from __future__ import absolute_import, division, print_function import time import mmtbx.model import iotbx.pdb from libtbx.utils import null_out neutral_atoms_list = ['Ru', 'Re', 'Ra', 'Rb', 'Rn', 'Rh', 'Be', 'Ba', 'Bi', 'Bk', 'Br', 'H', 'P', 'Os', 'Ge', 'Gd', 'Ga', 'Pr', 'Pt', 'Pu', 'C', 'Pb', 'Pa', 'Pd', 'Xe', 'Po', 'Pm', 'Ho', 'Hf', 'Hg', 'He', 'Mg', 'K', 'Mn', 'O', 'S', 'W', 'Zn', 'Eu', 'Zr', 'Er', 'Ni', 'Na', 'Nb', 'Nd', 'Ne', 'Np', 'Fr', 'Fe', 'B', 'F', 'Sr', 'N', 'Kr', 'Si', 'Sn', 'Sm', 'V', 'Sc', 'Sb', 'Se', 'Co', 'Cm', 'Cl', 'Ca', 'Cf', 'Ce', 'Cd', 'Tm', 'Cs', 'Cr', 'Cu', 'La', 'Li', 'Tl', 'Lu', 'Th', 'Ti', 'Te', 'Tb', 'Tc', 'Ta', 'Yb', 'Dy', 'I', 'U', 'Y', 'Ac', 'Ag', 'Ir', 'Am', 'Al', 'As', 'Ar', 'Au', 'At', 'In', 'Mo'] def run_tst_xrs_and_hierarchy(): # Check if scatterers in xrs are neutral after calling function pdb_inp = iotbx.pdb.input(source_info=None, lines=pdb_str) model = mmtbx.model.manager( model_input = pdb_inp, log = null_out()) model.neutralize_scatterers() xrs = model.get_xray_structure() for scatterer in xrs.scatterers(): assert (scatterer.scattering_type in neutral_atoms_list) # Check if pdb_hierarchy has neutral atoms as well pdb_str_neutralized = model.model_as_pdb() pdb_inp_neutralized = iotbx.pdb.input( source_info=None, lines=pdb_str_neutralized) model_neutralized = mmtbx.model.manager( model_input = pdb_inp_neutralized, log = null_out()) xrs_neutralized = model_neutralized.get_xray_structure() for scatterer in xrs_neutralized.scatterers(): assert (scatterer.scattering_type in neutral_atoms_list) def run_tst_grm_after_neutralize_scatterers(): # Look at nonbonded interaction CB - OE2 in Glu # OE2 has negative charge # vdw distance is 2.560 A when OE2 is neutral # vdw distance is 2.752 A when OE1 has O1- charge pdb_inp = iotbx.pdb.input(source_info=None, lines=pdb_str_2) model = mmtbx.model.manager( model_input = pdb_inp, log = null_out()) model.process(make_restraints=True) atoms = model.get_hierarchy().atoms() grm = model.get_restraints_manager() # with open('1.geo', 'w') as f: # f.write(model.restraints_as_geo()) nonbonded_proxies = grm.geometry.pair_proxies().nonbonded_proxies.simple for nb_proxy in nonbonded_proxies: iseq, jseq = nb_proxy.i_seqs if (iseq==4 and jseq==8): vdw_distance1 = nb_proxy.vdw_distance assert(atoms[iseq].name.strip()=='CB') assert(atoms[jseq].name.strip()=='OE2') model = mmtbx.model.manager( model_input = pdb_inp, log = null_out()) model.process(make_restraints=False) model.neutralize_scatterers() model.process(make_restraints=True) atoms2 = model.get_hierarchy().atoms() grm2 = model.get_restraints_manager() # with open('2.geo', 'w') as f: # f.write(model.restraints_as_geo()) nonbonded_proxies2 = grm2.geometry.pair_proxies().nonbonded_proxies.simple for nb_proxy in nonbonded_proxies2: iseq, jseq = nb_proxy.i_seqs if (iseq==4 and jseq==8): vdw_distance2 = nb_proxy.vdw_distance assert(atoms2[iseq].name.strip()=='CB') assert(atoms2[jseq].name.strip()=='OE2') assert(vdw_distance1 != vdw_distance2) pdb_str = """ CRYST1 36.960 124.370 41.010 90.00 116.55 90.00 P 1 21 1 SCALE1 0.027056 0.000000 0.013519 0.00000 SCALE2 0.000000 0.008041 0.000000 0.00000 SCALE3 0.000000 0.000000 0.027259 0.00000 HETATM 6628 H H A5000 6.345 4.777 15.778 1.00 7.19 H1- HETATM 6629 He He A5001 0.898 -11.608 9.059 1.00 4.52 He HETATM 6630 Li Li A5002 -9.341 15.181 18.207 1.00 4.40 Li HETATM 6631 Li Li A5003 -8.813 -4.503 15.152 1.00 4.49 Li1+ HETATM 6632 Be Be A5004 -9.819 4.216 22.563 1.00 3.89 Be HETATM 6633 Be Be A5005 7.293 18.903 22.780 1.00 6.69 Be2+ HETATM 6634 B B A5006 0.173 6.286 15.367 1.00 4.17 B HETATM 6635 C C A5007 -0.383 1.594 13.039 1.00 4.58 C HETATM 6636 N N A5008 -2.356 2.761 28.626 1.00 4.48 N HETATM 6637 O O A5009 -1.579 -5.998 16.103 1.00 4.95 O HETATM 6638 O O A5010 -13.313 18.722 16.219 1.00 7.64 O1- HETATM 6639 O O A5011 4.042 -17.542 13.901 1.00 5.04 O2- HETATM 6640 F F A5012 1.813 -15.513 8.453 1.00 4.89 F HETATM 6641 F F A5013 -3.818 15.582 34.975 1.00 6.70 F1- HETATM 6642 Ne Ne A5014 0.310 -17.405 7.121 1.00 5.09 Ne HETATM 6643 Na Na A5015 -15.880 -13.960 21.123 1.00 5.49 Na HETATM 6644 Na Na A5016 3.948 -16.112 11.472 1.00 5.30 Na1+ HETATM 6645 Mg Mg A5017 -5.457 -5.035 27.632 1.00 5.33 Mg HETATM 6646 Mg Mg A5018 -1.033 -20.162 14.712 1.00 5.86 Mg2+ HETATM 6647 Al Al A5019 -4.100 13.292 7.498 1.00 5.86 Al HETATM 6648 Al Al A5020 -9.492 -26.443 15.424 1.00 6.73 Al3+ HETATM 6649 Si Si A5021 -17.549 -17.302 8.636 1.00 6.46 Si HETATM 6650 Si Si A5022 4.404 -7.020 14.825 1.00 6.87 Si4+ HETATM 6651 P P A5023 -10.836 7.859 11.832 1.00 5.89 P HETATM 6652 S S A5024 0.998 3.980 13.754 1.00 5.70 S HETATM 6653 Cl Cl A5025 -5.365 12.486 5.272 1.00 6.33 Cl HETATM 6654 Cl Cl A5026 -15.556 -14.292 17.362 1.00 5.92 Cl1- HETATM 6655 Ar Ar A5027 3.867 -15.378 22.380 1.00 7.31 Ar HETATM 6656 K K A5028 -7.693 6.919 26.782 1.00 5.96 K HETATM 6657 K K A5029 -6.978 30.897 25.968 0.80 5.32 K1+ HETATM 6658 Ca Ca A5030 -6.322 -25.130 8.738 1.00 5.59 Ca HETATM 6659 Ca Ca A5031 6.962 7.229 16.925 1.00 6.08 Ca2+ HETATM 6660 Sc Sc A5032 -16.532 19.553 26.386 1.00 5.96 Sc HETATM 6661 Sc Sc A5033 2.846 -13.052 7.763 1.00 5.81 Sc3+ HETATM 6662 Ti Ti A5034 1.784 0.090 -2.170 1.00 7.02 Ti HETATM 6663 Ti Ti A5035 2.605 -14.287 0.491 1.00 6.70 Ti2+ HETATM 6664 Ti Ti A5036 -20.529 -8.793 13.734 1.00 6.46 Ti3+ HETATM 6665 Ti Ti A5037 -1.062 -0.582 14.744 1.00 6.45 Ti4+ HETATM 6666 V V A5038 -14.665 0.020 25.868 0.80 5.37 V HETATM 6667 V V A5039 -1.000 3.064 31.898 1.00 6.58 V2+ HETATM 6668 V V A5040 -3.011 18.109 34.071 1.00 6.71 V3+ HETATM 6669 V V A5041 -8.717 31.117 28.097 1.00 8.45 V5+ HETATM 6670 Cr Cr A5042 -19.474 -9.238 17.375 1.00 7.04 Cr HETATM 6671 Cr Cr A5043 2.577 12.013 31.099 1.00 7.46 Cr2+ HETATM 6672 Cr Cr A5044 -1.803 18.594 31.768 1.00 9.12 Cr3+ HETATM 6673 Mn Mn A5045 -5.340 -10.857 -4.897 1.00 9.22 Mn HETATM 6674 Mn Mn A5046 -8.923 4.751 25.261 1.00 6.53 Mn2+ HETATM 6675 Mn Mn A5047 -14.493 -4.667 4.322 1.00 5.71 Mn3+ HETATM 6676 Mn Mn A5048 -7.935 12.827 4.276 1.00 7.36 Mn4+ HETATM 6677 Fe Fe A5049 -16.603 -15.963 22.859 1.00 6.52 Fe HETATM 6678 Fe Fe A5050 5.273 -15.598 15.395 1.00 6.29 Fe2+ HETATM 6679 Fe Fe A5051 3.235 9.285 30.877 1.00 6.67 Fe3+ HETATM 6680 Co Co A5052 3.025 -18.039 22.544 1.00 6.99 Co HETATM 6681 Co Co A5053 -0.542 -15.322 -4.060 1.00 7.59 Co2+ HETATM 6682 Co Co A5054 -15.891 10.115 10.580 1.00 8.16 Co3+ HETATM 6683 Ni Ni A5055 -18.117 2.800 31.652 1.00 8.25 Ni HETATM 6684 Ni Ni A5056 4.325 -0.300 22.401 1.00 8.80 Ni2+ HETATM 6685 Ni Ni A5057 -10.666 -4.255 5.624 1.00 7.56 Ni3+ HETATM 6686 Cu Cu A5058 7.586 19.226 29.730 1.00 9.19 Cu HETATM 6687 Cu Cu A5059 -8.448 26.719 21.195 1.00 8.94 Cu1+ HETATM 6688 Cu Cu A5060 1.615 -22.177 9.005 0.70 6.61 Cu2+ HETATM 6689 Zn Zn A5061 -17.611 31.917 21.108 1.00 7.51 Zn HETATM 6690 Zn Zn A5062 -9.590 -3.484 29.577 1.00 6.73 Zn2+ HETATM 6691 Ga Ga A5063 -9.010 -23.725 17.437 1.00 6.62 Ga HETATM 6692 Ga Ga A5064 -11.495 -2.227 4.073 0.79 5.34 Ga3+ HETATM 6693 Ge Ge A5065 -5.323 -27.884 9.135 1.00 7.29 Ge HETATM 6694 Ge Ge A5066 -11.995 -24.557 19.436 1.00 7.76 Ge4+ HETATM 6695 As As A5067 8.866 12.749 23.235 1.00 9.38 As HETATM 6696 Se Se A5068 -20.992 -5.261 6.751 1.00 10.30 Se HETATM 6697 Br Br A5069 -11.955 16.592 37.039 1.00 10.09 Br HETATM 6698 Br Br A5070 -4.929 -13.595 -5.436 1.00 9.30 Br1- HETATM 6699 Kr Kr A5071 -5.562 -22.177 1.544 1.00 7.55 Kr HETATM 6700 Rb Rb A5072 -1.071 2.859 -0.759 0.80 6.86 Rb HETATM 6701 Rb Rb A5073 -16.938 -10.770 -0.110 1.00 9.09 Rb1+ HETATM 6702 Sr Sr A5074 -7.582 -21.920 19.111 0.70 5.55 Sr HETATM 6703 Sr Sr A5075 6.197 12.147 11.582 1.00 7.42 Sr2+ HETATM 6704 Y Y A5076 -23.796 -1.956 8.962 0.70 19.49 Y HETATM 6705 Y Y A5077 9.894 4.496 22.239 1.00 9.32 Y3+ HETATM 6706 Zr Zr A5078 -21.108 -13.726 13.696 1.00 8.40 Zr HETATM 6707 Zr Zr A5079 5.444 -2.244 -0.988 1.00 10.26 Zr4+ HETATM 6708 Nb Nb A5080 1.428 -32.632 10.473 1.00 7.70 Nb HETATM 6709 Nb Nb A5081 -11.489 22.783 34.873 1.00 9.91 Nb3+ HETATM 6710 Nb Nb A5082 -5.022 8.426 -0.521 1.00 9.46 Nb5+ HETATM 6711 Mo Mo A5083 4.245 -26.322 18.944 1.00 9.17 Mo HETATM 6712 Mo Mo A5084 -21.686 31.635 22.531 1.00 8.64 Mo3+ HETATM 6713 Mo Mo A5085 5.619 0.799 8.811 1.00 9.02 Mo5+ HETATM 6714 Mo Mo A5086 -20.860 -2.905 5.430 1.00 10.43 Mo6+ HETATM 6715 Tc Tc A5087 10.698 16.257 24.585 1.00 8.87 Tc HETATM 6716 Ru Ru A5088 -13.683 -23.315 21.718 0.80 8.64 Ru HETATM 6717 Ru Ru A5089 -15.661 11.589 8.016 1.00 8.65 Ru3+ HETATM 6718 Ru Ru A5090 -12.698 2.182 34.354 1.00 8.53 Ru4+ HETATM 6719 Rh Rh A5091 -17.937 -14.404 3.222 1.00 11.95 Rh HETATM 6720 Rh Rh A5092 9.630 8.424 8.317 1.00 9.93 Rh3+ HETATM 6721 Rh Rh A5093 4.321 -24.967 11.322 1.00 10.50 Rh4+ HETATM 6722 Pd Pd A5094 2.854 22.947 17.184 1.00 9.90 Pd HETATM 6723 Pd Pd A5095 -18.873 15.498 20.461 1.00 9.71 Pd2+ HETATM 6724 Pd Pd A5096 5.173 -14.697 1.413 1.00 8.92 Pd4+ HETATM 6725 Ag Ag A5097 13.750 8.522 14.089 0.90 8.83 Ag HETATM 6726 Ag Ag A5098 3.960 -14.391 24.920 1.00 10.92 Ag1+ HETATM 6727 Ag Ag A5099 -17.719 14.157 22.605 1.00 8.67 Ag2+ HETATM 6728 Cd Cd A5100 -13.886 -0.324 33.947 1.00 8.25 Cd HETATM 6729 Cd Cd A5101 -0.211 -8.780 26.524 1.00 7.97 Cd2+ HETATM 6730 In In A5102 7.556 -13.249 0.737 0.70 6.51 In HETATM 6731 In In A5103 -21.951 -11.151 14.274 1.00 8.87 In3+ HETATM 6732 Sn Sn A5104 -14.061 -1.934 27.862 0.80 5.90 Sn HETATM 6733 Sn Sn A5105 -14.045 20.753 14.529 1.00 10.10 Sn2+ HETATM 6734 Sn Sn A5106 -8.571 -21.026 26.684 1.00 8.59 Sn4+ HETATM 6735 Sb Sb A5107 -3.422 -29.610 15.693 1.00 8.74 Sb HETATM 6736 Sb Sb A5108 -17.171 8.243 8.941 0.80 8.41 Sb3+ HETATM 6737 Sb Sb A5109 -1.387 18.424 36.218 1.00 10.11 Sb5+ HETATM 6738 Te Te A5110 -18.238 8.843 16.853 1.00 8.90 Te HETATM 6739 I I A5111 -12.911 -10.114 -3.539 1.00 10.15 I HETATM 6740 I I A5112 -14.718 0.056 29.622 0.80 6.93 I1- HETATM 6741 Xe Xe A5113 3.198 24.539 23.772 1.00 10.25 Xe HETATM 6742 Cs Cs A5114 -9.544 -5.654 -3.780 1.00 12.88 Cs HETATM 6743 Cs Cs A5115 -14.304 29.432 17.958 1.00 10.60 Cs1+ HETATM 6744 Ba Ba A5116 0.027 -31.416 18.068 1.00 11.49 Ba HETATM 6745 Ba Ba A5117 2.957 -22.353 -4.387 0.70 8.04 Ba2+ HETATM 6746 La La A5118 5.044 8.538 33.082 1.00 12.08 La HETATM 6747 La La A5119 -18.925 -19.092 7.000 1.00 14.18 La3+ HETATM 6748 Ce Ce A5120 3.686 -31.641 11.616 1.00 12.00 Ce HETATM 6749 Ce Ce A5121 4.314 -21.047 4.935 1.00 13.08 Ce3+ HETATM 6750 Ce Ce A5122 -12.952 -11.779 -1.393 1.00 10.99 Ce4+ HETATM 6751 Pr Pr A5123 -22.006 -1.983 17.485 1.00 10.26 Pr HETATM 6752 Pr Pr A5124 -3.968 -5.120 30.009 1.00 8.71 Pr3+ HETATM 6753 Pr Pr A5125 -16.808 -13.442 32.754 1.00 10.21 Pr4+ HETATM 6754 Nd Nd A5126 -18.522 -19.217 21.909 1.00 11.45 Nd HETATM 6755 Nd Nd A5127 7.389 -14.736 13.689 0.79 9.38 Nd3+ HETATM 6756 Pm Pm A5128 -6.170 0.637 -4.572 1.00 11.33 Pm HETATM 6757 Pm Pm A5129 -14.747 4.266 34.323 0.70 7.31 Pm3+ HETATM 6758 Sm Sm A5130 10.579 11.382 21.519 1.00 8.24 Sm HETATM 6759 Sm Sm A5131 -19.700 -16.238 30.105 1.00 9.42 Sm3+ HETATM 6760 Eu Eu A5132 -22.579 -14.695 17.219 1.00 9.41 Eu HETATM 6761 Eu Eu A5133 0.431 22.503 15.354 1.00 10.83 Eu2+ HETATM 6762 Eu Eu A5134 3.775 -0.454 4.787 1.00 10.46 Eu3+ HETATM 6763 Gd Gd A5135 8.736 -13.435 3.171 0.70 7.33 Gd HETATM 6764 Gd Gd A5136 0.738 -6.147 26.648 0.60 5.75 Gd3+ HETATM 6765 Tb Tb A5137 1.394 -23.570 -0.951 0.70 9.59 Tb HETATM 6766 Tb Tb A5138 -19.678 6.552 16.380 1.00 9.94 Tb3+ HETATM 6767 Dy Dy A5139 -2.871 -28.584 20.001 1.00 9.75 Dy HETATM 6768 Dy Dy A5140 -13.866 27.937 31.785 1.00 11.94 Dy3+ HETATM 6769 Ho Ho A5141 3.567 -2.449 6.680 1.00 10.18 Ho HETATM 6770 Ho Ho A5142 -9.008 -27.341 6.794 1.00 12.93 Ho3+ HETATM 6771 Er Er A5143 -23.728 12.240 13.099 0.60 8.45 Er HETATM 6772 Er Er A5144 -11.400 -26.489 5.781 1.00 10.82 Er3+ HETATM 6773 Tm Tm A5145 0.539 8.340 4.707 1.00 11.51 Tm HETATM 6774 Tm Tm A5146 -4.464 -31.333 4.295 1.00 14.23 Tm3+ HETATM 6775 Yb Yb A5147 1.679 -13.251 26.060 1.00 10.97 Yb HETATM 6776 Yb Yb A5148 16.068 6.165 7.249 1.00 9.59 Yb2+ HETATM 6777 Yb Yb A5149 -12.354 -3.161 29.667 1.00 10.37 Yb3+ HETATM 6778 Lu Lu A5150 -3.325 -9.756 -6.517 1.00 13.33 Lu HETATM 6779 Lu Lu A5151 -0.150 -0.784 -3.769 1.00 11.21 Lu3+ HETATM 6780 Hf Hf A5152 0.864 -27.670 20.944 1.00 13.15 Hf HETATM 6781 Hf Hf A5153 5.277 14.822 9.726 0.80 8.80 Hf4+ HETATM 6782 Ta Ta A5154 -0.920 25.709 32.136 1.00 12.95 Ta HETATM 6783 Ta Ta A5155 -7.440 14.897 39.637 1.00 13.70 Ta5+ HETATM 6784 W W A5156 -1.897 16.311 9.508 0.30 8.01 W HETATM 6785 W W A5157 9.876 -7.712 22.676 0.70 12.19 W6+ HETATM 6786 Re Re A5158 7.075 23.333 22.508 1.00 10.79 Re HETATM 6787 Os Os A5159 -3.347 13.709 3.688 0.80 12.93 Os HETATM 6788 Os Os A5160 4.584 25.908 28.447 0.70 11.73 Os4+ HETATM 6789 Ir Ir A5161 -10.135 14.821 39.519 1.00 12.17 Ir HETATM 6790 Ir Ir A5162 7.822 15.920 12.630 0.80 11.10 Ir3+ HETATM 6791 Ir Ir A5163 -15.533 -9.718 -4.075 1.00 13.25 Ir4+ HETATM 6792 Pt Pt A5164 -21.586 15.788 20.362 1.00 12.26 Pt HETATM 6793 Pt Pt A5165 1.617 -10.551 25.406 0.60 6.76 Pt2+ HETATM 6794 Pt Pt A5166 2.331 15.845 10.907 1.00 12.82 Pt4+ HETATM 6795 Au Au A5167 -20.388 24.283 25.576 0.80 10.02 Au HETATM 6796 Au Au A5168 -16.045 -22.074 21.225 0.80 9.72 Au1+ HETATM 6797 Au Au A5169 0.061 -9.313 -3.705 1.00 11.60 Au3+ HETATM 6798 Hg Hg A5170 7.492 -17.244 12.425 1.00 13.30 Hg HETATM 6799 Hg Hg A5171 -19.752 9.771 34.130 0.60 7.87 Hg1+ HETATM 6800 Hg Hg A5172 8.647 -12.463 12.618 0.76 9.72 Hg2+ HETATM 6801 Tl Tl A5173 3.978 9.179 37.165 1.00 13.43 Tl HETATM 6802 Tl Tl A5174 -17.402 22.538 31.902 1.00 14.63 Tl1+ HETATM 6803 Tl Tl A5175 6.354 18.018 31.924 1.00 10.88 Tl3+ HETATM 6804 Pb Pb A5176 1.089 19.502 35.743 0.80 9.96 Pb HETATM 6805 Pb Pb A5177 -0.157 11.746 38.584 1.00 11.69 Pb2+ HETATM 6806 Pb Pb A5178 -2.909 7.593 -2.014 1.00 11.66 Pb4+ HETATM 6807 Bi Bi A5179 8.977 13.583 13.488 0.86 7.85 Bi HETATM 6808 Bi Bi A5180 6.665 -23.693 10.766 1.00 12.76 Bi3+ HETATM 6809 Bi Bi A5181 -11.604 1.117 -0.345 1.00 12.54 Bi5+ HETATM 6810 Po Po A5182 -17.302 0.369 30.581 1.00 10.82 Po HETATM 6811 At At A5183 -19.659 -11.610 29.687 1.00 11.09 At HETATM 6812 Rn Rn A5184 -3.968 1.929 -3.764 1.00 12.35 Rn HETATM 6813 Fr Fr A5185 11.407 -18.267 17.735 1.00 12.98 Fr HETATM 6814 Ra Ra A5186 5.397 25.468 22.317 1.00 12.46 Ra HETATM 6815 Ra Ra A5187 -4.717 4.208 -2.299 0.60 11.91 Ra2+ HETATM 6816 Ac Ac A5188 -24.859 13.594 20.904 0.80 10.07 Ac HETATM 6817 Ac Ac A5189 -0.525 -29.946 20.292 1.00 11.70 Ac3+ HETATM 6818 Th Th A5190 -24.085 -10.808 12.682 0.80 9.23 Th HETATM 6819 Th Th A5191 2.450 17.612 37.060 1.00 14.59 Th4+ HETATM 6820 Pa Pa A5192 -8.704 -4.915 31.699 0.90 9.67 Pa HETATM 6821 U U A5193 -4.418 -30.056 18.178 0.60 5.84 U HETATM 6822 U U A5194 -2.425 -5.196 -4.808 1.00 14.11 U3+ HETATM 6823 U U A5195 -16.770 28.630 18.033 1.00 13.65 U4+ HETATM 6824 U U A5196 -17.157 23.223 16.403 0.70 11.62 U6+ HETATM 6825 Np Np A5197 -17.100 -11.582 -2.706 1.00 14.26 Np HETATM 6826 Np Np A5198 4.790 5.726 -0.392 0.50 14.83 Np3+ HETATM 6827 Np Np A5199 0.569 27.671 27.800 1.00 16.07 Np4+ HETATM 6828 Np Np A5200 5.999 -4.767 -2.338 0.60 8.51 Np6+ HETATM 6829 Pu Pu A5201 -15.871 26.197 30.725 1.00 15.27 Pu HETATM 6830 Pu Pu A5202 6.613 -0.513 20.819 1.00 14.76 Pu3+ HETATM 6831 Pu Pu A5203 -15.579 -3.630 26.346 0.70 7.25 Pu4+ HETATM 6832 Pu Pu A5204 -2.469 7.614 37.998 1.00 15.95 Pu6+ HETATM 6833 Am Am A5205 -23.621 -8.303 15.805 0.80 9.45 Am HETATM 6834 Cm Cm A5206 -19.652 -9.388 23.334 0.80 16.78 Cm HETATM 6835 Bk Bk A5207 -21.063 -13.891 29.633 0.69 9.58 Bk HETATM 6836 Cf Cf A5208 6.155 -19.205 4.041 1.00 13.10 Cf """ pdb_str_2 = """ CRYST1 15.167 14.392 12.685 90.00 90.00 90.00 P 1 SCALE1 0.065933 0.000000 0.000000 0.00000 SCALE2 0.000000 0.069483 0.000000 0.00000 SCALE3 0.000000 0.000000 0.078833 0.00000 ATOM 70 N GLU A 131 84.638 135.033 68.928 1.00204.16 N ATOM 71 CA GLU A 131 84.231 134.007 69.881 1.00204.16 C ATOM 72 C GLU A 131 83.568 134.620 71.099 1.00204.16 C ATOM 73 O GLU A 131 82.575 134.096 71.613 1.00204.16 O ATOM 74 CB GLU A 131 85.437 133.189 70.332 1.00204.16 C ATOM 75 CG GLU A 131 86.031 132.285 69.302 1.00204.16 C ATOM 76 CD GLU A 131 87.218 131.539 69.858 1.00204.16 C ATOM 77 OE1 GLU A 131 87.626 131.851 70.997 1.00204.16 O ATOM 78 OE2 GLU A 131 87.742 130.641 69.167 1.00204.16 O1- """ if (__name__ == "__main__"): t0 = time.time() run_tst_xrs_and_hierarchy() run_tst_grm_after_neutralize_scatterers() print("OK. Time:", round(time.time()-t0, 2))