When copying sequences, copy features [#16804]

Author: e-pettersen

src/bundles/atomic/bundle_info.xml

@@ -1,5 +1,5 @@
 <!-- Edit bundle_info.xml.in, not bundle_info.xml; then run make_selectors.py  -->
-<BundleInfo name="ChimeraX-Atomic" version="1.60.2"
+<BundleInfo name="ChimeraX-Atomic" version="1.60.3"
             package="chimerax.atomic"
             purePython="false"
             customInit="true"

src/bundles/atomic/bundle_info.xml.in

@@ -1,5 +1,5 @@
 <!-- Edit bundle_info.xml.in, not bundle_info.xml; then run make_selectors.py  -->
-<BundleInfo name="ChimeraX-Atomic" version="1.60.2"
+<BundleInfo name="ChimeraX-Atomic" version="1.60.3"
             package="chimerax.atomic"
             purePython="false"
             customInit="true"

src/bundles/atomic/src/molobject.py

@@ -867,6 +867,8 @@ def __copy__(self, copy_seq=None):
         copy_seq.attrs = copy(self.attrs)
         copy_seq.markups = copy(self.markups)
         copy_seq.numbering_start = self.numbering_start
+        if hasattr(self, '_features'):
+            copy_seq._features = self._features
         return copy_seq
 
     def __del__(self):

src/bundles/uniprot/src/fetch_uniprot.py

@@ -46,7 +46,7 @@ def fetch_uniprot(session, ident, ignore_cache=False, *, associate=None):
     seq.accession_id["UniProt"] = accession
     seq.set_features("UniProt", expand_features(features))
     session.logger.status("Opening UniProt %s" % ident)
-    aln = session.alignments.new_alignment([seq], ident, auto_associate=(associate is None))
+    aln = session.alignments.new_alignment([seq], ident, auto_associate=(associate is None), copy_seqs=False)
     if associate is not None:
         for chain in associate:
             aln.associate(chain, min_length=2)