schrodinger.test.stu.outcomes.custom.glide module

schrodinger.test.stu.outcomes.custom.glide.property_is_consistent(filename, propname, tolerance=0.0)[source]

Check that the value of a numeric property for all structures in a file are within ‘tolerance’ of the value for the first structure in the file.

schrodinger.test.stu.outcomes.custom.glide.properties_do_not_exist(filename, *properties)[source]

Check that none of the structures in the specified file have any of the specified properties.

schrodinger.test.stu.outcomes.custom.glide.score_input_pose_test(dock_raw, sip_raw)[source]

Compare the second pose from the docking raw file with the first pose from the score-in-place raw file. The GlideScore and coordinates should be essentially identical, and the docked pose should have the b_i_glide_inputpose property.

schrodinger.test.stu.outcomes.custom.glide.check_constraint(filename, ctype, label, atom, index)[source]

Check that a grid file has the expected constraint by type, label, atom, and index. The index is 1-based. The atom argument is ignored if <= 0.

schrodinger.test.stu.outcomes.custom.glide.check_dihedral(filename, smarts, expected_value, tolerance)[source]

Measure the dihedrals matching ‘smarts’ on the first structure in ‘filename’, and make sure that they are within ‘tolerance’ of ‘expected_value’. All values are in degrees. It is considered a failure for the pattern not to match the structure, or for the pattern not to match four atoms.

schrodinger.test.stu.outcomes.custom.glide.check_libfile_for_required_constraints(basename, nreqcons)[source]

Checks to see that all of the returned poses satisfy the minimum number of constraints. Should no poses be reported, this test will pass. We are only trying to catch returned poses lacking the required number of constraints here.

schrodinger.test.stu.outcomes.custom.glide.check_for_distorted_angles(filename, tolerance=15.0, first=1, last=None)[source]

Passes if all the structures in a file are “clean”, meaning that no bond angles are more than ‘tolerance’ degrees away from their expected values.

schrodinger.test.stu.outcomes.custom.glide.check_xp_components(filename)[source]

Given a lib file generated by an XP job with descriptors, make sure that the sum of all the scoring components equals the total score.

schrodinger.test.stu.outcomes.custom.glide.check_wscore_components(filename)[source]

Given a lib file generated by a Glide docking job with WScore mode active, make sure that the sum of all the scoring components equals the total score.

schrodinger.test.stu.outcomes.custom.glide.check_poses_for_specific_scoring_term(filename, expected_term, expected_value=None, min_abs_expected_value=None, expected_i_lig_atom=None, expected_i_prot_atom=None)[source]

Make sure that a particular scoring term has a non-zero value for each of the ct’s in the input filename. Note, we will skip any cts which have the Glide receptor property, “b_glide_receptor” set to True.

If the term is expected to have a specific value, the expected_value optional argument can be used.

If the term is expected to have a minimum value, min_abs_expected_value can be supplied. The absolute value is used so that this can refer to a reward which may be negative, or a penalty which may be positive. This is a less than or equal comparison.

If the term is expected to only occur on a specific ligand or protein atom, then expected_i_lig_atom or expected_i_prot_atom can be set. If both are supplied, then both are used.

expected_i_lig_atom and expected_i_prot_atom can be an int or a list of int if the penalty applies to multiple atoms.

To pass a list of ints in a stu workup, enclose the list in quotes. For example: expected_i_lig_atom=”[10, 11, 14, 16]”

schrodinger.test.stu.outcomes.custom.glide.measure_smarts(filename, smarts, expected_value, tolerance)[source]

Measure the distance/angle/dihedral matching smarts on each structure in filename, and make sure that they are within tolerance of expected_value. The SMARTS pattern must match 2, 3, or 4 atoms for measuring distance, angle, or dihedrals, respectively.