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# Last updated: 2025-03-27 19:48:55 -egs-
  5
  6# pylint: disable=C0413
  7# pylint: disable=C0103
  8
  9"""
 10``proteusPy`` is a Python package specializing in the modeling and analysis
 11of proteins of known structure with an emphasis on disulfide bonds. This package
 12reprises the molecular modeling program [Proteus](https://doi.org/10.1021/bi00368a023),
 13a structure-based program developed as part of Eric Suchanek's graduate thesis,
 14which was originally written in Common Lisp, ported to C++ and ultimately to Python.
 15
 16The package utilizes several base classes to create and analyze disulfide bonds:
 17- Turtle3D: to build disulfides through the manipulation of local coordinate systems.
 18- DisulfideBase: basic characteristics of individual disulfide bonds, classes ``Disulfide`` and ``DisulfideList``
 19- DisulfideClassManager: to manage ``Disulfide`` classes
 20- DisulfideClassGenerator: to generate ``Disulfide`` structure ensembles from disulfide classes
 21- DisulfideStats: to calculate statistics on disulfide bonds
 22- DisulfideVisualization: to visualize disulfide bonds
 23- DisulfideLoader: to load disulfide bonds from the master list of Disulfides and create the
 24 various data structures needed to build the structural classes and physical properties of
 25 the disulfide bonds.
 26
 27
 28This implementation of ``proteusPy`` focuses on the ``Disulfide`` class. This class
 29implements methods to analyze the protein structure stabilizing element known as a
 30*Disulfide bond*. Its underlying methods  have been utilized to construct a database of over 36,000
 31high-quality disulfide bonds from the RCSB protein data bank (https://www.rcsb.org) for structural analysis.
 32"""
 33
 34__pdoc__ = {
 35    "version": None,
 36    "__all__": False,
 37    "_version": False,
 38}
 39
 40import logging
 41
 42# Set the default (global) logger level to CRITICAL
 43logging.basicConfig(level=logging.CRITICAL)
 44
 45# Suppress findfont debug messages
 46logging.getLogger("matplotlib.font_manager").setLevel(logging.ERROR)
 47
 48# Create a logger for the package itself. __name__ is the package name, proteusPy
 49_logger = logging.getLogger(__name__)
 50
 51from ._version import __version__
 52from .angle_annotation import AngleAnnotation, plot_angle
 53from .atoms import (
 54    ATOM_COLORS,
 55    ATOM_RADII_COVALENT,
 56    ATOM_RADII_CPK,
 57    BOND_COLOR,
 58    BOND_RADIUS,
 59    BS_SCALE,
 60    CAMERA_SCALE,
 61    SPEC_POWER,
 62    SPECULARITY,
 63)
 64from .DisulfideBase import Disulfide, DisulfideList
 65from .DisulfideClasses import (
 66    angle_within_range,
 67    filter_by_percentage,
 68    get_quadrant,
 69    is_between,
 70)
 71from .DisulfideClassGenerator import DisulfideClassGenerator
 72from .DisulfideClassManager import DisulfideClassManager
 73from .DisulfideExceptions import (
 74    DisulfideConstructionException,
 75    DisulfideConstructionWarning,
 76    DisulfideException,
 77    DisulfideIOException,
 78    DisulfideParseWarning,
 79)
 80from .DisulfideIO import (
 81    Initialize_Disulfide_From_Coords,
 82    extract_disulfide,
 83    load_disulfides_from_id,
 84)
 85from .DisulfideLoader import Bootstrap_PDB_SS, DisulfideLoader, Load_PDB_SS
 86from .DisulfideStats import DisulfideStats
 87from .DisulfideVisualization import DisulfideVisualization
 88from .logger_config import (
 89    DEFAULT_LOG_LEVEL,
 90    configure_master_logger,
 91    create_logger,
 92    disable_stream_handlers_for_namespace,
 93    list_all_loggers,
 94    list_handlers,
 95    set_logger_level,
 96    set_logger_level_for_module,
 97    set_logging_level_for_all_handlers,
 98    toggle_stream_handler,
 99)
100from .Plotting import plot_class_chart
101from .ProteusGlobals import (
102    _ANG_INIT,
103    _FLOAT_INIT,
104    _INT_INIT,
105    BINARY_CLASS_METRICS_CSV_FILE,
106    BINARY_CLASS_METRICS_FILE,
107    CA_CUTOFF,
108    CAMERA_POS,
109    FONTSIZE,
110    LOADER_ALL_MASTER_URL,
111    LOADER_FNAME,
112    LOADER_FNAME_URL,
113    LOADER_SUBSET_FNAME,
114    LOADER_SUBSET_FNAME_URL,
115    LOADER_SUBSET_MASTER_URL,
116    MODEL_DIR,
117    OCTANT_CLASS_METRICS_CSV_FILE,
118    OCTANT_CLASS_METRICS_FILE,
119    PDB_DIR,
120    PROBLEM_ID_FILE,
121    SG_CUTOFF,
122    SS_CLASS_DEFINITIONS,
123    SS_CLASS_DICT_FILE,
124    SS_CONSENSUS_BIN_FILE,
125    SS_CONSENSUS_OCT_FILE,
126    SS_ID_FILE,
127    SS_LIST_URL,
128    SS_MASTER_PICKLE_FILE,
129    SS_PICKLE_FILE,
130    SS_PROBLEM_SUBSET_ID_FILE,
131    SS_SUBSET_PICKLE_FILE,
132    WINFRAME,
133    WINSIZE,
134)
135from .ProteusPyWarning import ProteusPyWarning
136from .Residue import (
137    build_residue,
138    get_backbone_from_chain,
139    to_alpha,
140    to_carbonyl,
141    to_nitrogen,
142    to_oxygen,
143)
144from .ssparser import (
145    check_file,
146    extract_and_write_ssbonds_and_atoms,
147    extract_ssbonds_and_atoms,
148    get_atom_coordinates,
149    get_phipsi_atoms_coordinates,
150    get_residue_atoms_coordinates,
151    print_disulfide_bond_info_dict,
152)
153from .turtle3D import ORIENT_BACKBONE, ORIENT_SIDECHAIN, Turtle3D
154from .utility import (
155    Download_Disulfides,
156    Extract_Disulfides,
157    Extract_Disulfides_From_List,
158    display_ss_pymol,
159    distance_squared,
160    extract_firstchain_ss,
161    generate_vector_dataframe,
162    get_jet_colormap,
163    get_memory_usage,
164    get_object_size_mb,
165    get_theme,
166    grid_dimensions,
167    image_to_ascii_art,
168    load_list_from_file,
169    print_memory_used,
170    prune_extra_ss,
171    remove_duplicate_ss,
172    retrieve_git_lfs_files,
173    save_list_to_file,
174    set_plotly_theme,
175    set_pyvista_theme,
176    sort_by_column,
177)
178from .vector3D import (
179    Vector3D,
180    calc_angle,
181    calc_dihedral,
182    calculate_bond_angle,
183    distance3d,
184    rms_difference,
185)
186
187set_plotly_theme(theme="auto")
188set_pyvista_theme(theme="auto")
189
190
191def describe():
192    """
193    Describe the proteusPy package.
194    """
195    set_logger_level_for_module("proteusPy", logging.INFO)
196    _logger.info("ProteusPy %s initialized.", __version__)
197    _logger.info("Plotly theme set to: %s", set_plotly_theme(theme="auto"))
198    _logger.info("PyVista theme set to: %s", set_pyvista_theme(theme="auto"))
199    _logger.info("Logging level setting to default: %s", DEFAULT_LOG_LEVEL)
200    _logger.setLevel(DEFAULT_LOG_LEVEL)
201    return
202
203
204# end of file