockStream/dockstream/core/Schrodinger/Glide_docker.py", line 203, in init raise DockingRunFailed("Cannot initialize Glide docker, as Schrodinger backend is not available - abort.") dockstream.utils.dockstream_exceptions.DockingRunFailed: Cannot initialize Glide docker, as Schrodinger backend is not available - abort.

====================================================================== ERROR: test_token_guard_with_execution (tests.Schrodinger.test_token_guard.Test_Schrodinger_token_guard)

Traceback (most recent call last): File "/media/data/evehom/Projects/CompChem/DockStream/tests/Schrodinger/test_token_guard.py", line 37, in test_token_guard_with_execution self.assertTrue(token_guard.guard()) File "/media/data/evehom/Projects/CompChem/DockStream/dockstream/core/Schrodinger/license_token_guard.py", line 101, in guard licadmin_output = self._get_licstat_output() File "/media/data/evehom/Projects/CompChem/DockStream/dockstream/core/Schrodinger/license_token_guard.py", line 77, in _get_licstat_output result = self._executor.execute(command=_EE.LICADMIN, arguments=[_EE.LICADMIN_STAT], check=True) File "/media/data/evehom/Projects/CompChem/DockStream/dockstream/utils/execute_external/execute.py", line 57, in execute location=location) File "/media/data/evehom/Projects/CompChem/DockStream/dockstream/utils/execute_external/execute.py", line 38, in execute shell=True) File "/opt/anaconda3/envs/DockStream/lib/python3.7/subprocess.py", line 512, in run output=stdout, stderr=stderr) subprocess.CalledProcessError: Command '['module load schrodinger/2019-4 && licadmin STAT']' returned non-zero exit status 127.

Ran 22 tests in 1.395s

FAILED (errors=21)

Evert-Homan avatar Feb 02 '22 16:02 Evert-Homan

Hi Evert,

Yes, that's to be expected since Ligprep and Glide cannot be initialized. That brings me back to the question how you load them when you call them normally from the command-line: Are you using a module (then we need to set "prefix_execution") or do you set $SCHRODINGER manually and call a path (then exporting $SCHRODINGER in the header and setting the "binary_path" is necessary)?

CMargreitter avatar Feb 02 '22 16:02 CMargreitter

Hi,

I usually just click on the Maestro icon to start the Schrodinger software :-). But otherwise I set $SCHRODINGER manually to where the suite is installed through my .bashrc (export SCHRODINGER=/opt/schrodinger/2021-4). To be honest I am a novice when it comes to Python so how would I specify this in the unit_test.py file?

Thx/Evert

Evert-Homan avatar Feb 03 '22 08:02 Evert-Homan