Merge pull request #41 from chemkg/issue-39

Add optional context fields for pKa values

Author: cmungall

examples/output/Molecule-citric_acid_with_pka_context.json

@@ -0,0 +1,19 @@
+{
+  "id": "CHEBI:30769",
+  "name": "citric acid",
+  "type": "chemrof:Molecule",
+  "inchi_string": "InChI=1S/C6H8O7/c7-3(8)1-6(13,5(11)12)2-4(9)10/h13H,1-2H2,(H,7,8)(H,9,10)(H,11,12)",
+  "smiles_string": "OC(=O)CC(O)(C(=O)O)CC(=O)O",
+  "empirical_formula": "C6H8O7",
+  "molecular_mass": 192.124,
+  "pka_ionization_constant": [
+    3.13,
+    4.76,
+    6.4
+  ],
+  "pka_temperature": 25.0,
+  "pka_ionic_strength": 0.0,
+  "pka_solvent": "water",
+  "pka_pressure": 1.0,
+  "@type": "Molecule"
+}

examples/output/Molecule-citric_acid_with_pka_context.yaml

@@ -0,0 +1,15 @@
+id: CHEBI:30769
+name: citric acid
+type: chemrof:Molecule
+inchi_string: InChI=1S/C6H8O7/c7-3(8)1-6(13,5(11)12)2-4(9)10/h13H,1-2H2,(H,7,8)(H,9,10)(H,11,12)
+smiles_string: OC(=O)CC(O)(C(=O)O)CC(=O)O
+empirical_formula: C6H8O7
+molecular_mass: 192.124
+pka_ionization_constant:
+- 3.13
+- 4.76
+- 6.4
+pka_temperature: 25.0
+pka_ionic_strength: 0.0
+pka_solvent: water
+pka_pressure: 1.0

examples/output/README.md

@@ -561,6 +561,26 @@ smiles_string: CC(=O)O
 type: chemrof:SmallMolecule
 water_solubility: 1000000.0
 
+```
+## Molecule-citric_acid_with_pka_context
+### Input
+```yaml
+empirical_formula: C6H8O7
+id: CHEBI:30769
+inchi_string: InChI=1S/C6H8O7/c7-3(8)1-6(13,5(11)12)2-4(9)10/h13H,1-2H2,(H,7,8)(H,9,10)(H,11,12)
+molecular_mass: 192.124
+name: citric acid
+pka_ionic_strength: 0.0
+pka_ionization_constant:
+- 3.13
+- 4.76
+- 6.4
+pka_pressure: 1.0
+pka_solvent: water
+pka_temperature: 25.0
+smiles_string: OC(=O)CC(O)(C(=O)O)CC(=O)O
+type: chemrof:Molecule
+
 ```
 ## AtomCation-sodium
 ### Input