masster 0.3.19__tar.gz → 0.3.20__tar.gz

{masster-0.3.19 → masster-0.3.20}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: masster
-Version: 0.3.19
+Version: 0.3.20
 Summary: Mass spectrometry data analysis package
 Project-URL: homepage, https://github.com/zamboni-lab/masster
 Project-URL: repository, https://github.com/zamboni-lab/masster

{masster-0.3.19 → masster-0.3.20}/pyproject.toml

@@ -1,7 +1,7 @@
 
 [project]
 name = "masster"
-version = "0.3.19"
+version = "0.3.20"
 description = "Mass spectrometry data analysis package"
 authors = [
     { name = "Zamboni Lab" }

{masster-0.3.19 → masster-0.3.20}/src/masster/__init__.py

@@ -12,6 +12,7 @@ from masster._version import __version__
 
 # from masster._version import get_version
 from masster.chromatogram import Chromatogram
+from masster.lib import Lib
 from masster.sample.sample import Sample
 from masster.spectrum import Spectrum
 from masster.study.study import Study
@@ -19,6 +20,7 @@ from masster.study.study import Study
 
 __all__ = [
     "Chromatogram",
+    "Lib",
     "Sample",
     "Spectrum",
     "Study",

{masster-0.3.19 → masster-0.3.20}/src/masster/_version.py

@@ -1,7 +1,7 @@
 from __future__ import annotations
 
 
-__version__ = "0.3.19"
+__version__ = "0.3.20"
 
 
 def get_version():

masster-0.3.20/src/masster/data/libs/README.md

@@ -0,0 +1,17 @@
+metabolite lib CSVs
+
+This folder contains programmatically generated metabolite lists used as example libs for the masster package.
+
+Files (generated by scripts in the repository root):
+- `urine_metabolites.csv` - best-effort list of metabolites reported in human urine (generated by `urine.py`).
+- `central_carbon_metabolites.csv` - curated central carbon metabolism compound list (generated by `ccm.py`).
+
+Generation method:
+- Names were curated in the scripts and resolved to structural identifiers via PubChem PUG-REST.
+- `urine.py` attempts to parse local HMDB XML (if present) before falling back to the HMDB web listing.
+- Both scripts use retries and basic normalization to improve PubChem matching.
+
+Notes & recommendations:
+- For authoritative resource lists, download HMDB / ChEBI / KEGG bulk data and map IDs (preferred).
+- Respect HMDB licensing and attribution when using HMDB data.
+- Verify ambiguous or missing entries before use in production analyses.

masster-0.3.20/src/masster/data/libs/ccm.py

@@ -0,0 +1,533 @@
+"""Generate a cleaned CSV of central-carbon metabolism compounds.
+
+Workflow:
+- Use a curated list of central-carbon/metabolism-relevant names (glycolysis, TCA, PPP,
+    amino acids, common organic acids, nucleotides, fatty acids, cofactors, sugars).
+- Query PubChem's PUG-REST for MolecularFormula, CanonicalSMILES and InChIKey for each name
+    with retries and basic name normalization to improve matching.
+- Save results to `masster/data/examples/central_carbon_metabolites.csv`.
+- Test loading with `masster.lib.Lib.import_csv`.
+
+This is a best-effort programmatic lookup; ambiguous names may not resolve (those rows will
+have empty Formula/SMILES/InChIKey). For authoritative lists, prefer curated databases
+(e.g., HMDB, KEGG) and bulk downloads.
+"""
+
+from __future__ import annotations
+
+import csv
+import sys
+import time
+import os
+import re
+from urllib.parse import quote
+
+try:
+    import requests
+except Exception:
+    requests = None
+
+try:
+    from rdkit import Chem
+except Exception:
+    Chem = None
+
+try:
+    from rdkit import Chem
+except Exception:
+    Chem = None
+
+
+CCM_METABOLITES = [
+    # Central carbon metabolism core (glycolysis, TCA, PPP, gluconeogenesis, pyruvate metabolism)
+    "Glucose",
+    "Glucose-6-phosphate",
+    "Fructose-6-phosphate",
+    "Fructose-1,6-bisphosphate",
+    "Glyceraldehyde-3-phosphate",
+    "Dihydroxyacetone phosphate",
+    "3-Phosphoglycerate",
+    "2-Phosphoglycerate",
+    "Phosphoenolpyruvate",
+    "Pyruvate",
+    "Lactate",
+    "Acetyl-CoA",
+    "Citric acid",
+    "Isocitrate",
+    "Alpha-ketoglutaric acid",
+    "Succinyl-CoA",
+    "Succinic acid",
+    "Fumaric acid",
+    "Malic acid",
+    "Oxaloacetic acid",
+    "Ribose-5-phosphate",
+    "Ribulose-5-phosphate",
+    "Sedoheptulose-7-phosphate",
+    "Erythrose-4-phosphate",
+    "Sedoheptulose-1,7-bisphosphate",
+    "Glycerol-3-phosphate",
+    "Glycerate",
+    "Pentose",
+    "Acetaldehyde",
+    "Acetic acid",
+
+    # Proteinogenic amino acids (20 standard)
+    "Alanine",
+    "Arginine",
+    "Asparagine",
+    "Aspartic acid",
+    "Cysteine",
+    "Glutamic acid",
+    "Glutamine",
+    "Glycine",
+    "Histidine",
+    "Isoleucine",
+    "Leucine",
+    "Lysine",
+    "Methionine",
+    "Phenylalanine",
+    "Proline",
+    "Serine",
+    "Threonine",
+    "Tryptophan",
+    "Tyrosine",
+    "Valine",
+    # Additional amino acid related metabolites
+    "Ornithine",
+    "Citrulline",
+    "Homocysteine",
+    "S-adenosylmethionine",
+    "S-adenosylhomocysteine",
+
+    # Common organic acids / intermediates & related small metabolites
+    "Formic acid",
+    "Propionic acid",
+    "Butyric acid",
+    "Malonic acid",
+    "2-Hydroxyglutarate",
+    "3-Hydroxybutyrate",
+    "Acetoacetate",
+    "Beta-hydroxybutyrate",
+    "Pyruvic acid",
+    "Lactic acid",
+
+    # Fatty acids (common)
+    "Myristic acid",
+    "Palmitic acid",
+    "Stearic acid",
+    "Palmitoleic acid",
+    "Oleic acid",
+    "Linoleic acid",
+    "Alpha-linolenic acid",
+    "Arachidonic acid",
+
+    # Nucleobases and nucleosides
+    "Adenine",
+    "Guanine",
+    "Cytosine",
+    "Thymine",
+    "Uracil",
+    "Adenosine",
+    "Guanosine",
+    "Cytidine",
+    "Uridine",
+
+    # Nucleotides (mono/di/tri)
+    "AMP",
+    "ADP",
+    "ATP",
+    "GMP",
+    "GDP",
+    "GTP",
+    "CMP",
+    "CDP",
+    "CTP",
+    "UMP",
+    "UDP",
+    "UTP",
+
+    # Cofactors / common metabolites
+    "NAD+",
+    "NADH",
+    "NADP+",
+    "NADPH",
+    "FAD",
+    "FMN",
+    "Coenzyme A",
+    "Pantothenic acid",
+    "Riboflavin",
+    "Niacin",
+
+    # Sugar and sugar derivatives
+    "Fructose",
+    "Mannose",
+    "Mannose-6-phosphate",
+    "Ribose",
+    "Glucosamine",
+    "N-acetylglucosamine",
+
+    # Other common metabolites
+    "Choline",
+    "Betaine",
+    "Carnitine",
+    "Phosphocholine",
+    "Glycerol",
+    "Sorbitol",
+    "Inositol",
+    "Cholesterol",
+    "Pantothenate",
+]
+
+
+def fetch_from_pubchem(name: str):
+    """Fetch formula, smiles and inchikey from PubChem by compound name.
+
+    Uses basic normalization and retries with exponential backoff. Returns
+    (formula, smiles, inchikey) or (None, None, None) on failure.
+    """
+    props = (None, None, None)
+
+    def normalize_name(n: str) -> str:
+        if not n:
+            return n
+        s = n
+        s = re.sub(r"\(.*?\)", "", s)  # remove parentheses
+        s = s.replace("+", "+")
+        s = s.replace("–", "-")
+        s = re.sub(r"\s+", " ", s).strip()
+        # common abbreviation mapping
+        mapping = {
+            "AMP": "Adenosine monophosphate",
+            "ADP": "Adenosine diphosphate",
+            "ATP": "Adenosine triphosphate",
+            "GMP": "Guanosine monophosphate",
+            "GDP": "Guanosine diphosphate",
+            "GTP": "Guanosine triphosphate",
+            "NAD+": "Nicotinamide adenine dinucleotide",
+            "NADH": "Nicotinamide adenine dinucleotide (reduced)",
+            "CoA": "Coenzyme A",
+        }
+        up = s.upper()
+        if up in mapping:
+            return mapping[up]
+        return s
+
+    query = normalize_name(name)
+
+    def try_query(q: str):
+        url = (
+            f"https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/{quote(q)}/property/"
+            + "MolecularFormula,CanonicalSMILES,InChI,InChIKey/JSON"
+        )
+        try:
+            r = requests.get(url, timeout=15)
+            if r.status_code == 200:
+                return r.json()
+        except Exception:
+            return None
+        return None
+
+    def try_query_inchikey(ik: str):
+        url = (
+            f"https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/{quote(ik)}/property/"
+            + "MolecularFormula,CanonicalSMILES,InChI,InChIKey/JSON"
+        )
+        try:
+            r = requests.get(url, timeout=15)
+            if r.status_code == 200:
+                return r.json()
+        except Exception:
+            return None
+        return None
+
+    def try_query_cid(cid: int):
+        url = (
+            f"https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/{cid}/property/"
+            + "MolecularFormula,CanonicalSMILES,InChI,InChIKey/JSON"
+        )
+        try:
+            r = requests.get(url, timeout=15)
+            if r.status_code == 200:
+                return r.json()
+        except Exception:
+            return None
+        return None
+
+    def try_get_cids_from_inchikey(ik: str):
+        url = f"https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/{quote(ik)}/cids/JSON"
+        try:
+            r = requests.get(url, timeout=15)
+            if r.status_code == 200:
+                j = r.json()
+                if 'IdentifierList' in j and 'CID' in j['IdentifierList']:
+                    return j['IdentifierList']['CID']
+        except Exception:
+            return []
+        return []
+
+    if requests is None:
+        return props
+
+    # exponential backoff attempts
+    attempts = 3
+    for i in range(attempts):
+        j = try_query(query)
+        if j:
+            try:
+                if "PropertyTable" in j and "Properties" in j["PropertyTable"]:
+                    p = j["PropertyTable"]["Properties"][0]
+                    mf = p.get("MolecularFormula")
+                    sm = p.get("CanonicalSMILES")
+                    inchi = p.get("InChI")
+                    ik = p.get("InChIKey")
+                    # if SMILES missing, try a lookup by InChIKey (dedicated endpoint)
+                    if not sm and ik:
+                        j2 = try_query_inchikey(ik)
+                        if j2 and "PropertyTable" in j2 and "Properties" in j2["PropertyTable"]:
+                            p2 = j2["PropertyTable"]["Properties"][0]
+                            sm = p2.get("CanonicalSMILES") or sm
+                            inchi = inchi or p2.get("InChI")
+
+                    # if still no SMILES but InChI present and RDKit available, try InChI -> SMILES conversion
+                    if not sm and inchi and Chem is not None:
+                        try:
+                            m = Chem.MolFromInchi(inchi)
+                            if m is not None:
+                                sm = Chem.MolToSmiles(m, isomericSmiles=True)
+                        except Exception:
+                            pass
+
+                    # if still no SMILES, try fetching CIDs from InChIKey and query a CID record
+                    if not sm and ik:
+                        cids = try_get_cids_from_inchikey(ik)
+                        for cid in (cids or [])[:5]:
+                            j3 = try_query_cid(cid)
+                            if j3 and "PropertyTable" in j3 and "Properties" in j3["PropertyTable"]:
+                                p3 = j3["PropertyTable"]["Properties"][0]
+                                sm = p3.get("CanonicalSMILES") or sm
+                                if sm:
+                                    break
+
+                    return (mf, sm, ik)
+            except Exception:
+                pass
+        time.sleep(1 + 2 ** i)
+
+    # final fallback: try raw name without normalization
+    j = try_query(name)
+    if j and "PropertyTable" in j and "Properties" in j["PropertyTable"]:
+        p = j["PropertyTable"]["Properties"][0]
+        return (p.get("MolecularFormula"), p.get("CanonicalSMILES"), p.get("InChIKey"))
+
+    return props
+
+
+def generate_csv(out_path: str = "central_carbon_metabolites.csv"):
+    rows = []
+    for name in CCM_METABOLITES:
+        formula, smiles, inchikey = (None, None, None)
+        if requests is not None:
+            formula, smiles, inchikey = fetch_from_pubchem(name)
+
+        # Neutralize charged molecular formulas (e.g., trailing +, -, 2+, 3-)
+        # by adjusting the hydrogen count accordingly and removing the explicit charge.
+        def neutralize_formula(fmt: str) -> str:
+            if not fmt:
+                return fmt
+            s = fmt.strip()
+            # normalize common unicode superscripts (²³¹⁺⁻) to ascii
+            sup_map = str.maketrans({
+                "²": "2",
+                "³": "3",
+                "¹": "1",
+                "⁺": "+",
+                "⁻": "-",
+            })
+            s = s.translate(sup_map)
+            # Remove enclosing brackets if present, e.g. [C6H5O7]2-
+            if s.startswith("[") and s.endswith("]"):
+                s = s[1:-1]
+            # strip trailing punctuation or separators (commas, periods, parentheses)
+            s = s.rstrip(" \t\n\r,.;)")
+            # detect trailing charge formats e.g. '2-', '-','3+','+','-2','+2' optionally with whitespace
+            m = re.search(r"([+-]?\d+[+-]?|[+-])\s*$", s)
+            if not m:
+                return fmt
+
+            charge_str = m.group(1)
+            base = s[: m.start(1)].strip()
+            # determine magnitude and sign for patterns like '2-' or '-2' or '+2' or '3+'
+            sign = 1
+            mag = 1
+            if charge_str[0] in '+-':
+                # formats like '-2' or '+2' or '-' or '+'
+                sign = -1 if charge_str[0] == '-' else 1
+                mag = int(charge_str[1:]) if len(charge_str) > 1 and charge_str[1:].isdigit() else 1
+            elif charge_str[-1] in '+-':
+                # formats like '2-' or '3+'
+                sign = -1 if charge_str[-1] == '-' else 1
+                mag = int(charge_str[:-1]) if charge_str[:-1].isdigit() else 1
+
+            # parse element counts from base formula
+            tokens = re.findall(r"([A-Z][a-z]?)(\d*)", base)
+            if not tokens:
+                # if parsing failed, return base without charge marker
+                return base
+
+            elems = []
+            counts: dict[str, int] = {}
+            for el, num in tokens:
+                counts[el] = counts.get(el, 0) + (int(num) if num else 1)
+                if el not in elems:
+                    elems.append(el)
+
+            # adjust hydrogens: negative charge -> add H (protonation),
+            # positive charge -> remove H (deprotonation)
+            if sign == -1:
+                counts["H"] = counts.get("H", 0) + mag
+                if "H" not in elems:
+                    # place H after C if present, else at beginning
+                    if "C" in elems:
+                        idx = elems.index("C") + 1
+                        elems.insert(idx, "H")
+                    else:
+                        elems.insert(0, "H")
+            else:
+                if "H" in counts:
+                    counts["H"] = counts.get("H", 0) - mag
+                    if counts["H"] <= 0:
+                        counts.pop("H", None)
+                        if "H" in elems:
+                            elems.remove("H")
+                else:
+                    # can't remove hydrogens we don't have; leave base unchanged
+                    pass
+
+            # rebuild formula preserving original element order
+            parts = []
+            for el in elems:
+                if el in counts:
+                    n = counts[el]
+                    parts.append(f"{el}{n if n!=1 else ''}")
+            new_formula = "".join(parts)
+            return new_formula
+
+        try:
+            formula_neutral = neutralize_formula(formula) if formula else formula
+            if formula and formula_neutral != formula:
+                # prefer the neutralized formula in the output
+                formula = formula_neutral
+        except Exception:
+            # if anything goes wrong, keep original formula
+            pass
+
+        # neutralize SMILES using RDKit when available
+        def neutralize_smiles(smiles_str: str) -> str:
+            if not smiles_str or Chem is None:
+                return smiles_str
+            try:
+                m = Chem.MolFromSmiles(smiles_str, sanitize=True)
+                if m is None:
+                    return smiles_str
+                # Work on a read-write mol to adjust hydrogens and formal charges
+                rw = Chem.RWMol(Chem.AddHs(m))
+                to_remove = []
+                for a in list(rw.GetAtoms()):
+                    idx = a.GetIdx()
+                    q = a.GetFormalCharge()
+                    if q > 0:
+                        # remove up to q hydrogen neighbors (by index)
+                        h_neighbors = [nbr.GetIdx() for nbr in a.GetNeighbors() if nbr.GetSymbol() == "H"]
+                        remove = h_neighbors[: min(len(h_neighbors), q)]
+                        to_remove.extend(remove)
+                    elif q < 0:
+                        # add -q hydrogens bonded to this atom
+                        for _ in range(-q):
+                            h = Chem.Atom("H")
+                            new_idx = rw.AddAtom(h)
+                            rw.AddBond(idx, new_idx, Chem.BondType.SINGLE)
+                    # reset formal charge on this atom
+                    rw.GetAtomWithIdx(idx).SetFormalCharge(0)
+
+                # remove hydrogen atoms collected, in reverse order so indices stay valid
+                for ridx in sorted(set(to_remove), reverse=True):
+                    try:
+                        rw.RemoveAtom(ridx)
+                    except Exception:
+                        pass
+
+                newm = rw.GetMol()
+                try:
+                    Chem.SanitizeMol(newm)
+                except Exception:
+                    # best effort: continue
+                    pass
+                # remove explicit Hs to produce a clean canonical SMILES
+                try:
+                    no_h = Chem.RemoveHs(newm)
+                except Exception:
+                    no_h = newm
+                sm = Chem.MolToSmiles(no_h, isomericSmiles=True)
+                return sm
+            except Exception:
+                return smiles_str
+
+        try:
+            smiles = neutralize_smiles(smiles) if smiles else smiles
+        except Exception:
+            pass
+        rows.append({
+            "Name": name,
+            "Formula": formula or "",
+            "SMILES": smiles or "",
+            "InChIKey": inchikey or "",
+        })
+
+    # Ensure output directory exists (data/libs)
+    out_dir = os.path.join('masster', 'data', 'libs')
+    os.makedirs(out_dir, exist_ok=True)
+    out_path_full = os.path.join(out_dir, os.path.basename(out_path))
+
+    fieldnames = ["Name", "Formula", "SMILES", "InChIKey"]
+    with open(out_path_full, "w", newline="", encoding="utf-8") as f:
+        writer = csv.DictWriter(f, fieldnames=fieldnames)
+        writer.writeheader()
+        for r in rows:
+            writer.writerow(r)
+
+    print(f"Wrote {len(rows)} entries to {out_path_full}")
+    return out_path_full
+
+
+def test_load_with_lib(csv_path: str):
+    """Try to load the generated CSV using masster.lib.Lib.import_csv."""
+    try:
+        from masster.lib import Lib
+    except Exception as e:
+        print(f"Cannot import masster.lib.Lib: {e}")
+        return False
+
+    try:
+        lib = Lib()
+        # import_csv expects a path and optional polarity; use polarity=None to import both
+        lib.import_csv(csv_path, polarity=None)
+        print(f"Lib loaded: {len(lib)} entries")
+        # print a few entries (polars DataFrame -> head)
+        try:
+            print(lib.lib_df.select(["name", "formula", "adduct", "mz"]).head(8))
+        except Exception:
+            # older implementations might not have the same columns; just show length
+            pass
+        return True
+    except Exception as e:
+        print(f"Failed to load CSV with Lib.import_csv: {e}")
+        return False
+
+
+if __name__ == "__main__":
+    csv_file = generate_csv()
+    ok = test_load_with_lib(csv_file)
+    if not ok:
+        print("Test failed; please inspect messages above.")
+        sys.exit(2)
+    print("Done.")

masster-0.3.20/src/masster/data/libs/central_carbon_README.md

@@ -0,0 +1,17 @@
+central_carbon_metabolites.csv
+
+This folder contains example compound lists used by the masster package.
+
+Files:
+- central_carbon_metabolites.csv: a best-effort list of central carbon metabolism related
+  compounds (glycolysis, TCA cycle, pentose phosphate pathway, amino acids, organic acids,
+  nucleotides, fatty acids, cofactors). The CSV was generated by `ccm.py` which:
+  - Uses a curated name list included in the script.
+  - Resolves structural identifiers (MolecularFormula, CanonicalSMILES, InChIKey) via PubChem PUG-REST
+    with retries and basic normalization.
+  - Writes a CSV with columns: Name, Formula, SMILES, InChIKey.
+
+Notes:
+- This is a programmatically generated list. For authoritative lists, use database bulk downloads
+  (HMDB, KEGG, ChEBI) and provide explicit IDs. Prefer HMDB or ChEBI for metabolomics work.
+- Some compound names may be ambiguous; verify entries before use.