Module prime_workups

Iterator that returns the specified frames of the structures in filename {structure} By default return all frames, but if frames_to_check { list, set or anything with an "__in__" method" of integers} is set then the only frames for which their index (starting with 0) are in frames to check are returned. Note that even if a list is passed with integers out of order, the frames will always be yielded in the order that they are in the file.

STU workup that will check to see if a list of moved residues { string the residue names (__str__() evaluation of the structure._Residue class) separated by spaces} corresponds to the list of all residue that have an an atom that moved more than tolerance {float} between any of the frames_to_check in filename (see partial_structure_reader) and the first structure frame in reference_fn. Returns True if the lists match, False if they dont if check_bacbone_dihedrals{logical} is True then check use the residues that either their phi or psi angle moved by more than tolerance degrees are used instead of distance in cartesian space

Use the featurs in structurecheck to identify potential problems in the structure. By default this will find any instances where there is a steric clash of more than 30% of the vdW radius (set by steric delta {float}) or any bond length deviations of more than 0.15 angstroms (set by bond_length_deviation {float}) The number of allowable clashes, bond length deviations and other structual properties can be set by passing a dictionary into protein_health_kwargs {dict} as decirbed in the help for structurecheck.ProteinReportCheck. frames_to_check is descirbed above Note that protein_health_kwargs needs to have a dictionary passed to it to be useful as a STU test. Currently STU does not allow this.

For a given structure ct1 {structure.Structure} and the Plop residue or atom name name1 {string, described in psp_util.convertPlopResToAsl} and a second ct2 {structure.Structure}, name2 {string} pair following the same convention, return the minimum distance between the two. If either name matches no values in the structure then None is returned.

STU workup For the specified structure frames in a filename {string} return True if the minimum distance between the atom or residue name1 {string} is distance {float} +- tolerance{float} Angstroms. Otherwise return false (see partial_structrue_reader for description of frames_to check)

STU workup
For the specified structure frames in a filename {string} return True
if the residues match the residues listed in residues {string,
   space separted list of residue names as given by the __str__
   operator of structure._Residue} then return True 
(see partial_structrue_reader for description of frames_to check)

STU workup For the specified structure frames in a filename {string} return True if all contain the specified numbers of atoms{integer}, residues{integer}, and molecules{integer}, If any of these are not set then that test is skipped. Otherwise return False. (see partial_structrue_reader for description of frames_to check)

STU Workup For a specified structure in a filename {string} return True if the property named property_name{string} is equal to value {any type} If tolerance is ">", "<", ">=" or "<=" than use that operation instead of equals. Otherwise is tolerance is provided and not in the above list than return True iff all frames are within tolerance of value.