from __future__ import absolute_import, division, print_function import sys from six.moves import cStringIO as StringIO from six.moves import range pdbs = [ # 0 [""" ATOM 1 N ALA A 1 -1.521 3.898 0.713 1.00 20.00 A N+1 ATOM 2 H ALA A 1 -1.675 4.606 1.277 1.00 20.00 A H ATOM 3 H2 ALA A 1 -2.026 3.996 -0.045 1.00 20.00 A H ATOM 4 H3 ALA A 1 -0.632 3.875 0.487 1.00 20.00 A H ATOM 5 CA ALA A 1 -1.879 2.678 1.370 1.00 20.00 A C ATOM 6 HA ALA A 1 -1.349 2.598 2.189 1.00 20.00 A H ATOM 7 CB ALA A 1 -3.346 2.715 1.747 1.00 20.00 A C ATOM 8 HB1 ALA A 1 -3.507 3.466 2.360 1.00 20.00 A H ATOM 9 HB2 ALA A 1 -3.592 1.873 2.188 1.00 20.00 A H ATOM 10 HB3 ALA A 1 -3.886 2.831 0.942 1.00 20.00 A H ATOM 11 C ALA A 1 -1.551 1.486 0.458 1.00 20.00 A C ATOM 12 O ALA A 1 -2.007 1.439 -0.662 1.00 20.00 A O ATOM 13 N ALA A 2 -0.744 0.404 0.952 1.00 20.00 A N ATOM 14 H ALA A 2 -0.359 0.462 1.781 1.00 20.00 A H ATOM 15 CA ALA A 2 -0.493 -0.749 0.119 1.00 20.00 A C ATOM 16 HA ALA A 2 -0.668 -0.439 -0.791 1.00 20.00 A H ATOM 17 CB ALA A 2 -1.476 -1.885 0.331 1.00 20.00 A C ATOM 18 HB1 ALA A 2 -1.345 -2.266 1.221 1.00 20.00 A H ATOM 19 HB2 ALA A 2 -1.326 -2.579 -0.349 1.00 20.00 A H ATOM 20 HB3 ALA A 2 -2.395 -1.542 0.252 1.00 20.00 A H ATOM 21 C ALA A 2 0.972 -1.193 0.100 1.00 20.00 A C ATOM 22 O ALA A 2 1.603 -1.231 1.129 1.00 20.00 A O ATOM 23 N ALA A 3 1.569 -1.642 -1.120 1.00 20.00 A N ATOM 24 H ALA A 3 1.050 -1.766 -1.865 1.00 20.00 A H ATOM 25 CA ALA A 3 2.971 -1.947 -1.163 1.00 20.00 A C ATOM 26 HA ALA A 3 3.432 -1.386 -0.509 1.00 20.00 A H ATOM 27 CB ALA A 3 3.520 -1.630 -2.540 1.00 20.00 A C ATOM 28 HB1 ALA A 3 4.474 -1.845 -2.568 1.00 20.00 A H ATOM 29 HB2 ALA A 3 3.393 -0.674 -2.732 1.00 20.00 A H ATOM 30 HB3 ALA A 3 3.045 -2.163 -3.211 1.00 20.00 A H ATOM 31 C ALA A 3 3.187 -3.395 -0.790 1.00 20.00 A C ATOM 32 O ALA A 3 2.646 -4.306 -1.466 1.00 20.00 A O ATOM 33 OXT ALA A 3 3.917 -3.690 0.195 1.00 20.00 A O-1 """, """ ATOM 1 N ALA A 1 -1.521 3.898 0.713 1.00 20.00 A N+1 ATOM 2 CA ALA A 1 -1.879 2.678 1.370 1.00 20.00 A C ATOM 3 C ALA A 1 -1.551 1.486 0.458 1.00 20.00 A C ATOM 4 O ALA A 1 -2.007 1.439 -0.662 1.00 20.00 A O ATOM 5 CB ALA A 1 -3.346 2.715 1.747 1.00 20.00 A C ATOM 6 H ALA A 1 -1.675 4.606 1.277 1.00 20.00 A H ATOM 7 H2 ALA A 1 -2.026 3.996 -0.045 1.00 20.00 A H ATOM 8 H3 ALA A 1 -0.632 3.875 0.487 1.00 20.00 A H ATOM 9 HA ALA A 1 -1.349 2.598 2.189 1.00 20.00 A H ATOM 10 HB1 ALA A 1 -3.507 3.466 2.360 1.00 20.00 A H ATOM 11 HB2 ALA A 1 -3.592 1.873 2.188 1.00 20.00 A H ATOM 12 HB3 ALA A 1 -3.886 2.831 0.942 1.00 20.00 A H ATOM 13 N ALA A 2 -0.744 0.404 0.952 1.00 20.00 A N ATOM 14 CA ALA A 2 -0.493 -0.749 0.119 1.00 20.00 A C ATOM 15 C ALA A 2 0.972 -1.193 0.100 1.00 20.00 A C ATOM 16 O ALA A 2 1.603 -1.231 1.129 1.00 20.00 A O ATOM 17 CB ALA A 2 -1.476 -1.885 0.331 1.00 20.00 A C ATOM 18 H ALA A 2 -0.359 0.462 1.781 1.00 20.00 A H ATOM 19 HA ALA A 2 -0.668 -0.439 -0.791 1.00 20.00 A H ATOM 20 HB1 ALA A 2 -1.345 -2.266 1.221 1.00 20.00 A H ATOM 21 HB2 ALA A 2 -1.326 -2.579 -0.349 1.00 20.00 A H ATOM 22 HB3 ALA A 2 -2.395 -1.542 0.252 1.00 20.00 A H ATOM 23 N ALA A 3 1.569 -1.642 -1.120 1.00 20.00 A N ATOM 24 CA ALA A 3 2.971 -1.947 -1.163 1.00 20.00 A C ATOM 25 C ALA A 3 3.187 -3.395 -0.790 1.00 20.00 A C ATOM 26 O ALA A 3 2.646 -4.306 -1.466 1.00 20.00 A O ATOM 27 CB ALA A 3 3.520 -1.630 -2.540 1.00 20.00 A C ATOM 28 OXT ALA A 3 3.917 -3.690 0.195 1.00 20.00 A O-1 ATOM 29 H ALA A 3 1.050 -1.766 -1.865 1.00 20.00 A H ATOM 30 HA ALA A 3 3.432 -1.386 -0.509 1.00 20.00 A H ATOM 31 HB1 ALA A 3 4.474 -1.845 -2.568 1.00 20.00 A H ATOM 32 HB2 ALA A 3 3.393 -0.674 -2.732 1.00 20.00 A H ATOM 33 HB3 ALA A 3 3.045 -2.163 -3.211 1.00 20.00 A H """], # no H [""" ATOM 1 N ALA A 1 -1.521 3.898 0.713 1.00 20.00 A N+1 ATOM 5 CA ALA A 1 -1.879 2.678 1.370 1.00 20.00 A C ATOM 7 CB ALA A 1 -3.346 2.715 1.747 1.00 20.00 A C ATOM 11 C ALA A 1 -1.551 1.486 0.458 1.00 20.00 A C ATOM 12 O ALA A 1 -2.007 1.439 -0.662 1.00 20.00 A O ATOM 13 N ALA A 2 -0.744 0.404 0.952 1.00 20.00 A N ATOM 15 CA ALA A 2 -0.493 -0.749 0.119 1.00 20.00 A C ATOM 17 CB ALA A 2 -1.476 -1.885 0.331 1.00 20.00 A C ATOM 21 C ALA A 2 0.972 -1.193 0.100 1.00 20.00 A C ATOM 22 O ALA A 2 1.603 -1.231 1.129 1.00 20.00 A O ATOM 23 N ALA A 3 1.569 -1.642 -1.120 1.00 20.00 A N ATOM 25 CA ALA A 3 2.971 -1.947 -1.163 1.00 20.00 A C ATOM 27 CB ALA A 3 3.520 -1.630 -2.540 1.00 20.00 A C ATOM 31 C ALA A 3 3.187 -3.395 -0.790 1.00 20.00 A C ATOM 32 O ALA A 3 2.646 -4.306 -1.466 1.00 20.00 A O ATOM 33 OXT ALA A 3 3.917 -3.690 0.195 1.00 20.00 A O-1 """, """ ATOM 1 N ALA A 1 -1.521 3.898 0.713 1.00 20.00 A N+1 ATOM 2 CA ALA A 1 -1.879 2.678 1.370 1.00 20.00 A C ATOM 3 C ALA A 1 -1.551 1.486 0.458 1.00 20.00 A C ATOM 4 O ALA A 1 -2.007 1.439 -0.662 1.00 20.00 A O ATOM 5 CB ALA A 1 -3.346 2.715 1.747 1.00 20.00 A C ATOM 6 N ALA A 2 -0.744 0.404 0.952 1.00 20.00 A N ATOM 7 CA ALA A 2 -0.493 -0.749 0.119 1.00 20.00 A C ATOM 8 C ALA A 2 0.972 -1.193 0.100 1.00 20.00 A C ATOM 9 O ALA A 2 1.603 -1.231 1.129 1.00 20.00 A O ATOM 10 CB ALA A 2 -1.476 -1.885 0.331 1.00 20.00 A C ATOM 11 N ALA A 3 1.569 -1.642 -1.120 1.00 20.00 A N ATOM 12 CA ALA A 3 2.971 -1.947 -1.163 1.00 20.00 A C ATOM 13 C ALA A 3 3.187 -3.395 -0.790 1.00 20.00 A C ATOM 14 O ALA A 3 2.646 -4.306 -1.466 1.00 20.00 A O ATOM 15 CB ALA A 3 3.520 -1.630 -2.540 1.00 20.00 A C ATOM 16 OXT ALA A 3 3.917 -3.690 0.195 1.00 20.00 A O-1 """], # just CB [""" ATOM 1 N ALA A 1 -1.521 3.898 0.713 1.00 20.00 A N+1 ATOM 5 CA ALA A 1 -1.879 2.678 1.370 1.00 20.00 A C ATOM 7 CB ALA A 1 -3.346 2.715 1.747 1.00 20.00 A C ATOM 11 C ALA A 1 -1.551 1.486 0.458 1.00 20.00 A C ATOM 12 O ALA A 1 -2.007 1.439 -0.662 1.00 20.00 A O ATOM 13 N ALA A 2 -0.744 0.404 0.952 1.00 20.00 A N ATOM 15 CA ALA A 2 -0.493 -0.749 0.119 1.00 20.00 A C ATOM 17 CB AALA A 2 -1.476 -1.885 0.331 1.00 20.00 A C ATOM 17 CB BALA A 2 -1.476 -1.885 0.331 1.00 20.00 A C ATOM 21 C ALA A 2 0.972 -1.193 0.100 1.00 20.00 A C ATOM 22 O ALA A 2 1.603 -1.231 1.129 1.00 20.00 A O ATOM 23 N ALA A 3 1.569 -1.642 -1.120 1.00 20.00 A N ATOM 25 CA ALA A 3 2.971 -1.947 -1.163 1.00 20.00 A C ATOM 27 CB ALA A 3 3.520 -1.630 -2.540 1.00 20.00 A C ATOM 31 C ALA A 3 3.187 -3.395 -0.790 1.00 20.00 A C ATOM 32 O ALA A 3 2.646 -4.306 -1.466 1.00 20.00 A O ATOM 33 OXT ALA A 3 3.917 -3.690 0.195 1.00 20.00 A O-1 """, """ ATOM 1 N ALA A 1 -1.521 3.898 0.713 1.00 20.00 A N+1 ATOM 2 CA ALA A 1 -1.879 2.678 1.370 1.00 20.00 A C ATOM 3 C ALA A 1 -1.551 1.486 0.458 1.00 20.00 A C ATOM 4 O ALA A 1 -2.007 1.439 -0.662 1.00 20.00 A O ATOM 5 CB ALA A 1 -3.346 2.715 1.747 1.00 20.00 A C ATOM 6 N ALA A 2 -0.744 0.404 0.952 1.00 20.00 A N ATOM 7 CA ALA A 2 -0.493 -0.749 0.119 1.00 20.00 A C ATOM 8 C ALA A 2 0.972 -1.193 0.100 1.00 20.00 A C ATOM 9 O ALA A 2 1.603 -1.231 1.129 1.00 20.00 A O ATOM 10 CB AALA A 2 -1.476 -1.885 0.331 0.50 20.00 A C ATOM 11 CB BALA A 2 -1.476 -1.885 0.331 0.50 20.00 A C ATOM 12 N ALA A 3 1.569 -1.642 -1.120 1.00 20.00 A N ATOM 13 CA ALA A 3 2.971 -1.947 -1.163 1.00 20.00 A C ATOM 14 C ALA A 3 3.187 -3.395 -0.790 1.00 20.00 A C ATOM 15 O ALA A 3 2.646 -4.306 -1.466 1.00 20.00 A O ATOM 16 CB ALA A 3 3.520 -1.630 -2.540 1.00 20.00 A C ATOM 17 OXT ALA A 3 3.917 -3.690 0.195 1.00 20.00 A O-1 """], # just CB diff [""" ATOM 1 N ALA A 1 -1.521 3.898 0.713 1.00 20.00 A N+1 ATOM 5 CA ALA A 1 -1.879 2.678 1.370 1.00 20.00 A C ATOM 7 CB ALA A 1 -3.346 2.715 1.747 1.00 20.00 A C ATOM 11 C ALA A 1 -1.551 1.486 0.458 1.00 20.00 A C ATOM 12 O ALA A 1 -2.007 1.439 -0.662 1.00 20.00 A O ATOM 13 N ALA A 2 -0.744 0.404 0.952 1.00 20.00 A N ATOM 15 CA ALA A 2 -0.493 -0.749 0.119 1.00 20.00 A C ATOM 17 CB AALA A 2 -1.976 -1.885 0.331 1.00 20.00 A C ATOM 17 CB BALA A 2 -1.476 -1.885 0.331 1.00 20.00 A C ATOM 21 C ALA A 2 0.972 -1.193 0.100 1.00 20.00 A C ATOM 22 O ALA A 2 1.603 -1.231 1.129 1.00 20.00 A O ATOM 23 N ALA A 3 1.569 -1.642 -1.120 1.00 20.00 A N ATOM 25 CA ALA A 3 2.971 -1.947 -1.163 1.00 20.00 A C ATOM 27 CB ALA A 3 3.520 -1.630 -2.540 1.00 20.00 A C ATOM 31 C ALA A 3 3.187 -3.395 -0.790 1.00 20.00 A C ATOM 32 O ALA A 3 2.646 -4.306 -1.466 1.00 20.00 A O ATOM 33 OXT ALA A 3 3.917 -3.690 0.195 1.00 20.00 A O-1 """, """ ATOM 1 N ALA A 1 -1.521 3.898 0.713 1.00 20.00 A N+1 ATOM 2 CA ALA A 1 -1.879 2.678 1.370 1.00 20.00 A C ATOM 3 CB ALA A 1 -3.346 2.715 1.747 1.00 20.00 A C ATOM 4 C AALA A 1 -1.551 1.486 0.458 0.50 20.00 A C ATOM 5 O AALA A 1 -2.007 1.439 -0.662 0.50 20.00 A O ATOM 6 C BALA A 1 -1.551 1.486 0.458 0.50 20.00 A C ATOM 7 O BALA A 1 -2.007 1.439 -0.662 0.50 20.00 A O ATOM 8 CB AALA A 2 -1.976 -1.885 0.331 0.50 20.00 A C ATOM 9 N AALA A 2 -0.744 0.404 0.952 0.50 20.00 A N ATOM 10 CA AALA A 2 -0.493 -0.749 0.119 0.50 20.00 A C ATOM 11 C AALA A 2 0.972 -1.193 0.100 0.50 20.00 A C ATOM 12 O AALA A 2 1.603 -1.231 1.129 0.50 20.00 A O ATOM 13 CB BALA A 2 -1.476 -1.885 0.331 0.50 20.00 A C ATOM 14 N BALA A 2 -0.744 0.404 0.952 0.50 20.00 A N ATOM 15 CA BALA A 2 -0.493 -0.749 0.119 0.50 20.00 A C ATOM 16 C BALA A 2 0.972 -1.193 0.100 0.50 20.00 A C ATOM 17 O BALA A 2 1.603 -1.231 1.129 0.50 20.00 A O ATOM 18 CA ALA A 3 2.971 -1.947 -1.163 1.00 20.00 A C ATOM 19 C ALA A 3 3.187 -3.395 -0.790 1.00 20.00 A C ATOM 20 O ALA A 3 2.646 -4.306 -1.466 1.00 20.00 A O ATOM 21 CB ALA A 3 3.520 -1.630 -2.540 1.00 20.00 A C ATOM 22 OXT ALA A 3 3.917 -3.690 0.195 1.00 20.00 A O-1 ATOM 23 N AALA A 3 1.569 -1.642 -1.120 0.50 20.00 A N ATOM 24 N BALA A 3 1.569 -1.642 -1.120 0.50 20.00 A N """], # all 2 [""" ATOM 1 N ALA A 1 -1.521 3.898 0.713 1.00 20.00 A N+1 ATOM 5 CA ALA A 1 -1.879 2.678 1.370 1.00 20.00 A C ATOM 7 CB ALA A 1 -3.346 2.715 1.747 1.00 20.00 A C ATOM 11 C ALA A 1 -1.551 1.486 0.458 1.00 20.00 A C ATOM 12 O ALA A 1 -2.007 1.439 -0.662 1.00 20.00 A O ATOM 13 N AALA A 2 -0.744 0.404 0.952 1.00 20.00 A N ATOM 15 CA AALA A 2 -0.493 -0.749 0.119 1.00 20.00 A C ATOM 17 CB AALA A 2 -1.976 -1.885 0.331 1.00 20.00 A C ATOM 21 C AALA A 2 0.972 -1.193 0.100 1.00 20.00 A C ATOM 22 O AALA A 2 1.603 -1.231 1.129 1.00 20.00 A O ATOM 13 N BALA A 2 -0.744 0.404 0.952 1.00 20.00 A N ATOM 15 CA BALA A 2 -0.493 -0.749 0.119 1.00 20.00 A C ATOM 17 CB BALA A 2 -1.976 -1.885 0.331 1.00 20.00 A C ATOM 21 C BALA A 2 0.972 -1.193 0.100 1.00 20.00 A C ATOM 22 O BALA A 2 1.603 -1.231 1.129 1.00 20.00 A O ATOM 23 N ALA A 3 1.569 -1.642 -1.120 1.00 20.00 A N ATOM 25 CA ALA A 3 2.971 -1.947 -1.163 1.00 20.00 A C ATOM 27 CB ALA A 3 3.520 -1.630 -2.540 1.00 20.00 A C ATOM 31 C ALA A 3 3.187 -3.395 -0.790 1.00 20.00 A C ATOM 32 O ALA A 3 2.646 -4.306 -1.466 1.00 20.00 A O ATOM 33 OXT ALA A 3 3.917 -3.690 0.195 1.00 20.00 A O-1 """, """ ATOM 1 N ALA A 1 -1.521 3.898 0.713 1.00 20.00 A N+1 ATOM 2 CA ALA A 1 -1.879 2.678 1.370 1.00 20.00 A C ATOM 3 CB ALA A 1 -3.346 2.715 1.747 1.00 20.00 A C ATOM 4 C AALA A 1 -1.551 1.486 0.458 0.50 20.00 A C ATOM 5 O AALA A 1 -2.007 1.439 -0.662 0.50 20.00 A O ATOM 6 C BALA A 1 -1.551 1.486 0.458 0.50 20.00 A C ATOM 7 O BALA A 1 -2.007 1.439 -0.662 0.50 20.00 A O ATOM 8 N AALA A 2 -0.744 0.404 0.952 0.50 20.00 A N ATOM 9 CA AALA A 2 -0.493 -0.749 0.119 0.50 20.00 A C ATOM 10 C AALA A 2 0.972 -1.193 0.100 0.50 20.00 A C ATOM 11 O AALA A 2 1.603 -1.231 1.129 0.50 20.00 A O ATOM 12 CB AALA A 2 -1.976 -1.885 0.331 0.50 20.00 A C ATOM 13 N BALA A 2 -0.744 0.404 0.952 0.50 20.00 A N ATOM 14 CA BALA A 2 -0.493 -0.749 0.119 0.50 20.00 A C ATOM 15 C BALA A 2 0.972 -1.193 0.100 0.50 20.00 A C ATOM 16 O BALA A 2 1.603 -1.231 1.129 0.50 20.00 A O ATOM 17 CB BALA A 2 -1.976 -1.885 0.331 0.50 20.00 A C ATOM 18 CA ALA A 3 2.971 -1.947 -1.163 1.00 20.00 A C ATOM 19 C ALA A 3 3.187 -3.395 -0.790 1.00 20.00 A C ATOM 20 O ALA A 3 2.646 -4.306 -1.466 1.00 20.00 A O ATOM 21 CB ALA A 3 3.520 -1.630 -2.540 1.00 20.00 A C ATOM 22 OXT ALA A 3 3.917 -3.690 0.195 1.00 20.00 A O-1 ATOM 23 N AALA A 3 1.569 -1.642 -1.120 0.50 20.00 A N ATOM 24 N BALA A 3 1.569 -1.642 -1.120 0.50 20.00 A N """], # all 2 interlocked [""" ATOM 1 N ALA A 1 -1.521 3.898 0.713 1.00 20.00 A N+1 ATOM 5 CA ALA A 1 -1.879 2.678 1.370 1.00 20.00 A C ATOM 7 CB ALA A 1 -3.346 2.715 1.747 1.00 20.00 A C ATOM 11 C ALA A 1 -1.551 1.486 0.458 1.00 20.00 A C ATOM 12 O ALA A 1 -2.007 1.439 -0.662 1.00 20.00 A O ATOM 13 N AALA A 2 -0.744 0.404 0.952 1.00 20.00 A N ATOM 13 N BALA A 2 -0.744 0.404 0.952 1.00 20.00 A N ATOM 15 CA AALA A 2 -0.493 -0.749 0.119 1.00 20.00 A C ATOM 15 CA BALA A 2 -0.493 -0.749 0.119 1.00 20.00 A C ATOM 17 CB AALA A 2 -1.976 -1.885 0.331 1.00 20.00 A C ATOM 17 CB BALA A 2 -1.976 -1.885 0.331 1.00 20.00 A C ATOM 21 C AALA A 2 0.972 -1.193 0.100 1.00 20.00 A C ATOM 21 C BALA A 2 0.972 -1.193 0.100 1.00 20.00 A C ATOM 22 O AALA A 2 1.603 -1.231 1.129 1.00 20.00 A O ATOM 22 O BALA A 2 1.603 -1.231 1.129 1.00 20.00 A O ATOM 23 N ALA A 3 1.569 -1.642 -1.120 1.00 20.00 A N ATOM 25 CA ALA A 3 2.971 -1.947 -1.163 1.00 20.00 A C ATOM 27 CB ALA A 3 3.520 -1.630 -2.540 1.00 20.00 A C ATOM 31 C ALA A 3 3.187 -3.395 -0.790 1.00 20.00 A C ATOM 32 O ALA A 3 2.646 -4.306 -1.466 1.00 20.00 A O ATOM 33 OXT ALA A 3 3.917 -3.690 0.195 1.00 20.00 A O-1 """, """ ATOM 1 N ALA A 1 -1.521 3.898 0.713 1.00 20.00 A N+1 ATOM 2 CA ALA A 1 -1.879 2.678 1.370 1.00 20.00 A C ATOM 3 CB ALA A 1 -3.346 2.715 1.747 1.00 20.00 A C ATOM 4 C AALA A 1 -1.551 1.486 0.458 0.50 20.00 A C ATOM 5 O AALA A 1 -2.007 1.439 -0.662 0.50 20.00 A O ATOM 6 C BALA A 1 -1.551 1.486 0.458 0.50 20.00 A C ATOM 7 O BALA A 1 -2.007 1.439 -0.662 0.50 20.00 A O ATOM 8 N AALA A 2 -0.744 0.404 0.952 0.50 20.00 A N ATOM 9 CA AALA A 2 -0.493 -0.749 0.119 0.50 20.00 A C ATOM 10 C AALA A 2 0.972 -1.193 0.100 0.50 20.00 A C ATOM 11 O AALA A 2 1.603 -1.231 1.129 0.50 20.00 A O ATOM 12 CB AALA A 2 -1.976 -1.885 0.331 0.50 20.00 A C ATOM 13 N BALA A 2 -0.744 0.404 0.952 0.50 20.00 A N ATOM 14 CA BALA A 2 -0.493 -0.749 0.119 0.50 20.00 A C ATOM 15 C BALA A 2 0.972 -1.193 0.100 0.50 20.00 A C ATOM 16 O BALA A 2 1.603 -1.231 1.129 0.50 20.00 A O ATOM 17 CB BALA A 2 -1.976 -1.885 0.331 0.50 20.00 A C ATOM 18 CA ALA A 3 2.971 -1.947 -1.163 1.00 20.00 A C ATOM 19 C ALA A 3 3.187 -3.395 -0.790 1.00 20.00 A C ATOM 20 O ALA A 3 2.646 -4.306 -1.466 1.00 20.00 A O ATOM 21 CB ALA A 3 3.520 -1.630 -2.540 1.00 20.00 A C ATOM 22 OXT ALA A 3 3.917 -3.690 0.195 1.00 20.00 A O-1 ATOM 23 N AALA A 3 1.569 -1.642 -1.120 0.50 20.00 A N ATOM 24 N BALA A 3 1.569 -1.642 -1.120 0.50 20.00 A N """], # correcting partials [""" ATOM 757 N GLY A 103 21.999 10.712 0.961 1.00 4.33 N ATOM 758 CA GLY A 103 21.040 11.791 1.055 1.00 4.23 C ATOM 759 C GLY A 103 19.704 11.419 0.439 1.00 3.85 C ATOM 760 O GLY A 103 19.580 10.539 -0.422 1.00 4.32 O ATOM 761 N GLU A 104 18.680 12.148 0.879 1.00 3.87 N ATOM 762 CA GLU A 104 17.299 11.909 0.484 1.00 3.91 C ATOM 763 O GLU A 104 17.826 13.338 -1.410 1.00 4.76 O ATOM 764 CB GLU A 104 16.372 12.308 1.645 1.00 4.08 C ATOM 765 CG GLU A 104 16.686 11.548 2.930 1.00 4.59 C ATOM 766 CD GLU A 104 17.829 12.093 3.786 1.00 5.00 C ATOM 767 OE1 GLU A 104 18.152 11.408 4.823 1.00 6.45 O ATOM 768 OE2 GLU A 104 18.390 13.159 3.470 1.00 5.26 O ATOM 769 C AGLU A 104 16.973 12.646 -0.808 0.50 3.96 C ATOM 770 C BGLU A 104 16.975 12.684 -0.800 0.50 3.89 C ATOM 771 N ALEU A 105 15.717 12.499 -1.259 0.50 4.06 N ATOM 772 CA ALEU A 105 15.284 13.059 -2.541 0.50 4.88 C ATOM 773 C ALEU A 105 15.637 14.444 -2.871 0.50 4.43 C ATOM 774 O ALEU A 105 15.735 14.769 -4.050 0.50 6.07 O ATOM 775 CB ALEU A 105 13.730 13.346 -2.655 0.50 3.54 C ATOM 776 CG ALEU A 105 13.190 11.968 -3.122 0.50 3.81 C ATOM 777 CD1ALEU A 105 11.685 12.054 -3.263 0.50 4.54 C ATOM 778 CD2ALEU A 105 13.804 11.453 -4.425 0.50 4.05 C ATOM 779 N BLEU A 105 15.711 12.640 -1.220 0.50 3.57 N ATOM 780 CA BLEU A 105 15.237 13.396 -2.364 0.50 4.37 C ATOM 781 C BLEU A 105 15.537 14.890 -2.046 0.50 3.47 C ATOM 782 O BLEU A 105 15.411 15.372 -0.929 0.50 3.89 O ATOM 783 CB BLEU A 105 13.764 12.747 -2.519 0.50 4.65 C ATOM 784 CG BLEU A 105 13.014 12.862 -3.842 0.50 6.20 C ATOM 785 CD1BLEU A 105 13.508 11.889 -4.865 0.50 7.64 C ATOM 786 CD2BLEU A 105 11.548 12.657 -3.620 0.50 5.53 C ATOM 787 N AGLY A 106 15.734 15.299 -1.857 0.50 4.10 N ATOM 788 CA AGLY A 106 16.043 16.715 -2.048 0.50 5.76 C ATOM 789 C AGLY A 106 17.449 17.119 -1.650 0.50 4.81 C ATOM 790 O AGLY A 106 17.778 18.310 -1.696 0.50 5.91 O ATOM 791 N BGLY A 106 15.975 15.616 -3.081 0.50 3.71 N ATOM 792 CA BGLY A 106 16.294 17.031 -2.939 0.50 4.59 C ATOM 793 C BGLY A 106 17.649 17.368 -2.295 0.50 4.30 C ATOM 794 O BGLY A 106 18.056 18.524 -2.339 0.50 4.74 O ATOM 795 CA SER A 107 19.612 16.580 -0.930 1.00 4.51 C ATOM 796 C SER A 107 20.554 17.027 -2.048 1.00 4.08 C ATOM 797 O SER A 107 20.441 16.592 -3.191 1.00 4.85 O ATOM 798 CB SER A 107 20.205 15.355 -0.212 1.00 4.55 C ATOM 799 OG SER A 107 20.403 14.244 -1.072 1.00 4.35 O ATOM 800 N ASER A 107 18.312 16.190 -1.350 0.50 5.31 N ATOM 801 N BSER A 107 18.278 16.387 -1.593 0.50 5.42 N ATOM 802 N PRO A 108 21.538 17.876 -1.717 1.00 4.04 N ATOM 803 CA PRO A 108 22.472 18.325 -2.750 1.00 4.37 C ATOM 804 C PRO A 108 23.241 17.187 -3.437 1.00 4.03 C ATOM 805 O PRO A 108 23.746 16.255 -2.804 1.00 4.51 O ATOM 806 CB PRO A 108 23.413 19.264 -1.990 1.00 4.85 C ATOM 807 CG PRO A 108 22.520 19.852 -0.907 1.00 5.00 C ATOM 808 CD PRO A 108 21.676 18.668 -0.477 1.00 4.48 C """, """ ATOM 1 N GLY A 103 21.999 10.712 0.961 1.00 4.33 N ATOM 2 CA GLY A 103 21.040 11.791 1.055 1.00 4.23 C ATOM 3 C GLY A 103 19.704 11.419 0.439 1.00 3.85 C ATOM 4 O GLY A 103 19.580 10.539 -0.422 1.00 4.32 O ATOM 5 N GLU A 104 18.680 12.148 0.879 1.00 3.87 N ATOM 6 CA GLU A 104 17.299 11.909 0.484 1.00 3.91 C ATOM 7 CB GLU A 104 16.372 12.308 1.645 1.00 4.08 C ATOM 8 CG GLU A 104 16.686 11.548 2.930 1.00 4.59 C ATOM 9 CD GLU A 104 17.829 12.093 3.786 1.00 5.00 C ATOM 10 OE1 GLU A 104 18.152 11.408 4.823 1.00 6.45 O ATOM 11 OE2 GLU A 104 18.390 13.159 3.470 1.00 5.26 O ATOM 12 C AGLU A 104 16.973 12.646 -0.808 0.50 3.96 C ATOM 13 O AGLU A 104 17.826 13.338 -1.410 0.50 4.76 O ATOM 14 C BGLU A 104 16.975 12.684 -0.800 0.50 3.89 C ATOM 15 O BGLU A 104 17.826 13.338 -1.410 0.50 4.76 O ATOM 16 N ALEU A 105 15.717 12.499 -1.259 0.50 4.06 N ATOM 17 CA ALEU A 105 15.284 13.059 -2.541 0.50 4.88 C ATOM 18 C ALEU A 105 15.637 14.444 -2.871 0.50 4.43 C ATOM 19 O ALEU A 105 15.735 14.769 -4.050 0.50 6.07 O ATOM 20 CB ALEU A 105 13.730 13.346 -2.655 0.50 3.54 C ATOM 21 CG ALEU A 105 13.190 11.968 -3.122 0.50 3.81 C ATOM 22 CD1ALEU A 105 11.685 12.054 -3.263 0.50 4.54 C ATOM 23 CD2ALEU A 105 13.804 11.453 -4.425 0.50 4.05 C ATOM 24 N BLEU A 105 15.711 12.640 -1.220 0.50 3.57 N ATOM 25 CA BLEU A 105 15.237 13.396 -2.364 0.50 4.37 C ATOM 26 C BLEU A 105 15.537 14.890 -2.046 0.50 3.47 C ATOM 27 O BLEU A 105 15.411 15.372 -0.929 0.50 3.89 O ATOM 28 CB BLEU A 105 13.764 12.747 -2.519 0.50 4.65 C ATOM 29 CG BLEU A 105 13.014 12.862 -3.842 0.50 6.20 C ATOM 30 CD1BLEU A 105 13.508 11.889 -4.865 0.50 7.64 C ATOM 31 CD2BLEU A 105 11.548 12.657 -3.620 0.50 5.53 C ATOM 32 N AGLY A 106 15.734 15.299 -1.857 0.50 4.10 N ATOM 33 CA AGLY A 106 16.043 16.715 -2.048 0.50 5.76 C ATOM 34 C AGLY A 106 17.449 17.119 -1.650 0.50 4.81 C ATOM 35 O AGLY A 106 17.778 18.310 -1.696 0.50 5.91 O ATOM 36 N BGLY A 106 15.975 15.616 -3.081 0.50 3.71 N ATOM 37 CA BGLY A 106 16.294 17.031 -2.939 0.50 4.59 C ATOM 38 C BGLY A 106 17.649 17.368 -2.295 0.50 4.30 C ATOM 39 O BGLY A 106 18.056 18.524 -2.339 0.50 4.74 O ATOM 40 CA SER A 107 19.612 16.580 -0.930 1.00 4.51 C ATOM 41 C SER A 107 20.554 17.027 -2.048 1.00 4.08 C ATOM 42 O SER A 107 20.441 16.592 -3.191 1.00 4.85 O ATOM 43 CB SER A 107 20.205 15.355 -0.212 1.00 4.55 C ATOM 44 OG SER A 107 20.403 14.244 -1.072 1.00 4.35 O ATOM 45 N ASER A 107 18.312 16.190 -1.350 0.50 5.31 N ATOM 46 N BSER A 107 18.278 16.387 -1.593 0.50 5.42 N ATOM 47 N PRO A 108 21.538 17.876 -1.717 1.00 4.04 N ATOM 48 CA PRO A 108 22.472 18.325 -2.750 1.00 4.37 C ATOM 49 C PRO A 108 23.241 17.187 -3.437 1.00 4.03 C ATOM 50 O PRO A 108 23.746 16.255 -2.804 1.00 4.51 O ATOM 51 CB PRO A 108 23.413 19.264 -1.990 1.00 4.85 C ATOM 52 CG PRO A 108 22.520 19.852 -0.907 1.00 5.00 C ATOM 53 CD PRO A 108 21.676 18.668 -0.477 1.00 4.48 C """], ] ala_cif = """ data_comp_list loop_ _chem_comp.id _chem_comp.three_letter_code _chem_comp.name _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level _chem_comp.initial_date _chem_comp.modified_date _chem_comp.source ALA ALA Alanine L-peptide 10 5 . 2009-08-12 2012-12-06 ; Copy of CCP4 Monomer Library entry. eLBOW added bond orders. Added neutron distances ; data_comp_ALA loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.type_energy _chem_comp_atom.partial_charge ALA N N NH1 -0.204 ALA H H HNH1 0.204 ALA CA C CH1 0.058 ALA HA H HCH1 0.046 ALA CB C CH3 -0.120 ALA HB1 H HCH3 0.040 ALA HB2 H HCH3 0.040 ALA HB3 H HCH3 0.040 ALA C C C 0.318 ALA O O O -0.422 loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.type _chem_comp_bond.value_dist _chem_comp_bond.value_dist_esd _chem_comp_bond.value_dist_neutron ALA N H single 2.860 0.020 1.020 ALA N CA single 2.458 0.019 1.458 ALA CA HA single 2.970 0.020 1.090 ALA CA CB single 2.521 0.033 1.521 ALA CB HB1 single 2.970 0.020 1.090 ALA CB HB2 single 2.970 0.020 1.090 ALA CB HB3 single 2.970 0.020 1.090 ALA CA C single 2.525 0.021 1.525 ALA C O double 2.231 0.020 1.231 """ params_str = """pdb_interpretation { apply_cif_restraints { restraints_file_name = "%s" residue_selection = %s } } """ params = [ [params_str % ("ALA_different.cif", "chain A and resseq 2"), params_str % ("ALA_different.cif", 'chain A and resseq 2 and altloc "A"'), ], [params_str % ("ALA_different.cif", "chain A and resseq 2"), params_str % ("ALA_different.cif", 'chain A and resseq 2 and altloc "A"'), ], [params_str % ("ALA_different.cif", "chain A and resseq 2"), params_str % ("ALA_different.cif", 'chain A and resseq 2 and altloc "A"'), ], [params_str % ("ALA_different.cif", "chain A and resseq 2"), params_str % ("ALA_different.cif", 'chain A and resseq 2 and altloc "A"'), ], [params_str % ("ALA_different.cif", "chain A and resseq 2"), params_str % ("ALA_different.cif", 'chain A and resseq 2 and altloc "A"'), ], [params_str % ("ALA_different.cif", "chain A and resseq 2"), params_str % ("ALA_different.cif", 'chain A and resseq 2 and altloc "A"'), ], ] success = [ [1,0], [1,0], [0,0], [0,0], [0,1], [0,1], ] from libtbx import easy_run def assert_lines(s1, s2): def generate_lines(string): for line in string.split("\n"): if line.find("TER")>-1: continue if not line.strip(): continue yield line.strip() # for l1 in generate_lines(s1): for l2 in generate_lines(s2): if l1==l2: break else: print(l1) print(l2) assert 0 def run(): f=open("ALA_different.cif", "w") f.write(ala_cif) f.close() for i, (input_str, output_str) in enumerate(pdbs): if i==6: break preamble = "tst_altloc_specific_restraints_%02d" % i print('-'*80) print(input_str) print('-'*80) print(output_str) print('-'*80) for j in range(2): f=open("%s.pdb" % preamble, "w") f.write(input_str) f.close() f=open("%s_%02d.params" % (preamble, j), "w") f.write(params[i][j]) f.close() cmd = "phenix.pdb_interpretation %s %s" % ("%s.pdb" % preamble, "%s_%02d.params" % (preamble,j), ) cmd += " write_geo=1 cdl=0" print("\n ~> %s\n" % cmd) lines=StringIO() rc = easy_run.fully_buffered(cmd) rc.show_stdout(out=lines) finding=None not_finding=None if success[i][j]==0: finding = "were not modified by" elif success[i][j]==1: not_finding = "were not modified by" for line in lines.getvalue().split("\n"): if finding: if line.find(finding)>-1: finding = True break if not_finding: if line.find(not_finding)>-1: print(line) assert 0 if finding is not None: if finding==True: pass else: assert 0 for i, (input_str, output_str) in enumerate(pdbs): preamble = "tst_altloc_remediate_%02d" % i print('-'*80) print(input_str) print('-'*80) print(output_str) print('-'*80) f=open("%s.pdb" % preamble, "w") f.write(input_str) f.close() cmd = "mmtbx.altloc_remediate %s" % "%s.pdb" % preamble print(cmd) easy_run.call(cmd) f=open("%s_correct.pdb" % preamble, "r") lines = f.read() f.close() print(lines) print(output_str) assert_lines(lines, output_str) print("OK") if __name__=="__main__": run()#sys.argv[1])