from __future__ import absolute_import, division, print_function from mmtbx.geometry_restraints.afitt import finite_difference_test pdb_lines = """ CRYST1 94.100 94.100 131.400 90.00 90.00 120.00 P 61 2 2 ATOM 890 N ALA E 113 32.525 39.841 -1.660 1.00 15.64 N ATOM 891 CA ALA E 113 31.553 40.901 -1.907 1.00 15.53 C ATOM 893 C ALA E 113 31.742 41.398 -3.334 1.00 15.47 C ATOM 894 O ALA E 113 32.873 41.486 -3.811 1.00 15.46 O ATOM 892 CB ALA E 113 31.740 42.036 -0.918 1.00 15.53 C ATOM 2602 ZN ZN F 5 36.912 44.685 -7.131 1.00 13.76 ZN ATOM 2606 P1 LEP X 1 35.374 42.336 -6.280 1.00 14.03 P ATOM 2607 O2 LEP X 1 34.629 43.616 -5.992 1.00 14.13 O ATOM 2608 O3 LEP X 1 36.737 42.562 -6.884 1.00 13.72 O ATOM 2609 O4 LEP X 1 34.549 41.267 -6.954 1.00 14.26 O ATOM 2610 N5 LEP X 1 35.736 41.643 -4.701 1.00 14.42 N ATOM 2611 C6 LEP X 1 36.701 42.323 -3.815 1.00 14.69 C ATOM 2612 C7 LEP X 1 37.996 41.614 -4.069 1.00 14.79 C ATOM 2613 O8 LEP X 1 39.062 42.207 -4.117 1.00 15.05 O ATOM 2614 C9 LEP X 1 36.278 42.128 -2.373 1.00 14.85 C ATOM 2615 C10 LEP X 1 37.233 42.793 -1.403 1.00 15.12 C ATOM 2616 C11 LEP X 1 37.112 44.297 -1.488 1.00 15.24 C ATOM 2617 C12 LEP X 1 36.866 42.344 -0.010 1.00 15.23 C ATOM 2618 N13 LEP X 1 37.835 40.262 -4.227 1.00 14.73 N ATOM 2632 H1 LEP X 1 35.374 42.336 -6.280 1.00 20.00 H ATOM 2633 H2 LEP X 1 35.163 44.358 -6.248 1.00 20.00 H ATOM 2619 H5 LEP X 1 34.776 41.783 -4.384 1.00 14.42 H ATOM 2620 H6 LEP X 1 36.777 43.375 -4.099 1.00 14.69 H ATOM 2623 H10 LEP X 1 38.271 42.498 -1.590 1.00 15.12 H ATOM 2624 H111 LEP X 1 37.719 44.781 -0.714 1.00 15.24 H ATOM 2625 H112 LEP X 1 37.468 44.680 -2.449 1.00 15.24 H ATOM 2626 H113 LEP X 1 36.078 44.634 -1.353 1.00 15.24 H ATOM 2627 H121 LEP X 1 36.971 41.259 0.097 1.00 15.23 H ATOM 2628 H122 LEP X 1 37.521 42.806 0.737 1.00 15.23 H ATOM 2629 H123 LEP X 1 35.834 42.607 0.247 1.00 15.23 H ATOM 2630 H131 LEP X 1 38.608 39.742 -4.600 1.00 14.73 H ATOM 2631 H132 LEP X 1 36.892 40.088 -4.602 1.00 14.73 H ATOM 2621 H92 LEP X 1 35.260 42.517 -2.233 1.00 14.85 H ATOM 2622 H93 LEP X 1 36.213 41.054 -2.148 1.00 14.85 H """ cif_lines = """ 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 LEP LEP '(2S)-2-[(hydroxy-oxido-oxo-$l^{6}-phosphanyl)amino]-4-methyl-pentanamide' non-polymer 28 13 data_comp_LEP 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 LEP P1 P 'P1 ' 0.000 LEP O2 O 'OP ' 0.000 LEP O3 O 'OP ' 0.000 LEP O4 O 'OP ' 0.000 LEP N5 N 'NT1 ' 0.000 LEP C6 C 'CH1 ' 0.000 LEP C7 C 'C ' 0.000 LEP O8 O 'O ' 0.000 LEP C9 C 'CH2 ' 0.000 LEP C10 C 'CH1 ' 0.000 LEP C11 C 'CH3 ' 0.000 LEP C12 C 'CH3 ' 0.000 LEP N13 N 'NH2 ' 0.000 LEP H1 H 'HCH ' 0.000 LEP H2 H 'HOH1' 0.000 LEP H5 H 'HNH1' 0.000 LEP H6 H 'HCH1' 0.000 LEP H10 H 'HCH1' 0.000 LEP H111 H 'HCH3' 0.000 LEP H112 H 'HCH3' 0.000 LEP H113 H 'HCH3' 0.000 LEP H121 H 'HCH3' 0.000 LEP H122 H 'HCH3' 0.000 LEP H123 H 'HCH3' 0.000 LEP H131 H 'HNH2' 0.000 LEP H132 H 'HNH2' 0.000 LEP H92 H 'HCH2' 0.000 LEP H93 H 'HCH2' 0.000 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 LEP P1 O2 single 1.630 0.020 LEP P1 O3 single 1.510 0.020 LEP P1 O4 double 1.510 0.015 LEP P1 N5 single 1.762 0.020 LEP N5 C6 single 1.472 0.020 LEP N5 H5 single 1.028 0.020 LEP C6 C7 single 1.492 0.020 LEP C6 C9 single 1.508 0.020 LEP C6 H6 single 1.093 0.020 LEP C7 O8 double 1.222 0.015 LEP C7 N13 single 1.369 0.020 LEP C9 C10 single 1.508 0.020 LEP C9 H92 single 1.093 0.020 LEP C9 H93 single 1.093 0.020 LEP C10 C11 single 1.508 0.020 LEP C10 C12 single 1.508 0.020 LEP C10 H10 single 1.093 0.020 LEP C11 H111 single 1.093 0.020 LEP C11 H112 single 1.093 0.020 LEP C11 H113 single 1.093 0.020 LEP C12 H121 single 1.093 0.020 LEP C12 H122 single 1.093 0.020 LEP C12 H123 single 1.093 0.020 LEP N13 H131 single 1.015 0.020 LEP N13 H132 single 1.015 0.020 LEP P1 H1 single 1.411 0.020 LEP O2 H2 single 0.981 0.020 """ def run(pdb_file, cif_file, ligand_names,atom,scale,verbose): finite_difference_test(pdb_file, cif_file, ligand_names,atom,scale,verbose) if (__name__ == "__main__"): import sys if len(sys.argv)==1: f=open("afitt_fd.pdb", "w") f.write(pdb_lines) f.close() f=open("afitt_fd.cif", "w") f.write(cif_lines) f.close() run("afitt_fd.pdb", 'afitt_fd.cif', ["LEP"], 7, 1, True) else: import argparse parser = argparse.ArgumentParser() parser.add_argument("pdb_file", help="pdb file") parser.add_argument("cif_file", help="cif file", default=0) parser.add_argument("ligand_names", help="3-letter ligand names separated by commas") parser.add_argument("atom", help="i_seq of atom whose x-coord will be " "modified (to test AFITT this should " "be a ligand atom)") parser.add_argument( "-s", "--scale", default=1, help="weight applied" \ "to AFITT gradient/traget", type=float) parser.add_argument('-v', dest='verbose', action='store_true', help="verbose output") parser.epilog='Example: phenix.python afitt_fd.py vAla3.pdb vAla3.cif NME 37' args = parser.parse_args() ligand_names=args.ligand_names.split(',') run(args.pdb_file, args.cif_file, ligand_names, int(args.atom), args.scale, args.verbose)