Search: "structural"

Compares Trailmark code graphs at two source code snapshots (git commits, tags, or directories) to surface security-relevant structural changes. Detects new attack paths, complexity shifts, blast radius growth, taint propagation changes, and privilege boundary modifications that text diffs miss. Use when comparing code between commits or tags, analyzing structural evolution, detecting attack surface growth, reviewing what changed between audit snapshots, or finding security-relevant changes that text diffs miss.

Runs a Trailmark summary analysis on a codebase. Returns auto-detected languages, entry point count, and dependency list. Use when vivisect or galvanize needs a quick structural overview. Triggers: trailmark summary, code summary, structural overview.

Runs full Trailmark structural analysis by building a graph, running `preanalysis()`, and reporting hotspots, taint, blast radius, privilege boundaries, attack surface, and version-gated Trailmark 0.4+/0.5+ data such as proxy counts, subgraph edges, type/reference summaries, and entrypoint attributes. Use when vivisect needs detailed structural data for a target. Triggers: structural analysis, blast radius, taint analysis, complexity hotspots, proxy nodes, type references.

Runs a Trailmark structural review gate over a branch, pull request, fix commit, release diff, or git ref range to detect new entrypoints, new tainted paths, removed validation or authorization calls, privilege-boundary drift, blast-radius growth, complexity growth, and newly reachable sensitive sinks. Use when reviewing a PR, branch, remediation commit, or release diff where graph-level security regressions should be checked before merge.

Expands one confirmed or suspected vulnerability into a Trailmark graph neighborhood of variant candidates by finding sibling functions, shared callers and callees, common sensitive sinks, common entrypoint paths, interface implementations, override relationships, type/reference neighbors, and structurally similar nodes. Use after one issue is found to seed variant-analysis, semgrep-rule-creator, static-analysis, or manual review with graph-derived candidate locations.

Applies medicinal chemistry filters for compound triage, using drug-likeness rules (Lipinski, Veber, CNS), structural alert catalogs (PAINS, NIBR, ChEMBL), complexity metrics, and the medchem query language for library filtering.

Provides access to a collection of open-source molecular design and structural biology tools on the Tamarind Bio platform, via its REST API or MCP server — no local GPUs required. Tamarind bundles popular open-source models for structure prediction (AlphaFold, Boltz, Chai, ESMFold), protein, binder, and de novo design (RFdiffusion, ProteinMPNN, BoltzGen), antibody and nanobody design and developability, protein-ligand docking (DiffDock, Autodock Vina), binding-affinity prediction, MSA generation, and molecular dynamics. Use when the user mentions Tamarind or tamarind.bio, wants to run any of these open-source tools in the cloud, references app.tamarind.bio/api or the x-api-key header, or needs to submit batches of sequences for structural or biophysical characterization.

Formats and structurally validates local treatment-plan documentation after clinical decisions have already been supplied and verified by authorized licensed professionals. Use for source traceability, clinician-authored intervention records, goals and checkpoints, shared-decision records, reconciliation handoffs, and release gates—not for clinical decision-making.

Runs and analyzes molecular dynamics simulations with OpenMM and MDAnalysis. Sets up protein/small molecule systems, defines force fields, runs energy minimization and production MD, and analyzes trajectories (RMSD, RMSF, contact maps, free energy surfaces). For structural biology, drug binding, and biophysics.

Prepares and structurally reviews readiness evidence for ISO management-system and laboratory-competence standards - ISO 13485 medical device QMS, ISO 14971 device risk management, ISO/IEC 17025 testing and calibration laboratories, and ISO 15189 medical laboratories. Use when organizing declared scope, controlled documents, risk-management files, scope of accreditation, traceability, CAPA, external-provider controls, or bounded local evidence manifests, and when separating ISO certification from laboratory accreditation, FDA QMSR inspection, CLIA certification, MDSAP, and EU MDR/IVDR evidence boundaries. Not for legal applicability, compliance, certification, or accreditation decisions; contains no clause text.

Writes scientific Markdown documentation and Mermaid diagrams for workflows, relationships, timelines, and schemas. Provides syntax references, document templates, accessibility guidance, and version-aware rendering checks. Use when a user requests Markdown, Mermaid, or a text-based structural diagram; quantitative scientific figures require suitable plotting tools.

Builds and queries multi-language source and binary code graphs for security analysis. Includes pre-analysis passes for blast radius, taint propagation, privilege boundaries, entry point enumeration, proxy/unresolved-call tracking, type/reference queries, structural traversal, graph diffs, audit augmentation, declared cross-language/FFI/external links via `.trailmark/links.toml`, and SQL schema graphs. Use when analyzing call paths, mapping attack surface, finding complexity hotspots, enumerating entry points, tracing taint propagation, measuring blast radius, importing SARIF/weAudit/binary findings, linking source graphs across language or RPC boundaries, or building a code graph for audit prioritization. Feature-gate version-specific Trailmark APIs before using them; prefer `trailmark.parse.detect_languages()` or `--language auto` when the target language is unknown or polyglot.