inchi-identity 0.1.0__tar.gz

inchi_identity-0.1.0/-

@@ -0,0 +1 @@
+InChI=1S/C5H11NO2/c1-6(2,3)4-5(7)8/h4H2,1-3H3

inchi_identity-0.1.0/.gitignore

@@ -0,0 +1,29 @@
+.DS_Store
+
+node_modules/
+
+.env
+
+.venv/
+
+venv/
+
+.idea/
+
+.pytest_cache
+
+__pycache__/
+
+*/__pycache__/
+
+*.py[cod]
+
+*.pdb
+
+.conda/
+
+.vscode/
+
+*.swp
+
+*$py.class

inchi_identity-0.1.0/PKG-INFO

@@ -0,0 +1,138 @@
+Metadata-Version: 2.4
+Name: inchi-identity
+Version: 0.1.0
+Summary: Hierarchical molecular identity comparison framework for untargeted metabolomics
+Author-email: Alejandra O'Shea <alejandraosheafdez@gmail.com>
+License-File: LICENSE
+Requires-Python: >=3.10
+Requires-Dist: numpy
+Requires-Dist: openpyxl
+Requires-Dist: pandas
+Requires-Dist: python-dotenv
+Requires-Dist: requests
+Description-Content-Type: text/markdown
+
+# InChI Identity
+
+A hierarchical molecular identity comparison framework for untargeted metabolomics.
+
+Instead of binary exact matching, this tool evaluates molecular equivalence across six 
+progressive normalization layers, returning a structured equivalence profile that reflects 
+the structural resolution actually supported by the experimental evidence. For lipids, 
+a dedicated four-level hierarchy (Levels A–D) addresses cis/trans geometry, sn-position, 
+intra-chain double bond position, and global sum composition.
+---
+
+## Comparison Layers
+
+| Layer | Name | Description |
+|-------|------|-------------|
+| 1 | Complete Identity | Exact InChI string equality |
+| 2 | Isotopic Independence | Equality after /i layer removal |
+| 3 | Salt Independence | Equality after counterion removal |
+| 4 | Charge Independence | Equality after charge/protonation normalization |
+| 5 | Stereochemical/Isomeric Independence | Levels A–D (all molecules / lipids only) |
+| 6 | Tautomeric Independence | Equality after canonical tautomer generation |
+
+---
+
+## Installation
+
+RDKit must be installed via conda:
+
+```bash
+git clone https://github.com/alejandraoshea/identity-levels-inchi.git
+cd identity-levels-inchi
+conda env create -f conda_env.yml
+conda activate inchi-identity
+pip install -e .
+```
+
+Verify:
+
+```bash
+inchi --help
+```
+
+### InChI Trust (optional, for Layer 6)
+
+Download from https://www.inchi-trust.org/downloads/ then set the path:
+
+```bash
+export INCHITRUST_PATH=/path/to/inchi-1
+```
+
+If not available, Layer 6 falls back to RDKit's TautomerEnumerator automatically.
+
+---
+
+## CLI Usage
+
+### Compare two structures across all layers
+
+```bash
+inchi compare-pair "<inchi_1>" "<inchi_2>"
+```
+
+### Compare with selected layers only
+
+```bash
+inchi compare-pair-layers "<inchi_1>" "<inchi_2>" --layers isotope salt charge
+```
+
+### File-based comparison
+# Pairwise
+```bash
+inchi compare file1.txt file2.txt
+```
+# Cross-comparison (all vs all)
+```bash
+inchi compare file1.txt file2.txt --mode cross
+```
+
+# Only show equivalent pairs
+```bash
+inchi compare file1.txt file2.txt --only-equal
+inchi compare file1.txt file2.txt --mode cross --only-equal
+```
+
+### MGF spectral library unification
+```bash
+inchi compare-mgf file1.mgf file2.mgf \
+    --layer CHARGES_INDEPENDENCE \
+    --output-mgf unified.mgf \
+    --output-log unified_log.json
+```
+
+Available layers: `COMPLETE_IDENTITY`, `ISOTOPIC_INDEPENDENCE`, `SALTS_INDEPENDENCE`,
+`CHARGES_INDEPENDENCE`, `DOUBLE_BONDS_INDEPENDENCE`,
+`STEREOCHEMICAL_CIS_TRANS_INDEPENDENCE`, `TAUTOMER_INDEPENDENCE`
+
+---
+
+## Example output
+
+```json
+{
+    "inchi_1": "InChI=1S/C5H11NO2/c1-6(2,3)4-5(7)8/h4H2,1-3H3/p+1",
+    "inchi_2": "InChI=1S/C18H34O2/...",
+    "results": {
+        "COMPLETE_IDENTITY": false,
+        "ISOTOPIC_INDEPENDENCE": false,
+        "SALTS_INDEPENDENCE": false,
+        "CHARGES_INDEPENDENCE": false,
+        "DOUBLE_BONDS_INDEPENDENCE": false,
+        "STEREOCHEMICAL_CIS_TRANS_INDEPENDENCE": false,
+        "TAUTOMER_INDEPENDENCE": false
+    }
+}
+```
+
+---
+
+## Related repositories
+
+- [inchi-identity-api](https://github.com/alejandraoshea/inchi-identity-api) — Flask REST backend
+- [inchi-identity-app](https://github.com/alejandraoshea/inchi-identity-app) — Web frontend
+
+---

inchi_identity-0.1.0/README.md

@@ -0,0 +1,124 @@
+# InChI Identity
+
+A hierarchical molecular identity comparison framework for untargeted metabolomics.
+
+Instead of binary exact matching, this tool evaluates molecular equivalence across six 
+progressive normalization layers, returning a structured equivalence profile that reflects 
+the structural resolution actually supported by the experimental evidence. For lipids, 
+a dedicated four-level hierarchy (Levels A–D) addresses cis/trans geometry, sn-position, 
+intra-chain double bond position, and global sum composition.
+---
+
+## Comparison Layers
+
+| Layer | Name | Description |
+|-------|------|-------------|
+| 1 | Complete Identity | Exact InChI string equality |
+| 2 | Isotopic Independence | Equality after /i layer removal |
+| 3 | Salt Independence | Equality after counterion removal |
+| 4 | Charge Independence | Equality after charge/protonation normalization |
+| 5 | Stereochemical/Isomeric Independence | Levels A–D (all molecules / lipids only) |
+| 6 | Tautomeric Independence | Equality after canonical tautomer generation |
+
+---
+
+## Installation
+
+RDKit must be installed via conda:
+
+```bash
+git clone https://github.com/alejandraoshea/identity-levels-inchi.git
+cd identity-levels-inchi
+conda env create -f conda_env.yml
+conda activate inchi-identity
+pip install -e .
+```
+
+Verify:
+
+```bash
+inchi --help
+```
+
+### InChI Trust (optional, for Layer 6)
+
+Download from https://www.inchi-trust.org/downloads/ then set the path:
+
+```bash
+export INCHITRUST_PATH=/path/to/inchi-1
+```
+
+If not available, Layer 6 falls back to RDKit's TautomerEnumerator automatically.
+
+---
+
+## CLI Usage
+
+### Compare two structures across all layers
+
+```bash
+inchi compare-pair "<inchi_1>" "<inchi_2>"
+```
+
+### Compare with selected layers only
+
+```bash
+inchi compare-pair-layers "<inchi_1>" "<inchi_2>" --layers isotope salt charge
+```
+
+### File-based comparison
+# Pairwise
+```bash
+inchi compare file1.txt file2.txt
+```
+# Cross-comparison (all vs all)
+```bash
+inchi compare file1.txt file2.txt --mode cross
+```
+
+# Only show equivalent pairs
+```bash
+inchi compare file1.txt file2.txt --only-equal
+inchi compare file1.txt file2.txt --mode cross --only-equal
+```
+
+### MGF spectral library unification
+```bash
+inchi compare-mgf file1.mgf file2.mgf \
+    --layer CHARGES_INDEPENDENCE \
+    --output-mgf unified.mgf \
+    --output-log unified_log.json
+```
+
+Available layers: `COMPLETE_IDENTITY`, `ISOTOPIC_INDEPENDENCE`, `SALTS_INDEPENDENCE`,
+`CHARGES_INDEPENDENCE`, `DOUBLE_BONDS_INDEPENDENCE`,
+`STEREOCHEMICAL_CIS_TRANS_INDEPENDENCE`, `TAUTOMER_INDEPENDENCE`
+
+---
+
+## Example output
+
+```json
+{
+    "inchi_1": "InChI=1S/C5H11NO2/c1-6(2,3)4-5(7)8/h4H2,1-3H3/p+1",
+    "inchi_2": "InChI=1S/C18H34O2/...",
+    "results": {
+        "COMPLETE_IDENTITY": false,
+        "ISOTOPIC_INDEPENDENCE": false,
+        "SALTS_INDEPENDENCE": false,
+        "CHARGES_INDEPENDENCE": false,
+        "DOUBLE_BONDS_INDEPENDENCE": false,
+        "STEREOCHEMICAL_CIS_TRANS_INDEPENDENCE": false,
+        "TAUTOMER_INDEPENDENCE": false
+    }
+}
+```
+
+---
+
+## Related repositories
+
+- [inchi-identity-api](https://github.com/alejandraoshea/inchi-identity-api) — Flask REST backend
+- [inchi-identity-app](https://github.com/alejandraoshea/inchi-identity-app) — Web frontend
+
+---

inchi_identity-0.1.0/conda_env.yml

@@ -0,0 +1,16 @@
+name: inchi-identity
+
+channels:
+  - conda-forge
+
+dependencies:
+  - python=3.12
+  - rdkit
+  - numpy
+  - pandas
+  - requests
+  - openpyxl
+  - python-dotenv
+  - pip
+  - pip:
+      - pytest

inchi_identity-0.1.0/files_examples/file1.txt

@@ -0,0 +1,5 @@
+InChI=1S/C23H45NO4.ClH/c1-5-6-7-8-9-10-11-12-13-14-15-16-17-18-23(27)28-21(19-22(25)26)20-24(2,3)4;/h21H,5-20H2,1-4H3;1H
+InChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
+InChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/p-2/t4-,6-,7-,10-/m1/s1
+InChI=1S/C5H11NO2/c1-6(2,3)4-5(7)8/h4H2,1-3H3/p+1
+InChI=1S/C26H46NO8P/c1-5-6-7-8-9-10-11-16-19-26(30)33-22-24(17-14-12-13-15-18-25(28)29)23-35-36(31,32)34-21-20-27(2,3)4/h5-6,12-15,24H,7-11,16-23H2,1-4H3,(H-,28,29,31,32)/b6-5-,14-12+,15-13+/t24-/m1/s1

inchi_identity-0.1.0/files_examples/file1_smiles.txt

@@ -0,0 +1,3 @@
+CC(=O)O
+CCO
+CN(C)(C)CC(=O)O

inchi_identity-0.1.0/files_examples/file2.txt

@@ -0,0 +1,5 @@
+InChI=1S/C23H45NO4.ClH/c1-5-6-7-8-9-10-11-12-13-14-15-16-17-18-23(27)28-21(19-22(25)26)20-24(2,3)4;/h21H,5-20H2,1-4H3;1H
+InChI=1S/C18H34O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h9-10H,2-8,11-17H2,1H3,(H,19,20)/b10-9-
+InChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/p-1/t4-,6-,7-,10-/m1/s1
+InChI=1S/C5H11NO2/c1-6(2,3)4-5(7)8/h4H2,1-3H3
+InChI=1S/C5H10O/c1-3-4-5(2)6/h4,6H,3H2,1-2H3/b5-4-

inchi_identity-0.1.0/files_examples/file2_smiles.txt

@@ -0,0 +1,3 @@
+CC(=O)[O-].[Na+]
+CCO
+C[N+](C)(C)CC(=O)[O-]

inchi_identity-0.1.0/files_examples/test_file1.mgf

@@ -0,0 +1,120 @@
+BEGIN IONS
+TITLE=Adenosine triphosphate
+PEPMASS=507.9810
+CHARGE=1-
+RTINSECONDS=120.5
+INCHI=InChI=1S/C10H16N5O13P3/c11-8-5-9(13-3-12-8)15(4-14-5)10-7(17)6(16)4(26-10)2-25-30(21,22)28-31(23,24)27-29(18,19)20/h3-4,6-7,10,16-17H,2H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
+SCANS=1
+101.5 999.0
+136.1 5000.0
+159.0 2500.0
+END IONS
+
+BEGIN IONS
+TITLE=ATP (duplicate)
+PEPMASS=507.9815
+CHARGE=1-
+RTINSECONDS=120.8
+INCHI=InChI=1S/C10H16N5O13P3/c11-8-5-9(13-3-12-8)15(4-14-5)10-7(17)6(16)4(26-10)2-25-30(21,22)28-31(23,24)27-29(18,19)20/h3-4,6-7,10,16-17H,2H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
+SCANS=2
+101.5 850.0
+136.1 4800.0
+159.0 2300.0
+END IONS
+
+BEGIN IONS
+TITLE=Nicotinamide adenine dinucleotide
+PEPMASS=663.1091
+CHARGE=1-
+RTINSECONDS=145.2
+INCHI=InChI=1S/C21H27N7O14P2/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(32)14(30)11(41-21)6-39-44(36,37)42-43(34,35)38-5-10-13(29)15(31)20(40-10)27-3-1-2-9(4-27)18(23)33/h1-4,7-8,10-11,13-16,20-21,29-32H,5-6H2,(H2,22,24,25)(H2,23,33)(H,34,35)(H,36,37)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
+SCANS=3
+123.1 1200.0
+136.0 8000.0
+428.0 3500.0
+END IONS
+
+BEGIN IONS
+TITLE=Glucose 6-phosphate
+PEPMASS=259.0224
+CHARGE=1-
+RTINSECONDS=85.3
+INCHI=InChI=1S/C6H13O9P/c7-3-2(1-14-16(11,12)13)15-6(10)5(9)4(3)8/h2-10H,1H2,(H2,11,12,13)/t2-,3-,4+,5-,6?/m1/s1
+SCANS=4
+97.0 2000.0
+139.0 1500.0
+199.0 4500.0
+END IONS
+
+BEGIN IONS
+TITLE=Glucose-6-P (replicate)
+PEPMASS=259.0227
+CHARGE=1-
+RTINSECONDS=85.5
+INCHI=InChI=1S/C6H13O9P/c7-3-2(1-14-16(11,12)13)15-6(10)5(9)4(3)8/h2-10H,1H2,(H2,11,12,13)/t2-,3-,4+,5-,6?/m1/s1
+SCANS=5
+97.0 2100.0
+139.0 1450.0
+199.0 4600.0
+END IONS
+
+BEGIN IONS
+TITLE=Citric acid
+PEPMASS=191.0197
+CHARGE=1-
+RTINSECONDS=65.8
+INCHI=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)
+SCANS=6
+87.0 1800.0
+111.0 3200.0
+173.0 2500.0
+END IONS
+
+BEGIN IONS
+TITLE=L-Glutamic acid
+PEPMASS=146.0459
+CHARGE=1-
+RTINSECONDS=55.2
+INCHI=InChI=1S/C5H9NO4/c6-3(5(9)10)1-2-4(7)8/h3H,1-2,6H2,(H,7,8)(H,9,10)/t3-/m0/s1
+SCANS=7
+84.0 1500.0
+102.0 2800.0
+128.0 3500.0
+END IONS
+
+BEGIN IONS
+TITLE=Pyruvic acid
+PEPMASS=87.0082
+CHARGE=1-
+RTINSECONDS=45.5
+INCHI=InChI=1S/C3H4O3/c1-2(4)3(5)6/h1H3,(H,5,6)
+SCANS=8
+43.0 2500.0
+59.0 1200.0
+87.0 5000.0
+END IONS
+
+BEGIN IONS
+TITLE=Acetyl-CoA
+PEPMASS=808.1145
+CHARGE=1-
+RTINSECONDS=155.8
+INCHI=InChI=1S/C23H38N7O17P3S/c1-12(31)51-7-6-25-14(32)4-5-26-21(35)18(34)23(2,3)9-44-50(41,42)47-49(39,40)43-8-13-17(46-48(36,37)38)16(33)22(45-13)30-11-29-15-19(24)27-10-28-20(15)30/h10-11,13,16-18,22,33-34H,4-9H2,1-3H3,(H,25,32)(H,26,35)(H,39,40)(H,41,42)(H2,24,27,28)(H2,36,37,38)/t13-,16-,17-,18+,22-/m1/s1
+SCANS=9
+134.0 1800.0
+428.0 4200.0
+507.0 2800.0
+END IONS
+
+BEGIN IONS
+TITLE=Fructose 1,6-bisphosphate
+PEPMASS=338.9888
+CHARGE=1-
+RTINSECONDS=92.4
+INCHI=InChI=1S/C6H14O12P2/c7-3(1-17-19(11,12)13)5(9)6(10,2-18-20(14,15)16)4(8)3/h3,5,7,9-10H,1-2H2,(H2,11,12,13)(H2,14,15,16)/t3-,5-,6-/m1/s1
+SCANS=10
+97.0 3500.0
+139.0 2200.0
+199.0 4800.0
+END IONS
+

inchi_identity-0.1.0/files_examples/test_file2.mgf

@@ -0,0 +1,144 @@
+BEGIN IONS
+TITLE=ATP from database
+PEPMASS=507.9812
+CHARGE=1-
+RTINSECONDS=121.0
+INCHI=InChI=1S/C10H16N5O13P3/c11-8-5-9(13-3-12-8)15(4-14-5)10-7(17)6(16)4(26-10)2-25-30(21,22)28-31(23,24)27-29(18,19)20/h3-4,6-7,10,16-17H,2H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
+SCANS=101
+101.5 920.0
+136.1 4900.0
+159.0 2400.0
+END IONS
+
+BEGIN IONS
+TITLE=NAD+ reference
+PEPMASS=663.1095
+CHARGE=1-
+RTINSECONDS=145.5
+INCHI=InChI=1S/C21H27N7O14P2/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(32)14(30)11(41-21)6-39-44(36,37)42-43(34,35)38-5-10-13(29)15(31)20(40-10)27-3-1-2-9(4-27)18(23)33/h1-4,7-8,10-11,13-16,20-21,29-32H,5-6H2,(H2,22,24,25)(H2,23,33)(H,34,35)(H,36,37)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
+SCANS=102
+123.1 1150.0
+136.0 8200.0
+428.0 3600.0
+END IONS
+
+BEGIN IONS
+TITLE=Citrate
+PEPMASS=191.0199
+CHARGE=1-
+RTINSECONDS=66.0
+INCHI=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)
+SCANS=103
+87.0 1750.0
+111.0 3150.0
+173.0 2550.0
+END IONS
+
+BEGIN IONS
+TITLE=L-Lactate
+PEPMASS=89.0239
+CHARGE=1-
+RTINSECONDS=38.5
+INCHI=InChI=1S/C3H6O3/c1-2(4)3(5)6/h2,4H,1H3,(H,5,6)/t2-/m1/s1
+SCANS=104
+43.0 3200.0
+45.0 1800.0
+89.0 6500.0
+END IONS
+
+BEGIN IONS
+TITLE=Succinate
+PEPMASS=117.0193
+CHARGE=1-
+RTINSECONDS=52.3
+INCHI=InChI=1S/C4H6O4/c5-3(6)1-2-4(7)8/h1-2H2,(H,5,6)(H,7,8)
+SCANS=105
+73.0 2100.0
+99.0 1500.0
+117.0 4200.0
+END IONS
+
+BEGIN IONS
+TITLE=Acetyl coenzyme A
+PEPMASS=808.1148
+CHARGE=1-
+RTINSECONDS=156.0
+INCHI=InChI=1S/C23H38N7O17P3S/c1-12(31)51-7-6-25-14(32)4-5-26-21(35)18(34)23(2,3)9-44-50(41,42)47-49(39,40)43-8-13-17(46-48(36,37)38)16(33)22(45-13)30-11-29-15-19(24)27-10-28-20(15)30/h10-11,13,16-18,22,33-34H,4-9H2,1-3H3,(H,25,32)(H,26,35)(H,39,40)(H,41,42)(H2,24,27,28)(H2,36,37,38)/t13-,16-,17-,18+,22-/m1/s1
+SCANS=106
+134.0 1750.0
+428.0 4300.0
+507.0 2750.0
+END IONS
+
+BEGIN IONS
+TITLE=Alpha-ketoglutarate
+PEPMASS=145.0142
+CHARGE=1-
+RTINSECONDS=58.8
+INCHI=InChI=1S/C5H6O5/c6-3(5(9)10)1-2-4(7)8/h1-2H2,(H,7,8)(H,9,10)
+SCANS=107
+57.0 1200.0
+101.0 3800.0
+145.0 5200.0
+END IONS
+
+BEGIN IONS
+TITLE=Oxaloacetate
+PEPMASS=131.0001
+CHARGE=1-
+RTINSECONDS=48.2
+INCHI=InChI=1S/C4H4O5/c5-2(4(8)9)1-3(6)7/h1H2,(H,6,7)(H,8,9)
+SCANS=108
+87.0 2800.0
+113.0 1900.0
+131.0 4500.0
+END IONS
+
+BEGIN IONS
+TITLE=Glucose-6-phosphate reference
+PEPMASS=259.0226
+CHARGE=1-
+RTINSECONDS=85.4
+INCHI=InChI=1S/C6H13O9P/c7-3-2(1-14-16(11,12)13)15-6(10)5(9)4(3)8/h2-10H,1H2,(H2,11,12,13)/t2-,3-,4+,5-,6?/m1/s1
+SCANS=109
+97.0 2050.0
+139.0 1480.0
+199.0 4550.0
+END IONS
+
+BEGIN IONS
+TITLE=Coenzyme A
+PEPMASS=766.1041
+CHARGE=1-
+RTINSECONDS=152.5
+INCHI=InChI=1S/C21H36N7O16P3S/c1-21(2,16(31)19(32)24-4-3-12(29)23-5-6-48)8-41-47(38,39)44-46(36,37)40-7-11-15(43-45(33,34)35)14(30)20(42-11)28-10-27-13-17(22)25-9-26-18(13)28/h9-11,14-16,20,30-31,48H,3-8H2,1-2H3,(H,23,29)(H,24,32)(H,36,37)(H,38,39)(H2,22,25,26)(H2,33,34,35)/t11-,14-,15-,16+,20-/m1/s1
+SCANS=110
+134.0 2200.0
+261.0 1500.0
+428.0 3800.0
+END IONS
+
+BEGIN IONS
+TITLE=Malate
+PEPMASS=133.0142
+CHARGE=1-
+RTINSECONDS=61.5
+INCHI=InChI=1S/C4H6O5/c5-2(4(8)9)1-3(6)7/h2,5H,1H2,(H,6,7)(H,8,9)/t2-/m0/s1
+SCANS=111
+71.0 1600.0
+115.0 2900.0
+133.0 5100.0
+END IONS
+
+BEGIN IONS
+TITLE=Fumarate
+PEPMASS=115.0037
+CHARGE=1-
+RTINSECONDS=55.8
+INCHI=InChI=1S/C4H4O4/c5-3(6)1-2-4(7)8/h1-2H,(H,5,6)(H,7,8)/b2-1+
+SCANS=112
+71.0 3500.0
+99.0 2100.0
+115.0 6200.0
+END IONS
+

inchi_identity-0.1.0/files_examples/test_protonation_file1.mgf

@@ -0,0 +1,21 @@
+BEGIN IONS
+TITLE=ATP neutral
+PEPMASS=507.0
+INCHI=InChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
+101.5 999.0
+136.1 5000.0
+END IONS
+
+BEGIN IONS
+TITLE=Glucose-6-phosphate neutral
+PEPMASS=260.0
+INCHI=InChI=1S/C6H13O9P/c7-3-2(1-14-16(11,12)13)15-6(10)5(9)4(3)8/h2-10H,1H2,(H2,11,12,13)/t2-,3-,4+,5-,6?/m1/s1
+97.0 1500.0
+END IONS
+
+BEGIN IONS
+TITLE=Citric acid
+PEPMASS=192.0
+INCHI=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)
+111.0 2000.0
+END IONS

inchi_identity-0.1.0/files_examples/test_protonation_file2.mgf

@@ -0,0 +1,22 @@
+BEGIN IONS
+TITLE=ATP deprotonated -1
+PEPMASS=507.0
+INCHI=InChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/p-1/t4-,6-,7-,10-/m1/s1
+101.5 920.0
+136.1 4900.0
+END IONS
+
+BEGIN IONS
+TITLE=ATP deprotonated -2
+PEPMASS=507.0
+INCHI=InChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/p-2/t4-,6-,7-,10-/m1/s1
+101.5 880.0
+136.1 4800.0
+END IONS
+
+BEGIN IONS
+TITLE=G6P deprotonated -2
+PEPMASS=260.0
+INCHI=InChI=1S/C6H13O9P/c7-3-2(1-14-16(11,12)13)15-6(10)5(9)4(3)8/h2-10H,1H2,(H2,11,12,13)/p-2/t2-,3-,4+,5-,6?/m1/s1
+97.0 1450.0
+END IONS

inchi_identity-0.1.0/files_examples/test_salts_file1.mgf

@@ -0,0 +1,20 @@
+BEGIN IONS
+TITLE=Sodium acetate
+PEPMASS=82.0
+INCHI=InChI=1S/C2H4O2.Na/c1-2(3)4;/h1H3,(H,3,4);/q;+1/p-1
+100.0 1200.0
+END IONS
+
+BEGIN IONS
+TITLE=Potassium acetate
+PEPMASS=98.0
+INCHI=InChI=1S/C2H4O2.K/c1-2(3)4;/h1H3,(H,3,4);/q;+1/p-1
+100.0 1150.0
+END IONS
+
+BEGIN IONS
+TITLE=Succinic acid
+PEPMASS=118.0
+INCHI=InChI=1S/C4H6O4/c5-3(6)1-2-4(7)8/h1-2H2,(H,5,6)(H,7,8)
+117.0 3000.0
+END IONS

inchi_identity-0.1.0/files_examples/test_salts_file2.mgf

@@ -0,0 +1,20 @@
+BEGIN IONS
+TITLE=Calcium acetate
+PEPMASS=158.0
+INCHI=InChI=1S/2C2H4O2.Ca/c2*1-2(3)4;/h2*1H3,(H,3,4);/q;;+2/p-2
+100.0 1100.0
+END IONS
+
+BEGIN IONS
+TITLE=Acetic acid neutral
+PEPMASS=60.0
+INCHI=InChI=1S/C2H4O2/c1-2(3)4/h1H3,(H,3,4)
+100.0 1050.0
+END IONS
+
+BEGIN IONS
+TITLE=Succinic acid sodium salt
+PEPMASS=140.0
+INCHI=InChI=1S/C4H6O4.Na/c5-3(6)1-2-4(7)8;/h1-2H2,(H,5,6)(H,7,8);/q;+1/p-1
+117.0 2950.0
+END IONS