From 3f66ce6ec0e44ab8f422edb27c37540ae33db010 Mon Sep 17 00:00:00 2001
From: Rodrigo V Honorato <r.vargashonorato@uu.nl>
Date: Thu, 19 Sep 2024 15:10:47 +0200
Subject: [PATCH] add fallback logic to define `cns_exec`

---
 src/haddock/core/defaults.py                    | 16 ++++++++++++++--
 src/haddock/modules/topology/topoaa/__init__.py |  7 +++----
 2 files changed, 17 insertions(+), 6 deletions(-)

diff --git a/src/haddock/core/defaults.py b/src/haddock/core/defaults.py
index fa8a8805f..d957e6676 100644
--- a/src/haddock/core/defaults.py
+++ b/src/haddock/core/defaults.py
@@ -1,19 +1,31 @@
 """All default parameters used by the framework."""
 
 import importlib.resources
+import os
 import string
+import sys
 from pathlib import Path
 
 import yaml
 from pkg_resources import resource_filename
 
 import haddock
-from haddock import core_path
+from haddock import core_path, log
 
 
 BINARY_DIR = Path(importlib.resources.files(haddock) / "bin")  # type: ignore
 
-cns_exec = Path(resource_filename("haddock", "bin/cns"))
+cns_exec = Path(resource_filename("haddock", "bin/cns_"))
+if not cns_exec.exists():
+    log.warning("CNS executable not found at %s", cns_exec)
+    _cns_exec = os.environ.get("CNS_EXEC")
+    if _cns_exec is None:
+        log.error(
+            "Please define the location the CNS binary by setting a CNS_EXEC system variable"
+        )
+        sys.exit(1)
+    else:
+        cns_exec = Path(_cns_exec)
 
 CONTACT_FCC_EXEC = Path(resource_filename("haddock", "bin/contact_fcc"))
 FAST_RMSDMATRIX_EXEC = Path(resource_filename("haddock", "bin/fast-rmsdmatrix"))
diff --git a/src/haddock/modules/topology/topoaa/__init__.py b/src/haddock/modules/topology/topoaa/__init__.py
index b8b5ed111..29f556b3d 100644
--- a/src/haddock/modules/topology/topoaa/__init__.py
+++ b/src/haddock/modules/topology/topoaa/__init__.py
@@ -29,7 +29,7 @@
 from functools import partial
 from pathlib import Path
 
-from haddock.core.defaults import MODULE_DEFAULT_YAML
+from haddock.core.defaults import MODULE_DEFAULT_YAML, cns_exec
 from haddock.core.typing import FilePath, Optional, ParamDict, ParamMap, Union
 from haddock.libs import libpdb
 from haddock.libs.libcns import (
@@ -37,7 +37,7 @@
     load_workflow_params,
     prepare_output,
     prepare_single_input,
-)
+    )
 from haddock.libs.libontology import Format, PDBFile, TopologyFile
 from haddock.libs.libstructure import make_molecules
 from haddock.libs.libsubprocess import CNSJob
@@ -262,13 +262,12 @@ def _run(self) -> None:
                 # Add new job to the pool
                 output_filename = Path(f"{model.stem}.{Format.CNS_OUTPUT}")
                 err_fname = f"{model.stem}.cnserr"
-
                 job = CNSJob(
                     topoaa_input,
                     output_filename,
                     err_fname,
                     envvars=self.envvars,
-                    cns_exec=self.params["cns_exec"],
+                    cns_exec=cns_exec,
                 )
 
                 jobs.append(job)