Merge pull request #225 from UC-Davis-molecular-computing/dev

Dev

nuad/constraints.py

@@ -3163,7 +3163,7 @@ def write_design_file(self, directory: str = '.', filename: str | None = None,
         Write JSON file representing this :any:`Design`,
         which can be imported via the method :meth:`Design.from_design_file`,
         with the output file having the same name as the running script but with ``.py`` changed to
-        :attr:`default_scadnano_file_extension`,
+        ``.json``,
         unless `filename` is explicitly specified.
         For instance, if the script is named ``my_design.py``,
         then the design will be written to ``my_design.json``.
@@ -3612,9 +3612,11 @@ def domains_by_pool_name(self, domain_pool_name: str) -> List[Domain[DomainLabel
         return domains_in_pool
 
     @staticmethod
-    def from_scadnano_file(sc_filename: str,
-                           fix_assigned_sequences: bool = True,
-                           ignored_strands: Iterable[Strand] | None = None) -> Design[StrandLabel, DomainLabel]:
+    def from_scadnano_file(
+            sc_filename: str,
+            fix_assigned_sequences: bool = True,
+            ignored_strands: Iterable[Strand] | None = None
+    ) -> Design[StrandLabel, DomainLabel]:
         """
         Converts a scadnano Design stored in file named `sc_filename` to a a :any:`Design` for doing
         DNA sequence design.
@@ -3775,17 +3777,35 @@ def get_group_name_from_strand_label(sc_strand: Strand) -> Any:
         else:
             raise AssertionError(f'label does not have either an attribute or a dict key "{group_key}"')
 
+    def assign_fields_to_scadnano_design(self, sc_design: sc.Design[StrandLabel, DomainLabel],
+                                         ignored_strands: Iterable[Strand] = (),
+                                         overwrite: bool = False):
+        """
+        Assigns DNA sequence, IDTFields, and StrandGroups (as a key in a scadnano String.label dict
+        under key "group").
+        TODO: document more
+        """
+        self.assign_sequences_to_scadnano_design(sc_design, ignored_strands, overwrite)
+        self.assign_strand_groups_to_labels(sc_design, ignored_strands, overwrite)
+        self.assign_idt_fields_to_scadnano_design(sc_design, ignored_strands, overwrite)
+        self.assign_modifications_to_scadnano_design(sc_design, ignored_strands, overwrite)
+
     def assign_sequences_to_scadnano_design(self, sc_design: sc.Design[StrandLabel, DomainLabel],
                                             ignored_strands: Iterable[Strand] = (),
                                             overwrite: bool = False) -> None:
         """
         Assigns sequences from this :any:`Design` into `sc_design`.
 
+        Also writes a label to each scadnano strand. If the label is None a new one is created as
+        a dict with a key `group`. The name of the StrandGroup of the nuad design is the value
+        to assign to this key. If the scadnano strand label is already a dict, it adds this key.
+        If the strand label is not None or a dict, an exception is raised.
+
         Assumes that each domain name in domains in `sc_design` is a :py:data:`Domain.name` of a
         :any:`Domain` in this :any:`Design`.
 
         If multiple strands in `sc_design` share the same name, then all of them are assigned the
-        DNA sequence of the dsd :any:`Strand` with that name.
+        DNA sequence of the nuad :any:`Strand` with that name.
 
         :param sc_design:
             a scadnano design.
@@ -3824,8 +3844,60 @@ def assign_sequences_to_scadnano_design(self, sc_design: sc.Design[StrandLabel,
                                f'Make sure that this is a strand you intended to leave out of the '
                                f'sequence design process')
 
+    def shared_strands_with_scadnano_design(self, sc_design: sc.Design,
+                                            ignored_strands: Iterable[Strand] = ()) \
+            -> List[Tuple[Strand, List[sc.Strand]]]:
+        """
+        Returns a list of pairs (nuad_strand, sc_strands), where nuad_strand has the same name
+        as all scadnano Strands in sc_strands, but only scadnano strands are included in the
+        list that do not appear in `ignored_strands`.
+        """
+        sc_strands_to_include = [strand for strand in sc_design.strands if strand not in ignored_strands]
+        nuad_strands_by_name = {strand.name: strand for strand in self.strands}
+
+        sc_strands_by_name: Dict[str, List[sc.Strand]] = defaultdict(list)
+        for sc_strand in sc_strands_to_include:
+            sc_strands_by_name[sc_strand.name].append(sc_strand)
+
+        pairs = []
+        for name, nuad_strand in nuad_strands_by_name.items():
+            if name in sc_strands_by_name:
+                sc_strands = sc_strands_by_name[name]
+                pairs.append((nuad_strand, sc_strands))
+
+        return pairs
+
+    def assign_strand_groups_to_labels(self, sc_design: sc.Design,
+                                       ignored_strands: Iterable[Strand] = (),
+                                       overwrite: bool = False) -> None:
+        """
+        TODO: document this
+        """
+        strand_pairs = self.shared_strands_with_scadnano_design(sc_design, ignored_strands)
+
+        for nuad_strand, sc_strands in strand_pairs:
+            for sc_strand in sc_strands:
+                if nuad_strand.group is not None:
+                    if sc_strand.label is None:
+                        sc_strand.label = {}
+                    elif not isinstance(sc_strand.label, dict):
+                        raise ValueError(f'cannot assign strand group to strand {sc_strand.name} '
+                                         f'because it already has a label that is not a dict. '
+                                         f'It must either have label None or a dict.')
+
+                    # if we get here, then sc_strand.label is a dict. Need to check whether
+                    # it already has a 'group' key.
+                    if group_key in sc_strand.label is not None and not overwrite:
+                        raise ValueError(f'Cannot assign strand group from nuad strand to scadnano strand '
+                                         f'{sc_strand.name} (through its label field) because the '
+                                         f'scadnano strand already has a label with group key '
+                                         f'\n{sc_strand.label[group_key]}. '
+                                         f'Set overwrite to True to force an overwrite.')
+                    sc_strand.label[group_key] = nuad_strand.group
+
     def assign_idt_fields_to_scadnano_design(self, sc_design: sc.Design[StrandLabel, DomainLabel],
-                                             ignored_strands: Iterable[Strand] = ()) -> None:
+                                             ignored_strands: Iterable[Strand] = (),
+                                             overwrite: bool = False) -> None:
         """
         Assigns :any:`IDTFields` from this :any:`Design` into `sc_design`.
 
@@ -3836,25 +3908,27 @@ def assign_idt_fields_to_scadnano_design(self, sc_design: sc.Design[StrandLabel,
             a scadnano design.
         :param ignored_strands:
             strands in the scadnano design that are to be not assigned.
+        :param overwrite:
+            whether to overwrite existing fields.
         :raises ValueError:
             if scadnano strand already has any modifications assigned
         """
         # filter out ignored strands
-        sc_strands_to_include = [strand for strand in sc_design.strands if strand not in ignored_strands]
-
-        nuad_strands_by_name = {strand.name: strand for strand in self.strands}
+        strand_pairs = self.shared_strands_with_scadnano_design(sc_design, ignored_strands)
 
-        for sc_strand in sc_strands_to_include:
-            nuad_strand = nuad_strands_by_name[sc_strand.name]
-            if nuad_strand.idt is not None:
-                if sc_strand.idt is not None:
-                    raise ValueError(f'Cannot assign IDT fields from dsd strand to scadnano strand '
-                                     f'{sc_strand.name} because the scadnano strand already has IDT fields '
-                                     f'assigned:\n{sc_strand.idt}')
-                sc_strand.idt = nuad_strand.idt.to_scadnano_idt()
+        for nuad_strand, sc_strands in strand_pairs:
+            for sc_strand in sc_strands:
+                if nuad_strand.idt is not None:
+                    if sc_strand.idt is not None and not overwrite:
+                        raise ValueError(f'Cannot assign IDT fields from dsd strand to scadnano strand '
+                                         f'{sc_strand.name} because the scadnano strand already has '
+                                         f'IDT fields assigned:\n{sc_strand.idt}. '
+                                         f'Set overwrite to True to force an overwrite.')
+                    sc_strand.idt = nuad_strand.idt.to_scadnano_idt()
 
     def assign_modifications_to_scadnano_design(self, sc_design: sc.Design[StrandLabel, DomainLabel],
-                                                ignored_strands: Iterable[Strand] = ()) -> None:
+                                                ignored_strands: Iterable[Strand] = (),
+                                                overwrite: bool = False) -> None:
         """
         Assigns :any:`modifications.Modification`'s from this :any:`Design` into `sc_design`.
 
@@ -3865,6 +3939,8 @@ def assign_modifications_to_scadnano_design(self, sc_design: sc.Design[StrandLab
             a scadnano design.
         :param ignored_strands:
             strands in the scadnano design that are to be not assigned.
+        :param overwrite:
+            whether to overwrite existing fields in scadnano design
         :raises ValueError:
             if scadnano strand already has any modifications assigned
         """
@@ -3877,26 +3953,29 @@ def assign_modifications_to_scadnano_design(self, sc_design: sc.Design[StrandLab
         for sc_strand in sc_strands_to_include:
             dsd_strand: Strand = dsd_strands_by_name[sc_strand.name]
             if dsd_strand.modification_5p is not None:
-                if sc_strand.modification_5p is not None:
+                if sc_strand.modification_5p is not None and not overwrite:
                     raise ValueError(f'Cannot assign 5\' modification from dsd strand to scadnano strand '
                                      f'{sc_strand.name} because the scadnano strand already has a 5\''
-                                     f'modification assigned:\n{sc_strand.modification_5p}')
+                                     f'modification assigned:\n{sc_strand.modification_5p}. '
+                                     f'Set overwrite to True to force an overwrite.')
                 sc_strand.modification_5p = dsd_strand.modification_5p.to_scadnano_modification()
 
             if dsd_strand.modification_3p is not None:
-                if sc_strand.modification_3p is not None:
+                if sc_strand.modification_3p is not None and not overwrite:
                     raise ValueError(f'Cannot assign 3\' modification from dsd strand to scadnano strand '
                                      f'{sc_strand.name} because the scadnano strand already has a 3\''
-                                     f'modification assigned:\n{sc_strand.modification_3p}')
+                                     f'modification assigned:\n{sc_strand.modification_3p}. '
+                                     f'Set overwrite to True to force an overwrite.')
                 sc_strand.modification_3p = dsd_strand.modification_3p.to_scadnano_modification()
 
             for offset, mod_int in dsd_strand.modifications_int.items():
-                if offset in sc_strand.modifications_int is not None:
+                if offset in sc_strand.modifications_int is not None and not overwrite:
                     raise ValueError(f'Cannot assign internal modification from dsd strand to '
                                      f'scadnano strand {sc_strand.name} at offset {offset} '
                                      f'because the scadnano strand already has an internal '
                                      f'modification assigned at that offset:\n'
-                                     f'{sc_strand.modifications_int[offset]}')
+                                     f'{sc_strand.modifications_int[offset]} .'
+                                     f'Set overwrite to True to force an overwrite.')
                 sc_strand.modifications_int[offset] = mod_int.to_scadnano_modification()
 
     def _assign_to_strand_without_checking_existing_sequence(
@@ -4244,7 +4323,7 @@ def parse_and_normalize_quantity(quantity: float | int | str | pint.Quantity) \
     return quantity
 
 
-def Q_(qty: int | str | Decimal | float, unit: str | pint.Unit) -> pint.Quantity[Decimal]:
+def Q_(qty: int | str | Decimal | float, unit: str | pint.Unit) -> pint.Quantity[Decimal]:  # noqa
     # Convenient constructor for units, eg, :code:`Q_(5.0, 'nM')`.
     # Ensures that the quantity is a Decimal.
     if isinstance(qty, Decimal):
@@ -4687,7 +4766,7 @@ def _check_nupack_installed() -> None:
      Raises ImportError if nupack module is not installed.
     """
     try:
-        import nupack
+        import nupack  # noqa
     except ModuleNotFoundError:
         raise ImportError(
             'NUPACK 4 must be installed to create a constraint that uses NUPACK. '
@@ -4956,7 +5035,7 @@ def evaluate(seqs: Tuple[str, ...], domain_pair: DomainPair | None) -> Result:
                                 pairs=pairs)
 
 
-def nupack_strand_pair_constraint_by_number_matching_domains(
+def nupack_strand_pair_constraints_by_number_matching_domains(
         thresholds: Dict[int, float],
         temperature: float = nv.default_temperature,
         sodium: float = nv.default_sodium,
@@ -5012,9 +5091,9 @@ def nupack_strand_pair_constraint_by_number_matching_domains(
 
     if descriptions is None:
         descriptions = {
-            num_matching: _pair_default_description('strand', 'NUPACK', threshold, temperature) +
-                          f'\nfor strands with {num_matching} complementary '
-                          f'{"domain" if num_matching == 1 else "domains"}'
+            num_matching: (_pair_default_description('strand', 'NUPACK', threshold, temperature) +
+                           f'\nfor strands with {num_matching} complementary '
+                           f'{"domain" if num_matching == 1 else "domains"}')
             for num_matching, threshold in thresholds.items()
         }
 
@@ -5452,9 +5531,9 @@ def rna_cofold_strand_pairs_constraints_by_number_matching_domains(
                           parameters_filename=parameters_filename)
     if descriptions is None:
         descriptions = {
-            num_matching: _pair_default_description('strand', 'RNAcofold', threshold, temperature) +
-                          f'\nfor strands with {num_matching} complementary '
-                          f'{"domain" if num_matching == 1 else "domains"}'
+            num_matching: (_pair_default_description('strand', 'RNAcofold', threshold, temperature) +
+                           f'\nfor strands with {num_matching} complementary '
+                           f'{"domain" if num_matching == 1 else "domains"}')
             for num_matching, threshold in thresholds.items()
         }
     return _strand_pairs_constraints_by_number_matching_domains(
@@ -5526,9 +5605,9 @@ def rna_duplex_strand_pairs_constraints_by_number_matching_domains(
 
     if descriptions is None:
         descriptions = {
-            num_matching: _pair_default_description('strand', 'RNAduplex', threshold, temperature) +
-                          f'\nfor strands with {num_matching} complementary '
-                          f'{"domain" if num_matching == 1 else "domains"}'
+            num_matching: (_pair_default_description('strand', 'RNAduplex', threshold, temperature) +
+                           f'\nfor strands with {num_matching} complementary '
+                           f'{"domain" if num_matching == 1 else "domains"}')
             for num_matching, threshold in thresholds.items()
         }
 

nuad/search.py

@@ -4,8 +4,8 @@
 :any:`Domain`'s in a :any:`Design` to satisfy all :any:`Constraint`'s.
 Various parameters of the search can be controlled using :any:`SearchParameters`.
 
-Instructions for using the dsd library are available at
-https://github.com/UC-Davis-molecular-computing/dsd#data-model
+Instructions for using the nuad library are available at
+https://github.com/UC-Davis-molecular-computing/nuad#data-model
 """
 
 from __future__ import annotations