B d@sddlmZmZmZddlmZddlZddlmZddl m Z ddZ d.dd Z d/d d Z ddZddZddZddZddZddZGdddeZddZddZd d!Zd0d"d#Zd1d$d%Zd2d'd(Zd3d)d*Zd4d,d-ZdS)5)absolute_importdivisionprint_function)objectN)matrix)rangecCs||k||kS)zT cmp(x, y) -> integer Return negative if xy. )xyrrp/mnt/filia/a/genomebrowser/www/genomebrowser/fleming/tools/molprobity/modules/cctbx_project/libtbx/math_utils.pycmpsr cCsHd|}|dkr*tt||d|Stt||d|SdS)a Python 3 defaults to rounding to the nearest even number (round half to even), so this function keeps the Python 2 behavior, which is rounding half away from zero. References: https://docs.python.org/3.7/library/functions.html#round https://en.wikipedia.org/wiki/Rounding#Round_half_to_even https://docs.python.org/2.7/library/functions.html#round https://en.wikipedia.org/wiki/Rounding#Round_half_away_from_zero Function from: http://python3porting.com/differences.html#rounding-behavior rg?N)floatmathfloorceil)r dprrr round2srFcCst|tr~t|rtdSt|td|ksDt|td|krtdd|}|d|7}||}|rl|St|St||St|trx"t|D]\}}t||||<qWt|t rt|}x"t|D]\}}t||||<qWt |}t|t j r0t|}x$t|D]\}}t||||<q Wt |}t|t j r|j }t|}x$t|D]\}}t||||<qVWt j ||d}|S)a{ round off all floats in a list (or tuple) of list (or tuples) recursively using round2() defined above as in: >>> math_utils.roundoff( [12.3454, 7.4843, ["foo", (35.3581, -0.3856, [4.2769, 3.2147] )] ]) [12.345, 7.484, ['foo', (35.358, -0.386, [4.277, 3.215])]] If value is less than 10**-precision or greater than 10**precision then return with scientific notation nanz1e-%dz9e%d%z%dz.%de)Zelemsn) isinstancerrisnanabsrlist enumerateroundofftuplerZsqrZrecr)val precisionZ as_stringZfstrZval2strivZvalnrrr r%s>  (      rcCs |dkrt|dSt|dS)Nrg?)int)r rrr iroundMs r%cCstt|S)N)r%rr)r rrr iceilQsr&cCstt|S)N)r%rr)r rrr ifloorTsr'cCs t|dS)Ng?)r')r rrr nearest_integerWsr(cCs | p|S)z2 does p => q in the sense of logical implication? r)rqrrr does_implyZsr*cCst||ot||S)z3 does p <=> q in the sense of logical equivalence? )r*)rr)rrr are_equivalent^sr+c@s&eZdZd ddZddZddZdS) nested_loopNTcCs|dkrdgt|}nt|t|ks,t|s^t|}x$tt|D]}||d7<qFWx(tt|D]}||||ksltqlW||_||_t||_x8tt|D](}||||kr|jdd8<PqWdS)Nr)lenAssertionErrorrrbeginendcurrent)Or2r1Z open_ranger"rrr __init__ds  znested_loop.__init__cCs|S)Nr)r4rrr __iter__wsznested_loop.__iter__cCsh|j}|j}|j}t|}xD|dkr^|d8}||d7<||||krP|S||||<qWtdS)Nrr-)r1r2r3r/ StopIteration)r4becr"rrr __next__zs znested_loop.__next__)NT)__name__ __module__ __qualname__r5r6r;rrrr r,bs r,cCst|dkrdSt|d}x|}|d8}||||krt|}x|d8}||||krDPqDW||||||<||<||d}||d=|||dS|dkr|dSqWdS)aFEmulation of C++ std::next_permutation: Treats all permutations of seq as a set of "dictionary" sorted sequences. Permutes the current sequence into the next one of this set. Returns true if there are more sequences to generate. If the sequence is the largest of the set, the smallest is generated and false returned. r-FNTr)r/reverseextend)seqr"Ziijtailrrr next_permutations*     rDcCsJddl}t|}x4t|D](}||}||||||<||<qWdS)Nr)randomr/r randrange)rrErr"rBrrr random_permutation_in_places  rGcCsFg}d}x8|dkr@x"||dkr4||||}qW|d7}q W|S)zs.     ($