Python loopmodel_template Examples

Example #1

File: test_loopmodel.py Project: MehtapIsik/ensembler

def test_loopmodel_KC1D_HUMAN_D0_4HNF_A():
    with integrationtest_context(set_up_project_stage='templates_resolved'):
        template = Mock()
        template.id = 'KC1D_HUMAN_D0_4HNF_A'
        template.seq = 'YRLGRKIGSGSFGDIYLGTDIAAGEEVAIKLECVKTKHPQLHIESKIYKMMQGGVGIPTIRWCGAEGDYNVMVMELLGPSLEDLFNFCSRKFSLKTVLLLADQMISRIEYIHSKNFIHRDVKPDNFLMGLGKKGNLVYIIDFGLAKKYRDARTHQHIPYRENKNLTGTARYASINTHLGIEQSRRDDLESLGYVLMYFNLGSLPWQGLKAATKRQKYERISEKKMSTPIEVLCKGYPSEFATYLNFCRSLRFDDKPDYSYLRQLFRNLF'

        missing_residues = pdbfix_template(template)
        loopmodel_template(template, missing_residues)

        assert os.path.exists(os.path.join('templates', 'structures-modeled-loops', 'KC1D_HUMAN_D0_4HNF_A.pdb'))

Example #2

def test_loopmodel_KC1D_HUMAN_D0_4HNF_A():
    with integrationtest_context(set_up_project_stage='templates_resolved'):
        template = Mock()
        template.id = 'KC1D_HUMAN_D0_4HNF_A'
        template.seq = 'YRLGRKIGSGSFGDIYLGTDIAAGEEVAIKLECVKTKHPQLHIESKIYKMMQGGVGIPTIRWCGAEGDYNVMVMELLGPSLEDLFNFCSRKFSLKTVLLLADQMISRIEYIHSKNFIHRDVKPDNFLMGLGKKGNLVYIIDFGLAKKYRDARTHQHIPYRENKNLTGTARYASINTHLGIEQSRRDDLESLGYVLMYFNLGSLPWQGLKAATKRQKYERISEKKMSTPIEVLCKGYPSEFATYLNFCRSLRFDDKPDYSYLRQLFRNLF'

        missing_residues = pdbfix_template(template)
        loopmodel_template(template, missing_residues)

        assert os.path.exists(os.path.join('templates', 'structures-modeled-loops', 'KC1D_HUMAN_D0_4HNF_A.pdb'))

Example #3

File: test_loopmodel.py Project: MehtapIsik/ensembler

def test_loopmodel_KC1D_HUMAN_D0_3UZP_A():
    """
    No missing residues
    """
    with integrationtest_context(set_up_project_stage='templates_resolved'):
        template = Mock()
        template.id = 'KC1D_HUMAN_D0_3UZP_A'
        template.seq = 'YRLGRKIGSGSFGDIYLGTDIAAGEEVAIKLECVKTKHPQLHIESKIYKMMQGGVGIPTIRWCGAEGDYNVMVMELLGPSLEDLFNFCSRKFSLKTVLLLADQMISRIEYIHSKNFIHRDVKPDNFLMGLGKKGNLVYIIDFGLAKKYRDARTHQHIPYRENKNLTGTARYASINTHLGIEQSRRDDLESLGYVLMYFNLGSLPWQGLKAATKRQKYERISEKKMSTPIEVLCKGYPSEFATYLNFCRSLRFDDKPDYSYLRQLFRNLF'

        missing_residues = pdbfix_template(template)
        loopmodel_template(template, missing_residues)

        assert not os.path.exists(os.path.join(ensembler.core.default_project_dirnames.templates_structures_modeled_loops, 'KC1D_HUMAN_D0_3UZP_A.pdb'))
        log = yaml.load(open(os.path.join(ensembler.core.default_project_dirnames.templates_structures_modeled_loops, 'KC1D_HUMAN_D0_3UZP_A-loopmodel-log.yaml')))
        assert log['no_missing_residues'] == True

Example #4

def test_loopmodel_KC1D_HUMAN_D0_3UZP_A():
    """
    No missing residues
    """
    with integrationtest_context(set_up_project_stage='templates_resolved'):
        template = Mock()
        template.id = 'KC1D_HUMAN_D0_3UZP_A'
        template.seq = 'YRLGRKIGSGSFGDIYLGTDIAAGEEVAIKLECVKTKHPQLHIESKIYKMMQGGVGIPTIRWCGAEGDYNVMVMELLGPSLEDLFNFCSRKFSLKTVLLLADQMISRIEYIHSKNFIHRDVKPDNFLMGLGKKGNLVYIIDFGLAKKYRDARTHQHIPYRENKNLTGTARYASINTHLGIEQSRRDDLESLGYVLMYFNLGSLPWQGLKAATKRQKYERISEKKMSTPIEVLCKGYPSEFATYLNFCRSLRFDDKPDYSYLRQLFRNLF'

        missing_residues = pdbfix_template(template)
        loopmodel_template(template, missing_residues)

        assert not os.path.exists(os.path.join(ensembler.core.default_project_dirnames.templates_structures_modeled_loops, 'KC1D_HUMAN_D0_3UZP_A.pdb'))
        log = yaml.load(open(os.path.join(ensembler.core.default_project_dirnames.templates_structures_modeled_loops, 'KC1D_HUMAN_D0_3UZP_A-loopmodel-log.yaml')))
        assert log['no_missing_residues'] == True