Crate molframe_core 

Core types, storage and analysis contracts for molframe.

This crate holds the vocabulary every other molframe crate speaks: the typed positions into a structure’s tables, the interned identifiers, the chunked columnar store the coordinates and annotations live in, the immutable Structure built over it, and the contract types that make an analysis state what it assumed.

It has almost no dependencies and no input or output of its own, so a project that wants only the types pays for only the types. Memory mapping and decompression are behind features for the same reason.

Layout

• index — typed positions; a residue position is not an atom position.
• element — element identity, and recovering one from an atom name.
• span — where in a source file something was.
• diagnostic — findings about data, returned alongside success.
• symbol — interned identifiers, so no kernel compares strings.
• numeric — the one home of every lossy numeric conversion.

Re-exports

pub use anisotropy::AnisotropicDisplacement;

pub use anisotropy::AnisotropyTable;

pub use anisotropy::AnisotropyTableBuilder;

pub use annotation::AROMATIC_ATOM_ANNOTATION;

pub use annotation::ATOM_RADIUS_ANNOTATION;

pub use annotation::AUTODOCK_TYPE_ANNOTATION;

pub use annotation::AnnotationColumn;

pub use annotation::AtomAnnotation;

pub use annotation::AtomAnnotations;

pub use annotation::COMPONENT_KIND_ANNOTATION;

pub use annotation::FORMAL_CHARGE_ANNOTATION;

pub use annotation::HBOND_ACCEPTOR_ANNOTATION;

pub use annotation::HBOND_DONOR_ANNOTATION;

pub use annotation::INSTANCE_ID_ANNOTATION;

pub use annotation::MISSING_BAND_CODE;

pub use annotation::PAE_ANNOTATION;

pub use annotation::PARTIAL_CHARGE_ANNOTATION;

pub use annotation::PLDDT_ANNOTATION;

pub use annotation::POLYMER_ATOM_ROLE_ANNOTATION;

pub use annotation::PlddtBand;

pub use annotation::SEGMENT_ID_ANNOTATION;

pub use annotation::STEREO_CONFIGURATION_ANNOTATION;

pub use bond::BondAdjacency;

pub use bond::BondOrder;

pub use bond::BondProvenance;

pub use bond::BondRecord;

pub use bond::BondTable;

pub use bond::BondTableBuilder;

pub use chunk::AtomChunk;

pub use chunk::AtomChunkStats;

pub use chunk::ChunkBuilder;

pub use chunk::ElementMask;

pub use chunk::Extremes;

pub use chunk::ParentMapping;

pub use chunk::TARGET_CHUNK_ATOMS;

pub use column::BitVec;

pub use column::EncodedColumn;

pub use column::Presence;

pub use column::ValidityMask;

pub use contract::Analysis;

pub use contract::AnalysisPolicy;

pub use contract::Coverage;

pub use contract::Provenance;

pub use contract::Status;

pub use coords::Aabb;

pub use coords::CoordinateBlock;

pub use coords::CoordinateGeneration;

pub use coords::CoordinateSample;

pub use coords::CoordinateSampleError;

pub use diagnostic::Class;

pub use diagnostic::Code;

pub use diagnostic::ContextItem;

pub use diagnostic::Diagnostic;

pub use diagnostic::Diagnostics;

pub use diagnostic::Findings;

pub use diagnostic::Kind;

pub use diagnostic::Rendered;

pub use diagnostic::Severity;

pub use diagnostic::Strictness;

pub use element::Element;

pub use execution::Backpressure;

pub use execution::Batch;

pub use execution::BatchDemand;

pub use execution::BatchLease;

pub use execution::BatchSource;

pub use execution::CancellationToken;

pub use execution::Cancelled;

pub use execution::ContextError;

pub use execution::ExecutionContext;

pub use execution::ExecutionContextBuilder;

pub use execution::MemoryBudget;

pub use execution::MemoryBudgetError;

pub use execution::MemoryReservation;

pub use execution::ScratchPolicy;

pub use execution::SpillArtifact;

pub use execution::SpillError;

pub use execution::SpillFile;

pub use execution::SpillReader;

pub use execution::TempStoragePolicy;

pub use index::AnisotropyIndex;

pub use index::AtomIndex;

pub use index::BondIndex;

pub use index::ChainIndex;

pub use index::EntityIndex;

pub use index::InstanceId;

pub use index::ModelIndex;

pub use index::ResidueIndex;

pub use io::AmbiguousResidueBoundaryPolicy;

pub use io::BatchContinuity;

pub use io::ByteWindow;

pub use io::CategoryFilter;

pub use io::ContinuityLevel;

pub use io::Format;

pub use io::InputBuffer;

pub use io::InputKind;

pub use io::MissingElementPolicy;

pub use io::OccupancyPolicy;

pub use io::ParseMode;

pub use io::ReadOptions;

pub use io::ReadResult;

pub use io::SourceBytes;

pub use io::SpillWindowedFile;

pub use io::StructureAtomRecord;

pub use io::StructureBatch;

pub use io::StructureBatchBuffer;

pub use io::StructureBatchBuilder;

pub use io::StructureBatchError;

pub use io::StructureBatchPool;

pub use io::WindowedFile;

pub use io::WindowedSourceFile;

pub use io::collect_structure;

pub use io::write_output;

pub use limits::CapacityError;

pub use limits::TableError;

pub use optional::OptionalI32;

pub use optional::OptionalSymbol;

pub use provider::AtomEndpoint;

pub use provider::BondChunk;

pub use provider::BondChunkProvider;

pub use provider::BondChunkRecord;

pub use provider::ChunkDescriptor;

pub use provider::ChunkId;

pub use provider::ChunkLayout;

pub use provider::DatasetCatalog;

pub use provider::DatasetDescriptor;

pub use provider::DatasetId;

pub use provider::FrameChunk;

pub use provider::FrameChunkProvider;

pub use provider::LocalRow;

pub use provider::LogicalRow;

pub use provider::PayloadKind;

pub use provider::PropertyChunk;

pub use provider::PropertyChunkProvider;

pub use provider::PropertyKind;

pub use provider::PropertyValue;

pub use provider::ProviderError;

pub use provider::StructureChunk;

pub use provider::StructureChunkProvider;

pub use provider::TARGET_CHUNK_BONDS;

pub use secondary::SecondaryAssignment;

pub use secondary::SecondarySource;

pub use secondary::SecondaryStructure;

pub use selection::AtomSelection;

pub use span::ByteSpan;

pub use span::Position;

pub use structure::CountDifference;

pub use structure::DifferenceError;

pub use structure::ExtensionStore;

pub use structure::MetadataDifference;

pub use structure::Structure;

pub use structure::StructureData;

pub use structure::StructureDifference;

pub use structure::StructureDifferenceOptions;

pub use structure::StructureView;

pub use structure::ValueDifference;

pub use structure::structure_difference;

pub use symbol::AltId;

pub use symbol::DictionaryFull;

pub use symbol::Interner;

pub use symbol::SymbolId;

pub use topology::EntityKind;

pub use topology::PolymerKind;

pub use topology::Topology;

Modules

anisotropy

Anisotropic displacement parameters as a sparse per-atom table.

annotation

Typed per-atom annotations.

bond

Bond graph storage and adjacency.

chunk

Atoms in chunks: columnar within a chunk, chunked across the structure.

column

Column storage: encodings, bit-level primitives, and why a value is absent.

contract

What an analysis assumed, and what it is therefore worth.

coords

Coordinate storage and bounds.

diagnostic

Findings about data, accumulated and returned alongside success.

element

Chemical element identity.

execution

Bounded execution contracts for streaming and out-of-core work.

hashing

Hashing for keys the engine assigned itself.

index

Typed table positions.

io

Getting bytes in, recognising what they are, and the contract readers meet.

limits

Explicit representation limits for public storage types.

numeric

The one place a numeric conversion that can lose information is written.

optional

Compact optional scalar representations.

parallel

Dividing work so that the answer does not depend on how many threads ran it.

provider

Out-of-core provider contracts for renderer and analysis consumers.

secondary

Per-residue secondary-structure vocabulary shared by readers and analyses.

selection

Atom selection representations.

span

Source byte and line locations.

structure

The normalised structure, the views over it, and the invariants it holds.

symbol

Interned identifiers.

topology

The hierarchy, stored as offset tables rather than nested collections.

Macros

diagnostic_from

Implements From<&E> and From<E> for Diagnostic.