feat(domain): add receptor domain/joint config + parser (Phase 4 task 1)#26
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May 18, 2026 03:27
Adds ReceptorDomainConfig / DomainSpec / JointSpec in inc/f3dock/domain/DomainSpec.h plus a DomainSpecParser that mirrors the existing FlexSampler::parse_param pattern. Three new parameter- file keys: receptorDomain, receptorJointFixed, receptorJointHinge. Validation covers duplicate ids, unknown joint endpoints, multi-parent edges, and multi-root graphs; build_graph() populates an f3dock::domain::DomainGraph with rest-pose joint transforms using Rodrigues rotation about an arbitrary axis line for hinges. PARAMS_IN::receptorDomains carries the parsed config; it is read but not yet acted on at runtime (atom partitioning is task 2, scoring-loop refactor is task 3). Existing F2Dock behaviour is untouched when no receptorDomain keys are present.
Drop the _MSC_VER/strings.h-conditional F3DOCK_STRCASECMP macro in FlexSampler.cpp and the ad-hoc tolower lambda in DomainSpec.cpp in favor of a single inline f3dock::util::iequals(string_view, string_view) in inc/f3dock/util/StringUtil.h. Pure C++20 standard library, no POSIX or MSVC-specific headers needed at the call site.
- .github/workflows/ci.yml: include feature/** branches so stacked feature PRs run CI. - tests/unit/test_f3dock_domain_spec.cpp: clang-format-18 reflow (flagged by CI on PR #26).
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Adds ReceptorDomainConfig / DomainSpec / JointSpec in inc/f3dock/domain/DomainSpec.h plus a DomainSpecParser that mirrors the existing FlexSampler::parse_param pattern. Three new parameter-file keys: receptorDomain, receptorJointFixed, receptorJointHinge. Validation covers duplicate ids, unknown joint endpoints, multi-parent edges, multi-root graphs; build_graph() populates an f3dock::domain::DomainGraph with rest-pose joint transforms using Rodrigues rotation about an arbitrary axis line for hinges. PARAMS_IN::receptorDomains carries the parsed config; it is read but not yet acted on at runtime (atom partitioning is task 2, scoring-loop refactor is task 3). Existing F2Dock behaviour is untouched when no receptorDomain keys are present. Unit tests in tests/unit/test_f3dock_domain_spec.cpp. Updates migration matrix. [Phase 4 task 1]