From 0fe3a32fcb39fbf575197d1a155b21a5a9df3ca7 Mon Sep 17 00:00:00 2001
From: David Doty <doty@ucdavis.edu>
Date: Fri, 31 Mar 2023 10:09:48 -0700
Subject: [PATCH] added p8634 variant of M13

---
 nuad/constraints.py | 19 +++++++++++++++----
 nuad/search.py      | 11 +++++------
 2 files changed, 20 insertions(+), 10 deletions(-)

diff --git a/nuad/constraints.py b/nuad/constraints.py
index 65bd55ea..98588230 100644
--- a/nuad/constraints.py
+++ b/nuad/constraints.py
@@ -140,6 +140,13 @@ class M13Variant(enum.Enum):
     https://www.tilibit.com/collections/scaffold-dna/products/single-stranded-scaffold-dna-type-p8064
     """
 
+    p8634 = "p8634"
+    """Variant of M13mp18 that is 8634 bases long. At the time of this writing, not listed as available
+    from any biotech vender, but Tilibit will make it for you if you ask. 
+    (https://www.tilibit.com/pages/contact-us)
+    """
+
+
     def length(self) -> int:
         """
         :return: length of this variant of M13 (e.g., 7249 for variant :data:`M13Variant.p7249`)
@@ -150,6 +157,8 @@ def length(self) -> int:
             return 7560
         if self is M13Variant.p8064:
             return 8064
+        if self is M13Variant.p8634:
+            return 8634
         raise AssertionError('should be unreachable')
 
     def scadnano_variant(self) -> sc.M13Variant:
@@ -159,6 +168,8 @@ def scadnano_variant(self) -> sc.M13Variant:
             return sc.M13Variant.p7560
         if self is M13Variant.p8064:
             return sc.M13Variant.p8064
+        if self is M13Variant.p8634:
+            return sc.M13Variant.p8634
         raise AssertionError('should be unreachable')
 
 
@@ -5763,7 +5774,7 @@ def longest_complementary_subsequences_two_loops(arr1: np.ndarray, arr2: np.ndar
     the sequences in `arr1` are assumed to be oriented 5' --> 3', and the sequences in `arr2`
     are assumed to be oriented 3' --> 5'.
 
-    Args
+    Args:
         arr1: 2D array of DNA sequences, with each sequence represented as a 1D array of 0, 1, 2, 3
               corresponding to A, C, G, T, respectively, with each row being a single DNA sequence
               oriented 5' --> 3'.
@@ -5771,7 +5782,7 @@ def longest_complementary_subsequences_two_loops(arr1: np.ndarray, arr2: np.ndar
               oriented 3' --> 5'.
         gc_double: Whether to double the score for G-C base pairs.
 
-    Returns
+    Returns:
         list `ret` of ints, where `ret[i]` is the length of the longest complementary subsequence
         between `arr1[i]` and `arr2[i]`.
     """
@@ -5821,7 +5832,7 @@ def longest_complementary_subsequences(arr1: np.ndarray, arr2: np.ndarray, gc_do
     the sequences in `arr1` are assumed to be oriented 5' --> 3', and the sequences in `arr2`
     are assumed to be oriented 3' --> 5'.
 
-    Args
+    Args:
         arr1: 2D array of DNA sequences, with each sequence represented as a 1D array of 0, 1, 2, 3
               corresponding to A, C, G, T, respectively, with each row being a single DNA sequence
               oriented 5' --> 3'.
@@ -5829,7 +5840,7 @@ def longest_complementary_subsequences(arr1: np.ndarray, arr2: np.ndarray, gc_do
               oriented 3' --> 5'.
         gc_double: Whether to double the score for G-C base pairs.
 
-    Returns
+    Returns:
         list `ret` of ints, where `ret[i]` is the length of the longest complementary subsequence
         between `arr1[i]` and `arr2[i]`.
     """
diff --git a/nuad/search.py b/nuad/search.py
index ea193ee6..4ecbfa77 100644
--- a/nuad/search.py
+++ b/nuad/search.py
@@ -1813,9 +1813,8 @@ def replace_with_new(self) -> None:
         _assert_violations_are_accurate(self.evaluations, self.violations)
 
     def update_scores_and_counts(self) -> None:
-        """
-        :return: Total score of all evaluations.
-        """
+        # return: Total score of all evaluations.
+
         self.total_score = self.total_score_fixed = self.total_score_nonfixed = 0.0
         self.num_evaluations = self.num_evaluations_nonfixed = self.num_evaluations_fixed = 0
         self.num_violations = self.num_violations_nonfixed = self.num_violations_fixed = 0
@@ -1949,11 +1948,11 @@ class Evaluation(Generic[DesignPart]):
 
     def __init__(self, constraint: Constraint, violated: bool, part: DesignPart, domains: Iterable[Domain],
                  score: float, summary: str, result: nc.Result) -> None:
-        # :param constraint:
+        # constraint:
         #     :any:`Constraint` that was violated to result in this
-        # :param domains:
+        # domains:
         #     :any:`Domain`'s that were involved in violating :py:data:`Evaluation.constraint`
-        # :param score:
+        # score:
         #     total "score" of this violation, typically something like an excess energy over a
         #     threshold, squared, multiplied by the :data:`Constraint.weight`
         self.constraint = constraint