Inchi mismatch error in QM

[connie]

Running into the following inchi mismatch error between log file and geometry for the second time now. Note that the only difference between the inchi's is the final 3 in the string. Seems like they are actually the same molecule. The geometry inchi is the accurate one, however.

Also we do not yet have methods for inchi key collisions..

1 radicals on C12(C(C)(C)OC1CC(C2)(C)OO)CO[O] exceeds limit of 0. Using HBI method.
Output file /home/connieg/QMfiles/LVZYJRSIGFYMQJ-UHFFFAOYSA.out does not (yet) exist.
Trying MopacMolPM3 attempt 1 of 10 on molecule C12(C(C)(C)OC1CC(C2)(C)OO)COO.
InChI in log file (InChI=1S/C10H18O5/c1-8(2)10(6-13-11)5-9(3,15-12)4-7(10)14-8/h7,11-12H,4-6H2,1-3H) didn't match that in geometry (InChI=1S/C10H18O5/c1-8(2)10(6-13-11)5-9(3,15-12)4-7(10)14-8/h7,11-12H,4-6H2,1-3H3).
InChI in log file (InChI=1S/C10H18O5/c1-8(2)10(6-13-11)5-9(3,15-12)4-7(10)14-8/h7,11-12H,4-6H2,1-3H) didn't match that in geometry (InChI=1S/C10H18O5/c1-8(2)10(6-13-11)5-9(3,15-12)4-7(10)14-8/h7,11-12H,4-6H2,1-3H3).
Traceback (most recent call last):
  File "/home/connieg/Code/RMG-Py/rmg.py", line 136, in <module>
    cProfile.runctx(command, global_vars, local_vars, stats_file)
  File "/usr/lib/python2.6/cProfile.py", line 49, in runctx
    prof = prof.runctx(statement, globals, locals)
  File "/usr/lib/python2.6/cProfile.py", line 140, in runctx
    exec cmd in globals, locals
  File "<string>", line 1, in <module>
  File "/home/connieg/Code/RMG-Py/rmgpy/rmg/main.py", line 400, in execute
    self.reactionModel.enlarge(objectsToEnlarge)
  File "/home/connieg/Code/RMG-Py/rmgpy/rmg/model.py", line 698, in enlarge
    spec.generateThermoData(database, quantumMechanics=self.quantumMechanics)
  File "/home/connieg/Code/RMG-Py/rmgpy/rmg/model.py", line 124, in generateThermoData
    tdata = database.thermo.estimateRadicalThermoViaHBI(molecule, quantumMechanics.getThermoData)
  File "/home/connieg/Code/RMG-Py/rmgpy/data/thermo.py", line 788, in estimateRadicalThermoViaHBI
    thermoData = stableThermoEstimator(saturatedStruct)
  File "/home/connieg/Code/RMG-Py/rmgpy/qm/main.py", line 147, in getThermoData
    thermo0 = qm_molecule_calculator.generateThermoData()
  File "/home/connieg/Code/RMG-Py/rmgpy/qm/molecule.py", line 252, in generateThermoData
    self.qmData = self.generateQMData()
  File "/home/connieg/Code/RMG-Py/rmgpy/qm/mopac.py", line 198, in generateQMData
    success = self.run()
  File "/home/connieg/Code/RMG-Py/rmgpy/qm/mopac.py", line 68, in run
    return self.verifyOutputFile()
  File "/home/connieg/Code/RMG-Py/rmgpy/qm/mopac.py", line 133, in verifyOutputFile
    return self.checkForInChiKeyCollision(logFileInChI) # Not yet implemented!
AttributeError: MopacMolPM3 instance has no attribute 'checkForInChiKeyCollision'

[rwest]

Any chance the log file was made before the switch to RDKit, and is being checked after?

[connie]

Yes this was still on the main branch. Will try with rdkit branch then.

[rwest]

I think your problem is fixed by 87a7ce9c720a9b28784c895332e43564535de784, but I will leave the issue open for now as a reminder to implement more rigorous checking (or explicitly decide not to).

[connie]

Still running into the same problem. The log file omits an H in the InChI. But I think it is the correct molecule. https://github.com/GreenGroup/RMG-Py/commit/87a7ce9c720a9b28784c895332e43564535de784 will still fail on this.

Warning: InChI in log file (InChI=1S/C10H18O5/c1-10(11,7-4-8-13-12)15-14-9-5-2-3-6-9/h4,7,9,11-12H,2-3,5-6,82,1H3) didn't match that in geometry (InChI=1S/C10H18O5/c1-10(11,7-4-8-13-12)15-14-9-5-2-3-6-9/h4,7,9,11-12H,2-3,5-6,8H2,1H3). Traceback (most recent call last): File "/files/RMG-Py/rmg.py", line 144, in rmg.execute(args) File "/files/RMG-Py/rmgpy/rmg/main.py", line 329, in execute self.initialize(args) File "/files/RMG-Py/rmgpy/rmg/main.py", line 317, in initialize self.reactionModel.enlarge([spec for spec in self.initialSpecies if spec.reactive]) File "/files/RMG-Py/rmgpy/rmg/model.py", line 698, in enlarge spec.generateThermoData(database, quantumMechanics=self.quantumMechanics) File "/files/RMG-Py/rmgpy/rmg/model.py", line 124, in generateThermoData tdata = database.thermo.estimateRadicalThermoViaHBI(molecule, quantumMechanics.getThermoData) File "/files/RMG-Py/rmgpy/data/thermo.py", line 788, in estimateRadicalThermoViaHBI thermoData = stableThermoEstimator(saturatedStruct) File "/files/RMG-Py/rmgpy/qm/main.py", line 147, in getThermoData thermo0 = qm_molecule_calculator.generateThermoData() File "/files/RMG-Py/rmgpy/qm/molecule.py", line 221, in generateThermoData self.qmData = self.generateQMData() File "/files/RMG-Py/rmgpy/qm/mopac.py", line 208, in generateQMData success = self.run() File "/files/RMG-Py/rmgpy/qm/mopac.py", line 67, in run return self.verifyOutputFile() File "/files/RMG-Py/rmgpy/qm/mopac.py", line 134, in verifyOutputFile return self.checkForInChiKeyCollision(logFileInChI) # Not yet implemented! AttributeError: MopacMolPM3 instance has no attribute 'checkForInChiKeyCollision'

[rwest]

Is the log file really just missing that one character? Why on earth would it? It isn't interpreted by MOPAC/GAUSSIAN, just read in and spat out!

Either MOPAC/Gaussian is deleting a character (string too long? Split across lines? Utter bizarreness)...

Or the log file dates from a previous job when we generated InChIs without a missing H (via OB) and are comparing it with a newly created one (via RDKit).

Could it be the latter? Can you figure out a test?

...or it's something else :-D

[connie]

I believe that MOPAC output file is giving the incorrect inchi- might be an internal MOPAC problem. The one from the geometry must be from RDKit(?) and it's the correct one- I checked using the website.

It's not an Openbabel problem because I just ran it fresh with the latest RMG.

In fact, the .mop file contains the correct inchi, but then the .out file contains the one missing the H!

[rwest]

Ok. What happens if you replace it with a string like 1234567890123456790... ? Does MOPAC delete the Nth character or is it something special about that ,8H2, ?

[connie]

There is nothing special about ,8H2, MOPAC appears to be removing the 81th character exactly in the output log file.

Tried a .mop file with this input: abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ1234567890thisisatestformopacwillitwork

Got this in the output (missing the 'c' in mopac): abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ1234567890thisisatestformopawillitwork

[connie]

Perhaps we can allow matching for the first 80 characters if the log file inchi happens to be longer?

[connie]

In any case, the checkForInChiKeyCollision function is missing in both Gaussian and Mopac classes. It appears in QMVerifier (but this class doesn't seem to be used anywhere- was it intended to be a parent class?).