Pull Request №681 RosettaCommons/rosetta/main ← everyday847/rosetta/differentiable-parametric
Merge: cf532f89b6bbb7e67fd75031f3cc2aa95fb5ce19←21d90cb52d1abe277b363e833609842144201b21
Add differentiable parametric backbone minimization
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Merge commit message:
Fix sidechain rebuild: use set_phi/psi/omega to sync atom tree
The previous approach (calling private/protected AtomTree methods)
didn't compile. Use public Pose::set_phi/set_psi/set_omega instead:
reading each backbone torsion from the new XYZ and writing it back
via set_torsion updates the atom tree's internal coordinates, which
triggers a coordinate rebuild that repositions all downstream atoms
including sidechains.
Rosetta Benchmark 2 months Tests for this revision was automatically canceled because newer set of tests for pull-request №681 was submitted!
Pull Request №681 RosettaCommons/rosetta/main ← everyday847/rosetta/differentiable-parametric
Merge: cf532f89b6bbb7e67fd75031f3cc2aa95fb5ce19←66ea3c3c82c9b9a8645bd6966946f26478975b02
Add differentiable parametric backbone minimization
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Merge commit message:
Fix sidechain drift during parametric minimization, add trajectory dump
Sidechain fix: after setting backbone XYZ from Crick equations,
sync the atom tree's internal coordinates by reading phi/psi/omega
back from the new Cartesian positions and writing them as torsions.
Without this, the atom tree retains the old backbone frame and
sidechains don't follow the backbone when it moves.
Trajectory visualization: ParametricAtomTreeMultifunc can now dump
a PDB at each function evaluation via set_trajectory_dump(). Enabled
automatically when the AtomTreeMinimizer tracer is at Debug level
(-out:levels core.optimization.AtomTreeMinimizer:debug).
Rosetta Benchmark 2 months Tests for this revision was automatically canceled because newer set of tests for pull-request №681 was submitted!
Pull Request №688 RosettaCommons/rosetta/main ← lyskov-ai/rosetta/refactor/core-signal-events-rule-of-zero
Merge: b8e64ecdc0338b77c231760f7f9bdcd4d500a240←532a3428f85793cb075127b7e01dea59ebbedbf8
Apply Rule of Zero to core signal event hierarchies
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Merge commit message:
Apply Rule of Zero to core signal event hierarchies
The signal event classes in core/conformation/signals/ and core/pose/signals/
each had hand-written copy constructor, copy assignment, and empty destructor
that did nothing the compiler-generated versions wouldn't do. Remove the
boilerplate and let the compiler generate the copy operations; keep the
destructor declared (defaulted) where the class is a polymorphic base.
Touched: GeneralEvent, ConnectionEvent, IdentityEvent, XYZEvent (conformation);
GeneralEvent, DestructionEvent, ConformationEvent, EnergyEvent (pose).
LengthEvent is intentionally left alone -- its copy constructor and copy
assignment invoke check_consistency() in debug builds, so they have semantic
content beyond member-wise copy.
Pull Request №681 RosettaCommons/rosetta/main ← everyday847/rosetta/differentiable-parametric
Merge: cf532f89b6bbb7e67fd75031f3cc2aa95fb5ce19←f971f5794aa3de2152dc17bc8f81f45c7bbd2fc5
Add differentiable parametric backbone minimization
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Merge commit message:
Add parametric DOF support to MoveMap/MoveMapFactory XML schema
The <Parametric enable="true"/> sub-element was not recognized by
the MoveMap XSD. Instead, add parametric as a top-level attribute
(like bb, chi, jump) on both MoveMapFactory and the legacy MoveMap:
<MinMover ... bb="false" chi="true" parametric="true"/>
or in MoveMapFactory style:
<MoveMap bb="false" chi="true" parametric="true"/>
Changes:
- MoveMapFactory: add all_parametric(bool), data members, parse
in parse_my_tag(), apply in edit_movemap_given_pose()
- MoveMapFactory XSD: add "parametric" attribute
- Legacy MoveMap schema (rosetta_scripts/util.cc): add "parametric"
attribute and parse in parse_movemap_tag()
- Integration test XMLs: use attribute form
Rosetta Benchmark 2 months Tests for this revision was automatically canceled because newer set of tests for pull-request №681 was submitted!
Pull Request №681 RosettaCommons/rosetta/main ← everyday847/rosetta/differentiable-parametric
Merge: cf532f89b6bbb7e67fd75031f3cc2aa95fb5ce19←ae639ae8cc56a638e2783f4f1ca61d9c4f2d0f05
Add differentiable parametric backbone minimization
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Merge commit message:
Fix library layer violation and compilation error in parametric minimization
- Remove protocols/helical_bundle/util.hh include from core-level
parametric_minimize_util.cc — core cannot depend on protocols
- Rewrite rebuild_parametric_backbone() to call
numeric::crick_equations::XYZ_BUNDLE() directly and set atom
coordinates via pose.set_xyz(), using only core/numeric dependencies
- Fix dofs scoping in AtomTreeMinimizer::run() (variable declared
inside if/else branches but used after)
- All modified files pass g++ -fsyntax-only with no errors
Rosetta Benchmark 2 months Tests for this revision was automatically canceled because newer set of tests for pull-request №681 was submitted!
Pull Request №685 RosettaCommons/rosetta/main ← lyskov-ai/rosetta/refactor/core-factory-copy-prevention
Merge: b8e64ecdc0338b77c231760f7f9bdcd4d500a240←c84621a02ce0a6cce0beb378ea0463316a2d1ade
Modernize copy prevention in core factory singletons and non-copyable classes
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Merge commit message:
Modernize copy prevention in core factory singletons and non-copyable classes
SilentStructFactory, ConstraintFactory, and SequenceFactory all inherit from
SingletonBase, which already = delete's copy construction and copy assignment.
Remove the now-redundant private unimplemented declarations from each derived
class.
OrbitalsStatistics and AtomTreeDiff had private-but-undefined copy constructors
(pre-C++11 idiom); replace with explicit = delete on both copy constructor and
copy assignment.
Pull Request №684 RosettaCommons/rosetta/main ← lyskov-ai/rosetta/refactor/metric-value-default-members
Merge: cf532f89b6bbb7e67fd75031f3cc2aa95fb5ce19←32851eb34495109eb51cb7da88258d6bbc5554e7
Default MetricValue special members
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Merge commit message:
Default MetricValue special members
Pull Request №676 RosettaCommons/rosetta/main ← everyday847/rosetta/origin/everyday847/parametric_helpers
Merge: 5c9f6db69d1a20db6353738e3724092516415bd3←3fec048183eb354c26030092edabd404582c57bf
Factor common logic out of add_*_parameter methods
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Merge commit message:
Factor common logic out of add_*_parameter methods
Extract a private configure_and_add_parameter() helper that handles
the shared configuration steps (name, description, units, type,
capabilities, global flag) and add_parameter() call. Each
add_*_parameter() and add_custom_parameter() now only constructs the
type-specific object, sets any conditional default value, and
delegates to the helper. Also replace bare new with make_shared.
Pull Request №677 RosettaCommons/rosetta/main ← everyday847/rosetta/origin/everyday847/parametric_make_shared
Merge: 5c9f6db69d1a20db6353738e3724092516415bd3←2ab90802a27b283be4fd87d779276b092a0b0c26
Use make_shared in ParametrizationCalculator
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Merge commit message:
Use make_shared in ParametrizationCalculator