Partial 2D Layout #205
Partial 2D Layout #205
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…e 'fixing' positions of atoms/bonds.
…istic. Also we sort the ring set a few lines later on by bond count.
…een flipped! Otherwise it may be wrong.
…hod call without the Java bean style getter/setter.
… them out one by one.
…oblems (stoichiometry).
johnmay
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…placed, rather than changing the draw direction we just ensure the winding of the bridged atoms and the other share atoms is consistent.
… before refined by wedges should be done after.
…- adjust refinement to count bonds instead of atoms and allow these to moved out of the way.
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| addAngle = addAngle * direction; | ||
| atomPlacer.populatePolygonCorners(atomsToDraw, ringCenter, startAngle, addAngle, radius); | ||
| logger.debug("placeBridgedRing->atomsToPlace: " + AtomPlacer.listNumbers(molecule, atoms)); |
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You can use a comma instead of a "+" here, which makes the code run faster when debugging is turned of:
logger.debug("placeBridgedRing->atomsToPlace: ", AtomPlacer.listNumbers(molecule, atoms));
It saves a bit of time but mostly a unneeded extra String in that case.
(This can be cleaned up later... it won't block merging the patch in...)
(BTW, not sure how fast the listNumbers() call is, but if that's relatively slow, you can even wrap the logger.debug() calls in an if logger.debugEnabled() {} or so...)
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Will update, but not my code :-) .. but yes I know the API but guess this was written before the logger. Incidentally string concatenation isn't super bad, the byte code inserts a string builder.
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Oh, it's a bit hard to see what code in the rendering stack is not yours by now :)
But then please don't worry! Let me fix it then.
Allows laying out of a structure when part of it has already been laid out. Or to put it another way, we can set the coordinates of a substructure and lock those in place. This allows structures to be aligned to a common substructure. There's also a critical patch in there that i'll make a release for right away.
This one has been a long time coming and there might be a few more bits to round up but seems to be working well. Something we can do automatically is align reaction reactants/products, with a incorrect atom-atom mapping (i.e. automatic from MCS) it can look awful and can be disabled, it generally works well.
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