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Feature/advanced sgroup rendering #151

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wants to merge 21 commits into from
Closed

Feature/advanced sgroup rendering #151

wants to merge 21 commits into from

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johnmay
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@johnmay johnmay commented Sep 9, 2015

Adds much better rendering - for example >2 brackets and their direction, multiple groups, and mixtures.

Still need to add data display but didn't to figure how that works first.

efficientbits.blogspot.co.uk/2015/09/bringing-molfile-sgroups-to-cdk-demo.html

@johnmay
General mechanism for hidding certain parts of the depiction.
294ddc8
@johnmay
Render abbreviaitons with zero or one attachment. We do this by hidin…
3177316 
…g parts we don't want to show, remapping some atom symbols or adding a label (for zero attach abbreviations).
@johnmay
Roundtrip parent atom list for display "multiple" groups.
904e2da
@johnmay
To display multiple groups correctly we need to hide certain atoms an…
5e495f5 
…d bonds. To hide atoms we take the set complement of the parent atom list in the atom list.
@johnmay
Document the display shortcut rendering methods.
5475014
@johnmay
Component ordering.
5446035
@johnmay
Rendering of mixtures and their components.
c44f05d
@johnmay
Additional Sgroup type - modification.
56ed7f2
@johnmay
Correct subscript display for polymer brackets.
07f9b0f
@johnmay
Remove NaN condition - this was being produced when atoms were on top…
a5d088c 
… of each other but actually for Sgroups we want these (carbons) to be hidden.
@johnmay
Sensible defaults for SRU display.
d0efb68
@johnmay
Improved bracket display - now displays cases when more than one brac…
046cc21 
…ket and they always point the right way.
@johnmay
Better median bond length when atoms are placed on top of each other …
bacacea 
…as in multiple group Sgroups.
@johnmay
Cleanup imports and correct name of modified polymer type.
6d08eca
@johnmay
Simplified remapped label generation.
a5d31ee
@johnmay
Utility to class to help with reversing and formatting abbrevation la…
516c21e 
…bels.
@johnmay
Use constants for style as having italics is also nice.
dfc60c4
@johnmay
Rendering of formatted abbreviation labels.
60fb8ae
@johnmay
Only certain chemical prefixes are italicised.
f181eb9
@johnmay
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johnmay commented Sep 11, 2015

Added some more commits for formatting labels nicely. All done now.

@johnmay
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johnmay commented Sep 11, 2015

Okay there was one more.

Code to generate them will be in a separate patch but here's a test file with some examples to try,

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M  STY  2   1 SUP   2 SUP
M  SAL   1  6   4   1   5   2   6   3
M  SBL   1  1   2
M  SMT   1 Ph
M  SAL   2  3  18  16  17
M  SBL   2  1  18
M  SMT   2 COOH
M  END
$$$$
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M  STY  6   1 SUP   2 SUP   3 SUP   4 SUP   5 SUP   6 SUP
M  SAL   1  4   1  51  50  49
M  SBL   1  1   1
M  SMT   1 OAc
M  SAL   2  4  16  46  48  47
M  SBL   2  1  20
M  SMT   2 OAc
M  SAL   3  4  55  54  56  53
M  SBL   3  1  57
M  SMT   3 OAc
M  SAL   4  4  59  58  61  60
M  SBL   4  1  61
M  SMT   4 OAc
M  SAL   5  4  70  63  64  65
M  SBL   5  1  67
M  SMT   5 OAc
M  SAL   6  4  68  71  69  67
M  SBL   6  1  71
M  SMT   6 OAc
M  END
$$$$
CHEBI:3756
  CDK     0911151902

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    4.5882   -5.1641    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7977   -4.0418    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4045   -4.3598    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0093   -3.7986    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0 
  3  1  2  0  0  0  0 
  7  1  1  0  0  0  0 
  5  2  2  0  0  0  0 
  8  2  1  0  0  0  0 
 13  3  1  0  0  0  0 
  9  4  1  0  0  0  0 
 11  4  1  0  0  0  0 
 12  4  2  0  0  0  0 
  6  5  1  0  0  0  0 
 15  5  1  0  0  0  0 
 10  6  1  0  0  0  0 
 14  7  2  0  0  0  0 
 19  7  1  0  0  0  0 
  9  8  2  0  0  0  0 
 16  9  1  0  0  0  0 
 13 10  1  0  0  0  0 
 17 10  2  0  0  0  0 
 18 14  1  0  0  0  0 
 20 14  1  0  0  0  0 
 16 15  2  0  0  0  0 
 21 19  2  0  0  0  0 
 22 20  2  0  0  0  0 
 22 21  1  0  0  0  0 
M  CHG  1   4   1
M  CHG  1  11  -1
M  STY  1   1 SUP
M  SAL   1  3  11   4  12
M  SBL   1  1   7
M  SMT   1 NO2
M  END
$$$$
CHEBI:15597
  CDK     0911151902

 14 13  0  0  0  0  0  0  0  0999 V2000
   11.6783  -15.6796    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.8301  -16.3446    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   13.9819  -17.0096    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.1651  -17.4964    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.8301  -18.6482    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.1601  -18.6482    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.8251  -19.8000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.8251  -17.4964    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.4951  -15.1927    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.1651  -19.8000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.8351  -18.4700    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.8351  -21.1300    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.8351  -19.8000    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    9.5051  -19.8000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0 
  3  2  2  0  0  0  0 
  4  2  1  0  0  0  0 
  5  4  1  0  0  0  0 
  6  5  1  0  0  0  0 
  7  6  1  0  0  0  0 
  8  6  2  0  0  0  0 
  9  2  1  0  0  0  0 
  5 10  1  1  0  0  0 
 12 13  1  0  0  0  0 
 11 13  1  0  0  0  0 
 14 13  2  0  0  0  0 
 10 13  1  0  0  0  0 
M  CHG  1   7  -1
M  CHG  1   9  -1
M  CHG  1  11  -1
M  CHG  1  12  -1
M  STY  3   1 SUP   2 SUP   3 SUP
M  SAL   1  3   7   8   6
M  SBL   1  1   5
M  SMT   1 COO-
M  SAL   2  5  13  14  10  11  12
M  SBL   2  1   9
M  SMT   2 OPO3-2
M  SAL   3  4   9   2   1   3
M  SBL   3  1   3
M  SMT   3 SO3-
M  END
$$$$

@egonw
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egonw commented Sep 12, 2015

A lot of code, but mostly internal. But looks good.

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egonw commented Sep 12, 2015

Applied and pushed.

@egonw egonw closed this Sep 12, 2015
@johnmay
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johnmay commented Sep 12, 2015

Thanks - yeah realising I needed the label reversing complicate things considerably.

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egonw commented Sep 13, 2015

There seem to be two more regressions: https://jenkins.bigcat.unimaas.nl/job/cdk/lastCompletedBuild/testReport/

org.openscience.cdk.io.MDLV2000WriterTest.sgroupParentAtomListRoundTrip
org.openscience.cdk.renderer.SymbolVisibilityTest.iupacCarbonCornerCase

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johnmay commented Sep 13, 2015

Darn - does travis not run the tests?

Regards,
John W May
john.wilkinsonmay@gmail.com

On 13 September 2015 at 07:51, Egon Willighagen notifications@github.com
wrote:

There seem to be two more regressions:
https://jenkins.bigcat.unimaas.nl/job/cdk/lastCompletedBuild/testReport/

org.openscience.cdk.io.MDLV2000WriterTest.sgroupParentAtomListRoundTrip
org.openscience.cdk.renderer.SymbolVisibilityTest.iupacCarbonCornerCase

—
Reply to this email directly or view it on GitHub
#151 (comment).

@johnmay johnmay deleted the feature/advanced-sgroup-rendering branch October 11, 2015 11:51
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