added percentage argument annotations

src/bundles/core/src/commands/__init__.py

@@ -48,13 +48,14 @@
     EnumOf,
     DynamicEnum,
 )
-from .cli import IntArg, Int2Arg, Int3Arg, IntsArg, NonNegativeIntArg, PositiveIntArg
+from .cli import IntArg, Int2Arg, Int3Arg, IntsArg, NonNegativeIntArg, PercentIntArg, PositiveIntArg
 from .cli import (
     FloatArg,
     Float2Arg,
     Float3Arg,
     FloatsArg,
     NonNegativeFloatArg,
+	PercentFloatArg,
     PositiveFloatArg,
 )
 from .cli import FloatOrDeltaArg

src/bundles/core/src/commands/cli.py

@@ -2136,6 +2136,8 @@ def unparse(value, session=None):
 PositiveIntArg = Bounded(IntArg, min=1, name="an integer >= 1")
 NonNegativeFloatArg = Bounded(FloatArg, min=0, name="a number >= 0")
 PositiveFloatArg = Bounded(FloatArg, min=0, inclusive=False, name="a number > 0")
+PercentFloatArg = Bounded(FloatArg, min=0, max=100, name="a percentage between 0 and 100")
+PercentIntArg = Bounded(IntArg, min=0, max=100, name="a percentage between 0 and 100")
 ModelIdArg = DottedTupleOf(PositiveIntArg, name="a model id", prefix="#")
 
 

src/bundles/seqalign/src/cmd.py

@@ -373,7 +373,8 @@ def seqalign_identity(session, src1, src2=None, *, denominator=IdentityDenominat
         session.logger.info("%s vs. %s: %.2f%% identity" % (seq1.name, src2.name, identity))
     return identity
 
-def seqalign_match(session, alignment, match_chains, to=None, *, iterate=-1, columns=None):
+def seqalign_match(session, alignment, match_chains, to=None, *,
+        iterate=-1, conservation=None, columns=None):
     if alignment is None:
         alignment = get_alignment_by_id(session, None)
     if columns is None:
@@ -385,7 +386,7 @@ def seqalign_match(session, alignment, match_chains, to=None, *, iterate=-1, col
             if col > length:
                 raise UserError("match column (%d) greater than alignment length (%d)" % (col, length))
             indices.append(col-1)
-    return alignment.match(to, match_chains, iterate=iterate, restriction=indices)
+    return alignment.match(to, match_chains, iterate=iterate, conservation=conservation, restriction=indices)
 
 def seqalign_refresh_attrs(session, alignment):
     alignment._set_residue_attributes()
@@ -497,7 +498,7 @@ def seqalign_align(session, seq_source, *, program=CLUSTAL_OMEGA, replace=False)
 def register_seqalign_command(logger):
     # REMINDER: update manager._builtin_subcommands as additional subcommands are added
     from chimerax.core.commands import CmdDesc, register, create_alias, Or, EmptyArg, RestOfLine, ListOf, \
-        EnumOf, BoolArg, NoneArg, PositiveIntArg
+        EnumOf, BoolArg, NoneArg, PositiveIntArg, PercentFloatArg
     from chimerax.atomic import UniqueChainsArg, SequencesArg, ChainArg
 
     apns = list(alignment_program_name_args.keys())
@@ -552,6 +553,7 @@ def register_seqalign_command(logger):
         required = [('alignment', Or(AlignmentArg, EmptyArg)), ('match_chains', UniqueChainsArg)],
         required_arguments = ['to'],
         keyword = [('to', ChainArg), ('iterate', Or(NoneArg, PositiveIntArg)),
+            ('conservation', PercentFloatArg),
             ('columns', ListOf(PositiveIntArg))],
         synopsis = "superimpose chains associated with sequence alignment"
     )