crevice 0.1.1__py3-none-any.whl

crevice/__init__.py

@@ -0,0 +1,296 @@
+"""CREVICE public API.
+
+CREVICE stands for Cavity and Residue Environment Visualisation, Interaction and
+Connectivity Evaluation.
+
+CREVICE measures empty space in protein structures and MD trajectories
+(channel radius profiles, cavities, pockets, tunnels and cast volumes) and
+relates it to the residues and waters around it (lining residues, contact
+networks, hydration and typed interactions). All lengths are in ångström,
+areas in Ų, volumes in ų and MD times in ps.
+
+The names imported here are the supported entry points; each is documented
+in its defining module. The main groups are:
+
+* loading: :func:`~crevice.parser.load_structure`, :func:`~crevice.pdb.resolve_structure`,
+  :func:`~crevice.trajectory.load_trajectory`;
+* geometry: :func:`~crevice.channels.pore_profile`, :func:`~crevice.rolling.rolling_probe_cast`,
+  :func:`~crevice.voids.void_cast`, :func:`~crevice.cavities.detect_cavities`, :func:`~crevice.tunnels.find_tunnels`;
+* residues and networks: :func:`~crevice.analysis.annotate_residues`,
+  :func:`~crevice.networks.build_residue_network`, :func:`~crevice.networks.build_cavity_network`;
+* trajectories and statistics: :func:`~crevice.trajectory.analyze_trajectory`,
+  :func:`~crevice.ensemble.profile_distribution`, :func:`~crevice.uncertainty.block_mean_confidence`;
+* outputs: the ``write_*`` exporters and ``plot_*`` figure functions.
+
+The same analyses are available from the ``crevice`` command line.
+
+Results are geometric measurements of the supplied coordinates. They depend
+on atomic radii, probe sizes and grid spacing, and are not by themselves
+evidence of biological function, permeation or solvent access.
+
+Examples
+--------
+>>> from crevice import Atom, StructureFrame, profile_along_path
+>>> frame = StructureFrame((Atom(1, "CA", "ALA", "A", 1, 4.0, 0.0, 0.0, "C"),))
+>>> round(profile_along_path(frame, [(0.0, 0.0, 0.0)]).min_radius, 2)
+2.3
+"""
+
+from .benchmarks import (
+    BENCHMARK_SYSTEMS,
+    DEFAULT_BENCHMARK_IDS,
+    BenchmarkSystem,
+    DownloadRecord,
+    benchmark_path,
+    benchmark_systems,
+    fetch_all_benchmark_structures,
+    fetch_benchmark_record,
+    fetch_benchmark_structure,
+    get_benchmark_system,
+    provenance_path,
+    read_provenance,
+    verify_cached_structure,
+)
+from .pdb import (
+    DownloadRecord,
+    StructureSource,
+    cached_structure_path,
+    fetch_structure,
+    is_accession,
+    normalize_accession,
+    resolve_structure,
+    structure_url,
+)
+from .cavities import cavity_surface_points, cavity_volume, classify_voids, detect_cavities
+from .channels import channel_volume, detect_bottlenecks, pore_profile, profile_along_path, trace_centerline
+from .figures import (
+    plot_cavity_summary,
+    plot_network_chord,
+    plot_network_summary,
+    plot_profile_radius,
+    plot_profile_radius_with_residues,
+    plot_residue_contacts,
+    plot_trajectory_profiles,
+    write_publication_pymol_script,
+    write_static_publication_bundle,
+)
+from .io import (
+    export_pymol_script,
+    write_cavities_csv,
+    write_connectivity_csv,
+    write_features_csv,
+    write_network_csv,
+    write_trajectory_csv,
+    write_tunnel_points_csv,
+    write_tunnels_csv,
+    write_void_cast_csv,
+    write_cavities_json,
+    write_cavities_pdb,
+    write_profile_csv,
+    write_network_json,
+    write_profile_json,
+    write_profile_pdb,
+    write_residue_contacts_csv,
+    write_residue_contacts_json,
+    write_tunnels_json,
+    write_trajectory_json,
+    write_tunnels_pdb,
+    write_void_cast_json,
+    write_void_cast_pdb,
+)
+from .ml import (
+    cluster_conformations,
+    cluster_profiles,
+    extract_features,
+    profile_features,
+    reduce_dimensions,
+    representative_frames,
+    representative_profile,
+    residue_importance,
+    transition_summary,
+)
+from .models import (
+    Atom,
+    Cavity,
+    ChannelPoint,
+    FrameAnalysis,
+    NetworkEdge,
+    NetworkNode,
+    PoreProfile,
+    ResidueContact,
+    ResidueInteractionNetwork,
+    StructureFrame,
+    TrajectoryAnalysis,
+    Tunnel,
+    VoidCast,
+    VoidComponent,
+)
+from .networks import build_cavity_network, build_residue_network, compare_networks, network_metrics
+from .parser import load_structure, load_structure_report
+from .volume_export import write_void_cast_dx, write_volume_viewer_bundle
+from .ensemble import profile_distribution, write_profile_distribution_csv
+from .connectivity import persistent_network, lining_connectivity, plot_lining_connectivity
+from .radii import RadiusSet, custom_radii_set, load_radius_file, radii_preset, use_radii
+from .residues import annotate_residues, bottleneck_residues, lining_residues, nearest_residues, residue_contact_table
+from .schemas import SCHEMA_VERSION, result_envelope
+from .static_suite import run_static_benchmark_suite
+from .trajectory import (
+    Trajectory,
+    analyze_trajectory,
+    cavity_timeseries,
+    inspect_trajectory,
+    load_static_frames,
+    load_trajectory,
+    load_trajectory_report,
+    network_timeseries,
+    profile_timeseries,
+    trajectory_from_frames,
+)
+from .tunnels import cluster_tunnels, find_tunnels, rank_tunnels, tunnel_profile
+from .voids import component_profile, validate_void_cast, void_cast
+
+__all__ = [
+    "write_void_cast_dx", "write_volume_viewer_bundle",
+    "profile_distribution", "write_profile_distribution_csv", "persistent_network",
+    "lining_connectivity", "plot_lining_connectivity",
+    "Atom",
+    "BENCHMARK_SYSTEMS",
+    "BenchmarkSystem",
+    "Cavity",
+    "ChannelPoint",
+    "DEFAULT_BENCHMARK_IDS",
+    "FrameAnalysis",
+    "NetworkEdge",
+    "NetworkNode",
+    "PoreProfile",
+    "RadiusSet",
+    "ResidueContact",
+    "ResidueInteractionNetwork",
+    "SCHEMA_VERSION",
+    "StructureFrame",
+    "Trajectory",
+    "TrajectoryAnalysis",
+    "Tunnel",
+    "VoidComponent",
+    "VoidCast",
+    "analyze_trajectory",
+    "annotate_residues",
+    "benchmark_path",
+    "benchmark_systems",
+    "bottleneck_residues",
+    "build_cavity_network",
+    "build_residue_network",
+    "cavity_surface_points",
+    "cavity_timeseries",
+    "cavity_volume",
+    "channel_volume",
+    "classify_voids",
+    "cluster_conformations",
+    "cluster_profiles",
+    "cluster_tunnels",
+    "void_cast",
+    "validate_void_cast",
+    "component_profile",
+    "compare_networks",
+    "custom_radii_set",
+    "detect_bottlenecks",
+    "detect_cavities",
+    "export_pymol_script",
+    "extract_features",
+    "fetch_all_benchmark_structures",
+    "fetch_benchmark_record",
+    "fetch_benchmark_structure",
+    "provenance_path",
+    "read_provenance",
+    "verify_cached_structure",
+    "StructureSource",
+    "cached_structure_path",
+    "fetch_structure",
+    "is_accession",
+    "normalize_accession",
+    "resolve_structure",
+    "structure_url",
+    "DownloadRecord",
+    "find_tunnels",
+    "get_benchmark_system",
+    "lining_residues",
+    "load_static_frames",
+    "load_structure_report",
+    "load_structure",
+    "load_trajectory_report",
+    "inspect_trajectory",
+    "load_trajectory",
+    "nearest_residues",
+    "network_metrics",
+    "network_timeseries",
+    "plot_cavity_summary",
+    "plot_network_chord",
+    "plot_profile_radius_with_residues",
+    "plot_network_summary",
+    "plot_profile_radius",
+    "plot_residue_contacts",
+    "plot_trajectory_profiles",
+    "write_publication_pymol_script",
+    "write_static_publication_bundle",
+    "pore_profile",
+    "profile_along_path",
+    "profile_features",
+    "profile_timeseries",
+    "radii_preset",
+    "load_radius_file",
+    "use_radii",
+    "rank_tunnels",
+    "reduce_dimensions",
+    "representative_frames",
+    "representative_profile",
+    "residue_contact_table",
+    "residue_importance",
+    "result_envelope",
+    "run_static_benchmark_suite",
+    "trace_centerline",
+    "trajectory_from_frames",
+    "transition_summary",
+    "tunnel_profile",
+    "write_cavities_json",
+    "write_cavities_pdb",
+    "write_network_json",
+    "write_trajectory_json",
+    "write_profile_csv",
+    "write_profile_json",
+    "write_profile_pdb",
+    "write_residue_contacts_csv",
+    "write_residue_contacts_json",
+    "write_tunnels_json",
+    "write_tunnels_pdb",
+    "write_void_cast_pdb",
+    "write_void_cast_json",
+    "write_cavities_csv",
+    "write_connectivity_csv",
+    "write_features_csv",
+    "write_network_csv",
+    "write_trajectory_csv",
+    "write_tunnel_points_csv",
+    "write_tunnels_csv",
+    "write_void_cast_csv",
+]
+
+from .rolling import rolling_probe_cast
+__all__.append("rolling_probe_cast")
+
+__version__ = "0.1.1"
+
+from .residue_evidence import boundary_residue_evidence,read_binary_dx,write_residue_evidence_bundle
+from .residue_dynamics import ResidueDynamics,write_dynamics_summary
+from .uncertainty import block_mean_confidence
+from .trajectory import align_frame_report
+__all__.extend(["boundary_residue_evidence","read_binary_dx","write_residue_evidence_bundle",
+                "ResidueDynamics","write_dynamics_summary","block_mean_confidence","align_frame_report"])
+
+from .residue_evidence import profile_constriction_evidence
+__all__.append("profile_constriction_evidence")
+
+from .residue_evidence import restore_viewer_identities
+__all__.append("restore_viewer_identities")
+
+from .residue_evidence import select_stick_residues
+__all__.append("select_stick_residues")

crevice/__main__.py

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+"""Run the CREVICE command line with ``python -m crevice``.
+
+Equivalent to the ``crevice`` console script: importing this module calls
+:func:`crevice.cli.main` and exits with its return code. It is therefore
+excluded from the API documentation and from doctest collection.
+"""
+
+from .cli import main
+
+raise SystemExit(main())