Handle alignments without maps

[Waztom]

@tdudgeon thinks this, alignment without maps, is the only thing fundamentally missing.

@ConorFWild will fix this.

Policy: fail unless user updates configuration to either process or ignore the offending datasets

[ConorFWild]

@kaliif @tdudgeon @Waztom

Changes merged in 791726b and 9a68494 and tested!

Can close issue one we verify this is handled by the upload and database correctly. This sounds like an @tdudgeon and @kaliif problem?

[tdudgeon]

That seems to work for the lb32627-65 data, but I encountered a further edge case. For XX01ZVNS2B-x1162 the ligand in the PDB is incompatible with the one in the CIF file.

PDB:

HETATM 2272  O4 CLIG B 301     -12.027   4.755 -16.642  0.20 32.76           O
ANISOU 2272  O4 CLIG B 301     4840   4814   2792   1021    650    506       O
HETATM 2273  O4 DLIG B 301     -12.027   4.755 -16.642  0.20 32.76           O
ANISOU 2273  O4 DLIG B 301     4840   4814   2792   1021    650    506       O
HETATM 2274  C7 CLIG B 301     -10.907   5.051 -15.839  0.20 32.50           C
ANISOU 2274  C7 CLIG B 301     4776   4794   2775    968    672    547       C
HETATM 2275  C7 DLIG B 301     -10.907   5.051 -15.839  0.20 32.50           C
ANISOU 2275  C7 DLIG B 301     4776   4794   2775    968    672    547       C
HETATM 2276  O5 CLIG B 301     -10.975   5.428 -14.685  0.20 30.91           O
ANISOU 2276  O5 CLIG B 301     4566   4562   2617    886    674    531       O
HETATM 2277  O5 DLIG B 301     -10.975   5.428 -14.685  0.20 30.91           O
ANISOU 2277  O5 DLIG B 301     4566   4562   2617    886    674    531       O
HETATM 2278  C8 CLIG B 301      -9.671   4.868 -16.625  0.20 32.73           C
ANISOU 2278  C8 CLIG B 301     4786   4886   2761   1029    692    611       C
HETATM 2279  C8 DLIG B 301      -9.671   4.868 -16.625  0.20 32.73           C
ANISOU 2279  C8 DLIG B 301     4786   4886   2761   1029    692    611       C
HETATM 2280  C9 CLIG B 301      -9.721   4.347 -17.912  0.20 33.12           C
ANISOU 2280  C9 CLIG B 301     4853   4974   2756   1128    686    618       C
HETATM 2281  C9 DLIG B 301      -9.721   4.347 -17.912  0.20 33.12           C
ANISOU 2281  C9 DLIG B 301     4853   4974   2756   1128    686    618       C
HETATM 2282  C10CLIG B 301      -8.558   4.206 -18.649  0.20 33.49           C
ANISOU 2282  C10CLIG B 301     4878   5088   2758   1189    709    678       C
HETATM 2283  C10DLIG B 301      -8.558   4.206 -18.649  0.20 33.49           C
ANISOU 2283  C10DLIG B 301     4878   5088   2758   1189    709    678       C
HETATM 2284  C11CLIG B 301      -7.349   4.590 -18.110  0.20 33.70           C
ANISOU 2284  C11CLIG B 301     4863   5141   2799   1147    737    734       C
HETATM 2285  C11DLIG B 301      -7.349   4.590 -18.110  0.20 33.70           C
ANISOU 2285  C11DLIG B 301     4863   5141   2799   1147    737    734       C
HETATM 2286  C12CLIG B 301      -7.295   5.119 -16.838  0.20 33.36           C
ANISOU 2286  C12CLIG B 301     4805   5054   2816   1047    739    728       C
HETATM 2287  C12DLIG B 301      -7.295   5.119 -16.838  0.20 33.36           C
ANISOU 2287  C12DLIG B 301     4805   5054   2816   1047    739    728       C
HETATM 2288  C13CLIG B 301      -8.453   5.262 -16.094  0.20 33.02           C
ANISOU 2288  C13CLIG B 301     4787   4947   2812    990    717    665       C
HETATM 2289  C13DLIG B 301      -8.453   5.262 -16.094  0.20 33.02           C
ANISOU 2289  C13DLIG B 301     4787   4947   2812    990    717    665       C

CIF:

loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
LIG     C1      C       CH3     0       6.954       0.668       2.395       
LIG     O1      O       O2      0       5.542       0.567       2.569       
LIG     C2      C       CR6     0       4.759       0.050       1.566       
LIG     C3      C       CR16    0       3.392       0.111       1.813       
LIG     C4      C       CR16    0       2.490       -0.378      0.886       
LIG     C5      C       CR6     0       2.957       -0.931      -0.296      
LIG     S1      S       S3      0       1.823       -1.551      -1.474      
LIG     O2      O       O       0       1.298       -2.797      -1.028      
LIG     O3      O       O       0       2.360       -1.413      -2.784      
LIG     N1      N       NR5     0       0.530       -0.461      -1.412      
LIG     N2      N       NRD5    0       -0.665      -0.812      -0.818      
LIG     C6      C       CR5     0       -1.464      0.238       -0.934      
LIG     O4      O       O2      0       -2.730      0.262       -0.457      
LIG     C7      C       C       0       -3.667      -0.690      -0.792      
LIG     O5      O       O       0       -3.389      -1.699      -1.363      
LIG     C8      C       CR6     0       -5.023      -0.300      -0.338      
LIG     C9      C       CR16    0       -5.496      1.001       -0.485      
LIG     C10     C       CR16    0       -6.774      1.333       -0.057      
LIG     C11     C       CR16    0       -7.589      0.375       0.509       
LIG     C12     C       CR16    0       -7.132      -0.920      0.653       
LIG     C13     C       CR16    0       -5.855      -1.260      0.230       
LIG     C14     C       CR15    0       -0.802      1.282       -1.571      
LIG     C15     C       CR5     0       0.462       0.818       -1.867      
LIG     N3      N       NH2     0       1.475       1.472       -2.494      
LIG     C16     C       CR16    0       4.316       -1.000      -0.556      
LIG     C17     C       CR16    0       5.216       -0.512      0.373       
LIG     H1      H       H       0       7.147       1.201       1.607       
LIG     H2      H       H       0       7.332       -0.220      2.288       
LIG     H3      H       H       0       7.345       1.093       3.176       
LIG     H4      H       H       0       3.078       0.485       2.613       
LIG     H5      H       H       0       1.570       -0.333      1.064       
LIG     H6      H       H       0       -4.947      1.661       -0.870      
LIG     H7      H       H       0       -7.086      2.217       -0.156      
LIG     H8      H       H       0       -8.458      0.604       0.799       
LIG     H9      H       H       0       -7.688      -1.575      1.041       
LIG     H10     H       H       0       -5.550      -2.145      0.331       
LIG     H11     H       H       0       -1.128      2.142       -1.777      
LIG     H12     H       H       0       2.181       1.029       -2.758      
LIG     H13     H       H       0       1.420       2.334       -2.627      
LIG     H14     H       H       0       4.631       -1.376      -1.357      
LIG     H15     H       H       0       6.134       -0.560      0.193

Look, for instance, the CIF contains 2 nitrogens, the pdb none.

The code has been adapted to handle this and report as a warning (no ligand files are generated in the output). Clearly this is a problem with the input data.

@kaliif is going to try to upload this data.

[tdudgeon]

I notice that @ConorFWild changed the error handling when panddas are missing so that you now get a nasty stacktrace rather than report a list of the errors. Personally I prefer not to scare the users that the world has blown up, just to guide them trough what went wrong.

[ConorFWild]

So, I'm inclined to say that both of these should be failure states that a user needs to explicitly handle in the config in order to get valid output/have the program proceed further. @phraenquex thoughts?

Also inclined to say we wrap running in a try block that will prevent raw stack traces and format known errors nicely.

[phraenquex]

@ConorFWild yes, the user should be made to explicitly declare the exceptions in the config.

I'm conscious that hanldling all corner cases would need a pretty extensive ontology. The full ontology is out of scope, stick to the exceptions you know about.

[ConorFWild]

In this case for purple release handling the error prettily is not a priority and we can close? @tdudgeon @phraenquex

[phraenquex]

@ConorFWild good point - it's covered by #1224 . So yes, in that case you can move this to Dev Done swimlane.