Molwitch chirality #332
Molwitch chirality #332
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The main issue here is just that we're re-loading and re-applying the parameters from the config whenever we are processing a structure. This is a problem for 2 reasons:
- It's unnecessary, we just need to call it once.
- It may not have been called in the right order. The renderer code doesn't use this stuff but still relies on these properties having been set in the past.
To remedy this we should add a new configuration class to read all chemical props, and then have the existing molwitchLoader class use that configuration class to apply params. That way it only happens once, it happens at the beginning, and it's future-proof to take any new parameter a molwitch implementation may allow without having to explicitly enumerate them.
| @@ -133,6 +146,30 @@ void instrument (StructureProcessorTask settings) { | |||
| Structure struc = settings.getStructure(); | |||
| Collection<Structure> components = settings.getComponents(); | |||
| Chemical mol = settings.getChemical().copy(); | |||
| if( maxUndefined !=null || complexityCutoff !=null ){ | |||
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This shouldn't be here ... it should be a global setting that happens when the application starts, since it's changing static settings once, right?
| @Slf4j | ||
| @Component | ||
| @Configuration | ||
| @ConfigurationProperties("gsrs.structure.processing") |
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I think we should just make a new class for this configuration, and make it so that it parses everything found under:
gsrs.structure.chemical.molwitch
into a Map<String, Object>. That is:
@ConfigurationProperties("gsrs.structure.chemical")
@Data
public class ChemicalParsingProperties
...
private Map<String,Object> molwitch;
And then in MolwitchLoader add a ChemicalParsingProperties autowired bean and then, at the end of invokeMolwitch do:
...
Map<String,Object> params = chemProps.getMolwitch();
ChemicalImplFactory defFAC = ImplUtil.getChemicalImplFactory();
defFAC.applyParameters(params);
Then we'll only be calling this once on load, and it'll be ready for everything, including the renderer (which may bypass the structure processor).
and MolwitchLoader
| @@ -27,6 +27,8 @@ public class StructureProcessor { | |||
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| private StructureHasher hasher; | |||
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| private List<String> processedFactoryClasses = new ArrayList<>(); | |||
In StructureProcessor, look for parameters that can be passed indirectly to a molwitch ChemicalImpl object