from __future__ import absolute_import, division, print_function import iotbx.pdb # All H ------------------------------------------------------------------------ pdb_str1_H = """ CRYST1 13.022 15.843 16.570 90.00 90.00 90.00 P 1 ATOM 1 N HIS 8.022 8.797 9.927 1.00 0.00 N ATOM 2 CA HIS 7.020 9.705 9.381 1.00 0.00 C ATOM 3 C HIS 6.734 10.843 10.354 1.00 0.00 C ATOM 4 O HIS 6.781 10.659 11.570 1.00 0.00 O ATOM 5 CB HIS 5.729 8.948 9.062 1.00 0.00 C ATOM 6 CG HIS 5.905 7.850 8.060 1.00 0.00 C ATOM 7 ND1 HIS 5.768 8.050 6.704 1.00 0.00 N ATOM 8 CD2 HIS 6.207 6.539 8.218 1.00 0.00 C ATOM 9 CE1 HIS 5.978 6.911 6.069 1.00 0.00 C ATOM 10 NE2 HIS 6.246 5.978 6.965 1.00 0.00 N ATOM 11 H HIS 7.644 8.098 10.566 1.00 0.00 H ATOM 12 HA HIS 7.398 10.137 8.454 1.00 0.00 H ATOM 13 HB2 HIS 5.000 9.652 8.660 1.00 0.00 H ATOM 14 HB3 HIS 5.346 8.504 9.981 1.00 0.00 H ATOM 15 HD1 HIS 5.540 8.939 6.259 1.00 0.00 H ATOM 16 HD2 HIS 6.384 6.030 9.154 1.00 0.00 H ATOM 17 HE1 HIS 5.937 6.766 5.000 1.00 0.00 H ATOM 18 HE2 HIS 6.450 5.000 6.760 1.00 0.00 H TER END """ pdb_str2_H = """ CRYST1 13.022 15.843 16.570 90.00 90.00 90.00 P 1 ATOM 1 N HIS 8.022 8.797 9.927 1.00 0.00 N ATOM 2 CA HIS 7.020 9.705 9.381 1.00 0.00 C ATOM 3 C HIS 6.734 10.843 10.354 1.00 0.00 C ATOM 4 O HIS 6.781 10.659 11.570 1.00 0.00 O ATOM 5 CB HIS 5.729 8.948 9.062 1.00 0.00 C ATOM 6 CG HIS 5.905 7.850 8.060 1.00 0.00 C ATOM 7 ND1 HIS 5.768 8.050 6.704 1.00 0.00 N ATOM 8 CD2 HIS 6.207 6.539 8.218 1.00 0.00 C ATOM 9 CE1 HIS 5.978 6.911 6.069 1.00 0.00 C ATOM 10 NE2 HIS 6.246 5.978 6.965 1.00 0.00 N ATOM 11 H HIS 7.644 8.098 10.566 1.00 0.00 H ATOM 12 HA HIS 7.398 10.137 8.454 1.00 0.00 H ATOM 13 HB2 HIS 5.000 9.652 8.660 1.00 0.00 H ATOM 14 HB3 HIS 5.346 8.504 9.981 1.00 0.00 H ATOM 15 HD1 HIS 5.540 8.939 6.259 1.00 0.00 H ATOM 16 HD2 HIS 6.384 6.030 9.154 1.00 0.00 H ATOM 17 HE1 HIS 5.937 6.766 5.000 1.00 0.00 H TER END """ pdb_str3_H = """ CRYST1 13.022 15.843 16.570 90.00 90.00 90.00 P 1 ATOM 1 N HIS 8.022 8.797 9.927 1.00 0.00 N ATOM 2 CA HIS 7.020 9.705 9.381 1.00 0.00 C ATOM 3 C HIS 6.734 10.843 10.354 1.00 0.00 C ATOM 4 O HIS 6.781 10.659 11.570 1.00 0.00 O ATOM 5 CB HIS 5.729 8.948 9.062 1.00 0.00 C ATOM 6 CG HIS 5.905 7.850 8.060 1.00 0.00 C ATOM 7 ND1 HIS 5.768 8.050 6.704 1.00 0.00 N ATOM 8 CD2 HIS 6.207 6.539 8.218 1.00 0.00 C ATOM 9 CE1 HIS 5.978 6.911 6.069 1.00 0.00 C ATOM 10 NE2 HIS 6.246 5.978 6.965 1.00 0.00 N ATOM 11 H HIS 7.644 8.098 10.566 1.00 0.00 H ATOM 12 HA HIS 7.398 10.137 8.454 1.00 0.00 H ATOM 13 HB2 HIS 5.000 9.652 8.660 1.00 0.00 H ATOM 14 HB3 HIS 5.346 8.504 9.981 1.00 0.00 H ATOM 16 HD2 HIS 6.384 6.030 9.154 1.00 0.00 H ATOM 17 HE1 HIS 5.937 6.766 5.000 1.00 0.00 H ATOM 18 HE2 HIS 6.450 5.000 6.760 1.00 0.00 H TER END """ # All D ------------------------------------------------------------------------ pdb_str1_D = """ CRYST1 13.022 15.843 16.570 90.00 90.00 90.00 P 1 ATOM 1 N HIS 8.022 8.797 9.927 1.00 0.00 N ATOM 2 CA HIS 7.020 9.705 9.381 1.00 0.00 C ATOM 3 C HIS 6.734 10.843 10.354 1.00 0.00 C ATOM 4 O HIS 6.781 10.659 11.570 1.00 0.00 O ATOM 5 CB HIS 5.729 8.948 9.062 1.00 0.00 C ATOM 6 CG HIS 5.905 7.850 8.060 1.00 0.00 C ATOM 7 ND1 HIS 5.768 8.050 6.704 1.00 0.00 N ATOM 8 CD2 HIS 6.207 6.539 8.218 1.00 0.00 C ATOM 9 CE1 HIS 5.978 6.911 6.069 1.00 0.00 C ATOM 10 NE2 HIS 6.246 5.978 6.965 1.00 0.00 N ATOM 11 D HIS 7.644 8.098 10.566 1.00 0.00 D ATOM 12 DA HIS 7.398 10.137 8.454 1.00 0.00 D ATOM 13 DB2 HIS 5.000 9.652 8.660 1.00 0.00 D ATOM 14 DB3 HIS 5.346 8.504 9.981 1.00 0.00 D ATOM 15 DD1 HIS 5.540 8.939 6.259 1.00 0.00 D ATOM 16 DD2 HIS 6.384 6.030 9.154 1.00 0.00 D ATOM 17 DE1 HIS 5.937 6.766 5.000 1.00 0.00 D ATOM 18 DE2 HIS 6.450 5.000 6.760 1.00 0.00 D TER END """ pdb_str2_D = """ CRYST1 13.022 15.843 16.570 90.00 90.00 90.00 P 1 ATOM 1 N HIS 8.022 8.797 9.927 1.00 0.00 N ATOM 2 CA HIS 7.020 9.705 9.381 1.00 0.00 C ATOM 3 C HIS 6.734 10.843 10.354 1.00 0.00 C ATOM 4 O HIS 6.781 10.659 11.570 1.00 0.00 O ATOM 5 CB HIS 5.729 8.948 9.062 1.00 0.00 C ATOM 6 CG HIS 5.905 7.850 8.060 1.00 0.00 C ATOM 7 ND1 HIS 5.768 8.050 6.704 1.00 0.00 N ATOM 8 CD2 HIS 6.207 6.539 8.218 1.00 0.00 C ATOM 9 CE1 HIS 5.978 6.911 6.069 1.00 0.00 C ATOM 10 NE2 HIS 6.246 5.978 6.965 1.00 0.00 N ATOM 11 D HIS 7.644 8.098 10.566 1.00 0.00 D ATOM 12 DA HIS 7.398 10.137 8.454 1.00 0.00 D ATOM 13 DB2 HIS 5.000 9.652 8.660 1.00 0.00 D ATOM 14 DB3 HIS 5.346 8.504 9.981 1.00 0.00 D ATOM 15 DD1 HIS 5.540 8.939 6.259 1.00 0.00 D ATOM 16 DD2 HIS 6.384 6.030 9.154 1.00 0.00 D ATOM 17 DE1 HIS 5.937 6.766 5.000 1.00 0.00 D TER END """ pdb_str3_D = """ CRYST1 13.022 15.843 16.570 90.00 90.00 90.00 P 1 ATOM 1 N HIS 8.022 8.797 9.927 1.00 0.00 N ATOM 2 CA HIS 7.020 9.705 9.381 1.00 0.00 C ATOM 3 C HIS 6.734 10.843 10.354 1.00 0.00 C ATOM 4 O HIS 6.781 10.659 11.570 1.00 0.00 O ATOM 5 CB HIS 5.729 8.948 9.062 1.00 0.00 C ATOM 6 CG HIS 5.905 7.850 8.060 1.00 0.00 C ATOM 7 ND1 HIS 5.768 8.050 6.704 1.00 0.00 N ATOM 8 CD2 HIS 6.207 6.539 8.218 1.00 0.00 C ATOM 9 CE1 HIS 5.978 6.911 6.069 1.00 0.00 C ATOM 10 NE2 HIS 6.246 5.978 6.965 1.00 0.00 N ATOM 11 D HIS 7.644 8.098 10.566 1.00 0.00 D ATOM 12 DA HIS 7.398 10.137 8.454 1.00 0.00 D ATOM 13 DB2 HIS 5.000 9.652 8.660 1.00 0.00 D ATOM 14 DB3 HIS 5.346 8.504 9.981 1.00 0.00 D ATOM 16 DD2 HIS 6.384 6.030 9.154 1.00 0.00 D ATOM 17 DE1 HIS 5.937 6.766 5.000 1.00 0.00 D ATOM 18 DE2 HIS 6.450 5.000 6.760 1.00 0.00 D TER END """ # All H/D ---------------------------------------------------------------------- pdb_str1_HD = """ CRYST1 13.022 15.843 16.570 90.00 90.00 90.00 P 1 ATOM 1 N HIS 8.022 8.797 9.927 1.00 0.00 N ATOM 2 CA HIS 7.020 9.705 9.381 1.00 0.00 C ATOM 3 C HIS 6.734 10.843 10.354 1.00 0.00 C ATOM 4 O HIS 6.781 10.659 11.570 1.00 0.00 O ATOM 5 CB HIS 5.729 8.948 9.062 1.00 0.00 C ATOM 6 CG HIS 5.905 7.850 8.060 1.00 0.00 C ATOM 7 ND1 HIS 5.768 8.050 6.704 1.00 0.00 N ATOM 8 CD2 HIS 6.207 6.539 8.218 1.00 0.00 C ATOM 9 CE1 HIS 5.978 6.911 6.069 1.00 0.00 C ATOM 10 NE2 HIS 6.246 5.978 6.965 1.00 0.00 N ATOM 11 H AHIS 7.644 8.098 10.566 0.50 0.00 H ATOM 11 D BHIS 7.644 8.098 10.566 0.50 0.00 D ATOM 12 HA HIS 7.398 10.137 8.454 1.00 0.00 H ATOM 13 HB2 HIS 5.000 9.652 8.660 1.00 0.00 H ATOM 14 HB3 HIS 5.346 8.504 9.981 1.00 0.00 H ATOM 15 HD1AHIS 5.540 8.939 6.259 0.50 0.00 H ATOM 15 DD1BHIS 5.540 8.939 6.259 0.50 0.00 D ATOM 16 HD2 HIS 6.384 6.030 9.154 1.00 0.00 H ATOM 17 HE1 HIS 5.937 6.766 5.000 1.00 0.00 H ATOM 18 HE2AHIS 6.450 5.000 6.760 0.50 0.00 H ATOM 18 DE2BHIS 6.450 5.000 6.760 0.50 0.00 D TER END """ pdb_str2_HD = """ CRYST1 13.022 15.843 16.570 90.00 90.00 90.00 P 1 ATOM 1 N HIS 8.022 8.797 9.927 1.00 0.00 N ATOM 2 CA HIS 7.020 9.705 9.381 1.00 0.00 C ATOM 3 C HIS 6.734 10.843 10.354 1.00 0.00 C ATOM 4 O HIS 6.781 10.659 11.570 1.00 0.00 O ATOM 5 CB HIS 5.729 8.948 9.062 1.00 0.00 C ATOM 6 CG HIS 5.905 7.850 8.060 1.00 0.00 C ATOM 7 ND1 HIS 5.768 8.050 6.704 1.00 0.00 N ATOM 8 CD2 HIS 6.207 6.539 8.218 1.00 0.00 C ATOM 9 CE1 HIS 5.978 6.911 6.069 1.00 0.00 C ATOM 10 NE2 HIS 6.246 5.978 6.965 1.00 0.00 N ATOM 11 H AHIS 7.644 8.098 10.566 0.50 0.00 H ATOM 11 D BHIS 7.644 8.098 10.566 0.50 0.00 D ATOM 12 HA HIS 7.398 10.137 8.454 1.00 0.00 H ATOM 13 HB2 HIS 5.000 9.652 8.660 1.00 0.00 H ATOM 14 HB3 HIS 5.346 8.504 9.981 1.00 0.00 H ATOM 15 HD1AHIS 5.540 8.939 6.259 0.50 0.00 H ATOM 15 DD1BHIS 5.540 8.939 6.259 0.50 0.00 D ATOM 16 HD2 HIS 6.384 6.030 9.154 1.00 0.00 H ATOM 17 HE1 HIS 5.937 6.766 5.000 1.00 0.00 H TER END """ pdb_str3_HD = """ CRYST1 13.022 15.843 16.570 90.00 90.00 90.00 P 1 ATOM 1 N HIS 8.022 8.797 9.927 1.00 0.00 N ATOM 2 CA HIS 7.020 9.705 9.381 1.00 0.00 C ATOM 3 C HIS 6.734 10.843 10.354 1.00 0.00 C ATOM 4 O HIS 6.781 10.659 11.570 1.00 0.00 O ATOM 5 CB HIS 5.729 8.948 9.062 1.00 0.00 C ATOM 6 CG HIS 5.905 7.850 8.060 1.00 0.00 C ATOM 7 ND1 HIS 5.768 8.050 6.704 1.00 0.00 N ATOM 8 CD2 HIS 6.207 6.539 8.218 1.00 0.00 C ATOM 9 CE1 HIS 5.978 6.911 6.069 1.00 0.00 C ATOM 10 NE2 HIS 6.246 5.978 6.965 1.00 0.00 N ATOM 11 H AHIS 7.644 8.098 10.566 0.50 0.00 H ATOM 11 D BHIS 7.644 8.098 10.566 0.50 0.00 D ATOM 12 HA HIS 7.398 10.137 8.454 1.00 0.00 H ATOM 13 HB2 HIS 5.000 9.652 8.660 1.00 0.00 H ATOM 14 HB3 HIS 5.346 8.504 9.981 1.00 0.00 H ATOM 16 HD2 HIS 6.384 6.030 9.154 1.00 0.00 H ATOM 17 HE1 HIS 5.937 6.766 5.000 1.00 0.00 H ATOM 18 HE2AHIS 6.450 5.000 6.760 0.50 0.00 H ATOM 18 DE2BHIS 6.450 5.000 6.760 0.50 0.00 D TER END """ class load(object): def __init__(self): self.r = {} all_his = [ ["h1", pdb_str1_H], ["h2", pdb_str2_H], ["h3", pdb_str3_H], ["d1", pdb_str1_D], ["d2", pdb_str2_D], ["d3", pdb_str3_D], ["hd1", pdb_str1_HD], ["hd2", pdb_str2_HD], ["hd3", pdb_str3_HD] ] for his in all_his: self.r[his[0]] = iotbx.pdb.input(source_info = None, lines = his[1] ).construct_hierarchy().only_residue_group().detached_copy() def main_three(self): result = [] for ps in ["h1", "h2", "h3"]: result.append(self.r[ps]) return result