from __future__ import division from mmtbx import monomer_library import mmtbx.monomer_library.pdb_interpretation import mmtbx.monomer_library.server from iotbx import pdb from cctbx.array_family import flex from libtbx.test_utils import show_diff from itertools import count from cStringIO import StringIO import sys pdb_records_gly_bnz = """\ CRYST1 56.470 56.470 80.520 90.00 90.00 90.00 P 43 21 2 8 ATOM 141 N GLY 1 19.851 38.691 38.859 1.00 14.08 N ATOM 142 CA GLY 1 19.095 38.743 40.099 1.00 15.88 C ATOM 143 C GLY 1 17.786 37.966 39.974 1.00 18.62 C ATOM 144 O GLY 1 17.440 37.187 40.865 1.00 18.84 O ATOM 145 CB GLY 1 18.798 40.190 40.494 1.00 15.26 C ATOM 146 CG BNZ 2 17.817 40.296 41.640 1.00 16.71 C ATOM 147 CD1 BNZ 2 18.228 40.074 42.953 1.00 19.01 C ATOM 148 CD2 BNZ 2 16.473 40.584 41.411 1.00 16.09 C ATOM 149 CE1 BNZ 2 17.322 40.135 44.011 1.00 17.90 C ATOM 150 CE2 BNZ 2 15.560 40.647 42.461 1.00 16.31 C ATOM 151 CZ BNZ 2 15.994 40.423 43.758 1.00 19.02 C ATOM 152 OH BNZ 2 15.111 40.507 44.807 1.00 21.58 O END """.splitlines() pdb_records_tyr = [line .replace(" GLY ", " TYR ") .replace(" BNZ 2 ", " TYR 1 ") for line in pdb_records_gly_bnz] cif_string = """\ # # Copy of monomer library entries 2006_01_03, to ensure the tests below # are independent of changes to the BNZ, GLY, TYR definitions. # Changes with respect to the original monomer library definitions # are marked with "# ADJUSTMENT". # data_comp_BNZ # 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 BNZ C6 C CR16 0.000 BNZ H6 H HCR6 0.000 BNZ C5 C CR16 0.000 BNZ H5 H HCR6 0.000 BNZ C4 C CR16 0.000 BNZ H4 H HCR6 0.000 BNZ C3 C CR16 0.000 BNZ H3 H HCR6 0.000 BNZ C2 C CR16 0.000 BNZ H2 H HCR6 0.000 BNZ C1 C CR16 0.000 BNZ H1 H HCR6 0.000 loop_ _chem_comp_tree.comp_id _chem_comp_tree.atom_id _chem_comp_tree.atom_back _chem_comp_tree.atom_forward _chem_comp_tree.connect_type BNZ C6 n/a C5 START BNZ H6 C6 . . BNZ C5 C6 C4 . BNZ H5 C5 . . BNZ C4 C5 C3 . BNZ H4 C4 . . BNZ C3 C4 C2 . BNZ H3 C3 . . BNZ C2 C3 C1 . BNZ H2 C2 . . BNZ C1 C2 H1 . BNZ H1 C1 . END BNZ C6 C1 . ADD 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 BNZ H6 C6 coval 0.960 0.020 BNZ C5 C6 coval 1.390 0.020 BNZ H5 C5 coval 0.960 0.020 BNZ C4 C5 coval 1.390 0.020 BNZ H4 C4 coval 0.960 0.020 BNZ C3 C4 coval 1.390 0.020 BNZ H3 C3 coval 0.960 0.020 BNZ C2 C3 coval 1.390 0.020 BNZ H2 C2 coval 0.960 0.020 BNZ C1 C2 coval 1.390 0.020 BNZ C1 C6 coval 1.390 0.020 BNZ H1 C1 coval 0.960 0.020 loop_ _chem_comp_angle.comp_id _chem_comp_angle.atom_id_1 _chem_comp_angle.atom_id_2 _chem_comp_angle.atom_id_3 _chem_comp_angle.value_angle _chem_comp_angle.value_angle_esd BNZ H6 C6 C5 120.000 3.000 BNZ H6 C6 C1 120.000 3.000 BNZ C5 C6 C1 120.000 3.000 BNZ C6 C5 H5 120.000 3.000 BNZ C6 C5 C4 120.000 3.000 BNZ H5 C5 C4 120.000 3.000 BNZ C5 C4 H4 120.000 3.000 BNZ C5 C4 C3 120.000 3.000 BNZ H4 C4 C3 120.000 3.000 BNZ C4 C3 H3 120.000 3.000 BNZ C4 C3 C2 120.000 3.000 BNZ H3 C3 C2 120.000 3.000 BNZ C3 C2 H2 120.000 3.000 BNZ C3 C2 C1 120.000 3.000 BNZ H2 C2 C1 120.000 3.000 BNZ C2 C1 H1 120.000 3.000 BNZ C2 C1 C6 120.000 3.000 BNZ H1 C1 C6 120.000 3.000 loop_ _chem_comp_tor.comp_id _chem_comp_tor.id _chem_comp_tor.atom_id_1 _chem_comp_tor.atom_id_2 _chem_comp_tor.atom_id_3 _chem_comp_tor.atom_id_4 _chem_comp_tor.value_angle _chem_comp_tor.value_angle_esd _chem_comp_tor.period BNZ CONST_1 C2 C1 C6 C5 0.000 0.000 0 BNZ CONST_2 C1 C6 C5 C4 0.000 0.000 0 BNZ CONST_4 C6 C5 C4 C3 0.000 0.000 0 BNZ CONST_5 C5 C4 C3 C2 0.000 0.000 0 BNZ CONST_6 C4 C3 C2 C1 0.000 0.000 0 BNZ CONST_7 C3 C2 C1 C6 0.000 0.000 0 loop_ _chem_comp_plane_atom.comp_id _chem_comp_plane_atom.plane_id _chem_comp_plane_atom.atom_id _chem_comp_plane_atom.dist_esd BNZ plan C1 0.020 # ADJUSTMENT: all "plan-1" renamed to "plan" BNZ plan C2 0.020 BNZ plan C3 0.020 BNZ plan C4 0.020 BNZ plan C5 0.020 BNZ plan C6 0.020 BNZ plan H1 0.020 BNZ plan H2 0.020 BNZ plan H3 0.020 BNZ plan H4 0.020 BNZ plan H5 0.020 BNZ plan H6 0.020 data_comp_GLY # 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 GLY N N NH1 -0.204 GLY H H HNH1 0.204 GLY CA C CH2 0.002 GLY HA1 H HCH2 0.051 GLY HA2 H HCH2 0.051 GLY C C C 0.318 GLY O O O -0.422 loop_ _chem_comp_tree.comp_id _chem_comp_tree.atom_id _chem_comp_tree.atom_back _chem_comp_tree.atom_forward _chem_comp_tree.connect_type GLY N n/a CA START GLY H N . . GLY CA N C . GLY HA1 CA . . GLY HA2 CA . . GLY C CA . END GLY O C . . 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 GLY N H coval 0.860 0.020 GLY N CA coval 1.451 0.016 GLY CA HA1 coval 0.970 0.020 GLY CA HA2 coval 0.970 0.020 GLY CA C coval 1.516 0.018 GLY C O coval 1.231 0.020 loop_ _chem_comp_angle.comp_id _chem_comp_angle.atom_id_1 _chem_comp_angle.atom_id_2 _chem_comp_angle.atom_id_3 _chem_comp_angle.value_angle _chem_comp_angle.value_angle_esd GLY H N CA 114.000 3.000 GLY HA1 CA HA2 109.000 3.000 GLY HA2 CA C 109.000 3.000 GLY HA1 CA C 109.000 3.000 GLY N CA HA1 110.000 3.000 GLY N CA HA2 110.000 3.000 GLY N CA C 112.500 2.900 GLY CA C O 120.800 2.100 data_comp_TYR # 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 TYR N N NH1 -0.204 TYR H H HNH1 0.204 TYR CA C CH1 0.058 TYR HA H HCH1 0.046 TYR CB C CH2 -0.054 TYR HB1 H HCH2 0.049 TYR HB2 H HCH2 0.049 TYR CG C CR6 -0.044 TYR CD1 C CR16 -0.053 TYR HD1 H HCR6 0.053 TYR CE1 C CR16 -0.099 TYR HE1 H HCR6 0.054 TYR CZ C CR6 0.176 TYR OH O OH1 -0.391 TYR HH H HOH1 0.305 TYR CE2 C CR16 -0.099 TYR HE2 H HCR6 0.054 TYR CD2 C CR16 -0.053 TYR HD2 H HCR6 0.053 TYR C C C 0.318 TYR O O O -0.422 loop_ _chem_comp_tree.comp_id _chem_comp_tree.atom_id _chem_comp_tree.atom_back _chem_comp_tree.atom_forward _chem_comp_tree.connect_type TYR N n/a CA START TYR H N . . TYR CA N C . TYR HA CA . . TYR CB CA CG . TYR HB1 CB . . TYR HB2 CB . . TYR CG CB CD1 . TYR CD1 CG CE1 . TYR HD1 CD1 . . TYR CE1 CD1 CZ . TYR HE1 CE1 . . TYR CZ CE1 CE2 . TYR OH CZ HH . TYR HH OH . . TYR CE2 CZ CD2 . TYR HE2 CE2 . . TYR CD2 CE2 HD2 . TYR HD2 CD2 . . TYR C CA . END TYR O C . . TYR CD2 CG . ADD 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 TYR N H coval 0.860 0.020 TYR N CA coval 1.458 0.019 TYR CA HA coval 0.980 0.020 TYR CA CB coval 1.530 0.020 TYR CB HB1 coval 0.970 0.020 TYR CB HB2 coval 0.970 0.020 TYR CB CG coval 1.512 0.022 TYR CG CD2 coval 1.389 0.021 TYR CG CD1 coval 1.389 0.021 TYR CD1 HD1 coval 0.930 0.020 TYR CD1 CE1 coval 1.382 0.030 TYR CE1 HE1 coval 0.930 0.020 TYR CE1 CZ coval 1.378 0.024 TYR CZ OH coval 1.376 0.021 TYR OH HH coval 0.820 0.020 TYR CZ CE2 coval 1.378 0.024 TYR CE2 HE2 coval 0.930 0.020 TYR CE2 CD2 coval 1.382 0.030 TYR CD2 HD2 coval 0.930 0.020 TYR CA C coval 1.525 0.021 TYR C O coval 1.231 0.020 loop_ _chem_comp_angle.comp_id _chem_comp_angle.atom_id_1 _chem_comp_angle.atom_id_2 _chem_comp_angle.atom_id_3 _chem_comp_angle.value_angle _chem_comp_angle.value_angle_esd TYR H N CA 114.000 3.000 TYR HA CA CB 109.000 3.000 TYR CB CA C 110.100 1.900 TYR HA CA C 109.000 3.000 TYR N CA HA 110.000 3.000 TYR N CA CB 110.500 1.700 TYR HB1 CB HB2 110.000 3.000 TYR HB2 CB CG 108.000 3.000 TYR HB1 CB CG 108.000 3.000 TYR CA CB HB1 109.000 3.000 TYR CA CB HB2 109.000 3.000 TYR CA CB CG 113.900 1.800 TYR CB CG CD2 120.800 1.500 TYR CD1 CG CD2 118.100 1.500 TYR CB CG CD1 120.800 1.500 TYR HD1 CD1 CE1 119.400 3.000 TYR CG CD1 HD1 119.400 3.000 TYR CG CD1 CE1 121.200 1.500 TYR HD2 CD2 CE2 119.400 3.000 TYR CG CD2 HD2 119.400 3.000 TYR CG CD2 CE2 121.200 1.500 TYR HE1 CE1 CZ 120.200 3.000 TYR CD1 CE1 HE1 120.200 3.000 TYR CD1 CE1 CZ 119.600 1.800 TYR OH CZ CE2 119.900 3.000 TYR CE1 CZ OH 119.900 3.000 TYR CZ OH HH 110.000 3.000 TYR CE1 CZ CE2 120.300 2.000 TYR HE2 CE2 CD2 120.200 3.000 TYR CZ CE2 HE2 120.200 3.000 TYR CZ CE2 CD2 119.600 1.800 TYR N CA C 111.200 2.800 TYR CA C O 120.800 1.700 loop_ _chem_comp_tor.comp_id _chem_comp_tor.id _chem_comp_tor.atom_id_1 _chem_comp_tor.atom_id_2 _chem_comp_tor.atom_id_3 _chem_comp_tor.atom_id_4 _chem_comp_tor.value_angle _chem_comp_tor.value_angle_esd _chem_comp_tor.period TYR chi1 N CA CB CG 180.000 15.000 3 TYR chi2 CA CB CG CD1 90.000 20.000 2 TYR CONST_01 CB CG CD1 CE1 180.000 0.000 0 TYR CONST_02 CG CD1 CE1 CZ 0.000 0.000 0 TYR CONST_03 CD1 CE1 CZ CE2 0.000 0.000 0 TYR hh1 CE1 CZ OH HH 60.000 30.000 2 TYR CONST_04 CE1 CZ CE2 CD2 0.000 0.000 0 TYR CONST_05 CZ CE2 CD2 CG 0.000 0.000 0 loop_ _chem_comp_chir.comp_id _chem_comp_chir.id _chem_comp_chir.atom_id_centre _chem_comp_chir.atom_id_1 _chem_comp_chir.atom_id_2 _chem_comp_chir.atom_id_3 _chem_comp_chir.volume_sign TYR chir_01 CA N CB C negativ loop_ _chem_comp_plane_atom.comp_id _chem_comp_plane_atom.plane_id _chem_comp_plane_atom.atom_id _chem_comp_plane_atom.dist_esd TYR plan CB 0.020 TYR plan CG 0.020 TYR plan CD1 0.020 TYR plan CE1 0.020 TYR plan CZ 0.020 TYR plan CE2 0.020 TYR plan CD2 0.020 TYR plan OH 0.020 TYR plan HD1 0.020 TYR plan HE1 0.020 TYR plan HE2 0.020 TYR plan HD2 0.020 # # end copy of monomer library entries # # # Modification of GLY, to add a CB # data_mod_gly_plus_c_beta loop_ _chem_mod_atom.mod_id _chem_mod_atom.function _chem_mod_atom.atom_id _chem_mod_atom.new_atom_id _chem_mod_atom.new_type_symbol _chem_mod_atom.new_type_energy _chem_mod_atom.new_partial_charge gly_plus_c_beta change CA . . CH1 0.058 gly_plus_c_beta change HA1 HA . HCH1 0.046 gly_plus_c_beta delete HA2 . . . . gly_plus_c_beta add . CB C CH2 -0.054 gly_plus_c_beta add . HB1 H HCH2 0.049 gly_plus_c_beta add . HB2 H HCH2 0.049 loop_ _chem_mod_bond.mod_id _chem_mod_bond.function _chem_mod_bond.atom_id_1 _chem_mod_bond.atom_id_2 _chem_mod_bond.new_type _chem_mod_bond.new_value_dist _chem_mod_bond.new_value_dist_esd gly_plus_c_beta change CA C . 1.525 0.021 gly_plus_c_beta change CA N . 1.458 0.019 gly_plus_c_beta change CA HA . 0.980 . gly_plus_c_beta add CA CB coval 1.530 0.020 gly_plus_c_beta add CB HB1 coval 0.970 0.020 gly_plus_c_beta add CB HB2 coval 0.970 0.020 loop_ _chem_mod_angle.mod_id _chem_mod_angle.function _chem_mod_angle.atom_id_1 _chem_mod_angle.atom_id_2 _chem_mod_angle.atom_id_3 _chem_mod_angle.new_value_angle _chem_mod_angle.new_value_angle_esd gly_plus_c_beta add C CA CB 110.1 1.900 gly_plus_c_beta change C CA N 111.2 2.800 gly_plus_c_beta change CA C O . 1.700 gly_plus_c_beta add CA CB HB1 109.0 3.000 gly_plus_c_beta add CA CB HB2 109.0 3.000 gly_plus_c_beta add CB CA HA 109.0 3.000 gly_plus_c_beta add CB CA N 110.5 1.700 gly_plus_c_beta add HB1 CB HB2 110.0 3.000 loop_ _chem_mod_chir.mod_id _chem_mod_chir.function _chem_mod_chir.atom_id_centre _chem_mod_chir.atom_id_1 _chem_mod_chir.atom_id_2 _chem_mod_chir.atom_id_3 _chem_mod_chir.new_volume_sign gly_plus_c_beta add CA N CB C negativ # # Modification of BNZ (benzene), to make it into a TYR sidechain, # but without the CB # data_mod_bnz_to_tyr_sidechain loop_ _chem_mod_atom.mod_id _chem_mod_atom.function _chem_mod_atom.atom_id _chem_mod_atom.new_atom_id _chem_mod_atom.new_type_symbol _chem_mod_atom.new_type_energy _chem_mod_atom.new_partial_charge bnz_to_tyr_sidechain change C1 CZ . CR6 0.176 bnz_to_tyr_sidechain delete H1 . . . . bnz_to_tyr_sidechain add . OH O OH1 -0.391 bnz_to_tyr_sidechain add . HH H HOH1 0.305 bnz_to_tyr_sidechain change C2 CE1 . CR16 -0.099 bnz_to_tyr_sidechain change H2 HE1 . HCR6 0.054 bnz_to_tyr_sidechain change C3 CD1 . CR16 -0.053 bnz_to_tyr_sidechain change H3 HD1 . HCR6 0.053 bnz_to_tyr_sidechain change C4 CG . CR6 -0.044 bnz_to_tyr_sidechain delete H4 . . . . bnz_to_tyr_sidechain change C5 CD2 . CR16 -0.053 bnz_to_tyr_sidechain change H5 HD2 . HCR6 0.053 bnz_to_tyr_sidechain change C6 CE2 . CR16 -0.099 bnz_to_tyr_sidechain change H6 HE2 . HCR6 0.054 loop_ _chem_mod_bond.mod_id _chem_mod_bond.function _chem_mod_bond.atom_id_1 _chem_mod_bond.atom_id_2 _chem_mod_bond.new_type _chem_mod_bond.new_value_dist _chem_mod_bond.new_value_dist_esd bnz_to_tyr_sidechain change CD1 CE1 . 1.382 0.030 bnz_to_tyr_sidechain change CD1 CG . 1.389 0.021 bnz_to_tyr_sidechain change CD1 HD1 . 0.930 0.020 bnz_to_tyr_sidechain change CD2 CE2 . 1.382 0.030 bnz_to_tyr_sidechain change CD2 CG . 1.389 0.021 bnz_to_tyr_sidechain change CD2 HD2 . 0.930 0.020 bnz_to_tyr_sidechain change CE1 CZ . 1.378 0.024 bnz_to_tyr_sidechain change CE1 HE1 . 0.930 0.020 bnz_to_tyr_sidechain change CE2 CZ . 1.378 0.024 bnz_to_tyr_sidechain change CE2 HE2 . 0.930 0.020 bnz_to_tyr_sidechain add CZ OH coval 1.376 0.021 bnz_to_tyr_sidechain add HH OH coval 0.820 0.020 loop_ _chem_mod_angle.mod_id _chem_mod_angle.function _chem_mod_angle.atom_id_1 _chem_mod_angle.atom_id_2 _chem_mod_angle.atom_id_3 _chem_mod_angle.new_value_angle _chem_mod_angle.new_value_angle_esd bnz_to_tyr_sidechain change CD1 CE1 CZ 119.6 1.800 bnz_to_tyr_sidechain change CD1 CE1 HE1 120.2 3.000 bnz_to_tyr_sidechain change CD1 CG CD2 118.1 1.500 bnz_to_tyr_sidechain change CD2 CE2 CZ 119.6 1.800 bnz_to_tyr_sidechain change CD2 CE2 HE2 120.2 . bnz_to_tyr_sidechain change CE1 CD1 CG 121.2 1.500 bnz_to_tyr_sidechain change CE1 CD1 CG 121.2 1.500 bnz_to_tyr_sidechain change CE1 CD1 HD1 119.4 . bnz_to_tyr_sidechain change CE1 CZ CE2 120.3 2.000 bnz_to_tyr_sidechain add CE1 CZ OH 119.9 3.000 bnz_to_tyr_sidechain change CE2 CD2 CG 121.2 1.500 bnz_to_tyr_sidechain change CE2 CD2 HD2 119.4 . bnz_to_tyr_sidechain add CE2 CZ OH 119.9 3.000 bnz_to_tyr_sidechain change CG CD1 HD1 119.4 . bnz_to_tyr_sidechain change CG CD2 HD2 119.4 . bnz_to_tyr_sidechain change CZ CE1 HE1 120.2 . bnz_to_tyr_sidechain change CZ CE2 HE2 120.2 . bnz_to_tyr_sidechain add CZ OH HH 110.0 3.000 loop_ _chem_mod_tor.mod_id _chem_mod_tor.function _chem_mod_tor.id _chem_mod_tor.atom_id_1 _chem_mod_tor.atom_id_2 _chem_mod_tor.atom_id_3 _chem_mod_tor.atom_id_4 _chem_mod_tor.new_value_angle _chem_mod_tor.new_value_angle_esd _chem_mod_tor.new_period bnz_to_tyr_sidechain delete CONST_1 CE1 CZ CE2 CD2 . . . bnz_to_tyr_sidechain add CONST_04 CE1 CZ CE2 CD2 0.0 0.0 0 bnz_to_tyr_sidechain delete CONST_2 CZ CE2 CD2 CG . . . bnz_to_tyr_sidechain add CONST_05 CZ CE2 CD2 CG 0.0 0.0 0 bnz_to_tyr_sidechain delete CONST_4 CE2 CD2 CG CD1 . . . bnz_to_tyr_sidechain delete CONST_5 CD2 CG CD1 CE1 . . . bnz_to_tyr_sidechain add hh1 CE1 CZ OH HH 60.0 30.0 2 bnz_to_tyr_sidechain delete CONST_6 CG CD1 CE1 CZ . . . bnz_to_tyr_sidechain add CONST_02 CG CD1 CE1 CZ 0.0 0.0 0 bnz_to_tyr_sidechain delete CONST_7 CD1 CE1 CZ CE2 . . . bnz_to_tyr_sidechain add CONST_03 CD1 CE1 CZ CE2 0.0 0.0 0 loop_ _chem_mod_plane_atom.mod_id _chem_mod_plane_atom.function _chem_mod_plane_atom.plane_id _chem_mod_plane_atom.atom_id _chem_mod_plane_atom.new_dist_esd bnz_to_tyr_sidechain add plan OH 0.020 data_link_list loop_ _chem_link.id _chem_link.comp_id_1 _chem_link.mod_id_1 _chem_link.group_comp_1 _chem_link.comp_id_2 _chem_link.mod_id_2 _chem_link.group_comp_2 _chem_link.name gly_bnz_to_tyr GLY gly_plus_c_beta . BNZ bnz_to_tyr_sidechain . . data_link_gly_bnz_to_tyr loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd gly_bnz_to_tyr 1 CB 2 CG . 1.512 0.022 loop_ _chem_link_angle.link_id _chem_link_angle.atom_1_comp_id _chem_link_angle.atom_id_1 _chem_link_angle.atom_2_comp_id _chem_link_angle.atom_id_2 _chem_link_angle.atom_3_comp_id _chem_link_angle.atom_id_3 _chem_link_angle.value_angle _chem_link_angle.value_angle_esd gly_bnz_to_tyr 1 CA 1 CB 2 CG 113.900 1.800 gly_bnz_to_tyr 1 CB 2 CG 2 CD1 120.800 1.500 gly_bnz_to_tyr 1 CB 2 CG 2 CD2 120.800 1.500 gly_bnz_to_tyr 2 CG 1 CB 1 HB1 108.000 3.000 gly_bnz_to_tyr 2 CG 1 CB 1 HB2 108.000 3.000 loop_ _chem_link_tor.link_id _chem_link_tor.id _chem_link_tor.atom_1_comp_id _chem_link_tor.atom_id_1 _chem_link_tor.atom_2_comp_id _chem_link_tor.atom_id_2 _chem_link_tor.atom_3_comp_id _chem_link_tor.atom_id_3 _chem_link_tor.atom_4_comp_id _chem_link_tor.atom_id_4 _chem_link_tor.value_angle _chem_link_tor.value_angle_esd _chem_link_tor.period gly_bnz_to_tyr CONST_01 1 CB 2 CG 2 CD1 2 CE1 180.00 0.0 0 gly_bnz_to_tyr chi1 1 N 1 CA 1 CB 2 CG 180.00 15.0 3 gly_bnz_to_tyr chi2 1 CA 1 CB 2 CG 2 CD1 90.00 20.0 2 loop_ _chem_link_plane.link_id _chem_link_plane.plane_id _chem_link_plane.atom_comp_id _chem_link_plane.atom_id _chem_link_plane.dist_esd gly_bnz_to_tyr plan 1 CB 0.020 """ def exercise(args): if ("--verbose" in args): out = sys.stdout else: out = StringIO() mon_lib_srv = monomer_library.server.server() ener_lib = monomer_library.server.ener_lib() open("tmp.cif", "w").write(cif_string) mon_lib_srv.process_cif(file_name="tmp.cif") mod_gly_plus_c_beta = mon_lib_srv.mod_mod_id_dict[ "gly_plus_c_beta"] mod_bnz_to_tyr_sidechain = mon_lib_srv.mod_mod_id_dict[ "bnz_to_tyr_sidechain"] # pdb_inp = pdb.input( source_info=None, lines=flex.std_string(pdb_records_gly_bnz)) pdb_hierarchy = pdb_inp.construct_hierarchy() residues = pdb_hierarchy.only_conformer().residues() assert len(residues) == 2 monomer_definitions = [] for residue in residues: md, ani = mon_lib_srv.get_comp_comp_id_and_atom_name_interpretation( residue_name=residue.resname, atom_names=residue.atoms().extract_name()) if (ani is not None): assert residue.resname == "GLY" assert ani.mon_lib_names() == ["N", "CA", "C", "O", None] monomer_definitions.append(md) gly_plus_c_beta = monomer_definitions[0].apply_mod(mod=mod_gly_plus_c_beta) gly_plus_c_beta.show(f=out) sidechain = monomer_definitions[1].apply_mod(mod=mod_bnz_to_tyr_sidechain) sidechain.show(f=out) # tyr_definition = mon_lib_srv.get_comp_comp_id_direct("TYR") tyr_atoms = [] for atom in tyr_definition.atom_list: s = StringIO() atom.show(f=s) tyr_atoms.append(s.getvalue()) tyr_atoms.sort() # mod_atoms = [] for atom in gly_plus_c_beta.atom_list + sidechain.atom_list: s = StringIO() atom.show(f=s) mod_atoms.append(s.getvalue()) mod_atoms.sort() assert not show_diff("".join(mod_atoms), "".join(tyr_atoms)) # tyr_bonds = [] for bond in tyr_definition.normalized_bond_list(): s = StringIO() bond.show(f=s) tyr_bonds.append(s.getvalue()) tyr_bonds.sort() # mod_bonds = [] for bond in gly_plus_c_beta.normalized_bond_list() \ + sidechain.normalized_bond_list(): s = StringIO() bond.show(f=s) mod_bonds.append(s.getvalue()) mod_bonds.sort() mod_bonds.insert(5, None) mod_bonds += [None] * (len(tyr_bonds) - len(mod_bonds)) for i,t,m in zip(count(), tyr_bonds, mod_bonds): print >> out, "bond index:", i if (m is None): print >> out, t else: t = t.splitlines() m = m.splitlines() assert len(m) == len(t) for ti,mi in zip(t, m): print >> out, "%-39s %-39s" % (ti,mi) print >> out assert not show_diff("".join(mod_bonds[:5]), "".join(tyr_bonds[:5])) assert not show_diff("".join(mod_bonds[6]), "".join(tyr_bonds[6])) assert not show_diff("".join(mod_bonds[8:]), "".join(tyr_bonds[8:])) # tyr_angles = [] for angle in tyr_definition.normalized_angle_list(): s = StringIO() angle.show(f=s) tyr_angles.append(s.getvalue()) tyr_angles.sort() # mod_angles = [] for angle in gly_plus_c_beta.normalized_angle_list() \ + sidechain.normalized_angle_list(): s = StringIO() angle.show(f=s) mod_angles.append(s.getvalue()) mod_angles.sort() mod_angles.insert(4, None) mod_angles.insert(10, None) mod_angles.insert(11, None) mod_angles.insert(24, None) mod_angles.insert(25, None) mod_angles += [None] * (len(tyr_angles) - len(mod_angles)) for i,t,m in zip(count(), tyr_angles, mod_angles): print >> out, "angle index:", i if (m is None): print >> out, t else: t = t.splitlines() m = m.splitlines() assert len(m) == len(t) for ti,mi in zip(t, m): print >> out, "%-39s %-39s" % (ti,mi) print >> out assert not show_diff("".join(mod_angles[:4]), "".join(tyr_angles[:4])) assert not show_diff("".join(mod_angles[5:10]), "".join(tyr_angles[5:10])) assert not show_diff("".join(mod_angles[12:24]), "".join(tyr_angles[12:24])) assert not show_diff("".join(mod_angles[26:]), "".join(tyr_angles[26:])) # tyr_tors = [] for tor in tyr_definition.tor_list: s = StringIO() tor.show(f=s) tyr_tors.append(s.getvalue()) tyr_tors.sort() # mod_tors = [] for tor in gly_plus_c_beta.tor_list \ + sidechain.tor_list: s = StringIO() tor.show(f=s) mod_tors.append(s.getvalue()) mod_tors.sort() mod_tors.insert(0, None) mod_tors.insert(5, None) mod_tors.insert(6, None) for i,t,m in zip(count(), tyr_tors, mod_tors): print >> out, "tor index:", i if (m is None): print >> out, t else: t = t.splitlines() m = m.splitlines() assert len(m) == len(t) for ti,mi in zip(t, m): print >> out, "%-39s %-39s" % (ti,mi) print >> out assert not show_diff("".join(mod_tors[1:5]), "".join(tyr_tors[1:5])) assert not show_diff("".join(mod_tors[7]), "".join(tyr_tors[7])) # assert len(tyr_definition.chir_list) == 1 assert len(gly_plus_c_beta.chir_list) == 1 assert len(sidechain.chir_list) == 0 gly_plus_c_beta.chir_list[0].id = tyr_definition.chir_list[0].id s = StringIO() tyr_definition.chir_list[0].show(f=s) tyr_chir = s.getvalue() s = StringIO() gly_plus_c_beta.chir_list[0].show(f=s) mod_chir = s.getvalue() assert not show_diff(mod_chir, tyr_chir) # tyr_plane_atoms = [] for plane_atom in tyr_definition.plane_atom_list: s = StringIO() plane_atom.show(f=s) tyr_plane_atoms.append(s.getvalue()) tyr_plane_atoms.sort() # mod_plane_atoms = [] for plane_atom in gly_plus_c_beta.plane_atom_list \ + sidechain.plane_atom_list: s = StringIO() plane_atom.show(f=s) mod_plane_atoms.append(s.getvalue()) mod_plane_atoms.sort() mod_plane_atoms.insert(0, None) mod_plane_atoms += [None] * (len(tyr_plane_atoms) - len(mod_plane_atoms)) for i,t,m in zip(count(), tyr_plane_atoms, mod_plane_atoms): print >> out, "plane_atom index:", i if (m is None): print >> out, t else: t = t.splitlines() m = m.splitlines() assert len(m) == len(t) for ti,mi in zip(t, m): print >> out, "%-39s %-39s" % (ti,mi) print >> out assert not show_diff( "".join(mod_plane_atoms[1:]), "".join(tyr_plane_atoms[1:])) # processed_tyr = monomer_library.pdb_interpretation.process( mon_lib_srv=mon_lib_srv, ener_lib=ener_lib, params=None, raw_records=pdb_records_tyr, log=sys.stdout) print processed_gly_bnz = monomer_library.pdb_interpretation.process( mon_lib_srv=mon_lib_srv, ener_lib=ener_lib, params=None, raw_records=pdb_records_gly_bnz, log=sys.stdout) print print "geo_tyr" geo_tyr = processed_tyr.geometry_restraints_manager() print print "geo_gly_bnz" geo_gly_bnz = processed_gly_bnz.geometry_restraints_manager() print # print "TODO: compare geometry restraints" print "OK" if (__name__ == "__main__"): exercise(sys.argv[1:])