Molecule rendering overlaps

[kvarchenko]

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:

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\"}"

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

Attachments rendering_problem_smiles.txt

Indigo/Bingo version

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

[AlexanderSavelyev]

@kvarchenko please provide your code to reproduce

[kvarchenko]

For Indigo Service:

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\"}"

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\"}"