Impact class needs to be tested

[martimunicoy]

Impact class needs to be tested

[martimunicoy]

Cases to be tested

• Impact template should complain when a non parameterized molecule is fetched.
• Writer should be tested

[martimunicoy]

Support

Set of three templates to use as reference: reference_templates.zip

• metz: corresponds to the template we expect to obtain when loading the following molecule:

from offpele.topology import Molecule
from offpele.utils import get_data_file_path
from offpele.template import Impact

pdb_path = get_data_file_path('ligands/methane.pdb')
m = Molecule(pdb_path)
m.parameterize('openff_unconstrained-1.2.1.offxml')

impact = Impact(m)

• malz: corresponds to the template we expect to obtain when loading the following molecule:

from offpele.topology import Molecule
from offpele.utils import get_data_file_path
from offpele.template import Impact

pdb_path = get_data_file_path('ligands/malonate.pdb')
m = Molecule(pdb_path)
m.parameterize('openff_unconstrained-1.2.1.offxml')

impact = Impact(m)

• etlz: corresponds to the template we expect to obtain when loading the following molecule:

from offpele.topology import Molecule
from offpele.utils import get_data_file_path
from offpele.template import Impact

pdb_path = get_data_file_path('ligands/ethylene.pdb')
m = Molecule(pdb_path, tag='ETL')  # Note that in this case we are assigning a tag to the molecule which will be used in the Impact template
m.parameterize('openff_unconstrained-1.2.1.offxml')

impact = Impact(m)

[laumalo]

Implementation

The following script has been implemented in order to test the class Impact: test_templates.py

Example

from test_templates import TestImpactTemplate
test = TestImpactTemplate()

• Impact template should complain when a non parameterized molecule is fetched or the input format is incorrect:

test.test_input()

• Testing the writer with a reference template using OFF:

test.test_writer_OFF()

• Testing the writer with a reference template using OPLS:

test.test_writer_OPLS()

[martimunicoy]

Support 2

I am attaching three reference Impact templates (corresponding to the ligands introduced in my previous post) obtained with the OPLS2005 force field: OPLS_reference_templates.zip