feat: add --thiol3 arg

fealden/fealden.py

@@ -119,7 +119,12 @@ def main() -> None:
     parser.add_argument(
         "--fixed",
         action="store_true",
-        help="Fix methylene blue to 3' termini, no file output",
+        help="Fix methylene blue to 3' termini",
+    )
+    parser.add_argument(
+        "--thiol3",
+        action="store_false",
+        help="Fix thiol to 3' termini",
     )
     parser.add_argument(
         "-out",
@@ -161,11 +166,17 @@ def main() -> None:
         args.interactive,
         args.out,
         args.fixed,
+        args.thiol3,
     )
 
 
 def generate_sensor(
-    seed: seed.Seed, rec_seq: str, num_poss_sen: int, core: int, fixed: bool
+    seed: seed.Seed,
+    rec_seq: str,
+    num_poss_sen: int,
+    core: int,
+    fixed: bool,
+    thiol: bool,
 ) -> list[sensor.Sensor]:
     """
     generate_sensor() gens a # of possible sensors and returns a list of valid sensors.
@@ -190,7 +201,7 @@ def generate_sensor(
 
     while version < num_poss_sen:
         version += 1
-        sen = seed.build_sensor(core, version, rec_seq, fixed)
+        sen = seed.build_sensor(core, version, rec_seq, fixed, thiol)
 
         # only keep good sensors
         if sen is None:
@@ -239,6 +250,7 @@ def __init__(
         interactive: bool,
         output_file: str,
         fixed: bool,
+        thiol: bool,
     ) -> None:
         """Initialize new Fealden instance."""
         self.rec_seq = rec_seq
@@ -270,7 +282,10 @@ def __init__(
         while i < num_process:
             i += 1
             tasks.extend(
-                [(s, self.rec_seq, seed_sens_per_process, i, fixed) for s in seeds]
+                [
+                    (s, self.rec_seq, seed_sens_per_process, i, fixed, thiol)
+                    for s in seeds
+                ]
             )
 
         for t in tasks:

fealden/fold.py

@@ -162,10 +162,7 @@ def get_distance(self, index1: int, index2: int) -> int:
             distance   <- an integer, the calculated distance
         """
         if index1 > index2:
-            # TODO: Double-check this implementation
-            # temp = index1
-            index1 = index2
-            index2 = index1
+            index1, index2 = index2, index1
 
         node1 = self.ptr_list[index1 - 1]
         node2 = self.ptr_list[index2 - 1]

fealden/seed.py

@@ -182,7 +182,12 @@ def build_the_rest(
         self.build_the_rest(data[1:], nodes)
 
     def build_sensor(
-        self, core: int, version: int, base_seq: str, fixed: bool
+        self,
+        core: int,
+        version: int,
+        base_seq: str,
+        fixed: bool,
+        thiol: bool,
     ) -> sensor.Sensor | None:
         """
         build_sensor() first builds a 'Sensor' sequence using the 'Seed' of 'self'
@@ -225,6 +230,7 @@ def build_sensor(
             self.name,
             base_seq,
             fixed,
+            thiol,
         )
 
     def generate_node_sizes(self) -> None:

fealden/sensor.py

@@ -24,6 +24,7 @@ def __init__(
         seed_name: str,
         base_seq: str,
         fixed: bool,
+        thiol: bool = True,
     ):
         """
         This is the constructor for Sensor.
@@ -58,6 +59,7 @@ def __init__(
         self.on_to_off_dist = 0
         self.base_seq = base_seq
         self.fixed = fixed
+        self.thiol = thiol
         (self.tag_loc, self.score) = self.get_tag_and_score()
 
     def interpret_data(
@@ -235,8 +237,10 @@ def get_tag_locations(
         # various folds
 
         # Fixed Methylene blue at 3' terminus
+        thiol_loc = len(self.seq) if not self.thiol else 1
+
         if self.fixed is True:
-            distances = [f.get_distance(1, len(self.seq)) for f in self.folds]
+            distances = [f.get_distance(thiol_loc, len(self.seq)) for f in self.folds]
             tag_locs.append((len(self.seq), distances))
 
         # Else discover internal T placements
@@ -247,7 +251,7 @@ def get_tag_locations(
                     and (i + 1 < self.rec_seq["start"] or i + 1 > self.rec_seq["end"])
                     and (i + 1 < self.resp_seq["start"] or i + 1 > self.resp_seq["end"])
                 ):
-                    distances = [f.get_distance(1, i + 1) for f in self.folds]
+                    distances = [f.get_distance(thiol_loc, i + 1) for f in self.folds]
                     smallest_dist = min(distances)
                     if (
                         smallest_dist <= MAX_ON_DIST