Make coordinate library

[joaomcteixeira]

Addresses #27

I am currently working on this implementation. I create now this PR so that @AlaaShamandy @RobertVernon can easily follow the progression in real time. Parallel work is taking place at #23.

[joaomcteixeira]

This PR incorporates the Natural Extension Reference Frame (NeRF) algorithm to place new coordinates in the reference space given a theta and torsion angle and three parent coordinates.

Thanks to @RobertVernon for placing the math initially, here I have cleaned it, document it and implemented the tests.

@AlaaShamandy @RobertVernon please review and accept for Merge.

This PR aids on completing #27.

[AlaaShamandy]

good catch :D

[RobertVernon]

I'll note that this means the function is no longer "RT_to_plane"

(RT is the shorthand for a pair of Rotation + Translation objects)

[joaomcteixeira]

Thanks for your comment!

[joaomcteixeira]

Thanks for your review @AlaaShamandy .
I will add additional test cases to make sure this implementation follows exactly what was proposed by @RobertVernon on the first script.

[joaomcteixeira]

@RobertVernon @AlaaShamandy this PR is ready for review and merge. Please share your comments

[joaomcteixeira]

Thx @RobertVernon and @AlaaShamandy for your comments. We can have this merge now:

tests/test_libcalc.py::test_make_axis_vectors_1[av0-bv0-cv0-expected0] PASSED                                            [  2%]
tests/test_libcalc.py::test_make_axis_vectors_1[av1-bv1-cv1-expected1] PASSED                                            [  4%]
tests/test_libcalc.py::test_rotation_to_plane[av0-bv0-cv0-expected0] PASSED                                              [  7%]
tests/test_libcalc.py::test_make_coord_from_angles[1-1-1-expected0] PASSED                                               [  9%]
tests/test_libcalc.py::test_make_coord[1-1-1-parent0-xaxis0-yaxis0-expected0] PASSED                                     [ 11%]
tests/test_libcalc.py::test_make_coord[1.1-0.3-4.5-parent1-xaxis1-yaxis1-expected1] PASSED                               [ 14%]
tests/test_libcalc.py::test_make_coord[1-1-1-parent2-xaxis2-yaxis2-expected2] PASSED                                     [ 16%]


src/idpconfgen/libs/libcalc.py             29      0      6      0   100.00%