Fullerene and 3D molecules are not represented as 3D in the Miew 3D window

[AlexeyGirin]

Steps to Reproduce

1. Open CDX file from ChemDraw (Fullerene and 3D molecules)
   

2. Ketcher Mview
   

Actual behavior
Fullerene and 3D molecules are not represented as 3D in the Miew 3D window.
Kindly see pictures.
Task #4232

Expected behavior
Fullerene and 3D molecules should be represented as 3D in the Miew 3D window.

Attachments
FullereneCDX-example.zip

Environment details:
• OS: Windows 10 Pro (version 22H2) x64
• Browser: Сhrome
• Version: (122.0.6261.95) x64

Ketcher version 2.19.0 – rc.2
Indigo Toolkit
Version 1.18.0-rc.6.0-g98bf384e0-x86_64-linux-gnu-11.2.1

[AlexeyGirin]

Moved to Refined Backlog since no fix over 2 versions

[NataliaLoginova]

The issue was partially fixed in PR #3501 3d mol files appear as 2D in Miew

[AlexeyGirin]

Check with @even1024 if it is indigo problem and move to Indigo if yes
@NataliaLoginova will bring here her investigation results from ketcher side

[baranovdv]

If we open or save file in Ketcher, there are two different conversion flows(depends on file extension):

• .ket/.mol - Ketcher converts the file using its own methods
• Other extensions - Ketcher sends the contents of the file to the Indigo API to receive a file in .ket format

For example, there is 3D molecule from Chem3D app:

It’s saved in .cdx format
If we open this file in Ketcher. It will make API call to Indigo with such data:

format: "ket" options: { "smart-layout": true, "ignore-stereochemistry-errors": true, "mass-skip-error-on-pseudoatoms": false, "gross-formula-add-rsites": true, "aromatize-skip-superatoms": true, "dearomatize-on-load": false, "ignore-no-chiral-flag": false } struct: "base64::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"

Indigo responses with such .ket file:
{ "root": { "nodes": [ { "$ref": "mol0" } ] }, "mol0": { "type": "molecule", "atoms": [ { "label": "C", "location": [ 2.242333173751831, -2.685666561126709, 0.0 ] }, { "label": "O", "location": [ 3.424333333969116, -3.057999849319458, 0.0 ] }, { "label": "S", "location": [ 2.186000108718872, -1.0826666355133057, 0.0 ] }, { "label": "H", "location": [ 1.7910000085830689, -3.0293333530426027, 0.0 ] }, { "label": "H", "location": [ 1.7903332710266114, -3.0296666622161867, 0.0 ] }, { "label": "H", "location": [ 3.4160001277923586, -3.8906667232513429, 0.0 ] }, { "label": "H", "location":[ 1.0, -1.0, 0.0 ] } ], "bonds":[ { "type": 1, "atoms": [ 0, 1 ] }, { "type": 1, "atoms": [ 0, 2 ] }, { "type": 1, "atoms": [ 0, 3 ] }, { "type": 1, "atoms": [ 0, 4 ] }, { "type": 1, "atoms": [ 1, 5 ] }, { "type": 1, "atoms": [ 2, 6 ] } ] } }

All z-axis coordinates are zeroed, that causes 2D style drawing of molecule in Miew:

Correct .ket file should be like that:
{ "root": { "nodes": [ { "$ref": "mol0" } ], "connections": [], "templates": [] }, "mol0": { "type": "molecule", "atoms": [ { "label": "C", "location": [ 9.230228843914343, -5.76550492482726, 0.00017677686499614848 ] }, { "label": "O", "location": [ 10.412158963278591, -6.137797002509149, 0.00017677686499614848 ] }, { "label": "S", "location": [ 9.173748635548073, -4.162227147744692, 0.00017677686499614848 ] }, { "label": "H", "location": [ 8.77874073071418, -6.109070761947275, -0.803450851407495 ] }, { "label": "H", "location": [ 8.77829878855169, -6.10933592724477, 0.803450851407495 ] }, { "label": "H", "location": [ 10.403762062191275, -6.97032764820851, 0.00017677686499614848 ] }, { "label": "H", "location": [ 7.987841036721411, -4.079672351791491, 0.00017677686499614848 ] } ], "bonds": [ { "type": 1, "atoms": [ 0, 1 ] }, { "type": 1, "atoms": [ 0, 2 ] }, { "type": 1, "atoms": [ 0, 3 ] }, { "type": 1, "atoms": [ 0, 4 ] }, { "type": 1, "atoms": [ 1, 5 ] }, { "type": 1, "atoms": [ 2, 6 ] } ] } }

This .ket file Indigo converts to .cml correctly and Miew draws 3D molecule:

[AlexeyGirin]

Moved to Indigo - epam/Indigo#1944