From 7e66e2add624911350fae536d801448811ba803c Mon Sep 17 00:00:00 2001
From: Bill Hlavacek <bill.hlavacek@gmail.com>
Date: Sun, 10 May 2026 16:00:05 -0600
Subject: [PATCH] Render FunctionProduct rate-law type in resolve_ratelaw

`RuleBlockXML.resolve_ratelaw` and `PopulationMapBlockXML.resolve_ratelaw`
recognize Ele/Function/MM/Sat/Hill/Arrhenius but fall through to a
silent `print("don't recognize rate law type")` for FunctionProduct,
which then surfaces as the wrong rate constant in the regenerated BNGL.

FunctionProduct is a real BNG2.pl rate-law modifier
(`Perl2/RateLaw.pm:105`, `:137`, `:670`) used when a rule's rate is the
product of two local functions evaluated in different reactant-pattern
contexts (e.g. `mobility_factor(x) * mobility_factor(y)` in the
BLBR_immobilization model family). Vanilla NFsim already supports it
(`NFinput/NFinput.cpp:2251`), so the only thing standing between these
models and a successful round-trip is the parser refusing the shape.

Fix: add a FunctionProduct branch that emits

    FunctionProduct("name1(args1)","name2(args2)")

mirroring BNG2.pl's own serializer at `Perl2/RateLaw.pm:670-677`. New
helper `_ratelaw_arg_ids` accepts both single-Argument (dict) and
multi-Argument (list) shapes the same way the existing MM/Sat handler
does.

Patched in both `RuleBlockXML` and `PopulationMapBlockXML` since both
classes carry their own copy of `resolve_ratelaw`.
---
 bionetgen/modelapi/xmlparsers.py | 54 ++++++++++++++++++++++++++++++++
 1 file changed, 54 insertions(+)

diff --git a/bionetgen/modelapi/xmlparsers.py b/bionetgen/modelapi/xmlparsers.py
index bf529821..5fc41e5f 100644
--- a/bionetgen/modelapi/xmlparsers.py
+++ b/bionetgen/modelapi/xmlparsers.py
@@ -600,6 +600,17 @@ def resolve_ratelaw(self, xml):
             rate_cts = rate_cts_xml["RateConstant"]["@value"]
         elif rate_type == "Function":
             rate_cts = xml["@name"]
+        elif rate_type == "FunctionProduct":
+            # Mirror BNG2.pl/Perl2/RateLaw.pm:670-677 — emit
+            # FunctionProduct("name1(args1)","name2(args2)") so the
+            # regenerated BNGL round-trips through BNG2.pl's parser
+            # and reaches NFsim, which supports FunctionProduct
+            # natively (NFinput.cpp:2251).
+            name1 = xml["@name1"]
+            name2 = xml["@name2"]
+            a1 = self._ratelaw_arg_ids(xml.get("ListOfArguments1"))
+            a2 = self._ratelaw_arg_ids(xml.get("ListOfArguments2"))
+            rate_cts = f'FunctionProduct("{name1}({a1})","{name2}({a2})")'
         elif (
             rate_type == "MM"
             or rate_type == "Sat"
@@ -621,6 +632,22 @@ def resolve_ratelaw(self, xml):
             print("don't recognize rate law type")
         return rate_cts
 
+    def _ratelaw_arg_ids(self, args_xml):
+        """Join the ``@id`` of each Argument in a ListOfArguments[N] element.
+
+        BNG-XML packs a single Argument as a dict and multiple as a list,
+        so we accept both shapes. Returns "" when ``args_xml`` is None
+        or empty so callers can render zero-arg ``f()`` consistently.
+        """
+        if not args_xml:
+            return ""
+        args = args_xml.get("Argument") if hasattr(args_xml, "get") else None
+        if args is None:
+            return ""
+        if isinstance(args, list):
+            return ",".join(str(a["@id"]) for a in args)
+        return str(args["@id"])
+
     def resolve_rxn_side(self, xml):
         # this is either reactant or product
         if xml is None:
@@ -849,6 +876,17 @@ def resolve_ratelaw(self, xml):
             rate_cts = rate_cts_xml["RateConstant"]["@value"]
         elif rate_type == "Function":
             rate_cts = xml["@name"]
+        elif rate_type == "FunctionProduct":
+            # Mirror BNG2.pl/Perl2/RateLaw.pm:670-677 — emit
+            # FunctionProduct("name1(args1)","name2(args2)") so the
+            # regenerated BNGL round-trips through BNG2.pl's parser
+            # and reaches NFsim, which supports FunctionProduct
+            # natively (NFinput.cpp:2251).
+            name1 = xml["@name1"]
+            name2 = xml["@name2"]
+            a1 = self._ratelaw_arg_ids(xml.get("ListOfArguments1"))
+            a2 = self._ratelaw_arg_ids(xml.get("ListOfArguments2"))
+            rate_cts = f'FunctionProduct("{name1}({a1})","{name2}({a2})")'
         elif (
             rate_type == "MM"
             or rate_type == "Sat"
@@ -870,6 +908,22 @@ def resolve_ratelaw(self, xml):
             print("don't recognize rate law type")
         return rate_cts
 
+    def _ratelaw_arg_ids(self, args_xml):
+        """Join the ``@id`` of each Argument in a ListOfArguments[N] element.
+
+        BNG-XML packs a single Argument as a dict and multiple as a list,
+        so we accept both shapes. Returns "" when ``args_xml`` is None
+        or empty so callers can render zero-arg ``f()`` consistently.
+        """
+        if not args_xml:
+            return ""
+        args = args_xml.get("Argument") if hasattr(args_xml, "get") else None
+        if args is None:
+            return ""
+        if isinstance(args, list):
+            return ",".join(str(a["@id"]) for a in args)
+        return str(args["@id"])
+
 
 # TODO: Store operations!
 class Operation: