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_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.

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.

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])]