from __future__ import absolute_import, division, print_function from six.moves import cStringIO as StringIO from mmtbx.ncs import ncs import sys from six.moves import zip from six.moves import range def remove_blank(text): return text.replace("\n"," ").replace(".0 "," ").replace(". "," ").replace(" ","") text1=""" Summary of NCS information Wed Jul 1 10:54:17 2015 source_info ncs.ncs_spec new_ncs_group new_operator rota_matrix 1.0000 0.0000 0.0000 rota_matrix 0.0000 1.0000 0.0000 rota_matrix 0.0000 0.0000 1.0000 tran_orth 0.0000 0.0000 0.0000 center_orth 3.2161 -7.6562 -13.0956 CHAIN A RMSD 0 MATCHING 7 RESSEQ 92:98 new_operator rota_matrix 0.4525 -0.3091 -0.8365 rota_matrix 0.7737 0.6025 0.1959 rota_matrix 0.4434 -0.7359 0.5118 tran_orth -0.1318 4.4033 -9.9054 center_orth -9.2303 -5.9527 -6.7960 CHAIN R RMSD 0.0007 MATCHING 7 RESSEQ 92:98 """ expected_text_group_specification=text1 expected_text_resolve=""" new_ncs_group rota_matrix 1.0000 0.0000 0.0000 rota_matrix 0.0000 1.0000 0.0000 rota_matrix 0.0000 0.0000 1.0000 tran_orth 0.0000 0.0000 0.0000 center_orth 3.2161 -7.6562 -13.0956 rota_matrix 0.4525 -0.3091 -0.8365 rota_matrix 0.7737 0.6025 0.1959 rota_matrix 0.4434 -0.7359 0.5118 tran_orth -0.1318 4.4033 -9.9054 center_orth -9.2303 -5.9527 -6.7960 """ expected_text_refine=""" refinement.pdb_interpretation.ncs_group { reference = chain 'A' and (resseq 92:98 ) selection = chain 'R' and (resseq 92:98 ) } """ def tst_01(): print("Read ncs-spec file and write out text...", end=' ') f=open('ncs.ncs_spec','w') print(text1, file=f) f.close() from mmtbx.ncs.ncs import ncs ncs_object=ncs() ncs_object.read_ncs('ncs.ncs_spec',quiet=True) f=StringIO() ncs_object.format_all_for_group_specification(out=f) found_text=f.getvalue() expected_text=expected_text_group_specification if remove_blank(" ".join(found_text.split("source_info")[1:]) ) != \ remove_blank(" ".join(expected_text.split("source_info")[1:])): print("Expected: \n%s \nFound: \n%s" %(expected_text_group_specification,found_text)) raise AssertionError("FAILED") f=StringIO() ncs_object.format_all_for_resolve(out=f) found_text=f.getvalue() if remove_blank(found_text)!=remove_blank(expected_text_resolve): print("Expected: \n%s \nFound: \n%s" %(expected_text_resolve,found_text)) raise AssertionError("FAILED") f=StringIO() ncs_object.format_all_for_phenix_refine(out=f) found_text=f.getvalue() if remove_blank(found_text)!=remove_blank(expected_text_refine): print("Expected: \n%s \nFound: \n%s" %(expected_text_refine,found_text)) raise AssertionError("FAILED") print("OK") text_helical=""" REMARK 350 BIOMT1 1 -0.982450 -0.186524 0.000000 0.00000 REMARK 350 BIOMT2 1 0.186524 -0.982450 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 -35.25000 REMARK 350 BIOMT1 2 -0.980683 0.195604 0.000000 0.00000 REMARK 350 BIOMT2 2 -0.195604 -0.980683 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 -33.84000 REMARK 350 BIOMT1 3 -0.835712 0.549169 0.000000 0.00000 REMARK 350 BIOMT2 3 -0.549169 -0.835712 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 -32.43000 REMARK 350 BIOMT1 4 -0.568705 0.822541 0.000000 0.00000 REMARK 350 BIOMT2 4 -0.822541 -0.568705 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 -31.02000 REMARK 350 BIOMT1 5 -0.218654 0.975802 0.000000 0.00000 REMARK 350 BIOMT2 5 -0.975802 -0.218654 0.000000 0.00000 REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 -29.61000 REMARK 350 BIOMT1 6 0.163326 0.986572 0.000000 0.00000 REMARK 350 BIOMT2 6 -0.986572 0.163326 0.000000 0.00000 REMARK 350 BIOMT3 6 0.000000 0.000000 1.000000 -28.20000 REMARK 350 BIOMT1 7 0.521456 0.853278 0.000000 0.00000 REMARK 350 BIOMT2 7 -0.853278 0.521456 0.000000 0.00000 REMARK 350 BIOMT3 7 0.000000 0.000000 1.000000 -26.79000 REMARK 350 BIOMT1 8 0.803441 0.595384 0.000000 0.00000 REMARK 350 BIOMT2 8 -0.595384 0.803441 0.000000 0.00000 REMARK 350 BIOMT3 8 0.000000 0.000000 1.000000 -25.38000 REMARK 350 BIOMT1 9 0.968104 0.250549 0.000000 0.00000 REMARK 350 BIOMT2 9 -0.250549 0.968104 0.000000 0.00000 REMARK 350 BIOMT3 9 0.000000 0.000000 1.000000 -23.97000 REMARK 350 BIOMT1 10 0.991399 -0.130872 0.000000 0.00000 REMARK 350 BIOMT2 10 0.130872 0.991399 0.000000 0.00000 REMARK 350 BIOMT3 10 0.000000 0.000000 1.000000 -22.56000 REMARK 350 BIOMT1 11 0.869926 -0.493183 0.000000 0.00000 REMARK 350 BIOMT2 11 0.493183 0.869926 0.000000 0.00000 REMARK 350 BIOMT3 11 0.000000 0.000000 1.000000 -21.15000 REMARK 350 BIOMT1 12 0.621421 -0.783477 0.000000 0.00000 REMARK 350 BIOMT2 12 0.783477 0.621421 0.000000 0.00000 REMARK 350 BIOMT3 12 0.000000 0.000000 1.000000 -19.74000 REMARK 350 BIOMT1 13 0.282174 -0.959363 0.000000 0.00000 REMARK 350 BIOMT2 13 0.959363 0.282174 0.000000 0.00000 REMARK 350 BIOMT3 13 0.000000 0.000000 1.000000 -18.33000 REMARK 350 BIOMT1 14 -0.098278 -0.995159 0.000000 0.00000 REMARK 350 BIOMT2 14 0.995159 -0.098278 0.000000 0.00000 REMARK 350 BIOMT3 14 0.000000 0.000000 1.000000 -16.92000 REMARK 350 BIOMT1 15 -0.464378 -0.885637 0.000000 0.00000 REMARK 350 BIOMT2 15 0.885637 -0.464378 0.000000 0.00000 REMARK 350 BIOMT3 15 0.000000 0.000000 1.000000 -15.51000 REMARK 350 BIOMT1 16 -0.762668 -0.646790 0.000000 0.00000 REMARK 350 BIOMT2 16 0.646790 -0.762668 0.000000 0.00000 REMARK 350 BIOMT3 16 0.000000 0.000000 1.000000 -14.10000 REMARK 350 BIOMT1 17 -0.949590 -0.313495 0.000000 0.00000 REMARK 350 BIOMT2 17 0.313495 -0.949590 0.000000 0.00000 REMARK 350 BIOMT3 17 0.000000 0.000000 1.000000 -12.69000 REMARK 350 BIOMT1 18 -0.997847 0.065577 0.000000 0.00000 REMARK 350 BIOMT2 18 -0.065577 -0.997847 0.000000 0.00000 REMARK 350 BIOMT3 18 0.000000 0.000000 1.000000 -11.28000 REMARK 350 BIOMT1 19 -0.900395 0.435074 0.000000 0.00000 REMARK 350 BIOMT2 19 -0.435074 -0.900395 0.000000 0.00000 REMARK 350 BIOMT3 19 0.000000 0.000000 1.000000 -9.87000 REMARK 350 BIOMT1 20 -0.671462 0.741039 0.000000 0.00000 REMARK 350 BIOMT2 20 -0.741039 -0.671462 0.000000 0.00000 REMARK 350 BIOMT3 20 0.000000 0.000000 1.000000 -8.46000 REMARK 350 BIOMT1 21 -0.344479 0.938794 0.000000 0.00000 REMARK 350 BIOMT2 21 -0.938794 -0.344479 0.000000 0.00000 REMARK 350 BIOMT3 21 0.000000 0.000000 1.000000 -7.05000 REMARK 350 BIOMT1 22 0.032806 0.999462 0.000000 0.00000 REMARK 350 BIOMT2 22 -0.999462 0.032806 0.000000 0.00000 REMARK 350 BIOMT3 22 0.000000 0.000000 1.000000 -5.64000 REMARK 350 BIOMT1 23 0.405301 0.914183 0.000000 0.00000 REMARK 350 BIOMT2 23 -0.914183 0.405301 0.000000 0.00000 REMARK 350 BIOMT3 23 0.000000 0.000000 1.000000 -4.23000 REMARK 350 BIOMT1 24 0.718612 0.695411 0.000000 0.00000 REMARK 350 BIOMT2 24 -0.695411 0.718612 0.000000 0.00000 REMARK 350 BIOMT3 24 0.000000 0.000000 1.000000 -2.82000 REMARK 350 BIOMT1 25 0.926988 0.375092 0.000000 0.00000 REMARK 350 BIOMT2 25 -0.375092 0.926988 0.000000 0.00000 REMARK 350 BIOMT3 25 0.000000 0.000000 1.000000 -1.41000 REMARK 350 BIOMT1 26 1.000000 -0.000000 0.000000 0.00000 REMARK 350 BIOMT2 26 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 26 0.000000 0.000000 1.000000 -0.00000 REMARK 350 BIOMT1 27 0.926988 -0.375092 0.000000 0.00000 REMARK 350 BIOMT2 27 0.375092 0.926988 0.000000 0.00000 REMARK 350 BIOMT3 27 0.000000 0.000000 1.000000 1.41000 REMARK 350 BIOMT1 28 0.718612 -0.695411 0.000000 0.00000 REMARK 350 BIOMT2 28 0.695411 0.718612 0.000000 0.00000 REMARK 350 BIOMT3 28 0.000000 0.000000 1.000000 2.82000 REMARK 350 BIOMT1 29 0.405301 -0.914183 0.000000 0.00000 REMARK 350 BIOMT2 29 0.914183 0.405301 0.000000 0.00000 REMARK 350 BIOMT3 29 0.000000 0.000000 1.000000 4.23000 REMARK 350 BIOMT1 30 0.032806 -0.999462 0.000000 0.00000 REMARK 350 BIOMT2 30 0.999462 0.032806 0.000000 0.00000 REMARK 350 BIOMT3 30 0.000000 0.000000 1.000000 5.64000 REMARK 350 BIOMT1 31 -0.344479 -0.938794 0.000000 0.00000 REMARK 350 BIOMT2 31 0.938794 -0.344479 0.000000 0.00000 REMARK 350 BIOMT3 31 0.000000 0.000000 1.000000 7.05000 REMARK 350 BIOMT1 32 -0.671462 -0.741039 0.000000 0.00000 REMARK 350 BIOMT2 32 0.741039 -0.671462 0.000000 0.00000 REMARK 350 BIOMT3 32 0.000000 0.000000 1.000000 8.46000 REMARK 350 BIOMT1 33 -0.900395 -0.435074 0.000000 0.00000 REMARK 350 BIOMT2 33 0.435074 -0.900395 0.000000 0.00000 REMARK 350 BIOMT3 33 0.000000 0.000000 1.000000 9.87000 REMARK 350 BIOMT1 34 -0.997847 -0.065577 0.000000 0.00000 REMARK 350 BIOMT2 34 0.065577 -0.997847 0.000000 0.00000 REMARK 350 BIOMT3 34 0.000000 0.000000 1.000000 11.28000 REMARK 350 BIOMT1 35 -0.949590 0.313495 0.000000 0.00000 REMARK 350 BIOMT2 35 -0.313495 -0.949590 0.000000 0.00000 REMARK 350 BIOMT3 35 0.000000 0.000000 1.000000 12.69000 REMARK 350 BIOMT1 36 -0.762668 0.646790 0.000000 0.00000 REMARK 350 BIOMT2 36 -0.646790 -0.762668 0.000000 0.00000 REMARK 350 BIOMT3 36 0.000000 0.000000 1.000000 14.10000 REMARK 350 BIOMT1 37 -0.464378 0.885637 0.000000 0.00000 REMARK 350 BIOMT2 37 -0.885637 -0.464378 0.000000 0.00000 REMARK 350 BIOMT3 37 0.000000 0.000000 1.000000 15.51000 REMARK 350 BIOMT1 38 -0.098278 0.995159 0.000000 0.00000 REMARK 350 BIOMT2 38 -0.995159 -0.098278 0.000000 0.00000 REMARK 350 BIOMT3 38 0.000000 0.000000 1.000000 16.92000 REMARK 350 BIOMT1 39 0.282174 0.959363 0.000000 0.00000 REMARK 350 BIOMT2 39 -0.959363 0.282174 0.000000 0.00000 REMARK 350 BIOMT3 39 0.000000 0.000000 1.000000 18.33000 REMARK 350 BIOMT1 40 0.621421 0.783477 0.000000 0.00000 REMARK 350 BIOMT2 40 -0.783477 0.621421 0.000000 0.00000 REMARK 350 BIOMT3 40 0.000000 0.000000 1.000000 19.74000 REMARK 350 BIOMT1 41 0.869926 0.493183 0.000000 0.00000 REMARK 350 BIOMT2 41 -0.493183 0.869926 0.000000 0.00000 REMARK 350 BIOMT3 41 0.000000 0.000000 1.000000 21.15000 REMARK 350 BIOMT1 42 0.991399 0.130872 0.000000 0.00000 REMARK 350 BIOMT2 42 -0.130872 0.991399 0.000000 0.00000 REMARK 350 BIOMT3 42 0.000000 0.000000 1.000000 22.56000 REMARK 350 BIOMT1 43 0.968104 -0.250549 0.000000 0.00000 REMARK 350 BIOMT2 43 0.250549 0.968104 0.000000 0.00000 REMARK 350 BIOMT3 43 0.000000 0.000000 1.000000 23.97000 REMARK 350 BIOMT1 44 0.803441 -0.595384 0.000000 0.00000 REMARK 350 BIOMT2 44 0.595384 0.803441 0.000000 0.00000 REMARK 350 BIOMT3 44 0.000000 0.000000 1.000000 25.38000 REMARK 350 BIOMT1 45 0.521456 -0.853278 0.000000 0.00000 REMARK 350 BIOMT2 45 0.853278 0.521456 0.000000 0.00000 REMARK 350 BIOMT3 45 0.000000 0.000000 1.000000 26.79000 REMARK 350 BIOMT1 46 0.163326 -0.986572 0.000000 0.00000 REMARK 350 BIOMT2 46 0.986572 0.163326 0.000000 0.00000 REMARK 350 BIOMT3 46 0.000000 0.000000 1.000000 28.20000 REMARK 350 BIOMT1 47 -0.218654 -0.975802 0.000000 0.00000 REMARK 350 BIOMT2 47 0.975802 -0.218654 0.000000 0.00000 REMARK 350 BIOMT3 47 0.000000 0.000000 1.000000 29.61000 REMARK 350 BIOMT1 48 -0.568705 -0.822541 0.000000 0.00000 REMARK 350 BIOMT2 48 0.822541 -0.568705 0.000000 0.00000 REMARK 350 BIOMT3 48 0.000000 0.000000 1.000000 31.02000 REMARK 350 BIOMT1 49 -0.835712 -0.549169 0.000000 0.00000 REMARK 350 BIOMT2 49 0.549169 -0.835712 0.000000 0.00000 REMARK 350 BIOMT3 49 0.000000 0.000000 1.000000 32.43000 REMARK 350 BIOMT1 50 -0.980683 -0.195604 0.000000 0.00000 REMARK 350 BIOMT2 50 0.195604 -0.980683 0.000000 0.00000 REMARK 350 BIOMT3 50 0.000000 0.000000 1.000000 33.84000 """ text_point_group=""" new_ncs_group new_operator rota_matrix 1.0000 0.0000 0.0000 rota_matrix 0.0000 1.0000 0.0000 rota_matrix 0.0000 0.0000 1.0000 tran_orth 0.0000 0.0000 0.0000 center_orth 18.1267 39.0869 16.3485 new_operator rota_matrix 0.6235 0.7818 0.0000 rota_matrix -0.7818 0.6235 0.0000 rota_matrix -0.0000 -0.0000 1.0000 tran_orth -14.8728 23.9186 0.0000 center_orth 8.7170 35.2568 16.3490 new_operator rota_matrix -0.2225 0.9749 0.0000 rota_matrix -0.9749 -0.2225 0.0000 rota_matrix 0.0000 -0.0000 1.0000 tran_orth -5.4432 50.4629 -0.0007 center_orth 5.8467 25.5100 16.3495 new_operator rota_matrix -0.9010 0.4339 -0.0000 rota_matrix -0.4339 -0.9010 0.0000 rota_matrix -0.0000 0.0000 1.0000 tran_orth 21.1858 59.6326 0.0000 center_orth 11.6703 17.1839 16.3485 new_operator rota_matrix -0.9010 -0.4339 -0.0000 rota_matrix 0.4339 -0.9010 -0.0000 rota_matrix -0.0000 -0.0000 1.0000 tran_orth 44.9594 44.5364 -0.0006 center_orth 21.8108 16.5521 16.3495 new_operator rota_matrix -0.2225 -0.9749 0.0000 rota_matrix 0.9749 -0.2225 -0.0000 rota_matrix 0.0000 0.0000 1.0000 tran_orth 47.9895 16.5293 0.0005 center_orth 28.6368 24.0954 16.3473 new_operator rota_matrix 0.6235 -0.7818 0.0000 rota_matrix 0.7818 0.6235 0.0000 rota_matrix -0.0000 0.0000 1.0000 tran_orth 27.9737 -3.2911 0.0000 center_orth 26.9919 34.1217 16.3485 """ text_nothing=""" new_ncs_group new_operator rota_matrix 1.0000 0.0000 0.0000 rota_matrix 0.0000 1.0000 0.0000 rota_matrix 0.0000 0.0000 1.0000 tran_orth 0.0000 0.0000 0.0000 center_orth 18.1267 39.0869 16.3485 new_operator rota_matrix 0.6235 0.7818 0.0000 rota_matrix -0.7818 0.6235 0.0000 rota_matrix -0.0000 -0.0000 1.0000 tran_orth -14.8728 23.9186 0.0000 center_orth 8.7170 35.2568 16.3490 new_operator rota_matrix -0.2225 0.9749 0.0000 rota_matrix -0.9749 -0.2225 0.0000 rota_matrix 0.0000 -0.0000 1.0000 tran_orth -5.4432 50.4629 -0.0007 center_orth 5.8467 25.5100 16.3495 new_operator rota_matrix -0.9010 0.4339 -0.0000 rota_matrix -0.4339 -0.9010 0.0000 rota_matrix -0.0000 0.0000 1.0000 tran_orth 21.1858 59.6326 0.0000 center_orth 11.6703 17.1839 16.3485 new_operator rota_matrix -0.9010 -0.4339 -0.0000 rota_matrix 0.4339 -0.9010 -0.0000 rota_matrix -0.0000 -0.0000 1.0000 tran_orth 44.9594 44.5364 -0.0006 center_orth 21.8108 16.5521 16.3495 new_operator rota_matrix -0.2225 -0.9749 0.0000 rota_matrix 0.9749 -0.2225 -0.0000 rota_matrix 0.0000 0.0000 1.0000 tran_orth 47.9895 16.5293 0.0005 center_orth 28.6368 24.0954 16.3473 """ text_helical_requires_reordering=""" REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 -0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 -0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 0.923478 -0.383651 0.000000 -0.00000 REMARK 350 BIOMT2 2 0.383651 0.923478 -0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 -0.000000 1.000000 -67.58400 REMARK 350 BIOMT1 3 0.712149 -0.702029 0.000000 -0.00000 REMARK 350 BIOMT2 3 0.702029 0.712149 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 -0.000000 1.000000 -66.17600 REMARK 350 BIOMT1 4 0.396828 -0.917893 0.000000 -0.00000 REMARK 350 BIOMT2 4 0.917893 0.396828 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 -0.000000 1.000000 -64.76800 REMARK 350 BIOMT1 5 0.023560 -0.999722 0.000000 -0.00000 REMARK 350 BIOMT2 5 0.999722 0.023560 0.000000 0.00000 REMARK 350 BIOMT3 5 0.000000 -0.000000 1.000000 -63.36000 REMARK 350 BIOMT1 6 -0.353148 -0.935567 0.000000 -0.00000 REMARK 350 BIOMT2 6 0.935567 -0.353148 0.000000 0.00000 REMARK 350 BIOMT3 6 0.000000 -0.000000 1.000000 -61.95200 REMARK 350 BIOMT1 7 -0.678288 -0.734796 0.000000 -0.00000 REMARK 350 BIOMT2 7 0.734796 -0.678288 0.000000 0.00000 REMARK 350 BIOMT3 7 0.000000 -0.000000 1.000000 -60.54400 REMARK 350 BIOMT1 8 -0.904381 -0.426727 0.000000 -0.00000 REMARK 350 BIOMT2 8 0.426727 -0.904381 0.000000 0.00000 REMARK 350 BIOMT3 8 -0.000000 -0.000000 1.000000 -59.13600 REMARK 350 BIOMT1 9 -0.998411 -0.056344 0.000000 -0.00000 REMARK 350 BIOMT2 9 0.056344 -0.998411 0.000000 0.00000 REMARK 350 BIOMT3 9 -0.000000 -0.000000 1.000000 -57.72800 REMARK 350 BIOMT1 10 -0.946649 0.322266 -0.000000 -0.00000 REMARK 350 BIOMT2 10 -0.322266 -0.946649 -0.000000 0.00000 REMARK 350 BIOMT3 10 0.000000 0.000000 1.000000 -56.32000 REMARK 350 BIOMT1 11 -0.756653 0.653817 0.000000 -0.00000 REMARK 350 BIOMT2 11 -0.653817 -0.756653 -0.000000 0.00000 REMARK 350 BIOMT3 11 0.000000 0.000000 1.000000 -54.91200 REMARK 350 BIOMT1 12 -0.456166 0.889895 0.000000 -0.00000 REMARK 350 BIOMT2 12 -0.889895 -0.456166 -0.000000 0.00000 REMARK 350 BIOMT3 12 0.000000 0.000000 1.000000 -53.50400 REMARK 350 BIOMT1 13 -0.089068 0.996026 0.000000 -0.00000 REMARK 350 BIOMT2 13 -0.996026 -0.089068 -0.000000 0.00000 REMARK 350 BIOMT3 13 0.000000 0.000000 1.000000 -52.09600 REMARK 350 BIOMT1 14 0.291036 0.956712 0.000000 -0.00000 REMARK 350 BIOMT2 14 -0.956712 0.291036 -0.000000 0.00000 REMARK 350 BIOMT3 14 0.000000 0.000000 1.000000 -50.68800 REMARK 350 BIOMT1 15 0.628642 0.777695 0.000000 -0.00000 REMARK 350 BIOMT2 15 -0.777695 0.628642 -0.000000 0.00000 REMARK 350 BIOMT3 15 0.000000 0.000000 1.000000 -49.28000 REMARK 350 BIOMT1 16 0.874450 0.485115 0.000000 -0.00000 REMARK 350 BIOMT2 16 -0.485115 0.874450 -0.000000 0.00000 REMARK 350 BIOMT3 16 0.000000 -0.000000 1.000000 -47.87200 REMARK 350 BIOMT1 17 0.992567 0.121696 0.000000 -0.00000 REMARK 350 BIOMT2 17 -0.121696 0.992567 -0.000000 0.00000 REMARK 350 BIOMT3 17 0.000000 -0.000000 1.000000 -46.46400 REMARK 350 BIOMT1 18 0.965745 -0.259493 0.000000 -0.00000 REMARK 350 BIOMT2 18 0.259493 0.965745 -0.000000 0.00000 REMARK 350 BIOMT3 18 0.000000 -0.000000 1.000000 -45.05600 REMARK 350 BIOMT1 19 0.797900 -0.602790 0.000000 -0.00000 REMARK 350 BIOMT2 19 0.602790 0.797900 0.000000 0.00000 REMARK 350 BIOMT3 19 0.000000 -0.000000 1.000000 -43.64800 REMARK 350 BIOMT1 20 0.513541 -0.858065 0.000000 -0.00000 REMARK 350 BIOMT2 20 0.858065 0.513541 0.000000 0.00000 REMARK 350 BIOMT3 20 0.000000 -0.000000 1.000000 -42.24000 REMARK 350 BIOMT1 21 0.154193 -0.988041 0.000000 -0.00000 REMARK 350 BIOMT2 21 0.988041 0.154193 0.000000 0.00000 REMARK 350 BIOMT3 21 0.000000 -0.000000 1.000000 -40.83200 REMARK 350 BIOMT1 22 -0.227671 -0.973738 0.000000 -0.00000 REMARK 350 BIOMT2 22 0.973738 -0.227671 0.000000 0.00000 REMARK 350 BIOMT3 22 0.000000 -0.000000 1.000000 -39.42400 REMARK 350 BIOMT1 23 -0.576290 -0.817245 0.000000 -0.00000 REMARK 350 BIOMT2 23 0.817245 -0.576290 0.000000 0.00000 REMARK 350 BIOMT3 23 0.000000 -0.000000 1.000000 -38.01600 REMARK 350 BIOMT1 24 -0.840756 -0.541415 0.000000 -0.00000 REMARK 350 BIOMT2 24 0.541415 -0.840756 0.000000 0.00000 REMARK 350 BIOMT3 24 0.000000 -0.000000 1.000000 -36.60800 REMARK 350 BIOMT1 25 -0.982450 -0.186524 0.000000 -0.00000 REMARK 350 BIOMT2 25 0.186524 -0.982450 0.000000 0.00000 REMARK 350 BIOMT3 25 -0.000000 -0.000000 1.000000 -35.20000 REMARK 350 BIOMT1 26 -0.980683 0.195604 -0.000000 -0.00000 REMARK 350 BIOMT2 26 -0.195604 -0.980683 -0.000000 0.00000 REMARK 350 BIOMT3 26 0.000000 0.000000 1.000000 -33.79200 REMARK 350 BIOMT1 27 -0.835712 0.549169 0.000000 -0.00000 REMARK 350 BIOMT2 27 -0.549169 -0.835712 -0.000000 0.00000 REMARK 350 BIOMT3 27 0.000000 0.000000 1.000000 -32.38400 REMARK 350 BIOMT1 28 -0.568705 0.822541 0.000000 -0.00000 REMARK 350 BIOMT2 28 -0.822541 -0.568705 -0.000000 0.00000 REMARK 350 BIOMT3 28 0.000000 0.000000 1.000000 -30.97600 REMARK 350 BIOMT1 29 -0.218654 0.975802 0.000000 -0.00000 REMARK 350 BIOMT2 29 -0.975802 -0.218654 -0.000000 0.00000 REMARK 350 BIOMT3 29 0.000000 0.000000 1.000000 -29.56800 REMARK 350 BIOMT1 30 0.163326 0.986572 0.000000 -0.00000 REMARK 350 BIOMT2 30 -0.986572 0.163326 -0.000000 0.00000 REMARK 350 BIOMT3 30 0.000000 0.000000 1.000000 -28.16000 REMARK 350 BIOMT1 31 0.521456 0.853278 0.000000 -0.00000 REMARK 350 BIOMT2 31 -0.853278 0.521456 -0.000000 0.00000 REMARK 350 BIOMT3 31 0.000000 0.000000 1.000000 -26.75200 REMARK 350 BIOMT1 32 0.803441 0.595384 0.000000 -0.00000 REMARK 350 BIOMT2 32 -0.595384 0.803441 -0.000000 0.00000 REMARK 350 BIOMT3 32 0.000000 0.000000 1.000000 -25.34400 REMARK 350 BIOMT1 33 0.968104 0.250549 0.000000 -0.00000 REMARK 350 BIOMT2 33 -0.250549 0.968104 -0.000000 0.00000 REMARK 350 BIOMT3 33 0.000000 -0.000000 1.000000 -23.93600 REMARK 350 BIOMT1 34 0.991399 -0.130872 0.000000 -0.00000 REMARK 350 BIOMT2 34 0.130872 0.991399 -0.000000 0.00000 REMARK 350 BIOMT3 34 0.000000 -0.000000 1.000000 -22.52800 REMARK 350 BIOMT1 35 0.869926 -0.493183 0.000000 -0.00000 REMARK 350 BIOMT2 35 0.493183 0.869926 -0.000000 0.00000 REMARK 350 BIOMT3 35 0.000000 -0.000000 1.000000 -21.12000 REMARK 350 BIOMT1 36 0.621421 -0.783477 0.000000 -0.00000 REMARK 350 BIOMT2 36 0.783477 0.621421 0.000000 0.00000 REMARK 350 BIOMT3 36 0.000000 -0.000000 1.000000 -19.71200 REMARK 350 BIOMT1 37 0.282174 -0.959363 0.000000 -0.00000 REMARK 350 BIOMT2 37 0.959363 0.282174 0.000000 0.00000 REMARK 350 BIOMT3 37 0.000000 -0.000000 1.000000 -18.30400 REMARK 350 BIOMT1 38 -0.098278 -0.995159 0.000000 -0.00000 REMARK 350 BIOMT2 38 0.995159 -0.098278 0.000000 0.00000 REMARK 350 BIOMT3 38 0.000000 -0.000000 1.000000 -16.89600 REMARK 350 BIOMT1 39 -0.464378 -0.885637 0.000000 -0.00000 REMARK 350 BIOMT2 39 0.885637 -0.464378 0.000000 -0.00000 REMARK 350 BIOMT3 39 0.000000 -0.000000 1.000000 -15.48800 REMARK 350 BIOMT1 40 -0.762668 -0.646790 0.000000 -0.00000 REMARK 350 BIOMT2 40 0.646790 -0.762668 0.000000 -0.00000 REMARK 350 BIOMT3 40 0.000000 -0.000000 1.000000 -14.08000 REMARK 350 BIOMT1 41 -0.949590 -0.313495 0.000000 -0.00000 REMARK 350 BIOMT2 41 0.313495 -0.949590 0.000000 -0.00000 REMARK 350 BIOMT3 41 -0.000000 -0.000000 1.000000 -12.67200 REMARK 350 BIOMT1 42 -0.997848 0.065577 -0.000000 -0.00000 REMARK 350 BIOMT2 42 -0.065577 -0.997848 -0.000000 -0.00000 REMARK 350 BIOMT3 42 0.000000 0.000000 1.000000 -11.26400 REMARK 350 BIOMT1 43 -0.900395 0.435074 -0.000000 -0.00000 REMARK 350 BIOMT2 43 -0.435074 -0.900395 -0.000000 -0.00000 REMARK 350 BIOMT3 43 0.000000 0.000000 1.000000 -9.85600 REMARK 350 BIOMT1 44 -0.671462 0.741039 0.000000 -0.00000 REMARK 350 BIOMT2 44 -0.741039 -0.671462 -0.000000 -0.00000 REMARK 350 BIOMT3 44 0.000000 0.000000 1.000000 -8.44800 REMARK 350 BIOMT1 45 -0.344479 0.938794 0.000000 -0.00000 REMARK 350 BIOMT2 45 -0.938794 -0.344479 -0.000000 -0.00000 REMARK 350 BIOMT3 45 0.000000 0.000000 1.000000 -7.04000 REMARK 350 BIOMT1 46 0.032806 0.999462 0.000000 -0.00000 REMARK 350 BIOMT2 46 -0.999462 0.032806 -0.000000 -0.00000 REMARK 350 BIOMT3 46 0.000000 0.000000 1.000000 -5.63200 REMARK 350 BIOMT1 47 0.405301 0.914183 0.000000 -0.00000 REMARK 350 BIOMT2 47 -0.914183 0.405301 -0.000000 -0.00000 REMARK 350 BIOMT3 47 0.000000 0.000000 1.000000 -4.22400 REMARK 350 BIOMT1 48 0.718612 0.695411 0.000000 -0.00000 REMARK 350 BIOMT2 48 -0.695411 0.718612 -0.000000 -0.00000 REMARK 350 BIOMT3 48 0.000000 0.000000 1.000000 -2.81600 REMARK 350 BIOMT1 49 0.926988 0.375092 0.000000 -0.00000 REMARK 350 BIOMT2 49 -0.375092 0.926988 -0.000000 0.00000 REMARK 350 BIOMT3 49 0.000000 -0.000000 1.000000 -1.40800 """ text_helical_requires_reordering_2=""" REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -0.956100 0.293039 0.000000 249.45917 REMARK 350 BIOMT2 2 -0.293039 -0.956100 0.000000 337.37095 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 -64.48000 REMARK 350 BIOMT1 3 -0.828842 0.559482 0.000000 190.40401 REMARK 350 BIOMT2 3 -0.559482 -0.828842 0.000000 358.24869 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 -63.24000 REMARK 350 BIOMT1 4 -0.629320 0.777146 0.000000 127.82616 REMARK 350 BIOMT2 4 -0.777146 -0.629320 0.000000 360.96995 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 -62.00000 REMARK 350 BIOMT1 5 -0.374930 0.927053 0.000000 67.18158 REMARK 350 BIOMT2 5 -0.927053 -0.374930 0.000000 345.29749 REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 -60.76000 REMARK 350 BIOMT1 6 -0.087851 0.996134 0.000000 13.75764 REMARK 350 BIOMT2 6 -0.996134 -0.087851 0.000000 312.59772 REMARK 350 BIOMT3 6 0.000000 0.000000 1.000000 -59.52000 REMARK 350 BIOMT1 7 0.206887 0.978365 0.000000 -27.78781 REMARK 350 BIOMT2 7 -0.978365 0.206887 0.000000 265.72163 REMARK 350 BIOMT3 7 0.000000 0.000000 1.000000 -58.28000 REMARK 350 BIOMT1 8 0.483588 0.875296 0.000000 -53.83256 REMARK 350 BIOMT2 8 -0.875296 0.483588 0.000000 208.75617 REMARK 350 BIOMT3 8 0.000000 0.000000 1.000000 -57.04000 REMARK 350 BIOMT1 9 0.718126 0.695913 0.000000 -62.10586 REMARK 350 BIOMT2 9 -0.695913 0.718126 0.000000 146.66797 REMARK 350 BIOMT3 9 0.000000 0.000000 1.000000 -55.80000 REMARK 350 BIOMT1 10 0.890054 0.455856 0.000000 -51.88640 REMARK 350 BIOMT2 10 -0.455856 0.890054 0.000000 84.87028 REMARK 350 BIOMT3 10 0.000000 0.000000 1.000000 -54.56000 REMARK 350 BIOMT1 11 0.984381 0.176054 0.000000 -24.06518 REMARK 350 BIOMT2 11 -0.176054 0.984381 0.000000 28.75102 REMARK 350 BIOMT3 11 0.000000 0.000000 1.000000 -53.32000 REMARK 350 BIOMT1 12 0.992883 -0.119097 0.000000 18.93218 REMARK 350 BIOMT2 12 0.119097 0.992883 0.000000 -16.79696 REMARK 350 BIOMT3 12 0.000000 0.000000 1.000000 -52.08000 REMARK 350 BIOMT1 13 0.914819 -0.403865 0.000000 73.35689 REMARK 350 BIOMT2 13 0.403865 0.914819 0.000000 -47.80251 REMARK 350 BIOMT3 13 0.000000 0.000000 1.000000 -50.84000 REMARK 350 BIOMT1 14 0.756995 -0.653421 0.000000 134.46383 REMARK 350 BIOMT2 14 0.653421 0.756995 0.000000 -61.56235 REMARK 350 BIOMT3 14 0.000000 0.000000 1.000000 -49.60000 REMARK 350 BIOMT1 15 0.533172 -0.846007 0.000000 196.92532 REMARK 350 BIOMT2 15 0.846007 0.533172 0.000000 -56.87681 REMARK 350 BIOMT3 15 0.000000 0.000000 1.000000 -48.36000 REMARK 350 BIOMT1 16 0.262863 -0.964833 0.000000 255.29556 REMARK 350 BIOMT2 16 0.964833 0.262863 0.000000 -34.15441 REMARK 350 BIOMT3 16 0.000000 0.000000 1.000000 -47.12000 REMARK 350 BIOMT1 17 -0.030364 -0.999539 0.000000 304.48545 REMARK 350 BIOMT2 17 0.999539 -0.030364 0.000000 4.62377 REMARK 350 BIOMT3 17 0.000000 0.000000 1.000000 -45.88000 REMARK 350 BIOMT1 18 -0.320944 -0.947098 0.000000 340.20629 REMARK 350 BIOMT2 18 0.947098 -0.320944 0.000000 56.07680 REMARK 350 BIOMT3 18 0.000000 0.000000 1.000000 -44.64000 REMARK 350 BIOMT1 19 -0.583541 -0.812084 0.000000 359.34371 REMARK 350 BIOMT2 19 0.812084 -0.583541 0.000000 115.71865 REMARK 350 BIOMT3 19 0.000000 0.000000 1.000000 -43.40000 REMARK 350 BIOMT1 20 -0.795262 -0.606266 0.000000 360.22919 REMARK 350 BIOMT2 20 0.606266 -0.795262 0.000000 178.34938 REMARK 350 BIOMT3 20 0.000000 0.000000 1.000000 -42.16000 REMARK 350 BIOMT1 21 -0.937646 -0.347590 0.000000 342.78553 REMARK 350 BIOMT2 21 0.347590 -0.937646 0.000000 238.50842 REMARK 350 BIOMT3 21 0.000000 0.000000 1.000000 -40.92000 REMARK 350 BIOMT1 22 -0.998281 -0.058609 0.000000 308.53357 REMARK 350 BIOMT2 22 0.058609 -0.998281 0.000000 290.95073 REMARK 350 BIOMT3 22 0.000000 0.000000 1.000000 -39.68000 REMARK 350 BIOMT1 23 -0.971879 0.235481 0.000000 260.45962 REMARK 350 BIOMT2 23 -0.235481 -0.971879 0.000000 331.10404 REMARK 350 BIOMT3 23 0.000000 0.000000 1.000000 -38.44000 REMARK 350 BIOMT1 24 -0.860742 0.509041 0.000000 202.75509 REMARK 350 BIOMT2 24 -0.509041 -0.860742 0.000000 355.46752 REMARK 350 BIOMT3 24 0.000000 0.000000 1.000000 -37.20000 REMARK 350 BIOMT1 25 -0.674560 0.738220 0.000000 140.45103 REMARK 350 BIOMT2 25 -0.738220 -0.674560 0.000000 361.91701 REMARK 350 BIOMT3 25 0.000000 0.000000 1.000000 -35.96000 REMARK 350 BIOMT1 26 -0.429566 0.903036 0.000000 78.97951 REMARK 350 BIOMT2 26 -0.903036 -0.429566 0.000000 349.89019 REMARK 350 BIOMT3 26 0.000000 0.000000 1.000000 -34.72000 REMARK 350 BIOMT1 27 -0.147119 0.989119 0.000000 23.70001 REMARK 350 BIOMT2 27 -0.989119 -0.147119 0.000000 320.43566 REMARK 350 BIOMT3 27 0.000000 0.000000 1.000000 -33.48000 REMARK 350 BIOMT1 28 0.148155 0.988964 0.000000 -20.56783 REMARK 350 BIOMT2 28 -0.988964 0.148155 0.000000 276.12144 REMARK 350 BIOMT3 28 0.000000 0.000000 1.000000 -32.24000 REMARK 350 BIOMT1 29 0.430511 0.902585 0.000000 -49.96446 REMARK 350 BIOMT2 29 -0.902585 0.430511 0.000000 220.81113 REMARK 350 BIOMT3 29 0.000000 0.000000 1.000000 -31.00000 REMARK 350 BIOMT1 30 0.675333 0.737513 0.000000 -61.92689 REMARK 350 BIOMT2 30 -0.737513 0.675333 0.000000 159.32705 REMARK 350 BIOMT3 30 0.000000 0.000000 1.000000 -29.76000 REMARK 350 BIOMT1 31 0.861275 0.508140 0.000000 -55.41216 REMARK 350 BIOMT2 31 -0.508140 0.861275 0.000000 97.02977 REMARK 350 BIOMT3 31 0.000000 0.000000 1.000000 -28.52000 REMARK 350 BIOMT1 32 0.972125 0.234463 0.000000 -30.98826 REMARK 350 BIOMT2 32 -0.234463 0.972125 0.000000 39.35079 REMARK 350 BIOMT3 32 0.000000 0.000000 1.000000 -27.28000 REMARK 350 BIOMT1 33 0.998219 -0.059655 0.000000 9.21536 REMARK 350 BIOMT2 33 0.059655 0.998219 0.000000 -8.68108 REMARK 350 BIOMT3 33 0.000000 0.000000 1.000000 -26.04000 REMARK 350 BIOMT1 34 0.937282 -0.348572 0.000000 61.69351 REMARK 350 BIOMT2 34 0.348572 0.937282 0.000000 -42.87811 REMARK 350 BIOMT3 34 0.000000 0.000000 1.000000 -24.80000 REMARK 350 BIOMT1 35 0.794627 -0.607098 0.000000 121.87079 REMARK 350 BIOMT2 35 0.607098 0.794627 0.000000 -60.25876 REMARK 350 BIOMT3 35 0.000000 0.000000 1.000000 -23.56000 REMARK 350 BIOMT1 36 0.582690 -0.812694 0.000000 184.50055 REMARK 350 BIOMT2 36 0.812694 0.582690 0.000000 -59.30770 REMARK 350 BIOMT3 36 0.000000 0.000000 1.000000 -22.32000 REMARK 350 BIOMT1 37 0.319952 -0.947434 0.000000 244.12234 REMARK 350 BIOMT2 37 0.947434 0.319952 0.000000 -40.10783 REMARK 350 BIOMT3 37 0.000000 0.000000 1.000000 -21.08000 REMARK 350 BIOMT1 38 0.029317 -0.999570 0.000000 295.53792 REMARK 350 BIOMT2 38 0.999570 0.029317 0.000000 -4.33312 REMARK 350 BIOMT3 38 0.000000 0.000000 1.000000 -19.84000 REMARK 350 BIOMT1 39 -0.263873 -0.964557 0.000000 334.26457 REMARK 350 BIOMT2 39 0.964557 -0.263873 0.000000 44.89734 REMARK 350 BIOMT3 39 0.000000 0.000000 1.000000 -18.60000 REMARK 350 BIOMT1 40 -0.534057 -0.845448 0.000000 356.92584 REMARK 350 BIOMT2 40 0.845448 -0.534057 0.000000 103.29134 REMARK 350 BIOMT3 40 0.000000 0.000000 1.000000 -17.36000 REMARK 350 BIOMT1 41 -0.757679 -0.652628 0.000000 361.54596 REMARK 350 BIOMT2 41 0.652628 -0.757679 0.000000 165.75771 REMARK 350 BIOMT3 41 0.000000 0.000000 1.000000 -16.12000 REMARK 350 BIOMT1 42 -0.915241 -0.402906 0.000000 347.72214 REMARK 350 BIOMT2 42 0.402906 -0.915241 0.000000 226.85021 REMARK 350 BIOMT3 42 0.000000 0.000000 1.000000 -14.88000 REMARK 350 BIOMT1 43 -0.993007 -0.118057 0.000000 316.65962 REMARK 350 BIOMT2 43 0.118057 -0.993007 0.000000 281.24241 REMARK 350 BIOMT3 43 0.000000 0.000000 1.000000 -13.64000 REMARK 350 BIOMT1 44 -0.984196 0.177085 0.000000 271.06663 REMARK 350 BIOMT2 44 -0.177085 -0.984196 0.000000 324.19205 REMARK 350 BIOMT3 44 0.000000 0.000000 1.000000 -12.40000 REMARK 350 BIOMT1 45 -0.889576 0.456787 0.000000 214.91827 REMARK 350 BIOMT2 45 -0.456787 -0.889576 0.000000 351.95450 REMARK 350 BIOMT3 45 0.000000 0.000000 1.000000 -11.16000 REMARK 350 BIOMT1 46 -0.717397 0.696664 0.000000 153.10991 REMARK 350 BIOMT2 46 -0.696664 -0.717397 0.000000 362.10924 REMARK 350 BIOMT3 46 0.000000 0.000000 1.000000 -9.92000 REMARK 350 BIOMT1 47 -0.482671 0.875802 0.000000 91.03041 REMARK 350 BIOMT2 47 -0.875802 -0.482671 0.000000 353.77092 REMARK 350 BIOMT3 47 0.000000 0.000000 1.000000 -8.68000 REMARK 350 BIOMT1 48 -0.205863 0.978581 0.000000 34.09226 REMARK 350 BIOMT2 48 -0.978581 -0.205863 0.000000 327.66653 REMARK 350 BIOMT3 48 0.000000 0.000000 1.000000 -7.44000 REMARK 350 BIOMT1 49 0.088894 0.996041 0.000000 -12.74030 REMARK 350 BIOMT2 49 -0.996041 0.088894 0.000000 286.07202 REMARK 350 BIOMT3 49 0.000000 0.000000 1.000000 -6.20000 REMARK 350 BIOMT1 50 0.375901 0.926660 0.000000 -45.38411 REMARK 350 BIOMT2 50 -0.926660 0.375901 0.000000 232.61386 REMARK 350 BIOMT3 50 0.000000 0.000000 1.000000 -4.96000 REMARK 350 BIOMT1 51 0.630134 0.776487 0.000000 -60.99306 REMARK 350 BIOMT2 51 -0.776487 0.630134 0.000000 171.95290 REMARK 350 BIOMT3 51 0.000000 0.000000 1.000000 -3.72000 REMARK 350 BIOMT1 52 0.829428 0.558614 0.000000 -58.20626 REMARK 350 BIOMT2 52 -0.558614 0.829428 0.000000 109.37793 REMARK 350 BIOMT3 52 0.000000 0.000000 1.000000 -2.48000 REMARK 350 BIOMT1 53 0.956407 0.292038 0.000000 -37.26669 REMARK 350 BIOMT2 53 -0.292038 0.956407 0.000000 50.34467 REMARK 350 BIOMT3 53 0.000000 0.000000 1.000000 -1.24000 REMARK 350 BIOMT1 54 0.956407 -0.292038 0.000000 50.34467 REMARK 350 BIOMT2 54 0.292038 0.956407 0.000000 -37.26669 REMARK 350 BIOMT3 54 0.000000 0.000000 1.000000 1.24000 REMARK 350 BIOMT1 55 0.829428 -0.558614 0.000000 109.37793 REMARK 350 BIOMT2 55 0.558614 0.829428 0.000000 -58.20626 REMARK 350 BIOMT3 55 0.000000 0.000000 1.000000 2.48000 REMARK 350 BIOMT1 56 0.630134 -0.776487 0.000000 171.95290 REMARK 350 BIOMT2 56 0.776487 0.630134 0.000000 -60.99306 REMARK 350 BIOMT3 56 0.000000 0.000000 1.000000 3.72000 REMARK 350 BIOMT1 57 0.375901 -0.926660 0.000000 232.61386 REMARK 350 BIOMT2 57 0.926660 0.375901 0.000000 -45.38411 REMARK 350 BIOMT3 57 0.000000 0.000000 1.000000 4.96000 REMARK 350 BIOMT1 58 0.088894 -0.996041 0.000000 286.07202 REMARK 350 BIOMT2 58 0.996041 0.088894 0.000000 -12.74030 REMARK 350 BIOMT3 58 0.000000 0.000000 1.000000 6.20000 REMARK 350 BIOMT1 59 -0.205863 -0.978581 0.000000 327.66653 REMARK 350 BIOMT2 59 0.978581 -0.205863 0.000000 34.09226 REMARK 350 BIOMT3 59 0.000000 0.000000 1.000000 7.44000 REMARK 350 BIOMT1 60 -0.482671 -0.875802 0.000000 353.77092 REMARK 350 BIOMT2 60 0.875802 -0.482671 0.000000 91.03041 REMARK 350 BIOMT3 60 0.000000 0.000000 1.000000 8.68000 REMARK 350 BIOMT1 61 -0.717397 -0.696664 0.000000 362.10924 REMARK 350 BIOMT2 61 0.696664 -0.717397 0.000000 153.10991 REMARK 350 BIOMT3 61 0.000000 0.000000 1.000000 9.92000 REMARK 350 BIOMT1 62 -0.889576 -0.456787 0.000000 351.95450 REMARK 350 BIOMT2 62 0.456787 -0.889576 0.000000 214.91827 REMARK 350 BIOMT3 62 0.000000 0.000000 1.000000 11.16000 REMARK 350 BIOMT1 63 -0.984196 -0.177085 0.000000 324.19205 REMARK 350 BIOMT2 63 0.177085 -0.984196 0.000000 271.06663 REMARK 350 BIOMT3 63 0.000000 0.000000 1.000000 12.40000 REMARK 350 BIOMT1 64 -0.993007 0.118057 0.000000 281.24241 REMARK 350 BIOMT2 64 -0.118057 -0.993007 0.000000 316.65962 REMARK 350 BIOMT3 64 0.000000 0.000000 1.000000 13.64000 REMARK 350 BIOMT1 65 -0.915241 0.402906 0.000000 226.85021 REMARK 350 BIOMT2 65 -0.402906 -0.915241 0.000000 347.72214 REMARK 350 BIOMT3 65 0.000000 0.000000 1.000000 14.88000 REMARK 350 BIOMT1 66 -0.757679 0.652628 0.000000 165.75771 REMARK 350 BIOMT2 66 -0.652628 -0.757679 0.000000 361.54596 REMARK 350 BIOMT3 66 0.000000 0.000000 1.000000 16.12000 REMARK 350 BIOMT1 67 -0.534057 0.845448 0.000000 103.29134 REMARK 350 BIOMT2 67 -0.845448 -0.534057 0.000000 356.92584 REMARK 350 BIOMT3 67 0.000000 0.000000 1.000000 17.36000 REMARK 350 BIOMT1 68 -0.263873 0.964557 0.000000 44.89734 REMARK 350 BIOMT2 68 -0.964557 -0.263873 0.000000 334.26457 REMARK 350 BIOMT3 68 0.000000 0.000000 1.000000 18.60000 REMARK 350 BIOMT1 69 0.029317 0.999570 0.000000 -4.33312 REMARK 350 BIOMT2 69 -0.999570 0.029317 0.000000 295.53792 REMARK 350 BIOMT3 69 0.000000 0.000000 1.000000 19.84000 REMARK 350 BIOMT1 70 0.319952 0.947434 0.000000 -40.10783 REMARK 350 BIOMT2 70 -0.947434 0.319952 0.000000 244.12234 REMARK 350 BIOMT3 70 0.000000 0.000000 1.000000 21.08000 REMARK 350 BIOMT1 71 0.582690 0.812694 0.000000 -59.30770 REMARK 350 BIOMT2 71 -0.812694 0.582690 0.000000 184.50055 REMARK 350 BIOMT3 71 0.000000 0.000000 1.000000 22.32000 REMARK 350 BIOMT1 72 0.794627 0.607098 0.000000 -60.25876 REMARK 350 BIOMT2 72 -0.607098 0.794627 0.000000 121.87079 REMARK 350 BIOMT3 72 0.000000 0.000000 1.000000 23.56000 REMARK 350 BIOMT1 73 0.937282 0.348572 0.000000 -42.87811 REMARK 350 BIOMT2 73 -0.348572 0.937282 0.000000 61.69351 REMARK 350 BIOMT3 73 0.000000 0.000000 1.000000 24.80000 REMARK 350 BIOMT1 74 0.998219 0.059655 0.000000 -8.68108 REMARK 350 BIOMT2 74 -0.059655 0.998219 0.000000 9.21536 REMARK 350 BIOMT3 74 0.000000 0.000000 1.000000 26.04000 REMARK 350 BIOMT1 75 0.972125 -0.234463 0.000000 39.35079 REMARK 350 BIOMT2 75 0.234463 0.972125 0.000000 -30.98826 REMARK 350 BIOMT3 75 0.000000 0.000000 1.000000 27.28000 REMARK 350 BIOMT1 76 0.861275 -0.508140 0.000000 97.02977 REMARK 350 BIOMT2 76 0.508140 0.861275 0.000000 -55.41216 REMARK 350 BIOMT3 76 0.000000 0.000000 1.000000 28.52000 REMARK 350 BIOMT1 77 0.675333 -0.737513 0.000000 159.32705 REMARK 350 BIOMT2 77 0.737513 0.675333 0.000000 -61.92689 REMARK 350 BIOMT3 77 0.000000 0.000000 1.000000 29.76000 REMARK 350 BIOMT1 78 0.430511 -0.902585 0.000000 220.81113 REMARK 350 BIOMT2 78 0.902585 0.430511 0.000000 -49.96446 REMARK 350 BIOMT3 78 0.000000 0.000000 1.000000 31.00000 REMARK 350 BIOMT1 79 0.148155 -0.988964 0.000000 276.12144 REMARK 350 BIOMT2 79 0.988964 0.148155 0.000000 -20.56783 REMARK 350 BIOMT3 79 0.000000 0.000000 1.000000 32.24000 REMARK 350 BIOMT1 80 -0.147119 -0.989119 0.000000 320.43566 REMARK 350 BIOMT2 80 0.989119 -0.147119 0.000000 23.70001 REMARK 350 BIOMT3 80 0.000000 0.000000 1.000000 33.48000 REMARK 350 BIOMT1 81 -0.429566 -0.903036 0.000000 349.89019 REMARK 350 BIOMT2 81 0.903036 -0.429566 0.000000 78.97951 REMARK 350 BIOMT3 81 0.000000 0.000000 1.000000 34.72000 REMARK 350 BIOMT1 82 -0.674560 -0.738220 0.000000 361.91701 REMARK 350 BIOMT2 82 0.738220 -0.674560 0.000000 140.45103 REMARK 350 BIOMT3 82 0.000000 0.000000 1.000000 35.96000 REMARK 350 BIOMT1 83 -0.860742 -0.509041 0.000000 355.46752 REMARK 350 BIOMT2 83 0.509041 -0.860742 0.000000 202.75509 REMARK 350 BIOMT3 83 0.000000 0.000000 1.000000 37.20000 REMARK 350 BIOMT1 84 -0.971879 -0.235481 0.000000 331.10404 REMARK 350 BIOMT2 84 0.235481 -0.971879 0.000000 260.45962 REMARK 350 BIOMT3 84 0.000000 0.000000 1.000000 38.44000 REMARK 350 BIOMT1 85 -0.998281 0.058609 0.000000 290.95073 REMARK 350 BIOMT2 85 -0.058609 -0.998281 0.000000 308.53357 REMARK 350 BIOMT3 85 0.000000 0.000000 1.000000 39.68000 REMARK 350 BIOMT1 86 -0.937646 0.347590 0.000000 238.50842 REMARK 350 BIOMT2 86 -0.347590 -0.937646 0.000000 342.78553 REMARK 350 BIOMT3 86 0.000000 0.000000 1.000000 40.92000 REMARK 350 BIOMT1 87 -0.795262 0.606266 0.000000 178.34938 REMARK 350 BIOMT2 87 -0.606266 -0.795262 0.000000 360.22919 REMARK 350 BIOMT3 87 0.000000 0.000000 1.000000 42.16000 REMARK 350 BIOMT1 88 -0.583541 0.812084 0.000000 115.71865 REMARK 350 BIOMT2 88 -0.812084 -0.583541 0.000000 359.34371 REMARK 350 BIOMT3 88 0.000000 0.000000 1.000000 43.40000 REMARK 350 BIOMT1 89 -0.320944 0.947098 0.000000 56.07680 REMARK 350 BIOMT2 89 -0.947098 -0.320944 0.000000 340.20629 REMARK 350 BIOMT3 89 0.000000 0.000000 1.000000 44.64000 REMARK 350 BIOMT1 90 -0.030364 0.999539 0.000000 4.62377 REMARK 350 BIOMT2 90 -0.999539 -0.030364 0.000000 304.48545 REMARK 350 BIOMT3 90 0.000000 0.000000 1.000000 45.88000 REMARK 350 BIOMT1 91 0.262863 0.964833 0.000000 -34.15441 REMARK 350 BIOMT2 91 -0.964833 0.262863 0.000000 255.29556 REMARK 350 BIOMT3 91 0.000000 0.000000 1.000000 47.12000 REMARK 350 BIOMT1 92 0.533172 0.846007 0.000000 -56.87681 REMARK 350 BIOMT2 92 -0.846007 0.533172 0.000000 196.92532 REMARK 350 BIOMT3 92 0.000000 0.000000 1.000000 48.36000 REMARK 350 BIOMT1 93 0.756995 0.653421 0.000000 -61.56235 REMARK 350 BIOMT2 93 -0.653421 0.756995 0.000000 134.46383 REMARK 350 BIOMT3 93 0.000000 0.000000 1.000000 49.60000 REMARK 350 BIOMT1 94 0.914819 0.403865 0.000000 -47.80251 REMARK 350 BIOMT2 94 -0.403865 0.914819 0.000000 73.35689 REMARK 350 BIOMT3 94 0.000000 0.000000 1.000000 50.84000 REMARK 350 BIOMT1 95 0.992883 0.119097 0.000000 -16.79696 REMARK 350 BIOMT2 95 -0.119097 0.992883 0.000000 18.93218 REMARK 350 BIOMT3 95 0.000000 0.000000 1.000000 52.08000 REMARK 350 BIOMT1 96 0.984381 -0.176054 0.000000 28.75102 REMARK 350 BIOMT2 96 0.176054 0.984381 0.000000 -24.06518 REMARK 350 BIOMT3 96 0.000000 0.000000 1.000000 53.32000 REMARK 350 BIOMT1 97 0.890054 -0.455856 0.000000 84.87028 REMARK 350 BIOMT2 97 0.455856 0.890054 0.000000 -51.88640 REMARK 350 BIOMT3 97 0.000000 0.000000 1.000000 54.56000 REMARK 350 BIOMT1 98 0.718126 -0.695913 0.000000 146.66797 REMARK 350 BIOMT2 98 0.695913 0.718126 0.000000 -62.10586 REMARK 350 BIOMT3 98 0.000000 0.000000 1.000000 55.80000 REMARK 350 BIOMT1 99 0.483588 -0.875296 0.000000 208.75617 REMARK 350 BIOMT2 99 0.875296 0.483588 0.000000 -53.83256 REMARK 350 BIOMT3 99 0.000000 0.000000 1.000000 57.04000 REMARK 350 BIOMT1 100 0.206887 -0.978365 0.000000 265.72163 REMARK 350 BIOMT2 100 0.978365 0.206887 0.000000 -27.78781 REMARK 350 BIOMT3 100 0.000000 0.000000 1.000000 58.28000 REMARK 350 BIOMT1 101 -0.087851 -0.996134 0.000000 312.59772 REMARK 350 BIOMT2 101 0.996134 -0.087851 0.000000 13.75764 REMARK 350 BIOMT3 101 0.000000 0.000000 1.000000 59.52000 REMARK 350 BIOMT1 102 -0.374930 -0.927053 0.000000 345.29749 REMARK 350 BIOMT2 102 0.927053 -0.374930 0.000000 67.18158 REMARK 350 BIOMT3 102 0.000000 0.000000 1.000000 60.76000 REMARK 350 BIOMT1 103 -0.629320 -0.777146 0.000000 360.96995 REMARK 350 BIOMT2 103 0.777146 -0.629320 0.000000 127.82616 REMARK 350 BIOMT3 103 0.000000 0.000000 1.000000 62.00000 REMARK 350 BIOMT1 104 -0.828842 -0.559482 0.000000 358.24869 REMARK 350 BIOMT2 104 0.559482 -0.828842 0.000000 190.40401 REMARK 350 BIOMT3 104 0.000000 0.000000 1.000000 63.24000 REMARK 350 BIOMT1 105 -0.956100 -0.293039 0.000000 337.37095 REMARK 350 BIOMT2 105 0.293039 -0.956100 0.000000 249.45917 REMARK 350 BIOMT3 105 0.000000 0.000000 1.000000 64.48000 REMARK 350 BIOMT1 106 -0.999999 -0.001047 0.000000 300.15700 REMARK 350 BIOMT2 106 0.001047 -0.999999 0.000000 299.84284 REMARK 350 BIOMT3 106 0.000000 0.000000 1.000000 65.72000 """ text_helical_short=""" new_operator rota_matrix 0.9270 0.3751 0.0000 rota_matrix -0.3751 0.9270 0.0000 rota_matrix 0.0000 0.0000 1.0000 tran_orth 0.0000 0.0000 -1.4100 center_orth 0.0000 0.0000 0.0000 new_operator rota_matrix 1.0000 -0.0000 0.0000 rota_matrix 0.0000 1.0000 0.0000 rota_matrix 0.0000 0.0000 1.0000 tran_orth 0.0000 0.0000 -0.0000 center_orth 0.0000 0.0000 0.0000 new_operator rota_matrix 0.9270 -0.3751 0.0000 rota_matrix 0.3751 0.9270 0.0000 rota_matrix 0.0000 0.0000 1.0000 tran_orth 0.0000 0.0000 1.4100 center_orth 0.0000 0.0000 0.0000 """ text_helical_short_a=""" new_operator rota_matrix 1.0000 0.0000 -0.0000 rota_matrix 0.0000 1.0000 0.0000 rota_matrix 0.0000 -0.0000 1.0000 tran_orth 0.0000 0.0000 0.0000 center_orth 0.0000 0.0000 0.0000 new_operator rota_matrix 0.9270 0.3751 -0.0000 rota_matrix -0.3751 0.9270 0.0000 rota_matrix 0.0000 -0.0000 1.0000 tran_orth 0.0000 0.0000 -1.4100 center_orth 0.0000 0.0000 0.0000 new_operator rota_matrix 0.7186 0.6954 -0.0000 rota_matrix -0.6954 0.7186 0.0000 rota_matrix 0.0000 -0.0000 1.0000 tran_orth 0.0000 0.0000 -2.8200 center_orth 0.0000 0.0000 0.0000 """ text_helical_short_b=""" new_operator rota_matrix 0.7186 -0.6954 0.0000 rota_matrix 0.6954 0.7186 -0.0000 rota_matrix -0.0000 0.0000 1.0000 tran_orth 0.0000 0.0000 2.8200 center_orth 0.0000 0.0000 0.0000 new_operator rota_matrix 0.9270 -0.3751 0.0000 rota_matrix 0.3751 0.9270 -0.0000 rota_matrix -0.0000 0.0000 1.0000 tran_orth 0.0000 0.0000 1.4100 center_orth 0.0000 0.0000 0.0000 new_operator rota_matrix 1.0000 0.0000 -0.0000 rota_matrix 0.0000 1.0000 0.0000 rota_matrix 0.0000 -0.0000 1.0000 tran_orth 0.0000 0.0000 0.0000 center_orth 0.0000 0.0000 0.0000 """ def tst_02(): print("Test short helical and point_group symmetry...", end=' ') from mmtbx.ncs.ncs import ncs f=open('helical.ncs_spec','w') print(text_helical_short, file=f) f.close() ncs_object=ncs() ncs_object.read_ncs('helical.ncs_spec',quiet=True) assert ncs_object.is_helical_along_z() assert not ncs_object.is_point_group_symmetry() print("OK") print("Test helical and point_group symmetry...", end=' ') from mmtbx.ncs.ncs import ncs f=open('helical.ncs_spec','w') print(text_helical, file=f) f.close() ncs_object=ncs() ncs_object.read_ncs('helical.ncs_spec',quiet=True) assert ncs_object.is_helical_along_z() assert not ncs_object.is_point_group_symmetry() f=open('point_group.ncs_spec','w') print(text_point_group, file=f) f.close() ncs_object=ncs() ncs_object.read_ncs('point_group.ncs_spec',quiet=True) assert not ncs_object.is_helical_along_z() assert ncs_object.is_point_group_symmetry() f=open('nothing.ncs_spec','w') print(text_nothing, file=f) f.close() ncs_object=ncs() ncs_object.read_ncs('nothing.ncs_spec',quiet=True) assert not ncs_object.is_helical_along_z() assert not ncs_object.is_point_group_symmetry() f=open('helical_requires_reordering.ncs_spec','w') print(text_helical_requires_reordering, file=f) f.close() ncs_object=ncs() ncs_object.read_ncs('helical_requires_reordering.ncs_spec',quiet=True) assert ncs_object.is_helical_along_z() assert not ncs_object.is_point_group_symmetry() f=open('helical_requires_reordering_2.ncs_spec','w') print(text_helical_requires_reordering_2, file=f) f.close() ncs_object=ncs() ncs_object.read_ncs('helical_requires_reordering_2.ncs_spec',quiet=True) assert ncs_object.is_helical_along_z() assert not ncs_object.is_point_group_symmetry() print("OK") print("Test helical extending z_range...", end=' ') from mmtbx.ncs.ncs import ncs f=open('helical.ncs_spec','w') print(text_helical_short, file=f) f.close() ncs_object=ncs() ncs_object.read_ncs('helical.ncs_spec',quiet=True) assert ncs_object.is_helical_along_z() ncs_object.invert_matrices() assert ncs_object.is_helical_along_z() ncs_group=ncs_object.ncs_groups()[0] r_forwards,t_forwards=ncs_group.helix_rt_forwards() found=False from mmtbx.ncs.ncs import is_same_transform for r2,t2 in zip( ncs_group.rota_matrices_inv(),ncs_group.translations_orth_inv()): if is_same_transform(r_forwards,t_forwards,r2,t2): found=True break assert found ncs_group.extend_helix_operators(z_range=40) assert ncs_group.n_ncs_oper()==57 assert ncs_group.is_helical_along_z() print("OK") def tst_02a(): print("Test short helical and point_group symmetry with identity at start...", end=' ') from mmtbx.ncs.ncs import ncs f=open('helical.ncs_spec','w') print(text_helical_short_a, file=f) f.close() ncs_object=ncs() ncs_object.read_ncs('helical.ncs_spec',quiet=True) assert ncs_object.is_helical_along_z() assert not ncs_object.is_point_group_symmetry() print("OK") def tst_02b(): print("Test short helical and point_group symmetry with identity at end...", end=' ') from mmtbx.ncs.ncs import ncs f=open('helical.ncs_spec','w') print(text_helical_short_b, file=f) f.close() ncs_object=ncs() ncs_object.read_ncs('helical.ncs_spec',quiet=True) assert ncs_object.is_helical_along_z() assert not ncs_object.is_point_group_symmetry() print("OK") text2=""" Summary of NCS information Wed Dec 30 10:36:10 2015 /Users/terwill/unix/misc/cryo/emd_3063 source_info temp_dir/pseudo_ha.pdb new_ncs_group NCS_CC 0.99 new_operator rota_matrix 1.0000 0.0000 0.0000 rota_matrix 0.0000 1.0000 0.0000 rota_matrix 0.0000 0.0000 1.0000 tran_orth -0.0000 -0.0000 -0.0000 center_orth -72.7684 -30.3322 -82.7957 new_operator rota_matrix -1.0000 -0.0023 -0.0059 rota_matrix 0.0024 -0.9998 -0.0209 rota_matrix -0.0059 -0.0209 0.9998 tran_orth -1.9886 -2.6166 1.3404 center_orth 71.2074 29.6271 -83.1177 new_operator rota_matrix 0.0108 -0.9999 0.0007 rota_matrix 0.9997 0.0108 -0.0241 rota_matrix 0.0241 0.0009 0.9997 tran_orth -0.7179 -2.8574 0.9201 center_orth -30.2612 71.6728 -83.0767 new_operator rota_matrix -0.0108 0.9999 0.0018 rota_matrix -0.9997 -0.0108 -0.0241 rota_matrix -0.0241 -0.0021 0.9997 tran_orth 0.4240 -3.6743 0.8246 center_orth 29.4566 -72.7242 -83.0880 """ expected_text2=""" source_info temp_dir/pseudo_ha.pdb new_ncs_group NCS_CC 0.99 new_operator rota_matrix 1.0000 0.0000 0.0000 rota_matrix 0.0000 1.0000 0.0000 rota_matrix 0.0000 0.0000 1.0000 tran_orth 0.0000 0.0000 0.0000 center_orth 100.9116 143.3478 102.3243 new_operator rota_matrix -1.0000 -0.0023 -0.0059 rota_matrix 0.0024 -0.9998 -0.0209 rota_matrix -0.0059 -0.0209 0.9998 tran_orth 172.7836 174.9324 1.3774 center_orth 71.2074 29.6271 102.0023 new_operator rota_matrix 0.0108 -0.9999 0.0007 rota_matrix 0.9997 0.0108 -0.0241 rota_matrix 0.0241 0.0009 0.9997 tran_orth 170.9568 1.6561 -3.2101 center_orth 143.4188 71.6728 102.0433 new_operator rota_matrix -0.0108 0.9999 0.0018 rota_matrix -0.9997 -0.0108 -0.0241 rota_matrix -0.0241 -0.0021 0.9997 tran_orth 0.1082 176.3428 1.2449 center_orth 29.4566 100.9558 102.0320 """ expected_text2b=""" Summary of NCS information Wed Dec 30 19:56:31 2015 /Users/terwill/unix/misc/junk source_info temp_dir/pseudo_ha.pdb new_ncs_group NCS_CC 0.99 new_operator rota_matrix 1.0000 0.0000 0.0000 rota_matrix 0.0000 1.0000 0.0000 rota_matrix 0.0000 0.0000 1.0000 tran_orth 0.0000 0.0000 0.0000 center_orth 27.2316 69.6678 -182.7957 new_operator rota_matrix -1.0000 -0.0023 -0.0059 rota_matrix 0.0024 -0.9998 -0.0209 rota_matrix -0.0059 -0.0209 0.9998 tran_orth 197.6514 195.0334 4.0004 center_orth 171.2074 129.6271 -183.1177 new_operator rota_matrix 0.0108 -0.9999 0.0007 rota_matrix 0.9997 0.0108 -0.0241 rota_matrix 0.0241 0.0009 0.9997 tran_orth 198.2621 -6.3174 -1.6099 center_orth 69.7388 171.6728 -183.0767 new_operator rota_matrix -0.0108 0.9999 0.0018 rota_matrix -0.9997 -0.0108 -0.0241 rota_matrix -0.0241 -0.0021 0.9997 tran_orth 1.6940 194.9657 3.4146 center_orth 129.4566 27.2758 -183.0880 """ expected_text2c=""" Summary of NCS information Fri May 20 15:01:59 2016 /Users/terwill/Desktop/working/Jan_2015/phenix/cryo-pdb/3j9c/build source_info temp_dir/pseudo_ha.pdb new_ncs_group NCS_CC 0.99 new_operator rota_matrix 1.0000 0.0000 0.0000 rota_matrix 0.0000 1.0000 0.0000 rota_matrix 0.0000 0.0000 1.0000 tran_orth -0.0000 -0.0000 -0.0000 center_orth -36.3842 -15.1661 -41.3978 new_operator rota_matrix -1.0000 -0.0023 -0.0059 rota_matrix 0.0024 -0.9998 -0.0209 rota_matrix -0.0059 -0.0209 0.9998 tran_orth -0.9943 -1.3083 0.6702 center_orth 35.6037 14.8135 -41.5588 new_operator rota_matrix 0.0108 -0.9999 0.0007 rota_matrix 0.9997 0.0108 -0.0241 rota_matrix 0.0241 0.0009 0.9997 tran_orth -0.3589 -1.4287 0.4601 center_orth -15.1306 35.8364 -41.5384 new_operator rota_matrix -0.0108 0.9999 0.0018 rota_matrix -0.9997 -0.0108 -0.0241 rota_matrix -0.0241 -0.0021 0.9997 tran_orth 0.2120 -1.8372 0.4123 center_orth 14.7283 -36.3621 -41.5440 """ def tst_03(): print("Map NCS operators to place them in (0,1)") f=open('ncs.ncs_spec','w') print(text2, file=f) f.close() from mmtbx.ncs.ncs import ncs ncs_object=ncs() ncs_object.read_ncs('ncs.ncs_spec',quiet=True) from cctbx import uctbx uc=uctbx.unit_cell((173.680,173.680,185.120,90.00,90.00,90.00)) f=StringIO() ncs_object.format_all_for_group_specification(out=f) start_text=f.getvalue() ncs_object.map_inside_unit_cell(unit_cell=uc) f=StringIO() ncs_object.format_all_for_group_specification(out=f) found_text=f.getvalue() if remove_blank(" ".join(found_text.split("source_info")[1:]) ) != \ remove_blank(" ".join(expected_text2.split("source_info")[1:])): print("Expected: \n%s \nFound: \n%s" %(expected_text_group_specification,found_text)) raise AssertionError("FAILED") print("OK") def tst_04(): print("Offset NCS operators") f=open('ncs.ncs_spec','w') print(text2, file=f) f.close() from mmtbx.ncs.ncs import ncs ncs_object=ncs() ncs_object.read_ncs('ncs.ncs_spec',quiet=True) f=StringIO() ncs_object.format_all_for_group_specification(out=f) start_text=f.getvalue() ncs_object=ncs_object.coordinate_offset(coordinate_offset=(100.,100.,-100.)) f=StringIO() ncs_object.format_all_for_group_specification(out=f) found_text=f.getvalue() if remove_blank(" ".join(found_text.split("source_info")[1:]) ) != \ remove_blank(" ".join(expected_text2b.split("source_info")[1:])): print("Expected: \n%s \nFound: \n%s" %(expected_text_group_specification,found_text)) raise AssertionError("FAILED") print("OK") def tst_05(): print("Magnify NCS operators") f=open('ncs.ncs_spec','w') print(text2, file=f) f.close() from mmtbx.ncs.ncs import ncs ncs_object=ncs() ncs_object.read_ncs('ncs.ncs_spec',quiet=True) f=StringIO() ncs_object.format_all_for_group_specification(out=f) start_text=f.getvalue() ncs_object.adjust_magnification(magnification=0.5) f=StringIO() ncs_object.format_all_for_group_specification(out=f) found_text=f.getvalue() if remove_blank(" ".join(found_text.split("source_info")[1:]) ) != \ remove_blank(" ".join(expected_text2c.split("source_info")[1:])): print("Expected: \n%s \nFound: \n%s" %(expected_text2c,found_text)) raise AssertionError("FAILED") print("OK") expected_text6=""" 11.70 22.34 39.00 :: 11.70 22.34 39.00 4.80 50.92 39.00 :: 4.80 50.92 39.00 -16.50 30.66 39.00 :: -16.50 30.66 39.00 41.70 5.02 5.67 :: 41.70 5.02 5.67 34.80 33.60 5.67 :: 34.80 33.60 5.67 13.50 13.34 5.67 :: 13.50 13.34 5.67 -18.30 39.66 72.33 :: -18.30 39.66 72.33 4.80 16.28 72.33 :: 4.80 16.28 72.33 13.50 47.98 72.33 :: 13.50 47.98 72.33 """ def tst_06(): print("Convert space group operators to NCS operators") from mmtbx.ncs.ncs import crystal_symmetry_to_ncs from cctbx import crystal from cctbx import sgtbx from cctbx import uctbx from scitbx import matrix from cctbx.array_family import flex SpaceGroup=sgtbx.space_group_info(symbol=str('h3')) unit_cell=uctbx.unit_cell((60.,60.,100.,90.,90.,120.,)) crystal_symmetry=crystal.symmetry( unit_cell=unit_cell,space_group_info=SpaceGroup) ncs_obj=crystal_symmetry_to_ncs(crystal_symmetry) # apply ncs or apply crystal symmetry and make sure we get same answer. xyz_fract=matrix.col((0.41,0.43,0.39)) sites_fract=flex.vec3_double() sites_fract.append(xyz_fract) sites_cart=crystal_symmetry.unit_cell().orthogonalize(sites_fract) ncs_group=ncs_obj.ncs_groups()[0] ncs_sites_cart=flex.vec3_double() for xyz_cart in sites_cart: for i0 in range(len(ncs_group.translations_orth())): r=ncs_group.rota_matrices_inv()[i0] # inverse maps pos 0 on to pos i t=ncs_group.translations_orth_inv()[i0] new_xyz_cart=r * matrix.col(xyz_cart) + t ncs_sites_cart.append(new_xyz_cart) cryst_sites_frac=flex.vec3_double() from mmtbx.ncs.ncs import offset_inside_cell for xyz_frac in sites_fract: for rt_mx in crystal_symmetry.space_group().all_ops(): xyz_frac_ncs=rt_mx*xyz_frac coordinate_offset=matrix.col(offset_inside_cell(xyz_frac_ncs, unit_cell=crystal_symmetry.unit_cell(),orthogonalize=False)) cryst_sites_frac.append(matrix.col(xyz_frac_ncs)+coordinate_offset) cryst_sites_cart=crystal_symmetry.unit_cell().orthogonalize(cryst_sites_frac) f=StringIO() for ncs_xx,cryst_xx in zip(ncs_sites_cart,cryst_sites_cart): text= "%7.2f %7.2f %7.2f :: %7.2f %7.2f %7.2f " %( tuple(list(ncs_xx)+list(cryst_xx))) print(text, file=f) assert "%7.2f %7.2f %7.2f" %(ncs_xx) == "%7.2f %7.2f %7.2f" %(cryst_xx) found_text=f.getvalue() if remove_blank(found_text) != remove_blank(expected_text6): print("Expected: \n%s \nFound: \n%s" %(expected_text6,found_text)) raise AssertionError("FAILED") print("OK") def tst_07(): print("Generate operators for point-group symmetries") from mmtbx.ncs.ncs import generate_ncs_ops ncs_list=generate_ncs_ops(symmetry="ALL",op_max=3, out=sys.stdout) helical_ncs_list=generate_ncs_ops(symmetry="helical",helical_rot_deg=23, helical_trans_z_angstrom=8, max_helical_ops_to_check=5, out=sys.stdout) ncs_list+=helical_ncs_list name_and_ops_list=[] for ncs_obj in ncs_list: print(ncs_obj.get_ncs_name(),ncs_obj.max_operators()) assert ncs_obj.is_helical_along_z() or ncs_obj.is_point_group_symmetry() #print ncs_obj.is_helical_along_z() or ncs_obj.is_point_group_symmetry() from six.moves import cStringIO as StringIO f=StringIO() ncs_obj.display_all(log=f) text=f.getvalue() #print text name_and_ops_list.append([ncs_obj.get_ncs_name(),ncs_obj.max_operators()]) print(name_and_ops_list) assert name_and_ops_list==[['I (b)', 60], ['I (d)', 60], ['I (f)', 60], ['I (a)', 60], ['I (c)', 60], ['I (e)', 60], ['O (a)', 24], ['O (b)', 24], ['T (a)', 12], ['T (b)', 12], ['T (c)', 12], ['C2 ', 2], ['C3 ', 3], ['D2 (a)', 4], ['D2 (b)', 4], ['D3 (a)', 6], ['D3 (b)', 6], ['Helical 23.00 deg 8.00 Z-trans ', 5]] print("OK") if __name__=="__main__": tst_07() tst_01() tst_02() tst_02a() tst_02b() tst_03() tst_04() tst_05() tst_06()