diff --git a/api/tests/integration/ref/formats/cdx.py.out b/api/tests/integration/ref/formats/cdx.py.out index 55eebe0726..bf2bd4bdf4 100644 --- a/api/tests/integration/ref/formats/cdx.py.out +++ b/api/tests/integration/ref/formats/cdx.py.out @@ -115,25 +115,21 @@ M STY 4 1 SUP 2 SUP 3 SUP 4 SUP M SLB 4 1 1 2 2 3 3 4 4 M SAL 1 5 1 2 3 4 5 M SMT 1 bAla -M SDS EXP 1 1 M SDI 1 4 0.0000 0.0000 0.0000 0.0000 M SDI 1 4 0.0000 0.0000 0.0000 0.0000 M SAL 2 8 6 7 8 9 10 11 12 13 M SAL 2 6 14 15 16 17 18 19 M SMT 2 D-Trp -M SDS EXP 1 2 M SDI 2 4 0.0000 0.0000 0.0000 0.0000 M SDI 2 4 0.0000 0.0000 0.0000 0.0000 M SAL 3 8 20 21 22 23 24 25 26 27 M SAL 3 6 28 29 30 31 32 33 M SMT 3 Trp -M SDS EXP 1 3 M SDI 3 4 0.0000 0.0000 0.0000 0.0000 M SDI 3 4 0.0000 0.0000 0.0000 0.0000 M SAL 4 8 34 35 36 37 38 39 40 41 M SAL 4 8 42 43 44 45 46 47 48 49 M SMT 4 PAThr -M SDS EXP 1 4 M SDI 4 4 0.0000 0.0000 0.0000 0.0000 M SDI 4 4 0.0000 0.0000 0.0000 0.0000 M END diff --git a/api/tests/integration/ref/formats/cdxml_ket_expanded.py.out b/api/tests/integration/ref/formats/cdxml_ket_expanded.py.out deleted file mode 100644 index 38d27e15dc..0000000000 --- a/api/tests/integration/ref/formats/cdxml_ket_expanded.py.out +++ /dev/null @@ -1,127 +0,0 @@ -*** CDXML to KET *** -{ - "root": { - "nodes": [ - { - "$ref": "mol0" - }, - { - "$ref": "mol1" - } - ] - }, - "mol0": { - "type": "molecule", - "atoms": [ - { - "label": "C", - "location": [ - 1.8660635948181153, - -2.6999735832214357, - 0.0 - ] - }, - { - "label": "C", - "location": [ - 1.0, - -3.199960231781006, - 0.0 - ] - }, - { - "label": "O", - "location": [ - 1.8660635948181153, - -1.700000286102295, - 0.0 - ] - } - ], - "bonds": [ - { - "type": 1, - "atoms": [ - 1, - 0 - ] - }, - { - "type": 2, - "atoms": [ - 0, - 2 - ] - } - ], - "sgroups": [ - { - "type": "SUP", - "atoms": [ - 0, - 1, - 2 - ], - "name": "Ac", - "expanded": true - } - ] - }, - "mol1": { - "type": "molecule", - "atoms": [ - { - "label": "C", - "location": [ - 6.266063213348389, - -1.9999737739562989, - 0.0 - ] - }, - { - "label": "C", - "location": [ - 5.400000095367432, - -2.499960422515869, - 0.0 - ] - }, - { - "label": "O", - "location": [ - 6.266063213348389, - -1.0, - 0.0 - ] - } - ], - "bonds": [ - { - "type": 1, - "atoms": [ - 1, - 0 - ] - }, - { - "type": 2, - "atoms": [ - 0, - 2 - ] - } - ], - "sgroups": [ - { - "type": "SUP", - "atoms": [ - 0, - 1, - 2 - ], - "name": "Ac", - "expanded": true - } - ] - } -} \ No newline at end of file diff --git a/api/tests/integration/ref/formats/cdxml_to_mol.py.out b/api/tests/integration/ref/formats/cdxml_to_mol.py.out index f3a9e618a7..9bfd7454be 100644 --- a/api/tests/integration/ref/formats/cdxml_to_mol.py.out +++ b/api/tests/integration/ref/formats/cdxml_to_mol.py.out @@ -101,28 +101,23 @@ M STY 5 1 SUP 2 SUP 3 SUP 4 SUP 5 SUP M SLB 5 1 1 2 2 3 3 4 4 5 5 M SAL 1 8 13 14 15 16 17 18 19 20 M SMT 1 OBn -M SDS EXP 1 1 M SDI 1 4 0.0000 0.0000 0.0000 0.0000 M SDI 1 4 0.0000 0.0000 0.0000 0.0000 M SAL 2 1 28 M SMT 2 OR -M SDS EXP 1 2 M SDI 2 4 0.0000 0.0000 0.0000 0.0000 M SDI 2 4 0.0000 0.0000 0.0000 0.0000 M SAL 3 2 31 32 M SMT 3 OCH3 -M SDS EXP 1 3 M SDI 3 4 0.0000 0.0000 0.0000 0.0000 M SDI 3 4 0.0000 0.0000 0.0000 0.0000 M SAL 4 2 35 36 M SMT 4 OCH3 -M SDS EXP 1 4 M SDI 4 4 0.0000 0.0000 0.0000 0.0000 M SDI 4 4 0.0000 0.0000 0.0000 0.0000 M SAL 5 8 37 38 39 40 41 42 43 44 M SAL 5 1 45 M SMT 5 O2SPh -M SDS EXP 1 5 M SDI 5 4 0.0000 0.0000 0.0000 0.0000 M SDI 5 4 0.0000 0.0000 0.0000 0.0000 M END @@ -322,12 +317,10 @@ M STY 2 1 SUP 2 SUP M SLB 2 1 1 2 2 M SAL 1 2 9 10 M SMT 1 HATU -M SDS EXP 1 1 M SDI 1 4 0.0000 0.0000 0.0000 0.0000 M SDI 1 4 0.0000 0.0000 0.0000 0.0000 M SAL 2 2 19 20 M SMT 2 DCM -M SDS EXP 1 2 M SDI 2 4 0.0000 0.0000 0.0000 0.0000 M SDI 2 4 0.0000 0.0000 0.0000 0.0000 M END @@ -418,7 +411,6 @@ M SLB 4 1 1 2 2 3 3 4 4 M SCN 1 4 HT M SAL 1 4 1 2 3 4 M SMT 1 test -M SDS EXP 1 1 M SDI 1 4 0.0000 0.0000 0.0000 0.0000 M SDI 1 4 0.0000 0.0000 0.0000 0.0000 M SAL 2 4 11 12 13 14 @@ -857,25 +849,21 @@ M STY 4 1 SUP 2 SUP 3 SUP 4 SUP M SLB 4 1 1 2 2 3 3 4 4 M SAL 1 5 1 2 3 4 5 M SMT 1 bAla -M SDS EXP 1 1 M SDI 1 4 0.0000 0.0000 0.0000 0.0000 M SDI 1 4 0.0000 0.0000 0.0000 0.0000 M SAL 2 8 6 7 8 9 10 11 12 13 M SAL 2 6 14 15 16 17 18 19 M SMT 2 D-Trp -M SDS EXP 1 2 M SDI 2 4 0.0000 0.0000 0.0000 0.0000 M SDI 2 4 0.0000 0.0000 0.0000 0.0000 M SAL 3 8 20 21 22 23 24 25 26 27 M SAL 3 6 28 29 30 31 32 33 M SMT 3 Trp -M SDS EXP 1 3 M SDI 3 4 0.0000 0.0000 0.0000 0.0000 M SDI 3 4 0.0000 0.0000 0.0000 0.0000 M SAL 4 8 34 35 36 37 38 39 40 41 M SAL 4 8 42 43 44 45 46 47 48 49 M SMT 4 PAThr -M SDS EXP 1 4 M SDI 4 4 0.0000 0.0000 0.0000 0.0000 M SDI 4 4 0.0000 0.0000 0.0000 0.0000 M END diff --git a/api/tests/integration/tests/formats/cdxml_ket_expanded.py b/api/tests/integration/tests/formats/cdxml_ket_expanded.py deleted file mode 100644 index 094722dddc..0000000000 --- a/api/tests/integration/tests/formats/cdxml_ket_expanded.py +++ /dev/null @@ -1,21 +0,0 @@ -import os -import sys - -sys.path.append( - os.path.normpath( - os.path.join(os.path.abspath(__file__), "..", "..", "..", "common") - ) -) - -from env_indigo import * # noqa - -indigo = Indigo() - -indigo.setOption("json-saving-pretty", True) -print("*** CDXML to KET ***") -ref_path = joinPathPy("ref/", __file__) -mol = indigo.loadMoleculeFromFile( - joinPathPy("ref/cdxml_ket_expanded.cdxml", __file__) -) - -print(mol.json()) diff --git a/api/tests/integration/tests/formats/ref/cdxml_ket_expanded.cdxml b/api/tests/integration/tests/formats/ref/cdxml_ket_expanded.cdxml deleted file mode 100644 index f56db97c3c..0000000000 --- a/api/tests/integration/tests/formats/ref/cdxml_ket_expanded.cdxml +++ /dev/null @@ -1,55 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - O - - - - - - - Ac - - - - - - - - - O - - - - - - - Ac - - - - - diff --git a/core/indigo-core/molecule/src/molecule_cdxml_loader.cpp b/core/indigo-core/molecule/src/molecule_cdxml_loader.cpp index 785dadfe54..1f40c265cc 100644 --- a/core/indigo-core/molecule/src/molecule_cdxml_loader.cpp +++ b/core/indigo-core/molecule/src/molecule_cdxml_loader.cpp @@ -628,7 +628,7 @@ void MoleculeCdxmlLoader::_addBracket(BaseMolecule& mol, const CdxmlBracket& bra if (bracket.is_superatom) { Superatom& sa = (Superatom&)sgroup; - sa.contracted = DisplayOption::Expanded; + sa.contracted = DisplayOption::Contracted; sa.subscript.readString(bracket.label.c_str(), true); } else