inchi-identity 0.2.5

Hierarchical molecular identity comparison framework for untargeted metabolomics

inchi-identity

A hierarchical molecular identity comparison framework for untargeted metabolomics, implemented as a Python CLI and published on PyPI.

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 — each reported individually.

Both InChI strings and SMILES are accepted as input — SMILES are automatically converted to canonical InChI before comparison.

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Comparison Layers

Layer	Key	Name	Description
1	complete_identity	Complete Identity	Exact InChI string equality
2	isotope	Isotopic Independence	Equality after /i layer removal
3	salt	Salt Independence	Equality after counterion removal (RDKit SaltRemover)
4	charge	Charge Independence	Equality after charge/protonation normalization
5	double_bond	Double Bond Independence	Position-independent comparison (any of A–D match)
5A	isomer_level_a	(A) Cis/Trans	Removes /b cis/trans geometry; applies to all molecules
5B	isomer_level_b	(B) sn-Position	Compares acyl chains as an unordered set; lipids only
5C	isomer_level_c	(C) Intra-Chain Position	Discards double bond position within each chain; lipids only
5D	isomer_level_d	(D) Sum Composition	Total carbon and double bond count only; lipids only
6	tautomer	Tautomeric Independence	Equality after canonical tautomer generation

Preprocessing is cumulative: each layer applies all normalizations from preceding layers before performing its own comparison.

Lipid sub-levels (Layer 5A–D)

Layer 5 (double_bond) returns a single true/false result: true if the two molecules match at any of the four sub-levels. Layers 5A–D are reported individually — each one tells you at which level of structural resolution the pair first becomes equivalent.

Sub-levels are also cumulative downward: if a pair matches at Level A, it automatically matches at B, C, and D as well (since each is more lenient).

Level	Key	Match criterion
A	isomer_level_a	Identical after removing cis/trans geometry
B	isomer_level_b	Same chains regardless of which sn-position they occupy
C	isomer_level_c	Same per-chain composition (C, DB, O) ignoring double bond position
D	isomer_level_d	Same total carbon count and total double bond count

For non-lipids, levels B, C, and D are not applicable — they are absent from the result (N/A in the web interface).

Lipid classification uses the ClassyFire API, with an RDKit-based heuristic fallback. Headgroup validation uses a library of 295 SMARTS patterns (40 manually curated + 255 generated at runtime by combining 15 glycolipid templates with 17 monosaccharide patterns).

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Installation

RDKit must be installed via conda before installing this package:

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 .

Or install directly from PyPI:

pip install inchi-identity

Verify the installation:

inchi --help

InChI Trust executable (optional, required for Layer 6)

Layer 6 uses the InChI Trust executable for canonical tautomer generation. Download it from https://www.inchi-trust.org/downloads/ and set the path:

export INCHITRUST_PATH=/path/to/inchi-1

If the executable is not available, Layer 6 automatically falls back to RDKit's TautomerEnumerator.

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CLI Usage

Mode 1 — Compare two structures across all layers

Runs every layer enabled in default_config.json (all layers on by default):

inchi compare-pair "<inchi_1>" "<inchi_2>"
inchi compare-pair "<inchi_1>" "<inchi_2>" 2>/dev/null > result.json

SMILES are also accepted:

inchi compare-pair "CC(=O)O" "CC(=O)[O-].[Na+]"

Using a custom config file

To run only a subset of layers without editing the default config, create a custom JSON file and pass it with --config:

inchi compare-pair "<inchi_1>" "<inchi_2>" --config path/to/my_config.json

A config file has the same structure as default_config.json — set any layer to false to skip it. Example that runs only the four isomer sub-levels:

{
  "identity_criteria": {
    "complete_identity":   { "enabled": false },
    "isotope_independence":  { "isotope_independent_identity": false },
    "salt_independence":     { "desalted_identity": false },
    "charge_independence":   { "charge_independent_identity": false },
    "isomer_independence": {
      "double_bond_position_independent_identity": false,
      "isomer_level_a_cis_trans":      true,
      "isomer_level_b_sn_position":    true,
      "isomer_level_c_intra_chain":    true,
      "isomer_level_d_sum_composition": true
    },
    "tautomer_independence": { "tautomer_independent_identity": false, "inchitrust_path": null }
  }
}

A ready-to-use version of this file is included at src/inchi_identity/configs/isomer_only_config.json.

Redirect output to a file (use 2>/dev/null on Linux/macOS or 2>$null on PowerShell to suppress the loading messages from stderr):

# Linux / macOS
inchi compare-pair "<inchi_1>" "<inchi_2>" \
    --config src/inchi_identity/configs/isomer_only_config.json \
    2>/dev/null > result.json

# PowerShell
inchi compare-pair "<inchi_1>" "<inchi_2>" `
    --config src/inchi_identity/configs/isomer_only_config.json `
    2>$null > result.json

Mode 2 — Compare with selected layers only (no config editing needed)

Pass layer keys directly on the command line with --layers. Only the specified layers are evaluated; the config file is ignored for layer selection.

inchi compare-pair-layers "<inchi_1>" "<inchi_2>" \
    --layers isotope charge double_bond tautomer

All available layer keys:

Key	Description
complete_identity	Exact match
isotope	Isotope independence
salt	Salt independence
charge	Charge independence
double_bond	Full double bond / stereochemical independence (A–D combined)
isomer_level_a	(A) Cis/Trans
isomer_level_b	(B) sn-Position
isomer_level_c	(C) Intra-Chain Position
isomer_level_d	(D) Sum Composition
tautomer	Tautomer independence

Multiple keys can be combined:

# Only the four isomer sub-levels:
inchi compare-pair-layers "<inchi_1>" "<inchi_2>" \
    --layers isomer_level_a isomer_level_b isomer_level_c isomer_level_d

# Double bond + all four sub-levels reported separately:
inchi compare-pair-layers "<inchi_1>" "<inchi_2>" \
    --layers double_bond isomer_level_a isomer_level_b isomer_level_c isomer_level_d

# Classic layers only:
inchi compare-pair-layers "<inchi_1>" "<inchi_2>" \
    --layers complete_identity isotope salt charge tautomer

Mode 3 — File-based comparison

Input files contain one InChI or SMILES per line. SMILES and InChI can be mixed.

Pairwise (entry i from file 1 vs entry i from file 2):

inchi compare file1.txt file2.txt > result_pairwise.json

Cross-comparison (all vs all, n×m pairs):

inchi compare file1.txt file2.txt --mode cross > result_cross.json

Filter to equivalent pairs only (works with both modes):

inchi compare file1.txt file2.txt --only-equal
inchi compare file1.txt file2.txt --mode cross --only-equal

When --only-equal is active, the output key changes from results to matches and only layers that evaluated to true are included.

A custom config can also be passed to file-based comparison:

inchi compare file1.txt file2.txt --config my_config.json

Mode 4 — MGF spectral library unification

Normalizes molecular identifiers embedded in two MGF files at a chosen equivalence layer, producing a unified MGF file and a JSON change log. InChI and SMILES identifiers are detected automatically per entry.

inchi compare-mgf file1.mgf file2.mgf \
    --layer CHARGES_INDEPENDENCE \
    --output-mgf unified.mgf \
    --output-log unified_log.json

Available --layer values:

COMPLETE_IDENTITY
ISOTOPIC_INDEPENDENCE
SALTS_INDEPENDENCE
CHARGES_INDEPENDENCE
DOUBLE_BONDS_INDEPENDENCE
ISOMER_INDEPENDENCE_A
ISOMER_INDEPENDENCE_B
ISOMER_INDEPENDENCE_C
ISOMER_INDEPENDENCE_D
TAUTOMER_INDEPENDENCE

The pipeline: (1) parses both files and extracts identifiers, (2) internally normalizes each file so equivalent entries share a canonical InChI, (3) performs a cross-file comparison and replaces identifiers in file 2 with the canonical form from file 1, (4) writes the unified MGF and a JSON log recording every transformation. Entries without identifiers and all spectral peak data are preserved unchanged.

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Output format

compare-pair — all layers

{
    "inchi_1": "InChI=1S/C18H34O2/.../b10-9-",
    "inchi_2": "InChI=1S/C18H34O2/.../b10-9+",
    "results": {
        "COMPLETE_IDENTITY": false,
        "ISOTOPIC_INDEPENDENCE": false,
        "SALTS_INDEPENDENCE": false,
        "CHARGES_INDEPENDENCE": false,
        "DOUBLE_BONDS_INDEPENDENCE": true,
        "ISOMER_INDEPENDENCE_A": true,
        "ISOMER_INDEPENDENCE_B": true,
        "ISOMER_INDEPENDENCE_C": true,
        "ISOMER_INDEPENDENCE_D": true,
        "TAUTOMER_INDEPENDENCE": true
    }
}

compare-pair — isomer sub-levels only (different double bond position)

cis-Oleic acid (Δ9) vs Vaccenic acid (Δ11): same 18:1 composition, different position.

{
    "inchi_1": "InChI=1S/C18H34O2/.../b10-9-",
    "inchi_2": "InChI=1S/C18H34O2/.../b12-11+",
    "results": {
        "ISOMER_INDEPENDENCE_A": false,
        "ISOMER_INDEPENDENCE_B": false,
        "ISOMER_INDEPENDENCE_C": true,
        "ISOMER_INDEPENDENCE_D": true
    }
}

Level A and B fail (position differs); Level C matches (both are 18:1 per chain); Level D matches (total C=18, DB=1).

compare-pair — charge normalization

{
    "inchi_1": "InChI=1S/C5H11NO2/c1-6(2,3)4-5(7)8/h4H2,1-3H3/p+1",
    "inchi_2": "InChI=1S/C5H11NO2/c1-6(2,3)4-5(7)8/h4H2,1-3H3",
    "results": {
        "COMPLETE_IDENTITY": false,
        "ISOTOPIC_INDEPENDENCE": false,
        "SALTS_INDEPENDENCE": false,
        "CHARGES_INDEPENDENCE": true,
        "DOUBLE_BONDS_INDEPENDENCE": true,
        "ISOMER_INDEPENDENCE_A": true,
        "ISOMER_INDEPENDENCE_B": null,
        "ISOMER_INDEPENDENCE_C": null,
        "ISOMER_INDEPENDENCE_D": null,
        "TAUTOMER_INDEPENDENCE": true
    }
}

null indicates the level is not applicable (non-lipid molecule).

With --only-equal

Only layers that evaluated to true are shown, under the matches key:

{
    "inchi_1": "InChI=1S/C5H11NO2/c1-6(2,3)4-5(7)8/h4H2,1-3H3/p+1",
    "inchi_2": "InChI=1S/C5H11NO2/c1-6(2,3)4-5(7)8/h4H2,1-3H3",
    "matches": {
        "CHARGES_INDEPENDENCE": true
    }
}

MGF change log

{
    "layer": "CHARGES_INDEPENDENCE",
    "total_changes": 3,
    "changes": [
        {
            "original_structure": "InChI=1S/.../p-1/t4-,6-,7-,10-/m1/s1",
            "structure_type": "INCHI",
            "smiles_to_inchi": null,
            "normalized_inchi": "InChI=1S/.../t4-,6-,7-,10-/m1/s1",
            "canonical_inchi":  "InChI=1S/.../t4-,6-,7-,10-/m1/s1"
        }
    ]
}

For SMILES entries, smiles_to_inchi contains the intermediate InChI produced by conversion. normalized_inchi is null when no charge layer was removed (only a SMILES→InChI conversion was performed).

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Example files

The files_examples/ directory contains ready-to-use input files and expected outputs for all four comparison modes, including InChI files, SMILES files, and MGF files covering salt normalization, charge normalization, and SMILES-in-MGF cases.

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Related repositories

Repository	Description
inchi-identity-api	Flask REST backend exposing the same comparison engine via HTTP endpoints
inchi-identity-app	Interactive web frontend for browser-based comparison, file upload, and molecular visualization

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