feat: SCHWED-5977 read charge if present in mmCIF reader

modules/io/src/mol/mmcif_reader.cc

@@ -141,6 +141,7 @@ bool MMCifReader::OnBeginLoop(const StarLoopDesc& header)
     indices_[AUTH_SEQ_ID]        = header.GetIndex("auth_seq_id");
     indices_[PDBX_PDB_INS_CODE]  = header.GetIndex("pdbx_PDB_ins_code");
     indices_[PDBX_PDB_MODEL_NUM] = header.GetIndex("pdbx_PDB_model_num");
+    indices_[FORMAL_CHARGE]     = header.GetIndex("pdbx_formal_charge");
 
     // post processing
     if (category_counts_[category_] > 0) {
@@ -482,6 +483,7 @@ void MMCifReader::ParseAndAddAtom(const std::vector<StringRef>& columns)
     return;                            
   }
   Real occ = 1.00f, temp = 0;
+  int charge = 0;
   geom::Vec3 apos;
   
   for (int i = CARTN_X; i <= CARTN_Z; ++i) {
@@ -505,6 +507,13 @@ void MMCifReader::ParseAndAddAtom(const std::vector<StringRef>& columns)
                               "atom_site.B_iso_or_equiv");
     }
   }
+  if (indices_[FORMAL_CHARGE] != -1) { // unit test
+    String charge_s = columns[indices_[FORMAL_CHARGE]].str();
+    if (charge_s != "?" && charge_s != ".") {
+      charge = this->TryGetInt(columns[indices_[FORMAL_CHARGE]],
+                               "atom_site.pdbx_formal_charge");
+    }
+  }
 
   // determine element
   String s_ele(columns[indices_[TYPE_SYMBOL]].str());
@@ -665,6 +674,8 @@ void MMCifReader::ParseAndAddAtom(const std::vector<StringRef>& columns)
 
   ah.SetOccupancy(occ);
 
+  ah.SetCharge(charge);
+
   // record type
   ah.SetHetAtom(indices_[GROUP_PDB] == -1 ? false :  
                 columns[indices_[GROUP_PDB]][0]=='H');

modules/io/src/mol/mmcif_reader.hh

@@ -359,7 +359,7 @@ protected:
 private:
   /// \enum magic numbers of this class
   typedef enum {
-    MAX_ITEMS_IN_ROW=18 ///< count for possible items in a loop row
+    MAX_ITEMS_IN_ROW=19 ///< count for possible items in a loop row
   } MMCifMagicNos;
 
   /// \enum items of the atom_site category
@@ -381,7 +381,8 @@ private:
     B_ISO_OR_EQUIV,
     PDBX_PDB_INS_CODE,
     GROUP_PDB,         ///< record name
-    PDBX_PDB_MODEL_NUM ///< model no. (especially NMR structures)
+    PDBX_PDB_MODEL_NUM,///< model no. (especially NMR structures)
+    FORMAL_CHARGE
   } AtomSiteItems;
 
   /// \enum items of the entity category

modules/io/tests/test_mmcif_reader.cc

@@ -1616,5 +1616,22 @@ BOOST_AUTO_TEST_CASE(mmcif_atom_site_B_iso_or_equiv_tests)
   BOOST_TEST_MESSAGE("  done.");
 }
 
+BOOST_AUTO_TEST_CASE(mmcif_formal_charge)
+{
+  mol::EntityHandle eh = mol::CreateEntity();
+  std::ifstream s("testfiles/mmcif/4C79_charged.cif");
+  IOProfile profile;
+  MMCifReader mmcif_p(s, eh, profile);
+  mmcif_p.Parse();
+
+  BOOST_CHECK_EQUAL(eh.FindAtom("A", 49, "OE2").GetCharge(), -1);
+  BOOST_CHECK_EQUAL(eh.FindAtom("A", 49, "OE1").GetCharge(), 0); // '?'
+  BOOST_CHECK_EQUAL(eh.FindAtom("A", 49, "CA").GetCharge(), 0);  // Explicit 0
+  BOOST_CHECK_EQUAL(eh.FindAtom("A", 49, "CB").GetCharge(), 0);  // '.'
+  BOOST_CHECK_EQUAL(eh.FindAtom("C", 1, "ZN").GetCharge(), 2);
+  BOOST_CHECK_EQUAL(eh.FindAtom("D", 1, "NA").GetCharge(), 1);
+
+}
+
 
 BOOST_AUTO_TEST_SUITE_END();

modules/io/tests/testfiles/mmcif/4C79_charged.cif

+data_4C79
+# taken and modified from 4C79.cif
+_entry.id   4C79
+# 
+loop_
+_entity.id 
+_entity.type 
+_entity.src_method 
+_entity.pdbx_description 
+_entity.formula_weight 
+_entity.pdbx_number_of_molecules 
+_entity.pdbx_ec 
+_entity.pdbx_mutation 
+_entity.pdbx_fragment 
+_entity.details 
+1 polymer     man SMOOTHENED   22144.174 2  ? ? 'CYSTEINE-RICH DOMAIN (CRD), RESIDUES 28-210' ? 
+2 non-polymer syn 'ZINC ION'   65.409    1  ? ? ?                                             ? 
+3 non-polymer syn 'SODIUM ION' 22.990    2  ? ? ?                                             ? 
+4 water       nat water        18.015    48 ? ? ?                                             ? 
+# 
+_entity_poly.entity_id                      1 
+_entity_poly.type                           'polypeptide(L)' 
+_entity_poly.nstd_linkage                   no 
+_entity_poly.nstd_monomer                   no 
+_entity_poly.pdbx_seq_one_letter_code       
+;MAVILHPNETIFNDFCKKSTTCEVLKYNTCLGSPLPYTHTSLILAEDSETQEEAFEKLAMWSGLRNAPRCWAVIQPLLCA
+VYMPKCENGKVELPSQHLCQATRNPCSIVERERGWPNFLKCENKEQFPKGCQNEVQKLKFNTSGQCEAPLVKTDIQASWY
+KDVEGCGIQCDNPLFTEDEHSDMHKLEHHHHHH
+;
+_entity_poly.pdbx_seq_one_letter_code_can   
+;MAVILHPNETIFNDFCKKSTTCEVLKYNTCLGSPLPYTHTSLILAEDSETQEEAFEKLAMWSGLRNAPRCWAVIQPLLCA
+VYMPKCENGKVELPSQHLCQATRNPCSIVERERGWPNFLKCENKEQFPKGCQNEVQKLKFNTSGQCEAPLVKTDIQASWY
+KDVEGCGIQCDNPLFTEDEHSDMHKLEHHHHHH
+;
+_entity_poly.pdbx_strand_id                 A
+_entity_poly.pdbx_target_identifier         ? 
+# 
+loop_
+_entity_poly_seq.entity_id 
+_entity_poly_seq.num 
+_entity_poly_seq.mon_id 
+_entity_poly_seq.hetero 
+1 1   MET n 
+1 2   ALA n 
+1 3   VAL n 
+1 4   ILE n 
+1 5   LEU n 
+1 6   HIS n 
+1 7   PRO n 
+1 8   ASN n 
+1 9   GLU n 
+1 10  THR n 
+1 11  ILE n 
+1 12  PHE n 
+1 13  ASN n 
+1 14  ASP n 
+1 15  PHE n 
+1 16  CYS n 
+1 17  LYS n 
+1 18  LYS n 
+1 19  SER n 
+1 20  THR n 
+1 21  THR n 
+1 22  CYS n 
+1 23  GLU n 
+1 24  VAL n 
+1 25  LEU n 
+1 26  LYS n 
+1 27  TYR n 
+1 28  ASN n 
+1 29  THR n 
+1 30  CYS n 
+1 31  LEU n 
+1 32  GLY n 
+1 33  SER n 
+1 34  PRO n 
+1 35  LEU n 
+1 36  PRO n 
+1 37  TYR n 
+1 38  THR n 
+1 39  HIS n 
+1 40  THR n 
+1 41  SER n 
+1 42  LEU n 
+1 43  ILE n 
+1 44  LEU n 
+1 45  ALA n 
+1 46  GLU n 
+1 47  ASP n 
+1 48  SER n 
+1 49  GLU n 
+1 50  THR n 
+1 51  GLN n 
+1 52  GLU n 
+1 53  GLU n 
+1 54  ALA n 
+1 55  PHE n 
+1 56  GLU n 
+1 57  LYS n 
+1 58  LEU n 
+1 59  ALA n 
+1 60  MET n 
+1 61  TRP n 
+1 62  SER n 
+1 63  GLY n 
+1 64  LEU n 
+1 65  ARG n 
+1 66  ASN n 
+1 67  ALA n 
+1 68  PRO n 
+1 69  ARG n 
+1 70  CYS n 
+1 71  TRP n 
+1 72  ALA n 
+1 73  VAL n 
+1 74  ILE n 
+1 75  GLN n 
+1 76  PRO n 
+1 77  LEU n 
+1 78  LEU n 
+1 79  CYS n 
+1 80  ALA n 
+1 81  VAL n 
+1 82  TYR n 
+1 83  MET n 
+1 84  PRO n 
+1 85  LYS n 
+1 86  CYS n 
+1 87  GLU n 
+1 88  ASN n 
+1 89  GLY n 
+1 90  LYS n 
+1 91  VAL n 
+1 92  GLU n 
+1 93  LEU n 
+1 94  PRO n 
+1 95  SER n 
+1 96  GLN n 
+1 97  HIS n 
+1 98  LEU n 
+1 99  CYS n 
+1 100 GLN n 
+1 101 ALA n 
+1 102 THR n 
+1 103 ARG n 
+1 104 ASN n 
+1 105 PRO n 
+1 106 CYS n 
+1 107 SER n 
+1 108 ILE n 
+1 109 VAL n 
+1 110 GLU n 
+1 111 ARG n 
+1 112 GLU n 
+1 113 ARG n 
+1 114 GLY n 
+1 115 TRP n 
+1 116 PRO n 
+1 117 ASN n 
+1 118 PHE n 
+1 119 LEU n 
+1 120 LYS n 
+1 121 CYS n 
+1 122 GLU n 
+1 123 ASN n 
+1 124 LYS n 
+1 125 GLU n 
+1 126 GLN n 
+1 127 PHE n 
+1 128 PRO n 
+1 129 LYS n 
+1 130 GLY n 
+1 131 CYS n 
+1 132 GLN n 
+1 133 ASN n 
+1 134 GLU n 
+1 135 VAL n 
+1 136 GLN n 
+1 137 LYS n 
+1 138 LEU n 
+1 139 LYS n 
+1 140 PHE n 
+1 141 ASN n 
+1 142 THR n 
+1 143 SER n 
+1 144 GLY n 
+1 145 GLN n 
+1 146 CYS n 
+1 147 GLU n 
+1 148 ALA n 
+1 149 PRO n 
+1 150 LEU n 
+1 151 VAL n 
+1 152 LYS n 
+1 153 THR n 
+1 154 ASP n 
+1 155 ILE n 
+1 156 GLN n 
+1 157 ALA n 
+1 158 SER n 
+1 159 TRP n 
+1 160 TYR n 
+1 161 LYS n 
+1 162 ASP n 
+1 163 VAL n 
+1 164 GLU n 
+1 165 GLY n 
+1 166 CYS n 
+1 167 GLY n 
+1 168 ILE n 
+1 169 GLN n 
+1 170 CYS n 
+1 171 ASP n 
+1 172 ASN n 
+1 173 PRO n 
+1 174 LEU n 
+1 175 PHE n 
+1 176 THR n 
+1 177 GLU n 
+1 178 ASP n 
+1 179 GLU n 
+1 180 HIS n 
+1 181 SER n 
+1 182 ASP n 
+1 183 MET n 
+1 184 HIS n 
+1 185 LYS n 
+1 186 LEU n 
+1 187 GLU n 
+1 188 HIS n 
+1 189 HIS n 
+1 190 HIS n 
+1 191 HIS n 
+1 192 HIS n 
+1 193 HIS n
+# 
+_struct.entry_id                  4C79 
+_struct.title                     'Crystal structure of the Smoothened CRD, native' 
+_struct.pdbx_descriptor           SMOOTHENED 
+_struct.pdbx_model_details        ? 
+_struct.pdbx_CASP_flag            ? 
+_struct.pdbx_model_type_details   ? 
+# 
+_struct_keywords.entry_id        4C79 
+_struct_keywords.pdbx_keywords   'SIGNALING PROTEIN' 
+_struct_keywords.text            'SIGNALING PROTEIN'
+# 
+loop_
+_atom_site.group_PDB 
+_atom_site.id 
+_atom_site.type_symbol 
+_atom_site.label_atom_id 
+_atom_site.label_alt_id 
+_atom_site.label_comp_id 
+_atom_site.label_asym_id 
+_atom_site.label_entity_id 
+_atom_site.label_seq_id 
+_atom_site.pdbx_PDB_ins_code 
+_atom_site.Cartn_x 
+_atom_site.Cartn_y 
+_atom_site.Cartn_z 
+_atom_site.occupancy 
+_atom_site.B_iso_or_equiv 
+_atom_site.pdbx_formal_charge 
+_atom_site.auth_seq_id 
+_atom_site.auth_comp_id 
+_atom_site.auth_asym_id 
+_atom_site.auth_atom_id 
+_atom_site.pdbx_PDB_model_num
+ATOM   262  N  N   . GLU A 1 49  ? -25.812 5.207   -4.954  1.00 35.58  ? 75   GLU A N   1
+ATOM   263  C  CA  . GLU A 1 49  ? -26.815 4.149   -4.979  1.00 36.58  0 75   GLU A CA  1
+ATOM   264  C  C   . GLU A 1 49  ? -27.600 4.155   -6.288  1.00 35.91  ? 75   GLU A C   1
+ATOM   265  O  O   . GLU A 1 49  ? -28.206 3.150   -6.663  1.00 35.94  ? 75   GLU A O   1
+ATOM   266  C  CB  . GLU A 1 49  ? -27.774 4.284   -3.794  1.00 38.91  . 75   GLU A CB  1
+ATOM   267  C  CG  . GLU A 1 49  ? -27.114 4.163   -2.426  1.00 40.64  ? 75   GLU A CG  1
+ATOM   268  C  CD  . GLU A 1 49  ? -26.931 2.725   -1.965  1.00 42.04  ? 75   GLU A CD  1
+ATOM   269  O  OE1 . GLU A 1 49  ? -26.905 1.807   -2.812  1.00 42.07  ? 75   GLU A OE1 1
+ATOM   270  O  OE2 . GLU A 1 49  ? -26.811 2.516   -0.740  1.00 42.97 -1 75   GLU A OE2 1
+HETATM 1881 ZN ZN  . ZN  C 2 .   ? -29.714 -4.622  -22.478 1.00 31.76  2 1159 ZN  A ZN  1 
+HETATM 1882 NA NA  . NA  D 3 .   ? -23.050 1.721   -4.584  1.00 26.51  1 1160 NA  A NA  1 
+#
+loop_
+_pdbx_entity_nonpoly.entity_id 
+_pdbx_entity_nonpoly.name 
+_pdbx_entity_nonpoly.comp_id 
+2 'ZINC ION'   ZN  
+3 'SODIUM ION' NA  
+4 water        HOH 
+#