Unidentifiable C++ Exception with FMCS

[proteneer]

Describe the bug
Using a custom AtomTyper and BondMCS parameters in conjunction results in an untranslated exception.

To Reproduce

mol_a = """338
                    3D
 Structure written by MMmdl.
 37 39  0  0  1  0            999 V2000
   27.6451    1.5396  -11.1263 O   0  0  0  0  0  0
   27.1573    0.3054  -11.6394 C   0  0  2  0  0  0
   26.5145    0.3811  -13.0370 C   0  0  0  0  0  0
   25.0296    0.6292  -12.8066 C   0  0  1  0  0  0
   24.8033   -0.0375  -11.4699 C   0  0  0  0  0  0
   26.0149   -0.2195  -10.7892 C   0  0  0  0  0  0
   26.0208   -0.7620   -9.4965 C   0  0  0  0  0  0
   24.8017   -1.0822   -8.8969 C   0  0  0  0  0  0
   23.6059   -0.9366   -9.5941 C   0  0  0  0  0  0
   23.6020   -0.4342  -10.9000 C   0  0  0  0  0  0
   22.4861   -0.2954  -11.6940 O   0  0  0  0  0  0
   21.2424   -0.5775  -11.1970 C   0  0  0  0  0  0
   20.6737   -1.8297  -11.4038 C   0  0  0  0  0  0
   19.4234   -2.1113  -10.8674 C   0  0  0  0  0  0
   18.8511   -3.3118  -11.0589 F   0  0  0  0  0  0
   18.7462   -1.1423  -10.1427 C   0  0  0  0  0  0
   19.2860    0.1245   -9.9701 C   0  0  0  0  0  0
   18.5760    1.1643   -9.2539 C   0  0  0  0  0  0
   20.5501    0.3903  -10.4736 C   0  0  0  0  0  0
   27.5283   -1.0639   -8.5710 S   0  0  0  0  0  0
   27.2110   -1.9989   -7.4925 O   0  0  0  0  0  0
   28.6000   -1.3708   -9.5178 O   0  0  0  0  0  0
   27.0777    1.2809  -13.8505 F   0  0  0  0  0  0
   18.0176    1.9927   -8.6784 N   0  0  0  0  0  0
   24.8400    1.9615  -12.6525 F   0  0  0  0  0  0
   26.6372   -0.7929  -13.6486 F   0  0  0  0  0  0
   27.9360    0.4657   -7.8636 N   0  0  0  0  0  0
   28.3611    1.8550  -11.6954 H   0  0  0  0  0  0
   27.9701   -0.4195  -11.7119 H   0  0  0  0  0  0
   24.3886    0.2707  -13.6271 H   0  0  0  0  0  0
   24.7736   -1.4789   -7.8939 H   0  0  0  0  0  0
   22.6914   -1.2459   -9.1138 H   0  0  0  0  0  0
   21.2074   -2.5951  -11.9425 H   0  0  0  0  0  0
   17.8099   -1.4198   -9.7083 H   0  0  0  0  0  0
   21.0016    1.3428  -10.2620 H   0  0  0  0  0  0
   27.2694    0.7696   -7.1547 H   0  0  0  0  0  0
   28.1746    1.1824   -8.5552 H   0  0  0  0  0  0
  1  2  1  0  0  0
  1 28  1  0  0  0
  2  3  1  0  0  0
  2  6  1  0  0  0
  2 29  1  0  0  0
  3  4  1  0  0  0
  3 23  1  0  0  0
  3 26  1  0  0  0
  4  5  1  0  0  0
  4 25  1  0  0  0
  4 30  1  0  0  0
  5  6  2  0  0  0
  5 10  1  0  0  0
  6  7  1  0  0  0
  7  8  2  0  0  0
  7 20  1  0  0  0
  8  9  1  0  0  0
  8 31  1  0  0  0
  9 10  2  0  0  0
  9 32  1  0  0  0
 10 11  1  0  0  0
 11 12  1  0  0  0
 12 13  2  0  0  0
 12 19  1  0  0  0
 13 14  1  0  0  0
 13 33  1  0  0  0
 14 15  1  0  0  0
 14 16  2  0  0  0
 16 17  1  0  0  0
 16 34  1  0  0  0
 17 18  1  0  0  0
 17 19  2  0  0  0
 18 24  3  0  0  0
 19 35  1  0  0  0
 20 21  2  0  0  0
 20 22  2  0  0  0
 20 27  1  0  0  0
 27 36  1  0  0  0
 27 37  1  0  0  0
M  END
$$$$"""

mol_b = """43
                    3D
 Structure written by MMmdl.
 34 35  0  0  1  0            999 V2000
   27.3206    0.2092  -11.5444 C   0  0  0  0  0  0
   24.8104   -0.0377  -11.5023 C   0  0  0  0  0  0
   26.0342   -0.2249  -10.8317 C   0  0  0  0  0  0
   26.0391   -0.7726   -9.5293 C   0  0  0  0  0  0
   24.8129   -1.0870   -8.9213 C   0  0  0  0  0  0
   23.6118   -0.9391   -9.6083 C   0  0  0  0  0  0
   23.6108   -0.4248  -10.9220 C   0  0  0  0  0  0
   22.4761   -0.3049  -11.6918 O   0  0  0  0  0  0
   21.2375   -0.5838  -11.1900 C   0  0  0  0  0  0
   20.6642   -1.8394  -11.3980 C   0  0  0  0  0  0
   19.4099   -2.1222  -10.8637 C   0  0  0  0  0  0
   18.7315   -1.1370  -10.1413 C   0  0  0  0  0  0
   19.2646    0.1136   -9.9710 C   0  0  0  0  0  0
   18.5795    1.1649   -9.2431 C   0  0  0  0  0  0
   20.5604    0.4002  -10.4797 C   0  0  0  0  0  0
   27.5401   -1.0912   -8.5545 S   0  0  0  0  0  0
   27.1859   -2.0084   -7.4841 O   0  0  0  0  0  0
   28.6206   -1.4509   -9.4586 O   0  0  0  0  0  0
   27.9627    0.5938   -7.7916 C   0  0  0  0  0  0
   27.7984    1.5671   -8.6677 F   0  0  0  0  0  0
   27.0861    0.7983   -6.7353 F   0  0  0  0  0  0
   24.7409    0.7017  -13.0762 Cl  0  0  0  0  0  0
   27.6879    1.5242  -11.1857 O   0  0  0  0  0  0
   18.0013    1.9953   -8.6849 N   0  0  0  0  0  0
   28.1313   -0.4949  -11.3851 H   0  0  0  0  0  0
   27.2003    0.1946  -12.6299 H   0  0  0  0  0  0
   24.7742   -1.4735   -7.9133 H   0  0  0  0  0  0
   22.6888   -1.2338   -9.1280 H   0  0  0  0  0  0
   21.2029   -2.5876  -11.9606 H   0  0  0  0  0  0
   18.9769   -3.1014  -11.0060 H   0  0  0  0  0  0
   17.7565   -1.3858   -9.7173 H   0  0  0  0  0  0
   21.0066    1.3603  -10.3264 H   0  0  0  0  0  0
   28.9730    0.5924   -7.4558 H   0  0  0  0  0  0
   28.4959    1.7705  -11.6621 H   0  0  0  0  0  0
  1  3  1  0  0  0
  1 23  1  0  0  0
  1 25  1  0  0  0
  1 26  1  0  0  0
  2  3  2  0  0  0
  2  7  1  0  0  0
  2 22  1  0  0  0
  3  4  1  0  0  0
  4  5  2  0  0  0
  4 16  1  0  0  0
  5  6  1  0  0  0
  5 27  1  0  0  0
  6  7  2  0  0  0
  6 28  1  0  0  0
  7  8  1  0  0  0
  8  9  1  0  0  0
  9 10  2  0  0  0
  9 15  1  0  0  0
 10 11  1  0  0  0
 10 29  1  0  0  0
 11 12  2  0  0  0
 11 30  1  0  0  0
 12 13  1  0  0  0
 12 31  1  0  0  0
 13 14  1  0  0  0
 13 15  2  0  0  0
 14 24  3  0  0  0
 15 32  1  0  0  0
 16 17  2  0  0  0
 16 18  2  0  0  0
 16 19  1  0  0  0
 19 20  1  0  0  0
 19 21  1  0  0  0
 19 33  1  0  0  0
 23 34  1  0  0  0
M  END
$$$$"""


import numpy as np
from rdkit import Chem
from rdkit.Chem import rdFMCS

romol_a = Chem.MolFromMolBlock(mol_a, removeHs=False)
romol_b = Chem.MolFromMolBlock(mol_b, removeHs=False)

class CompareDist(rdFMCS.MCSAtomCompare):

    def __init__(self, *args, **kwargs):
        super().__init__(*args, **kwargs)

    def compare(self, p, mol1, atom1, mol2, atom2):
        x_i = mol1.GetConformer(0).GetPositions()[atom1]
        x_j = mol2.GetConformer(0).GetPositions()[atom2]
        if np.linalg.norm(x_i-x_j) > 0.5:
            return False
        else:
            return True

# atom typer + complete rings fails
mcs_params = rdFMCS.MCSParameters()
mcs_params.AtomTyper = CompareDist()
mcs_params.BondCompareParameters.CompleteRingsOnly = 1 

# atom typer only works
# mcs_params = rdFMCS.MCSParameters()
# mcs_params.AtomTyper = CompareDist()
# mcs_params.BondCompareParameters.CompleteRingsOnly = 0 # Works

# complete rings only works
# mcs_params = rdFMCS.MCSParameters()
# mcs_params.BondCompareParameters.CompleteRingsOnly = 1 # Works

res = rdFMCS.FindMCS(
    [romol_a, romol_b],
    mcs_params
)

Expected behavior
CustomAtomTyper + CompleteRings fails with an untranslated exception but using either one alone proceeds without error.

Configuration (please complete the following information):

• RDKit version: 2020.03.01
• OS: Ubuntu 20.04
• Python version (if relevant): 3.6.7
• Are you using conda? yes
• If you are using conda, which channel did you install the rdkit from? rdkit

Additional context
Add any other context about the problem here.

[ptosco]

@proteneer Thanks for reporting this with a reproducible - I am on it.