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getKet duplicates items when macro molucules are used #5181

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doktordirk opened this issue Jul 26, 2024 · 3 comments
Closed

getKet duplicates items when macro molucules are used #5181

doktordirk opened this issue Jul 26, 2024 · 3 comments
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@aproskurnov
Labels
bug Customer Feedback Priority: High
Milestone
Ketcher 2.27.0-rc.1

Comments

@doktordirk
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Steps to Reproduce

  1. Add item in micro mode
  2. Switch to macro mode
  3. Add item in macro mode
  4. Switch to micro mode
  5. Get result from ketcher.getKet()

Actual behavior
All items in the ket data are duplicated

Expected behavior
No item duplicated. Output should be identical to using "Save as..." -> ket file

Screenshots

output of "Save as..." -> ket file 
{
    "root": {
        "nodes": [
            {
                "$ref": "monomer19"
            },
            {
                "$ref": "mol0"
            }
        ],
        "connections": [],
        "templates": [
            {
                "$ref": "monomerTemplate-Cya___3-sulfoalanine"
            }
        ]
    },
    "mol0": {
        "type": "molecule",
        "atoms": [
            {
                "label": "C",
                "location": [
                    10.208987298340658,
                    -8.74999266647844,
                    0
                ]
            },
            {
                "label": "C",
                "location": [
                    10.208987298340658,
                    -9.750007333521562,
                    0
                ]
            },
            {
                "label": "C",
                "location": [
                    11.075000000000001,
                    -10.250014667043123,
                    0
                ]
            },
            {
                "label": "C",
                "location": [
                    11.941012701659346,
                    -9.750007333521562,
                    0
                ]
            },
            {
                "label": "C",
                "location": [
                    11.941012701659346,
                    -8.74999266647844,
                    0
                ]
            },
            {
                "label": "C",
                "location": [
                    11.075000000000001,
                    -8.249985332956879,
                    0
                ]
            }
        ],
        "bonds": [
            {
                "type": 1,
                "atoms": [
                    5,
                    0
                ]
            },
            {
                "type": 1,
                "atoms": [
                    0,
                    1
                ]
            },
            {
                "type": 1,
                "atoms": [
                    1,
                    2
                ]
            },
            {
                "type": 1,
                "atoms": [
                    2,
                    3
                ]
            },
            {
                "type": 1,
                "atoms": [
                    3,
                    4
                ]
            },
            {
                "type": 1,
                "atoms": [
                    4,
                    5
                ]
            }
        ]
    },
    "monomer19": {
        "type": "monomer",
        "id": "19",
        "position": {
            "x": 13.5,
            "y": -6.775
        },
        "alias": "Cya",
        "templateId": "Cya___3-sulfoalanine"
    },
    "monomerTemplate-Cya___3-sulfoalanine": {
        "type": "monomerTemplate",
        "atoms": [
            {
                "label": "C",
                "location": [
                    0.5437,
                    0.778,
                    0
                ]
            },
            {
                "label": "C",
                "location": [
                    0.5429,
                    -0.7228,
                    0
                ],
                "stereoLabel": "abs"
            },
            {
                "label": "C",
                "location": [
                    1.8417,
                    -1.4748,
                    0
                ]
            },
            {
                "label": "O",
                "location": [
                    1.841,
                    -2.6748,
                    0
                ]
            },
            {
                "label": "O",
                "location": [
                    2.8815,
                    -0.8757,
                    0
                ]
            },
            {
                "label": "N",
                "location": [
                    -0.756,
                    -1.4748,
                    0
                ]
            },
            {
                "label": "H",
                "location": [
                    -1.7964,
                    -0.8767,
                    0
                ]
            },
            {
                "label": "S",
                "location": [
                    -0.7551,
                    1.53,
                    0
                ]
            },
            {
                "label": "O",
                "location": [
                    -0.7544,
                    2.73,
                    0
                ]
            },
            {
                "label": "O",
                "location": [
                    -1.7949,
                    0.9309,
                    0
                ]
            },
            {
                "label": "O",
                "location": [
                    -1.794,
                    2.1307,
                    0
                ]
            }
        ],
        "bonds": [
            {
                "type": 1,
                "atoms": [
                    1,
                    0
                ],
                "stereo": 1
            },
            {
                "type": 1,
                "atoms": [
                    1,
                    2
                ]
            },
            {
                "type": 2,
                "atoms": [
                    2,
                    3
                ]
            },
            {
                "type": 1,
                "atoms": [
                    2,
                    4
                ]
            },
            {
                "type": 1,
                "atoms": [
                    1,
                    5
                ]
            },
            {
                "type": 1,
                "atoms": [
                    5,
                    6
                ]
            },
            {
                "type": 1,
                "atoms": [
                    0,
                    7
                ]
            },
            {
                "type": 2,
                "atoms": [
                    7,
                    8
                ]
            },
            {
                "type": 2,
                "atoms": [
                    7,
                    9
                ]
            },
            {
                "type": 1,
                "atoms": [
                    7,
                    10
                ]
            }
        ],
        "class": "AminoAcid",
        "classHELM": "PEPTIDE",
        "id": "Cya___3-sulfoalanine",
        "fullName": "3-sulfoalanine",
        "alias": "Cya",
        "attachmentPoints": [
            {
                "attachmentAtom": 5,
                "leavingGroup": {
                    "atoms": [
                        6
                    ]
                },
                "type": "left"
            },
            {
                "attachmentAtom": 2,
                "leavingGroup": {
                    "atoms": [
                        4
                    ]
                },
                "type": "right"
            }
        ],
        "naturalAnalogShort": "A"
    }
}
output of ketcher.getKet()

{
"root": {
"nodes": [
{
"$ref": "monomer11"
},
{
"$ref": "monomer21"
},
{
"$ref": "mol0"
},
{
"$ref": "mol1"
}
],
"connections": [],
"templates": [
{
"$ref": "monomerTemplate-Cya___3-sulfoalanine"
}
]
},
"mol0": {
"type": "molecule",
"atoms": [
{
"label": "C",
"location": [
10.208987298340658,
-8.74999266647844,
0
]
},
{
"label": "C",
"location": [
10.208987298340658,
-9.750007333521562,
0
]
},
{
"label": "C",
"location": [
11.075000000000001,
-10.250014667043123,
0
]
},
{
"label": "C",
"location": [
11.941012701659346,
-9.750007333521562,
0
]
},
{
"label": "C",
"location": [
11.941012701659346,
-8.74999266647844,
0
]
},
{
"label": "C",
"location": [
11.075000000000001,
-8.249985332956879,
0
]
}
],
"bonds": [
{
"type": 1,
"atoms": [
5,
0
]
},
{
"type": 1,
"atoms": [
0,
1
]
},
{
"type": 1,
"atoms": [
1,
2
]
},
{
"type": 1,
"atoms": [
2,
3
]
},
{
"type": 1,
"atoms": [
3,
4
]
},
{
"type": 1,
"atoms": [
4,
5
]
}
]
},
"mol1": {
"type": "molecule",
"atoms": [
{
"label": "C",
"location": [
10.208987298340658,
-8.74999266647844,
0
]
},
{
"label": "C",
"location": [
10.208987298340658,
-9.750007333521562,
0
]
},
{
"label": "C",
"location": [
11.075000000000001,
-10.250014667043123,
0
]
},
{
"label": "C",
"location": [
11.941012701659346,
-9.750007333521562,
0
]
},
{
"label": "C",
"location": [
11.941012701659346,
-8.74999266647844,
0
]
},
{
"label": "C",
"location": [
11.075000000000001,
-8.249985332956879,
0
]
}
],
"bonds": [
{
"type": 1,
"atoms": [
5,
0
]
},
{
"type": 1,
"atoms": [
0,
1
]
},
{
"type": 1,
"atoms": [
1,
2
]
},
{
"type": 1,
"atoms": [
2,
3
]
},
{
"type": 1,
"atoms": [
3,
4
]
},
{
"type": 1,
"atoms": [
4,
5
]
}
]
},
"monomer11": {
"type": "monomer",
"id": "11",
"position": {
"x": 13.5,
"y": -6.775
},
"alias": "Cya",
"templateId": "Cya___3-sulfoalanine"
},
"monomerTemplate-Cya___3-sulfoalanine": {
"type": "monomerTemplate",
"atoms": [
{
"label": "C",
"location": [
0.5437,
0.778,
0
]
},
{
"label": "C",
"location": [
0.5429,
-0.7228,
0
],
"stereoLabel": "abs"
},
{
"label": "C",
"location": [
1.8417,
-1.4748,
0
]
},
{
"label": "O",
"location": [
1.841,
-2.6748,
0
]
},
{
"label": "O",
"location": [
2.8815,
-0.8757,
0
]
},
{
"label": "N",
"location": [
-0.756,
-1.4748,
0
]
},
{
"label": "H",
"location": [
-1.7964,
-0.8767,
0
]
},
{
"label": "S",
"location": [
-0.7551,
1.53,
0
]
},
{
"label": "O",
"location": [
-0.7544,
2.73,
0
]
},
{
"label": "O",
"location": [
-1.7949,
0.9309,
0
]
},
{
"label": "O",
"location": [
-1.794,
2.1307,
0
]
}
],
"bonds": [
{
"type": 1,
"atoms": [
1,
0
],
"stereo": 1
},
{
"type": 1,
"atoms": [
1,
2
]
},
{
"type": 2,
"atoms": [
2,
3
]
},
{
"type": 1,
"atoms": [
2,
4
]
},
{
"type": 1,
"atoms": [
1,
5
]
},
{
"type": 1,
"atoms": [
5,
6
]
},
{
"type": 1,
"atoms": [
0,
7
]
},
{
"type": 2,
"atoms": [
7,
8
]
},
{
"type": 2,
"atoms": [
7,
9
]
},
{
"type": 1,
"atoms": [
7,
10
]
}
],
"class": "AminoAcid",
"classHELM": "PEPTIDE",
"id": "Cya___3-sulfoalanine",
"fullName": "3-sulfoalanine",
"alias": "Cya",
"attachmentPoints": [
{
"attachmentAtom": 5,
"leavingGroup": {
"atoms": [
6
]
},
"type": "left"
},
{
"attachmentAtom": 2,
"leavingGroup": {
"atoms": [
4
]
},
"type": "right"
}
],
"naturalAnalogShort": "A"
},
"monomer21": {
"type": "monomer",
"id": "21",
"position": {
"x": 13.5,
"y": -6.775
},
"alias": "Cya",
"templateId": "Cya___3-sulfoalanine"
}
}

Desktop (please complete the following information):

  • OS: Ubuntu
  • Browser: chrome
  • Version : 127.0.6533.72 (Official Build) (64-bit)

Ketcher version
2.22.0-rc.9

Additional context
using

const structOrString = await window.ketcher.editor.struct();
const { struct } = await window.ketcher.indigo.convert(structOrString, {
        outputFormat: chemical/x-indigo-ket',
      });

gives the correct ket data (but has other issues since converting (basically) ket to ket flattes arrows
@doktordirk doktordirk added the bug label Jul 26, 2024
@rrodionov91
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Collaborator

Hi @doktordirk
Thank you for highlighting the issue. We reproduced it. Will plan the fix.

matejaivosevic added a commit that referenced this issue Aug 4, 2024
@matejaivosevic
#5181 - getKey duplicated items when macromolecules are used
3988c88
@matejaivosevic matejaivosevic linked a pull request Aug 4, 2024 that will close this issue
#5181 - getKey duplicated items when macromolecules are used #5213
Closed
9 tasks
@ivanmaslow ivanmaslow mentioned this issue Aug 6, 2024
Open
@NataliaLoginova NataliaLoginova removed a link to a pull request Oct 22, 2024
#5181 - getKey duplicated items when macromolecules are used #5213
Closed
9 tasks
@NataliaLoginova NataliaLoginova mentioned this issue Oct 22, 2024
Merged
9 tasks
@NataliaLoginova
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Collaborator

This issue was solved in PR #5181 - getKet duplicates items when macro molucules are use

@Zhirnoff
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Zhirnoff commented Nov 8, 2024

Tested. Bug fixed.
2024-11-08_10h47_28

Desktop:

  • OS: Windows 11
  • Browser Chrome
  • Version 128.0.6613.120 (Official Build) (64-bit)

Ketcher version
[Version 2.27.0-rc.1]
Indigo version
[Version 1.26.0-rc.1]

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@aproskurnov aproskurnov

Labels
bug Customer Feedback Priority: High
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Milestone
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7 participants
@aproskurnov @doktordirk @NataliaLoginova @rrodionov91 @AlexeyGirin @matejaivosevic @Zhirnoff