epam / epam/Indigo

Molecule rendering overlaps

Open
#758 2 comments 0 reactions 0 assignees View on GitHub
Dominant language
C++
Stars
406
Forks
134
Avg merge
2d 11h
Merged PRs (30d)
24

Description

**Steps to Reproduce**
While rendering SMILES from list attached overlapped substructures and wrong turns appear.
For example:
`c1ccccc1Oc1ccccc1F(C1C=CC=C2C=CC=CC=12)N(C1C=CC=C2C=CC=CC=12)Oc1ccccc1Br(C1C=CC=C2C=CC=CC=12)P[C-]BC1CCCC1Cl(C1C=CC=C2C=CC=CC=12)O`

`NC1CCCCC1[SiH2]C1CCCCC1PC1CCCC1CBrBrC1CCCCC1BNC1CCCCC1F[Br+]C1CCCC1`

For Indigo Service:
```bash
curl -X POST "http://localhost:8002/v2/indigo/render" -H "accept: application/json" -H "Content-Type: application/json" -d "{ \"output_format\": \"image/png\", \"struct\": \"c1ccccc1Oc1ccccc1F(C1C=CC=C2C=CC=CC=12)N(C1C=CC=C2C=CC=CC=12)Oc1ccccc1Br(C1C=CC=C2C=CC=CC=12)P[C-]BC1CCCC1Cl(C1C=CC=C2C=CC=CC=12)O\"}"
```

```bash
curl -X POST "http://localhost:8002/v2/indigo/render" -H "accept: application/json" -H "Content-Type: application/json" -d "{ \"output_format\": \"image/png\", \"struct\": \"NC1CCCCC1[SiH2]C1CCCCC1PC1CCCC1CBrBrC1CCCCC1BNC1CCCCC1F[Br+]C1CCCC1\"}"
```

**Expected behavior**
Rendered images without overlapping structures.

**Actual behavior**
![cfa7370e-4e22-4d7e-8bed-d2f3dfce798b](https://user-images.githubusercontent.com/104769439/172387563-1874aac0-0142-4882-80f8-f5de61f234dd.png)
![ba0acf38-5224-44ba-b791-729824c223b8](https://user-images.githubusercontent.com/104769439/172387585-4a7ac841-0049-42b6-8464-fce8adb5c909.png)

**Attachments**
[rendering_problem_smiles.txt](https://github.com/epam/Indigo/files/8853412/rendering_problem_smiles.txt)

**Indigo/Bingo version**

indigo_version: 1.7.0.44-gd16d27b64-x86_64-linux-gnu-11.2.1

Contributor guide

No contributing guide indexed for this repository

Assessment

This issue has not been assessed yet.

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.