Patch/sdg refine #169
Merged
Patch/sdg refine #169
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
… first bond did not always contain the first atom.
…buried") value allows us to prioritise atom placement and post layout modifications. The existing implementation had overflow meaning ranks weren't stable - otherwise it's simpler to canonical labelling.
… done through the JDK it looks like floating point coords get truncated. We are therefore better off rounding the coordinates ourself - I saw an improvement but still not perfect compared to a PDF/SVG displayed on the screen at the same scale..
|
Generally looks good to me. |
egonw
added a commit
that referenced
this pull request
Oct 24, 2015
Looks useful. I could not merge it immediately, not realizing it's just push button via the website...
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Refinement algorithm for improving a structure layout. Replaces the OverlapResolver (which was currently disabled but provided similar functionality) with a relatively standard algorithm for rotating, bending, and stretching bonds.
Examples (also comparing to OverlapResolver)
Clark 06
From CDK doc (Nina's doc - https://docs.google.com/document/d/1HEBrAscm__sXSJxjV3fT5SfzMouEJdT5gz60S2xdwHQ)
US20020149010A1_42
CHEMBL590010
CHEMBL1077020 (my favourite)
Still some are still not ideal:
Helson 99, Fig 8d
This one is okay... but I'm not super happy
CHEMBL604989
Here the chain place points the substituents (away from the ring centre). In cyclophanes we should flip the spiro connected rings so larger parts are on the outside. However the bonds would still be pointing the wrong way so more patches needed elsewhere (hence not resolved for now).
Full Album:
https://goo.gl/photos/W4KDRpTYSfVRLkLLA