Summary
MolSysMT currently lacks direct conversion support from molsysmt.MolSys to:
file:ciffile:cif.gzfile:bciffile:bcif.gz
This is now a concrete gap in the form ecosystem rather than a theoretical enhancement.
Why this matters
MolSysBuilder is now available as a deterministic native fixture source. We are already using it to declare molecular truth first and then export to target formats such as PDB, H5MSM, and OpenMM topology before testing round-trips.
That same strategy should also be available for CIF/BCIF workflows. At the moment it is blocked because MolSys cannot yet be materialized directly to CIF/BCIF outputs.
This affects:
- deterministic converter testing
- offline workflows
- symmetry and completeness of the form ecosystem
- future builder-driven fixture generation for mmCIF/BCIF parsers
Proposed direction
Prioritize a native route:
molsysmt.MolSys -> mmcif.PdbxContainers.DataContainermmcif.PdbxContainers.DataContainer -> file:cif / file:cif.gzmmcif.PdbxContainers.DataContainer -> file:bcif / file:bcif.gz
This should then allow MolSysBuilder -> MolSys -> CIF/BCIF fixture generation without adding builder-specific exporters.
Acceptance criteria
MolSys -> file:cif implementedMolSys -> file:cif.gz implementedMolSys -> file:bcif implementedMolSys -> file:bcif.gz implemented- deterministic tests based on
MolSysBuilder added for CIF/BCIF converter paths
- developer docs updated to reflect the new deterministic-fixture route
Notes
This is not only about export functionality. It is also about enabling trustworthy converter tests where the molecular truth is declared before the format under test is generated.
Summary
MolSysMT currently lacks direct conversion support from
molsysmt.MolSysto:file:ciffile:cif.gzfile:bciffile:bcif.gzThis is now a concrete gap in the form ecosystem rather than a theoretical enhancement.
Why this matters
MolSysBuilderis now available as a deterministic native fixture source. We are already using it to declare molecular truth first and then export to target formats such as PDB, H5MSM, and OpenMM topology before testing round-trips.That same strategy should also be available for CIF/BCIF workflows. At the moment it is blocked because MolSys cannot yet be materialized directly to CIF/BCIF outputs.
This affects:
Proposed direction
Prioritize a native route:
molsysmt.MolSys -> mmcif.PdbxContainers.DataContainermmcif.PdbxContainers.DataContainer -> file:cif/file:cif.gzmmcif.PdbxContainers.DataContainer -> file:bcif/file:bcif.gzThis should then allow
MolSysBuilder -> MolSys -> CIF/BCIFfixture generation without adding builder-specific exporters.Acceptance criteria
MolSys -> file:cifimplementedMolSys -> file:cif.gzimplementedMolSys -> file:bcifimplementedMolSys -> file:bcif.gzimplementedMolSysBuilderadded for CIF/BCIF converter pathsNotes
This is not only about export functionality. It is also about enabling trustworthy converter tests where the molecular truth is declared before the format under test is generated.