Flexicanvas cuts off bottom of reaction

[DavidACosgrove]

Drawing a reaction in a flexicanvas cuts off the bottom of the image:

To Reproduce

TEST_CASE("") {
  const char *rxnBlock = R"RXN($RXN

      Mrv1920  090120231611

  3  1
$MOL

  Mrv1920 09012316112D

  1  0  0  0  0  0            999 V2000
  -12.3227   -0.2785    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
M  END
$MOL

  Mrv1920 09012316112D

 11 11  0  0  0  0            999 V2000
   -6.0796   -0.5503    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -6.7352   -0.0493    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6291    0.7688    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4967   -0.3666    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.1522    0.1344    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.9137   -0.1829    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.5692    0.3181    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.3307    0.0008    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.4370   -0.8173    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.7813   -1.3182    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.0199   -1.0009    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  4  0  0  0  0
  7  8  4  0  0  0  0
  8  9  4  0  0  0  0
  9 10  4  0  0  0  0
 10 11  4  0  0  0  0
 11  6  4  0  0  0  0
M  END
$MOL

  Mrv1920 09012316112D

 10 10  0  0  0  0            999 V2000
   -3.2982    1.9786    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4043    1.1605    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7488    0.6596    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9872    0.9767    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8547   -0.1585    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1992   -0.6594    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3055   -1.4777    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0669   -1.7949    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7225   -1.2939    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6163   -0.4759    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10  5  1  0  0  0  0
M  END
$MOL

  Mrv1920 09012316112D

 20 21  0  0  0  0            999 V2000
    7.3862    1.9786    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2800    1.1605    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.9356    0.6596    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.6971    0.9768    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.8294   -0.1586    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.4850   -0.6595    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.3789   -1.4777    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6173   -1.7950    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9619   -1.2939    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0679   -0.4758    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.4124    0.0252    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5186    0.8432    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.6509   -0.2920    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9954    0.2089    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2337   -0.1084    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5784    0.3926    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8166    0.0753    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7107   -0.7427    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3661   -1.2438    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1276   -0.9266    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 11 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  4  0  0  0  0
 16 17  4  0  0  0  0
 17 18  4  0  0  0  0
 18 19  4  0  0  0  0
 19 20  4  0  0  0  0
 10  5  1  0  0  0  0
 20 15  4  0  0  0  0
M  END)RXN";

  std::string nameBase = "testGithub6683_";
  std::unique_ptr<ChemicalReaction> rxn(RxnBlockToChemicalReaction(rxnBlock));
  MolDraw2DSVG drawer(-1, -1);
  drawer.drawReaction(*rxn);
  drawer.finishDrawing();
  std::string text = drawer.getDrawingText();
  std::ofstream outs((nameBase + "1.svg").c_str());
  outs << text;
  outs.close();
}

Expected behavior
I would have hoped to have seen the bottom of the piperidine.

Screenshots
If applicable, add screenshots to help explain your problem.

Configuration (please complete the following information):

• RDKit version: current master branc
• OS: macOS

Additional context
This is a simpler version of the display of the reaction @paconius is using in #6683. This may or may not be the same bug, but clearly needs fixing. Looking into it now.

[paconius]

Hi David, I'm guessing that the clipping is not related to the svg issue in the orig. discussion based on the following. I've seen a number of cases where the image is clipped. usually on the left or right, but sometimes on the top/bottom as you observed. These clipping cases can be "fixed" by increasing the 'padding' parameter in draw options. However, no value of the padding parameter seems to be able to fix the negative widths in the SVG.
I could be wrong about this, as I am just speaking from limited observations.

[DavidACosgrove]

I think you’re right, now I’ve fixed it, but we can always hope! I’ll look at the other one early next week. It’s clearly a bug- whatever is going on, it should never produce negative values for width and height.

[paconius]

Here are a couple more rxn blocks that produce clipped svg images. Perhaps useful for testing your fix for the clipping problem. FIrst one is clipped on the left side. Second one is clipped on the right side. The images show the clipping produced when the padding parameter is left unchanged.

$RXN

      Mrv1920  090220231847

  2  1
$MOL

  Mrv1920 09022318472D          

  2  1  0  0  0  0            999 V2000
   -7.4817   -0.2130    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6567   -0.2130    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
M  END
$MOL

  Mrv1920 09022318472D          

  9  8  0  0  0  0            999 V2000
   -3.3781    2.1354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5235    1.3233    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2996    1.0435    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8932    0.7914    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0387   -0.0206    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7812   -0.3803    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8567   -1.3430    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4672   -0.6157    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6500   -0.5031    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8  5  1  0  0  0  0
M  END
$MOL

  Mrv1920 09022318472D          

  8  8  0  0  0  0            999 V2000
    5.5359   -0.2650    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3537    1.0574    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6115    0.6978    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7993    0.8433    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4102    0.1159    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.9815   -0.4790    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.7240   -0.1195    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5929    0.0033    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  3  1  0  0  0  0
  3  4  4  0  0  0  0
  4  5  4  0  0  0  0
  5  6  4  0  0  0  0
  6  7  4  0  0  0  0
  7  1  1  0  0  0  0
  7  3  4  0  0  0  0
  5  8  1  0  0  0  0
M  END

[paconius]

$RXN

      Mrv1920  090220231850

  1  2
$MOL

  Mrv1920 09022318502D          

 20 22  0  0  0  0            999 V2000
   -2.4533   -0.5079    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0179    0.0939    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8212   -0.0941    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0600   -0.8837    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8633   -1.0715    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4277   -0.4698    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2311   -0.6577    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7954   -0.0558    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5987   -0.2436    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.8377   -1.0333    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2734   -1.6351    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4701   -1.4473    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1888    0.3199    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3855    0.5077    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1465    1.2974    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7110    1.8993    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5142    1.7114    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7532    0.9218    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4957   -1.4854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6923   -1.2975    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  4  0  0  0  0
  2  3  4  0  0  0  0
  3  4  4  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  3  0  0  0
  6  7  1  0  0  0  0
  7  8  4  0  0  0  0
  8  9  4  0  0  0  0
  9 10  4  0  0  0  0
 10 11  4  0  0  0  0
 11 12  4  0  0  0  0
  6 13  1  0  0  0  0
 13 14  4  0  0  0  0
 14 15  4  0  0  0  0
 15 16  4  0  0  0  0
 16 17  4  0  0  0  0
 17 18  4  0  0  0  0
  4 19  4  0  0  0  0
 19 20  4  0  0  0  0
 20  1  4  0  0  0  0
 12  7  4  0  0  0  0
 18 13  4  0  0  0  0
M  END
$MOL

  Mrv1920 09022318502D          

  7  7  0  0  0  0            999 V2000
    5.5920    0.3948    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0277    0.9966    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2244    0.8087    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9855    0.0191    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1821   -0.1689    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.5499   -0.5827    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3531   -0.3949    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  4  0  0  0  0
  2  3  4  0  0  0  0
  3  4  4  0  0  0  0
  4  5  1  0  0  0  0
  4  6  4  0  0  0  0
  6  7  4  0  0  0  0
  7  1  4  0  0  0  0
M  END
$MOL

  Mrv1920 09022318502D          

  1  0  0  0  0  0            999 V2000
    8.3990    0.0732    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
M  END

[paconius]

@DavidACosgrove : I see your fixes were merged yesterday. Thanks for your help with this. I can further test and provide feedback whenever the next rdkit-dev becomes avaialble. Thanks again!