proteusPy

  1# Initialization for the proteusPy package
  2# Copyright (c) 2025 Eric G. Suchanek, PhD., all rights reserved
  3# Subject to the BSD public license.
  4
  5# pylint: disable=C0413
  6# pylint: disable=C0103
  7
  8"""
  9``proteusPy`` is a Python package specializing in the modeling and analysis
 10of proteins of known structure with an emphasis on disulfide bonds. This package
 11reprises the molecular modeling program [Proteus](https://doi.org/10.1021/bi00368a023),
 12a structure-based program developed as part of Eric Suchanek's graduate thesis,
 13which was originally written in Common Lisp, ported to C++ and ultimately to Python.
 14
 15The package utilizes several base classes to create and analyze disulfide bonds:
 16- Turtle3D: to build disulfides through the manipulation of local coordinate systems.
 17- DisulfideBase: basic characteristics of individual disulfide bonds, classes ``Disulfide`` and ``DisulfideList``
 18- DisulfideClassManager: to manage ``Disulfide`` classes
 19- DisulfideClassGenerator: to generate ``Disulfide`` structure ensembles from disulfide classes
 20- DisulfideStats: to calculate statistics on disulfide bonds
 21- DisulfideVisualization: to visualize disulfide bonds
 22- DisulfideLoader: to load disulfide bonds from the master list of Disulfides and create the
 23 various data structures needed to build the structural classes and physical properties of
 24 the disulfide bonds.
 25
 26
 27This implementation of ``proteusPy`` focuses on the ``Disulfide`` class. This class
 28implements methods to analyze the protein structure stabilizing element known as a
 29*Disulfide bond*. Its underlying methods  have been utilized to construct a database of over 36,000
 30high-quality disulfide bonds from the RCSB protein data bank (https://www.rcsb.org) for structural analysis.
 31"""
 32
 33__pdoc__ = {
 34    "version": None,
 35    "__all__": False,
 36    "_version": False,
 37}
 38
 39import logging
 40
 41# Set the default (global) logger level to CRITICAL
 42logging.basicConfig(level=logging.CRITICAL)
 43
 44# Suppress findfont debug messages
 45logging.getLogger("matplotlib.font_manager").setLevel(logging.ERROR)
 46
 47
 48from ._version import __version__
 49from .angle_annotation import AngleAnnotation, plot_angle
 50from .atoms import (
 51    ATOM_COLORS,
 52    ATOM_RADII_COVALENT,
 53    ATOM_RADII_CPK,
 54    BOND_COLOR,
 55    BOND_RADIUS,
 56    BS_SCALE,
 57    CAMERA_SCALE,
 58    SPEC_POWER,
 59    SPECULARITY,
 60)
 61from .backbone_loader import BackboneLoader, BackboneResidue
 62from .data_fetch import data_asset_url, fetch_data_file, sha256_file
 63from .disulfide_tree import (
 64    DisulfideTree,
 65    TreeNodeData,
 66    classify_angles,
 67    parent_class_id,
 68    snippet_for_disulfide,
 69    snippet_for_node,
 70)
 71from .DisulfideBase import Disulfide, DisulfideList
 72from .DisulfideClasses import (
 73    angle_within_range,
 74    filter_by_percentage,
 75    get_quadrant,
 76    is_between,
 77)
 78from .DisulfideClassGenerator import DisulfideClassGenerator
 79from .DisulfideClassManager import DisulfideClassManager
 80from .DisulfideExceptions import (
 81    DisulfideConstructionException,
 82    DisulfideConstructionWarning,
 83    DisulfideException,
 84    DisulfideIOException,
 85    DisulfideParseWarning,
 86)
 87from .DisulfideIO import (
 88    Initialize_Disulfide_From_Coords,
 89    extract_disulfide,
 90    load_disulfides_from_id,
 91)
 92from .DisulfideLoader import Bootstrap_PDB_SS, DisulfideLoader, Load_PDB_SS
 93from .DisulfideStats import DisulfideStats
 94from .DisulfideVisualization import DisulfideVisualization
 95from .graph_reasoner import (
 96    DirectedDiscoverer,
 97    EdgeDiscoverer,
 98    ExplorationSteering,
 99    GradientSteering,
100    GraphReasoner,
101    KNNDiscoverer,
102    KnowledgeGraph,
103    RadiusDiscoverer,
104    ReasoningPath,
105    SemanticEdge,
106    SteeringStrategy,
107    TargetSteering,
108    angular_distance,
109    euclidean_distance,
110    graph_from_disulfides,
111)
112from .logger_config import (
113    DEFAULT_LOG_LEVEL,
114    configure_master_logger,
115    create_logger,
116    disable_stream_handlers_for_namespace,
117    list_all_loggers,
118    list_handlers,
119    set_logger_level,
120    set_logger_level_for_module,
121    set_logging_level_for_all_handlers,
122    toggle_stream_handler,
123)
124from .manifold_model import (
125    ManifoldModel,
126    NodeGeometry,
127)
128from .manifold_observer import (
129    ManifoldObserver,
130    ObservedGeometry,
131)
132from .Plotting import plot_class_chart
133from .ProteusGlobals import (
134    _ANG_INIT,
135    _FLOAT_INIT,
136    _INT_INIT,
137    BINARY_CLASS_METRICS_CSV_FILE,
138    BINARY_CLASS_METRICS_FILE,
139    CA_CUTOFF,
140    CAMERA_POS,
141    DATA_RELEASE_BASE_URL,
142    DATA_RELEASE_SHA256,
143    DATA_RELEASE_TAG,
144    FONTSIZE,
145    LOADER_ALL_MASTER_URL,
146    LOADER_FNAME,
147    LOADER_FNAME_URL,
148    LOADER_SUBSET_FNAME,
149    LOADER_SUBSET_FNAME_URL,
150    LOADER_SUBSET_MASTER_URL,
151    MODEL_DIR,
152    OCTANT_CLASS_METRICS_CSV_FILE,
153    OCTANT_CLASS_METRICS_FILE,
154    PDB_DIR,
155    PROBLEM_ID_FILE,
156    SG_CUTOFF,
157    SS_CLASS_DEFINITIONS,
158    SS_CLASS_DICT_FILE,
159    SS_CONSENSUS_BIN_FILE,
160    SS_CONSENSUS_OCT_FILE,
161    SS_ID_FILE,
162    SS_LIST_URL,
163    SS_MASTER_PICKLE_FILE,
164    SS_PICKLE_FILE,
165    SS_PROBLEM_SUBSET_ID_FILE,
166    SS_SUBSET_PICKLE_FILE,
167    WINFRAME,
168    WINSIZE,
169)
170from .ProteusPyWarning import ProteusPyWarning
171from .Residue import (
172    build_residue,
173    get_backbone_from_chain,
174    to_alpha,
175    to_carbonyl,
176    to_nitrogen,
177    to_oxygen,
178)
179from .ssparser import (
180    check_file,
181    extract_and_write_ssbonds_and_atoms,
182    extract_ssbonds_and_atoms,
183    get_atom_coordinates,
184    get_phipsi_atoms_coordinates,
185    get_residue_atoms_coordinates,
186    print_disulfide_bond_info_dict,
187)
188from .tree_visualizer import (
189    png_tree,
190    text_tree,
191    tree_3d,
192)
193from .turtle3D import ORIENT_BACKBONE, ORIENT_SIDECHAIN, Turtle3D
194from .utility import (
195    Download_Disulfides,
196    Extract_Disulfides,
197    Extract_Disulfides_From_List,
198    display_ss_pymol,
199    distance_squared,
200    extract_firstchain_ss,
201    generate_vector_dataframe,
202    get_jet_colormap,
203    get_memory_usage,
204    get_object_size_mb,
205    get_theme,
206    grid_dimensions,
207    image_to_ascii_art,
208    load_list_from_file,
209    print_memory_used,
210    prune_extra_ss,
211    remove_duplicate_ss,
212    retrieve_git_lfs_files,
213    save_list_to_file,
214    set_plotly_theme,
215    set_pyvista_theme,
216    sort_by_column,
217)
218from .vector3D import (
219    Vector3D,
220    calc_angle,
221    calc_dihedral,
222    calculate_bond_angle,
223    distance3d,
224    rms_difference,
225)
226
227set_plotly_theme(theme="auto")
228set_pyvista_theme(theme="auto")
229
230# Create a logger for the package itself. __name__ is the package name, proteusPy
231
232_logger = create_logger(__name__, log_level=DEFAULT_LOG_LEVEL)
233configure_master_logger("proteusPy.log", disabled=True)
234
235
236def describe():
237    """
238    Describe the proteusPy package.
239    """
240    set_logger_level_for_module("proteusPy", logging.INFO)
241    _logger.info(
242        f"ProteusPy {__version__} initialized. Plotly theme set to: {set_plotly_theme(theme='auto')}. PyVista theme set to: {set_pyvista_theme(theme='auto')}. Logging level setting to default: {DEFAULT_LOG_LEVEL}"
243    )
244    _logger.setLevel(DEFAULT_LOG_LEVEL)
245    return
246
247
248# end of file