All Classes and Interfaces
Class
Description
A collection of algebraic or generic mathematical functions.
The result of an alignment.
The result of an alignment.
Superimpose sets of residues.
Binned representation of the angle between residues.
A wrapper which describes the correspondence between two collections of residues.
Schemes on which atoms (by name) to use to align residues.
Binned representation of the distance between residues.
The result of a structural motif search.
Scores hits by computing the RMSD with respect to the reference motif.
Indicates invalid query definitions.
A
ResiduePairIdentifier based on IndexSelection instances, created by the residue graph.Selects a residue by its index in the source structure file.
Keep structure data in memory? Requires ~30 GB of memory for 180k structures.
The specification on how to insert and select residue pair occurrences.
The implementation of the inverted index.
A
ResiduePairIdentifier defined by data from the inverted index.A motif may be best described by the minimal spanning tree which connects all vertices in the most compact fashion.
Enumerates all 'common' atoms by name.
Identifies a residue unambiguously by label_asym_id, struct_oper_id, and label_seq_id.
Pruning motifs is advantageous as it saves time (less lookups) and avoids too rigid criteria enforced during search.
How to simplify/prune motifs?
Motif definitions used in examples and tests.
The entry point to perform motif searches.
The entry point of the strucmotif-search application.
All properties used throughout the strucmotif-search application.
The immutable container for a structural motif query.
The state and results of a motif search run.
Performs motif search queries and returns the corresponding result object.
The default strucmotif-search runtime.
Don't prune query motif.
Describes the overlap between two
ResiduePairIdentifier instances.Defines a relation between 2 objects.
Immutable instance capturing all parameters of a given search job.
Partitions a collection into (roughly) equal-sized chunks.
Reports the polymer type for a component.
Defines a position-specific exchange for a particular position in the query structure.
Align 2 sets of residues by a quaternion-based characteristic polynomial.
The entry point to create
MotifSearchQuery instances.A query structure wraps a
Structure and provides additional functionality needed to employ it as motif
definition during a structural motif query job.Represents the pseudo-graph defined by all residues.
Efficiently determine residues in contacts by a spatial hashing approach.
Captures all properties of a residue pair (i.e.
Residue pair identifiers combine the
Selection of each residue making up this pair.A residue pair occurrence is the combination of its properties (
ResiduePairDescriptor) and both identifiers
(wrapped as ResiduePairIdentifier).Registry of known residues.
The version of a PDB entry.
A selection within a Structure.
The state of the application consists of two lists of structure identifiers:
known: entries that have been processed (might become invalid if e.g.
A file-system-based state repository.
The structure object wraps categories of a mmCIF file and allows access via some utility methods.
Access structure data.
Default implementation of a structure data provider.
Reports global properties of a structure.
Read structures from CIF files.
A simple structure reader that parses CIF data into structure instances.
The contract to write optimized structure data that don't contain non-polymers, hydrogen, model afters #1 etc.
This implementation keeps a sparse representation of structure data including:
label_asym_id
label_seq_id
label_comp_id
label_atom_id
coordinates
entry identifier and data used for assembly generation
Where the magic happens.
The default strucmotif-search target assembler.
A container keeping track of paths in a target structure.
An application-wide shared thread pool with a configurable number of threads.
Wraps a ForkJoinPool.
Tracks timings.
A helper class keeping track of internal timings.
A transformation described by a 4x4 matrix.