feat(domain): per-domain atom partition + libcvc 3.2.1 prebuilt fetch (Phase 4 task 2)#27
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… (Phase 4 task 2) Phase 4 task 2: introduce f3dock::domain::DomainPartition turning the receptor's flat atom array into a labelled atom-index -> domain-id map. Construction validates ReceptorDomainConfig against the actual receptor size (rejecting inverted ranges, out-of-range ranges, and overlapping domains); apply() rewrites baseline coordinates by composing each atom's owning world transform looked up in a DomainGraph. Unclaimed atoms ride with the implicit root rigid body unchanged, so receptors without any receptorDomain directive remain bit-for-bit identical. PARAMS_IN now carries the partition and a rest-pose DomainGraph alongside receptorDomains; setParamFromFile builds and validates both after the molecule is loaded so malformed configurations fail at parse time. No runtime use yet -- task 3 will swap per-state world transforms into the graph and feed apply() to the FFT scoring loop. Also bump the libcvc dependency to v3.2.1 (commit 08c15b5). The 3.2.1 release archives are named libcvc-3.2.0-* (project version not bumped before the release build), so the archive filename is now decoupled from the package version via a new LIBCVC_ARCHIVE_VERSION cache var. Unit tests in tests/unit/test_f3dock_domain_partition.cpp cover the build/validate paths and the apply() math; all 73 domain+flex tests pass locally on WSL Ubuntu-24.04 (gcc 13).
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This was referenced May 18, 2026
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Stacked on top of #26.
Phase 4 task 2 — per-domain atom partition
Introduces
f3dock::domain::DomainPartition(header ininc/f3dock/domain/DomainPartition.h, impl insrc/f3dock-domain/DomainPartition.cpp). It turns the receptor's flat atom array into a dense atom-index -> domain-id map.build(config, total_atoms, &err)validates aReceptorDomainConfigagainst the actual receptor size and rejects inverted ranges, out-of-range ranges, and overlapping domains.apply(graph, x_in, y_in, z_in, x_out, y_out, z_out, &err)rewrites baseline coordinates by composing each atom's owning world transform looked up in aDomainGraph. Output pointers may alias the inputs. Unclaimed atoms are copied through unchanged.PARAMS_INnow carries the partition and a rest-poseDomainGraphalongsidereceptorDomains;setParamFromFilebuilds and validates both immediately after the molecule is loaded so malformed configurations fail at parse time. No runtime use yet — task 3 will swap per-state world transforms into the graph and feedapply()to the FFT scoring loop. Receptors without anyreceptorDomaindirective remain bit-for-bit identical to today's behaviour.libcvc bump to v3.2.1 (commit 08c15b5)
The v3.2.1 release archives are named
libcvc-3.2.0-*(the project version in CMakeLists was not bumped before the release build), and the bundledcvcConfigVersion.cmakereports 3.2.0 too. To consume the v3.2.1 tag without breaking the find_package version check, the archive filename is now decoupled from the package version via a newLIBCVC_ARCHIVE_VERSIONcache var (defaults toLIBCVC_VERSION, overridable per-release).Tests
12 new
DomainPartition.*cases intests/unit/test_f3dock_domain_partition.cppcover the build/validate paths and the apply() math (identity rest pose, hinge-only-rotates-child, aliased output, missing graph node, unclaimed atoms unchanged). All 73domain|flextests pass locally on WSL Ubuntu-24.04 / gcc 13.Migration matrix
doc/F3DOCK_MIGRATION_MATRIX.mdPhase 4 task 2 is now marked landed.