Package schrodinger :: Package test :: Package stu :: Package outcomes :: Package custom :: Module glide

Module glide

Functions

_get_property(ct, propname, filename, index)
Thin wrapper to get a property from a CT, returning an error message that will be usable by users of STU if the property doesn't exist.

property_is_consistent(filename, propname, tolerance=0.0)
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.

properties_do_not_exist(filename, *properties)
Check that none of the structures in the specified file have any of the specified properties.

_compare_prop(ct1, ct2, prop, tol=1e-06)

score_input_pose_test(dock_raw, sip_raw)
Compare the second pose from the docking raw file with the first pose from the score-in-place raw file.

check_constraint(filename, ctype, label, atom, index)
Check that a grid file has the expected constraint by type, label, atom, and index.

check_dihedral(filename, smarts, expected_value, tolerance)
Measure the dihedrals matching 'smarts' on the first structure in 'filename', and make sure that they are within 'tolerance' of 'expected_value'.

_find_distortions(ct, tolerance=15.0, max_distortions=None)
Return a list of distortions given a structure.

check_libfile_for_required_constraints(basename, nreqcons)
Checks to see that all of the returned poses satisfy the minimum number of constraints.

check_for_distorted_angles(filename, tolerance=15.0, first=1, last=None)
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.

_check_xp_components(index, urh, tol=1e-06)
Make sure that the r_glide_XP properties present in the current block add up to r_glide_XP_GScore.

check_xp_components(filename)
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.

Variables

[hide private]

ALLOWED_ANGLES = [('*1**1', [60.0]), ('*1***1', [90.0]), ('*_,...

__package__ = 'schrodinger.test.stu.outcomes.custom'

Function Details

[hide private]

_get_property(ct, propname, filename, index)

Thin wrapper to get a property from a CT, returning an error message that will be usable by users of STU if the property doesn't exist. (filename and index are only used for constructing the error message.)

score_input_pose_test(dock_raw, sip_raw)

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.

check_constraint(filename, ctype, label, atom, index)

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.

check_dihedral(filename, smarts, expected_value, tolerance)

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.

_find_distortions(ct, tolerance=15.0, max_distortions=None)

Return a list of distortions given a structure. A distortion is an angle that's different from one of the ideal angles by more than "tolerance" in degrees. Returns a list of tuples (atoms, angle, distortion), where atoms is a tuple of three ints.

check_libfile_for_required_constraints(basename, nreqcons)

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.

Variables Details

[hide private]

ALLOWED_ANGLES

Value:

[('*1**1', [60.0]),
 ('*1***1', [90.0]),
 ('*_,~[#6,#7,#8,#16,#17]_,~*', [100.0, 120.0, 180.0])]