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feat: cardiolipins are now named according to the common convention #514

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Merged
comcon1 merged 1 commit into from
Jun 27, 2026
Merged

feat: cardiolipins are now named according to the common convention #514

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40 changes: 40 additions & 0 deletions src/fairmd/lipids/auxiliary/opconvertor.py
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Original file line number Diff line number Diff line change
Expand Up @@ -59,6 +59,7 @@ def _apply_naming(cls, opdic: dict) -> None:
# initialize the registry
@classmethod
def _initialize(cls):
# usual FA (glycerolipids)
def _snX_c_renamer(row: dict) -> dict: # noqa: N802
match = re.match(r"M_G[12]C([0-9]{1,2})_M", row["C"])
if match and len(match.groups()) == 1:
Expand All @@ -69,6 +70,20 @@ def _snX_c_renamer(row: dict) -> dict: # noqa: N802
cls._register("sn-1", _snX_c_renamer)
cls._register("sn-2", _snX_c_renamer)

# usual FA (cardiolipins)
def _snXX_c_renamer(row: dict) -> dict: # noqa: N802
match = re.match(r"M_G[12][12]C([0-9]{1,2})_M", row["C"])
if match and len(match.groups()) == 1:
idx = int(match[1])
row["C"] = str(idx - 1)
return row

cls._register("sn-1 1", _snXX_c_renamer)
cls._register("sn-1 2", _snXX_c_renamer)
cls._register("sn-2 1", _snXX_c_renamer)
cls._register("sn-2 2", _snXX_c_renamer)

# FA (sphingolipids)
def _fa_c_renamer(row: dict) -> dict:
match = re.match(r"M_N1C([0-9]{1,2})_M", row["C"])
if match and len(match.groups()) == 1:
Expand All @@ -78,6 +93,7 @@ def _fa_c_renamer(row: dict) -> dict:

cls._register("fa", _fa_c_renamer)

# glycerol backbone (glycerolipids)
def _gbb_c_renamer(row: dict) -> dict:
match = re.match(r"M_G([1-3])_M", row["C"])
if match and len(match.groups()) == 1:
Expand All @@ -87,6 +103,18 @@ def _gbb_c_renamer(row: dict) -> dict:

cls._register("glycerol backbone", _gbb_c_renamer)

# glycerol bb (cardiolipins)
def _gbbX_c_renamer(row: dict) -> dict:
match = re.match(r"M_G[1-2]([1-3])_M", row["C"])
if match and len(match.groups()) == 1:
idx = int(match[1])
row["C"] = f"g{idx}"
return row

cls._register("glycerol backbone 1", _gbbX_c_renamer)
cls._register("glycerol backbone 2", _gbbX_c_renamer)

# usual headgroup (phospholipids)
def _headgroup_c_renamer(row: dict) -> dict:
if row["C"] == "M_G3C4_M":
row["C"] = "伪"
Expand All @@ -98,6 +126,17 @@ def _headgroup_c_renamer(row: dict) -> dict:

cls._register("headgroup", _headgroup_c_renamer)

# intermediate glycerol (CL)
def _midglyc_c_renamer(row: dict) -> dict:
match = re.match(r"M_G0([1-3])_M", row["C"])
if match and len(match.groups()) == 1:
idx = int(match[1])
row["C"] = f"g{idx}'"
return row

cls._register("headgroup", _midglyc_c_renamer)

# universal H renamer
def _h_renamer(row: dict) -> dict:
match = re.match(r"M_.+H([1-4])_M", row["H"])
if match and len(match.groups()) == 1:
Expand All @@ -107,6 +146,7 @@ def _h_renamer(row: dict) -> dict:

cls._register("_all_", _h_renamer)

# universal plain C renamer
def _plain_c_renamer(row: dict) -> dict:
match = re.match(r"M_C([0-9]+)_M", row["C"])
if match and len(match.groups()) == 1:
Expand Down
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