Fatal error with explicit valence for nitrogen #91
Description
We're trying to build a mechanism for 2-nitrodiphenylamine:
species(
label='2NDPA',
reactive=True,
structure=adjacencyList(
"""
1 O u0 p3 c-1 {2,S}
2 N u0 p0 c+1 {1,S} {3,D} {4,S}
3 O u0 p2 c0 {2,D}
4 C u0 p0 c0 {2,S} {5,D} {9,S}
5 C u0 p0 c0 {4,D} {6,S} {17,S}
6 C u0 p0 c0 {5,S} {7,D} {18,S}
7 C u0 p0 c0 {6,D} {8,S} {19,S}
8 C u0 p0 c0 {7,S} {9,D} {20,S}
9 C u0 p0 c0 {4,S} {8,D} {10,S}
10 N u0 p1 c0 {9,S} {11,S} {21,S}
11 C u0 p0 c0 {10,S} {12,D} {16,S}
12 C u0 p0 c0 {11,D} {13,S} {22,S}
13 C u0 p0 c0 {12,S} {14,D} {23,S}
14 C u0 p0 c0 {13,D} {15,S} {24,S}
15 C u0 p0 c0 {14,S} {16,D} {25,S}
16 C u0 p0 c0 {11,S} {15,D} {26,S}
17 H u0 p0 c0 {5,S}
18 H u0 p0 c0 {6,S}
19 H u0 p0 c0 {7,S}
20 H u0 p0 c0 {8,S}
21 H u0 p0 c0 {10,S}
22 H u0 p0 c0 {12,S}
23 H u0 p0 c0 {13,S}
24 H u0 p0 c0 {14,S}
25 H u0 p0 c0 {15,S}
26 H u0 p0 c0 {16,S}
"""),
)
Once we comment out the forbidden structure "N_birad_singlet_2singleBonds", RMG-Py starts but then crashes with:
[15:01:43] Explicit valence for atom # 6 N, 4, is greater than permitted
[15:01:43] Explicit valence for atom # 6 N, 4, is greater than permitted
[15:01:43] Explicit valence for atom # 6 N, 4, is greater than permitted
[15:01:43] Explicit valence for atom # 6 N, 4, is greater than permitted
[15:01:43] Explicit valence for atom # 6 N, 4, is greater than permitted
[15:01:43] Explicit valence for atom # 6 N, 4, is greater than permitted
[15:01:43] Explicit valence for atom # 6 N, 4, is greater than permitted
[15:01:43] Explicit valence for atom # 6 N, 4, is greater than permitted
[15:01:43] Explicit valence for atom # 6 N, 4, is greater than permitted
[15:01:43] Explicit valence for atom # 6 N, 4, is greater than permitted
[15:01:43] Explicit valence for atom # 13 N, 4, is greater than permitted
[15:01:43] Explicit valence for atom # 13 N, 4, is greater than permitted
[15:01:43] Explicit valence for atom # 13 N, 4, is greater than permitted
[15:01:43] Explicit valence for atom # 13 N, 4, is greater than permitted
[15:01:43] Explicit valence for atom # 13 N, 4, is greater than permitted
[15:01:43] Explicit valence for atom # 13 N, 4, is greater than permitted
[15:01:43] Explicit valence for atom # 13 N, 4, is greater than permitted
[15:01:43] Explicit valence for atom # 13 N, 4, is greater than permitted
[15:01:43] Explicit valence for atom # 13 N, 4, is greater than permitted
[15:01:43] Explicit valence for atom # 13 N, 4, is greater than permitted
[15:01:43] Explicit valence for atom # 13 N, 4, is greater than permitted
[15:01:43] Explicit valence for atom # 13 N, 4, is greater than permitted
[15:01:43] Explicit valence for atom # 13 N, 4, is greater than permitted
[15:01:43] Explicit valence for atom # 13 N, 4, is greater than permitted
[15:01:43] Explicit valence for atom # 13 N, 4, is greater than permitted
[15:01:43] Explicit valence for atom # 12 N, 4, is greater than permitted
[15:01:43] Explicit valence for atom # 12 N, 4, is greater than permitted
[15:01:43] Explicit valence for atom # 12 N, 4, is greater than permitted
[15:01:43] Explicit valence for atom # 12 N, 4, is greater than permitted
[15:01:43] Explicit valence for atom # 13 N, 4, is greater than permitted
[15:01:43] Explicit valence for atom # 13 N, 4, is greater than permitted
[15:01:43] Explicit valence for atom # 13 N, 4, is greater than permitted
[15:01:43] Explicit valence for atom # 13 N, 4, is greater than permitted
[15:01:43] Explicit valence for atom # 13 N, 4, is greater than permitted
[15:01:43] Explicit valence for atom # 13 N, 4, is greater than permitted
[15:01:43] Explicit valence for atom # 13 N, 4, is greater than permitted
[15:01:43] Explicit valence for atom # 13 N, 4, is greater than permitted
[15:01:43] Explicit valence for atom # 13 N, 4, is greater than permitted
[15:01:43] Explicit valence for atom # 13 N, 4, is greater than permitted
[15:01:43] Explicit valence for atom # 13 N, 4, is greater than permitted
[15:01:43] Explicit valence for atom # 13 N, 4, is greater than permitted
[15:01:43] Explicit valence for atom # 13 N, 4, is greater than permitted
[15:01:43] Explicit valence for atom # 10 N, 4, is greater than permitted
[15:01:43] Explicit valence for atom # 10 N, 4, is greater than permitted
[15:01:43] Explicit valence for atom # 10 N, 4, is greater than permitted
[15:01:43] Explicit valence for atom # 10 N, 4, is greater than permitted
[15:01:43] Explicit valence for atom # 12 N, 4, is greater than permitted
[15:01:43] Explicit valence for atom # 12 N, 4, is greater than permitted
[15:01:43] Explicit valence for atom # 13 N, 4, is greater than permitted
[15:01:43] Explicit valence for atom # 13 N, 4, is greater than permitted
[15:01:43] Explicit valence for atom # 13 N, 4, is greater than permitted
[15:01:43] Explicit valence for atom # 13 N, 4, is greater than permitted
[15:01:43] Explicit valence for atom # 13 N, 4, is greater than permitted
[15:01:43] Explicit valence for atom # 13 N, 4, is greater than permitted
[15:01:43] Explicit valence for atom # 13 N, 4, is greater than permitted
[15:01:43] Explicit valence for atom # 13 N, 4, is greater than permitted
[15:01:43] Explicit valence for atom # 13 N, 4, is greater than permitted
[15:01:43] Explicit valence for atom # 13 N, 4, is greater than permitted
[15:01:43] Explicit valence for atom # 13 N, 4, is greater than permitted
[15:01:43] Explicit valence for atom # 13 N, 4, is greater than permitted
[15:01:43] Explicit valence for atom # 13 N, 4, is greater than permitted
[15:01:43] Explicit valence for atom # 13 N, 4, is greater than permitted
[15:01:43] Explicit valence for atom # 13 N, 4, is greater than permitted
[15:01:43] Explicit valence for atom # 13 N, 4, is greater than permitted
[15:01:43] Explicit valence for atom # 13 N, 4, is greater than permitted
[15:01:43] Explicit valence for atom # 13 N, 4, is greater than permitted
[15:01:43] Explicit valence for atom # 13 N, 4, is greater than permitted
[15:01:43] Explicit valence for atom # 13 N, 4, is greater than permitted
[15:01:43] Explicit valence for atom # 13 N, 4, is greater than permitted
[15:01:43] Explicit valence for atom # 13 N, 4, is greater than permitted
[15:01:43] Explicit valence for atom # 13 N, 4, is greater than permitted
[15:01:43] Explicit valence for atom # 13 N, 4, is greater than permitted
[15:01:43] Explicit valence for atom # 13 N, 4, is greater than permitted
[15:01:43] Explicit valence for atom # 13 N, 4, is greater than permitted
[15:01:43] Explicit valence for atom # 13 N greater than permitted
[15:01:43] Explicit valence for atom # 13 N, 4, is greater than permitted
[15:01:43] Explicit valence for atom # 13 N greater than permitted
Traceback (most recent call last):
File "../../../rmg.py", line 165, in
rmg.execute(inputFile, output_dir, **kwargs)
File "/Users/etierney/RMG-Py/rmgpy/rmg/main.py", line 541, in execute
bimolecularReact=self.bimolecularReact)
File "/Users/etierney/RMG-Py/rmgpy/rmg/model.py", line 748, in enlarge
self.processNewReactions(self.react(database, self.core.species[i]), self.core.species[i], None)
File "/Users/etierney/RMG-Py/rmgpy/rmg/model.py", line 649, in react
reactionList.extend(database.kinetics.generateReactionsFromFamilies([moleculeA], products=None, only_families=only_families))
File "/Users/etierney/RMG-Py/rmgpy/data/kinetics/database.py", line 419, in generateReactionsFromFamilies
reactionList.extend(family.generateReactions(reactants))
File "/Users/etierney/RMG-Py/rmgpy/data/kinetics/family.py", line 1244, in generateReactions
reactionList.extend(self.__generateReactions(reactants, forward=False))
File "/Users/etierney/RMG-Py/rmgpy/data/kinetics/family.py", line 1414, in __generateReactions
products0 = [product.generateResonanceIsomers() for product in products0]
File "rmgpy/molecule/molecule.py", line 1463, in rmgpy.molecule.molecule.Molecule.generateResonanceIsomers (build/pyrex/rmgpy/molecule/molecule.c:27204)
File "rmgpy/molecule/molecule.py", line 1464, in rmgpy.molecule.molecule.Molecule.generateResonanceIsomers (build/pyrex/rmgpy/molecule/molecule.c:27141)
File "rmgpy/molecule/resonance.py", line 10, in rmgpy.molecule.resonance.generateResonanceIsomers (build/pyrex/rmgpy/molecule/resonance.c:2463)
File "rmgpy/molecule/resonance.py", line 26, in rmgpy.molecule.resonance.generateResonanceIsomers (build/pyrex/rmgpy/molecule/resonance.c:2255)
File "rmgpy/molecule/resonance.py", line 254, in rmgpy.molecule.resonance.generateKekulizedResonanceIsomers (build/pyrex/rmgpy/molecule/resonance.c:5615)
File "rmgpy/molecule/resonance.py", line 267, in rmgpy.molecule.resonance.generateKekulizedResonanceIsomers (build/pyrex/rmgpy/molecule/resonance.c:5446)
File "rmgpy/molecule/generator.py", line 288, in rmgpy.molecule.generator.toRDKitMol (build/pyrex/rmgpy/molecule/generator.c:6645)
File "rmgpy/molecule/generator.py", line 328, in rmgpy.molecule.generator.toRDKitMol (build/pyrex/rmgpy/molecule/generator.c:6387)
ValueError: Sanitization error: Explicit valence for atom # 13 N greater than permitted
Since the atom number for the Nitrogen changes, I wonder if it happens during a check for resonance structures? Either way, how do we fix it?