diff --git a/modules/io/src/mol/mmcif_reader.cc b/modules/io/src/mol/mmcif_reader.cc
index 7ddde3b2cf53f36807b659cb943f13207ed0a203..e550d96f83dfc160819f860055561534606b48fd 100644
--- a/modules/io/src/mol/mmcif_reader.cc
+++ b/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');
diff --git a/modules/io/src/mol/mmcif_reader.hh b/modules/io/src/mol/mmcif_reader.hh
index 1f21c3928cac354f5f69197e763443d37a2dc9f6..f2f2d2dbd78069a778c6cd3ccab9d49abb7b0cb1 100644
--- a/modules/io/src/mol/mmcif_reader.hh
+++ b/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
diff --git a/modules/io/tests/test_mmcif_reader.cc b/modules/io/tests/test_mmcif_reader.cc
index e03eb0073be2133e959420e390e3c6f07ec07fde..6d81b46033ab1143be596f7464020706a4645abd 100644
--- a/modules/io/tests/test_mmcif_reader.cc
+++ b/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();
diff --git a/modules/io/tests/testfiles/mmcif/4C79_charged.cif b/modules/io/tests/testfiles/mmcif/4C79_charged.cif
new file mode 100644
index 0000000000000000000000000000000000000000..c5089608ff706068345942fb2240a2f7394c5a52
--- /dev/null
+++ b/modules/io/tests/testfiles/mmcif/4C79_charged.cif
@@ -0,0 +1,289 @@
+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
+#