Ligands parsed by LigandParserService and PDB HETID show wrong connectivity

singa-bio / singa

:leaves: SiNGA (Simulation of Natural Systems using Graph Automata) is an open-source library containing tools especially for structural bioinformatics and systems biology.

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Ligands parsed by LigandParserService and PDB HETID show wrong connectivity #92

Closed fkaiserbio closed 4 years ago

fkaiserbio commented 4 years ago

steps to reproduce:

LeafSubstructure<?> atp = LigandParserService.parseLeafSubstructureById("ATP");
MoleculeGraph moleculeGraph = MoleculeGraphs.createMoleculeGraphFromStructure((OakLeafSubstructure<?>) atp);

open molecule in GraphViewerPlayground.java
several atom connections missing

cleberecht commented 4 years ago

commit aecbe34 should fix the problem

seems that pdb has changed something in their ligand cif format let me know if this works for you

fkaiserbio commented 4 years ago

connectivity restored, thank you!