rcsb-api 1.5.0__py3-none-any.whl

rcsb_api-1.5.0.dist-info/METADATA

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+Metadata-Version: 2.4
+Name: rcsb-api
+Version: 1.5.0
+Summary: Python package interface for RCSB.org API services
+Project-URL: Homepage, https://github.com/rcsb/py-rcsb-api
+Project-URL: Repository, https://github.com/rcsb/py-rcsb-api
+Project-URL: Issues, https://github.com/rcsb/py-rcsb-api/issues
+Project-URL: Documentation, https://rcsbapi.readthedocs.io/
+Project-URL: Changelog, https://github.com/rcsb/py-rcsb-api/blob/master/CHANGELOG.md
+Author-email: Dennis Piehl <dennis.piehl@rcsb.org>
+License-Expression: MIT
+License-File: LICENSE
+License-File: NOTICE.md
+Keywords: API,PDB,RCSB,bioinformatics,protein,structure
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Science/Research
+Classifier: Natural Language :: English
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Typing :: Typed
+Requires-Python: <4.0,>=3.9
+Requires-Dist: graphql-core
+Requires-Dist: httpx>=0.26.0
+Requires-Dist: nest-asyncio>=1.6.0
+Requires-Dist: rustworkx
+Requires-Dist: tqdm
+Provides-Extra: docs
+Requires-Dist: myst-parser; extra == 'docs'
+Requires-Dist: sphinx; extra == 'docs'
+Requires-Dist: sphinx-rtd-theme; extra == 'docs'
+Provides-Extra: tests
+Requires-Dist: black>=21.5b1; extra == 'tests'
+Requires-Dist: coverage; extra == 'tests'
+Requires-Dist: flake8; extra == 'tests'
+Requires-Dist: pylint; extra == 'tests'
+Requires-Dist: tox; extra == 'tests'
+Description-Content-Type: text/markdown
+
+[![PyPi Release](https://img.shields.io/pypi/v/rcsb-api.svg)](https://pypi.org/project/rcsb-api/)
+[![Build Status](https://dev.azure.com/rcsb/RCSB%20PDB%20Python%20Projects/_apis/build/status/rcsb.py-rcsb-api?branchName=master)](https://dev.azure.com/rcsb/RCSB%20PDB%20Python%20Projects/_build/latest?definitionId=40&branchName=master)
+[![Documentation Status](https://readthedocs.org/projects/rcsbapi/badge/?version=latest)](https://rcsbapi.readthedocs.io/en/latest/?badge=latest)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.14052470.svg)](https://doi.org/10.5281/zenodo.14052470)
+[![OpenSSF Best Practices](https://www.bestpractices.dev/projects/10424/badge)](https://www.bestpractices.dev/projects/10424)
+[![FAIR checklist badge](https://fairsoftwarechecklist.net/badge.svg)](https://fairsoftwarechecklist.net/v0.2?f=31&a=30112&i=32111&r=133)
+[![fair-software.eu](https://img.shields.io/badge/fair--software.eu-%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F-green)](https://fair-software.eu)
+
+
+# <img src="https://github.com/user-attachments/assets/248d3e32-7644-46b2-bf18-b5248c9e6305" height="160"/> &nbsp;&nbsp; *rcsb-api*: Python Toolkit for Accessing RCSB.org APIs
+Python interface for RCSB Protein Data Bank API services at [RCSB.org](https://www.rcsb.org/).
+
+## Installation
+This package requires Python 3.9 or later.
+
+Install it from PyPI via `pip` or `uv`:
+
+    pip install rcsb-api
+    
+    # or, if using uv:
+    uv pip install rcsb-api
+
+Or, download from [GitHub](https://github.com/rcsb/py-rcsb-api/) and install locally:
+
+    git clone https://github.com/rcsb/py-rcsb-api.git
+    cd py-rcsb-api
+    pip install .
+
+## Getting Started
+Full documentation available at [readthedocs](https://rcsbapi.readthedocs.io/en/latest/).
+
+The [RCSB PDB Search API](https://search.rcsb.org) supports RESTful requests according to a defined [schema](https://search.rcsb.org/redoc/index.html). This package provides an `rcsbapi.search` module that simplifies generating complex search queries.
+
+The [RCSB PDB Data API](https://data.rcsb.org) supports requests using [GraphQL](https://graphql.org/), a language for API queries. This package provides an `rcsbapi.data` module that simplifies generating queries in GraphQL syntax.
+
+### Search API
+The `rcsbapi.search` module supports all available [Advanced Search](https://www.rcsb.org/search/advanced) services, as listed below. For more details on their usage, see [Search Service Types](https://rcsbapi.readthedocs.io/en/latest/search_api/query_construction.html#search-service-types).
+
+|Search service                    |QueryType                 |
+|----------------------------------|--------------------------|
+|Full-text                         |`TextQuery()`             |
+|Attribute (structure or chemical) |`AttributeQuery()`        |
+|Sequence similarity               |`SeqSimilarityQuery()`    |
+|Sequence motif                    |`SeqMotifQuery()`         |
+|Structure similarity              |`StructSimilarityQuery()` |
+|Structure motif                   |`StructMotifQuery()`      |
+|Chemical similarity               |`ChemSimilarityQuery()`   |
+
+#### Search API Examples
+To perform a search for all structures from humans associated with the term "Hemoglobin", you can combine a "full-text" query (`TextQuery`) with an "attribute" query (`AttributeQuery`):
+
+```python
+from rcsbapi.search import AttributeQuery, TextQuery
+from rcsbapi.search import search_attributes as attrs
+
+# Construct a "full-text" sub-query for structures associated with the term "Hemoglobin"
+q1 = TextQuery(value="Hemoglobin")
+
+# Construct an "attribute" sub-query to search for structures from humans
+q2 = AttributeQuery(
+    attribute="rcsb_entity_source_organism.scientific_name",
+    operator="exact_match",  # Other operators include "contains_phrase", "exists", and more
+    value="Homo sapiens"
+)
+# OR, do so by using Python bitwise operators:
+q2 = attrs.rcsb_entity_source_organism.scientific_name == "Homo sapiens"
+
+# Combine the sub-queries (can sub-group using parentheses and standard operators, "&", "|", etc.)
+query = q1 & q2
+
+# Fetch the results by iterating over the query execution
+for rId in query():
+    print(rId)
+
+# OR, capture them into a variable
+results = list(query())
+```
+
+These examples are in `operator` syntax. You can also make queries in `fluent` syntax. Learn more about both syntaxes and implementation details in [Query Syntax and Execution](https://rcsbapi.readthedocs.io/en/latest/search_api/query_construction.html#query-syntax-and-execution).
+
+
+### Data API
+The `rcsbapi.data` module allows you to easily construct GraphQL queries to the RCSB.org Data API.
+
+This is done by specifying the following input:
+- "input_type": the data hierarchy level you are starting from (e.g., "entry", "polymer_entity", etc.) (See full list [here](https://rcsbapi.readthedocs.io/en/latest/data_api/query_construction.html#input-type)).
+- "input_ids": the list of IDs for which to fetch data (corresponding to the specified "input_type")
+- "return_data_list": the list of data items ("fields") to retrieve. (Available fields can be explored [here](https://data.rcsb.org/data-attributes.html) or via  the [GraphiQL editor's Documentation Explorer panel](https://data.rcsb.org/graphql/index.html).)
+
+#### Data API Examples
+This is a [simple query](https://data.rcsb.org/graphql/index.html?query=%7B%0A%20%20entry(entry_id%3A%20%224HHB%22)%20%7B%0A%20%20%20%20exptl%20%7B%0A%20%20%20%20%20%20method%0A%20%20%20%20%7D%0A%20%20%7D%0A%7D) requesting the experimental method of a structure with PDB ID 4HHB (Hemoglobin).
+
+The query must be executed using the `.exec()` method, which will return the JSON response as well as store the response as an attribute of the `DataQuery` object. From the object, you can access the Data API response, get an interactive editor link, or access the arguments used to create the query.
+The package is able to automatically build queries based on the "input_type" and path segment passed into "return_data_list". If using this package in code intended for long-term use, it's recommended to use fully qualified paths. When autocompletion is being used, an WARNING message will be printed out as a reminder.
+
+```python
+from rcsbapi.data import DataQuery as Query
+query = Query(
+    input_type="entries",
+    input_ids=["4HHB"],
+    return_data_list=["exptl.method"]
+)
+print(query.exec())
+```
+Data is returned in JSON format
+```json
+{
+  "data": {
+    "entries": [
+      {
+        "rcsb_id": "4HHB",
+        "exptl": [
+          {
+            "method": "X-RAY DIFFRACTION"
+          }
+        ]
+      }
+    ]
+  }
+}
+```
+
+Here is a [more complex query](https://data.rcsb.org/graphql/index.html?query=%7B%0A%20%20polymer_entities(entity_ids%3A%5B%222CPK_1%22%2C%223WHM_1%22%2C%222D5Z_1%22%5D)%20%7B%0A%20%20%20%20rcsb_id%0A%20%20%20%20rcsb_entity_source_organism%20%7B%0A%20%20%20%20%20%20ncbi_taxonomy_id%0A%20%20%20%20%20%20ncbi_scientific_name%0A%20%20%20%20%7D%0A%20%20%20%20rcsb_cluster_membership%20%7B%0A%20%20%20%20%20%20cluster_id%0A%20%20%20%20%20%20identity%0A%20%20%20%20%7D%0A%20%20%7D%0A%7D). Note that periods can be used to further specify requested data in return_data_list. Also note multiple return data items and ids can be requested in one query.
+```python
+from rcsbapi.data import DataQuery as Query
+query = Query(
+    input_type="polymer_entities",
+    input_ids=["2CPK_1", "3WHM_1", "2D5Z_1"],
+    return_data_list=[
+        "polymer_entities.rcsb_id",
+        "rcsb_entity_source_organism.ncbi_taxonomy_id",
+        "rcsb_entity_source_organism.ncbi_scientific_name",
+        "cluster_id",
+        "identity"
+    ]
+)
+print(query.exec())
+```
+
+## Jupyter Notebooks
+Several Jupyter notebooks with example use cases and workflows for all package modules are provided under [notebooks](notebooks/).
+
+For example, one notebook using both Search and Data API packages for a COVID-19 related example is available in [notebooks/search_data_workflow.ipynb](notebooks/search_data_workflow.ipynb) or online through Google Colab <a href="https://colab.research.google.com/github/rcsb/py-rcsb-api/blob/master/notebooks/search_data_workflow.ipynb" target="_parent"><img src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open In Colab"/></a>.
+
+
+## Citing
+Please cite the ``rcsb-api`` package with the following reference:
+
+> Dennis W. Piehl, Brinda Vallat, Ivana Truong, Habiba Morsy, Rusham Bhatt, 
+> Santiago Blaumann, Pratyoy Biswas, Yana Rose, Sebastian Bittrich, Jose M. Duarte,
+> Joan Segura, Chunxiao Bi, Douglas Myers-Turnbull, Brian P. Hudson, Christine Zardecki,
+> Stephen K. Burley. rcsb-api: Python Toolkit for Streamlining Access to RCSB Protein 
+> Data Bank APIs, Journal of Molecular Biology, 2025.
+> DOI: [10.1016/j.jmb.2025.168970](https://doi.org/10.1016/j.jmb.2025.168970)
+
+You should also cite the RCSB.org API services this package utilizes:
+
+> Yana Rose, Jose M. Duarte, Robert Lowe, Joan Segura, Chunxiao Bi, Charmi
+> Bhikadiya, Li Chen, Alexander S. Rose, Sebastian Bittrich, Stephen K. Burley,
+> John D. Westbrook. RCSB Protein Data Bank: Architectural Advances Towards
+> Integrated Searching and Efficient Access to Macromolecular Structure Data
+> from the PDB Archive, Journal of Molecular Biology, 2020.
+> DOI: [10.1016/j.jmb.2020.11.003](https://doi.org/10.1016/j.jmb.2020.11.003)
+
+
+## Documentation and Support
+Please refer to the [readthedocs page](https://rcsbapi.readthedocs.io/en/latest/index.html) to learn more about package usage and other available features as well as to see more examples.
+
+If you experience any issues installing or using the package, please submit an issue on [GitHub](https://github.com/rcsb/py-rcsb-api/issues) and we will try to respond in a timely manner.

rcsb_api-1.5.0.dist-info/RECORD

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rcsb_api-1.5.0.dist-info/WHEEL

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+Wheel-Version: 1.0
+Generator: hatchling 1.27.0
+Root-Is-Purelib: true
+Tag: py3-none-any

rcsb_api-1.5.0.dist-info/licenses/LICENSE

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+MIT License
+
+Copyright (c) 2024 RCSB PDB
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

rcsb_api-1.5.0.dist-info/licenses/NOTICE.md

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+# Third-Party Copyright Notices
+`rcsb-api` uses third-party libraries or other resources that may
+be distributed under licenses different than the `rcsb-api` software.
+
+In the event that we accidentally failed to list a required notice,
+please bring it to our attention through the creation of a [GitHub issue](https://github.com/rcsb/py-rcsb-api/issues).
+
+The attached notices are provided for information only.
+
+## [rcsbsearchapi](https://github.com/rcsb/py-rcsbsearchapi)
+
+BSD 3-Clause License
+--------------------
+
+Copyright 2024 rcsbsearchapi Contributors
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice,
+   this list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its contributors
+   may be used to endorse or promote products derived from this software
+   without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

rcsbapi/config.py

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+"""
+Configurable settings for rcsb-api
+
+These settings can be overridden at runtime.
+
+For example, you can turn off autocompletion warning messages by
+modifying the `SUPPRESS_AUTOCOMPLETE_WARNING` setting as follows:
+
+Example:
+    from rcsbapi.config import config
+
+    # Override the default warning suppression flag
+    config.SUPPRESS_AUTOCOMPLETE_WARNING = True
+"""
+from __future__ import annotations
+
+import logging
+from pydoc import locate
+from typing import Any
+
+logger = logging.getLogger(__name__)
+
+
+class Config:
+    API_TIMEOUT: int = 100                       # Timeout in seconds for all API calls
+    MAX_RETRIES: int = 5                         # Maximum number of retries to perform per request upon failure
+    RETRY_BACKOFF: int = 1                       # Delay in seconds to wait between retries; increases exponentially between retries (e.g., 1s, 2s, 4s, 8s, ...)
+    SEARCH_API_REQUESTS_PER_SECOND: int = 10     # Requests per second limit for the Search API
+    DATA_API_REQUESTS_PER_SECOND: int = 20       # Requests per second limit for the Data API
+    DATA_API_BATCH_ID_SIZE: int = 300            # Size of batches to use for batching input ID list to Data API (reduce this if encountering timeouts or errors)
+    DATA_API_MAX_CONCURRENT_REQUESTS: int = 4    # Max number of Data API requests to run concurrently (e.g., when input ID list is split into many small batches)
+    DATA_API_INPUT_ID_LIMIT: int = 50_000        # Threshold for warning user that input ID list for Data API query is very large and may hinder performance
+    MODEL_API_REQUESTS_PER_SECOND: int = 10      # Requests per second limit for the Model API
+    SUPPRESS_AUTOCOMPLETE_WARNING: bool = False  # Turn off autocompletion warnings from being raised for Data API queries
+
+    def __setattr__(self, name: str, value: Any) -> None:
+        """Verify attribute exists when a user tries to set a configuration parameter, and ensure proper typing.
+        Raises an error if user accidentally tries to create a new, unused attribute (e.g., due to a typo or misspelling),
+        or sets it to an unexpected type.
+        """
+        # Verify attribute exists
+        if not hasattr(self, name):
+            raise AttributeError(f"'{name}' is not a valid attribute of Config class")
+
+        # Enforce consistent typing
+        expected_type = locate(self.__annotations__.get(name, None))
+        if expected_type and not isinstance(value, expected_type):
+            raise TypeError(f"Expected type '{expected_type.__name__}' for attribute '{name}', but got '{type(value).__name__}'")
+        super().__setattr__(name, value)
+
+
+config = Config()

rcsbapi/const.py

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+"""
+Constants for rcsb-api (immutable and cannot be overridden)
+
+These constants define fixed values used throughout the rcsb-api package,
+including API endpoints, search services, and schema URLs. The values are
+immutable and protected from modification during runtime.
+"""
+
+from __future__ import annotations
+from dataclasses import dataclass, field
+from types import MappingProxyType
+from typing import List
+from importlib.metadata import version as get_package_version
+
+__version__ = get_package_version("rcsb-api")
+
+
+@dataclass(frozen=True)
+class Const:
+    # Search API constants
+    STRUCTURE_INDEX: int = 0
+    CHEMICAL_INDEX: int = 0
+    SEARCH_API_REQUEST_SCHEMA_URL: str = "https://search.rcsb.org/schema/search/request/json-schema-rcsb_search_query.json"
+    SEARCH_OPENAPI_SCHEMA_URL: str = "https://search.rcsb.org/openapi.json"
+    STRUCTURE_ATTRIBUTE_SEARCH_SERVICE: str = "text"
+    CHEMICAL_ATTRIBUTE_SEARCH_SERVICE: str = "text_chem"
+    FULL_TEXT_SEARCH_SERVICE: str = "full_text"
+    SEQUENCE_SEARCH_SERVICE: str = "sequence"
+    SEQMOTIF_SEARCH_SERVICE: str = "seqmotif"
+    STRUCT_SIM_SEARCH_SERVICE: str = "structure"
+    STRUCTMOTIF_SEARCH_SERVICE: str = "strucmotif"
+    CHEM_SIM_SEARCH_SERVICE: str = "chemical"
+    SEQUENCE_SEARCH_MIN_NUM_OF_RESIDUES: int = 25
+    SEQMOTIF_SEARCH_MIN_CHARACTERS: int = 2
+    STRUCT_MOTIF_MIN_RESIDUES: int = 2
+    STRUCT_MOTIF_MAX_RESIDUES: int = 10
+    RCSB_SEARCH_API_QUERY_URL: str = "https://search.rcsb.org/rcsbsearch/v2/query"
+    UPLOAD_URL: str = "https://user-upload.rcsb.org/v1/putMultipart"
+    RETURN_UP_URL: str = "https://user-upload.rcsb.org/v1/download/"
+
+    SEARCH_API_SCHEMA_DIR: str = "search/resources"
+    SEARCH_API_STRUCTURE_ATTRIBUTE_SCHEMA_URL: str = "https://search.rcsb.org/rcsbsearch/v2/metadata/schema"
+    SEARCH_API_STRUCTURE_ATTRIBUTE_SCHEMA_FILENAME: str = "structure_schema.json"
+    SEARCH_API_CHEMICAL_ATTRIBUTE_SCHEMA_URL: str = "https://search.rcsb.org/rcsbsearch/v2/metadata/chemical/schema"
+    SEARCH_API_CHEMICAL_ATTRIBUTE_SCHEMA_FILENAME: str = "chemical_schema.json"
+
+    # Data API constants
+    DATA_API_ENDPOINT: str = "https://data.rcsb.org/graphql"
+    DATA_API_SCHEMA_DIR: str = "data/resources"
+    DATA_API_SCHEMA_FILENAME: str = "data_api_schema.json"
+    DATA_API_SCHEMA_BASE_URL: str = "https://data.rcsb.org/rest/v1/schema/"
+    DATA_API_SCHEMA_ENDPOINT_TO_FILE: MappingProxyType[str, str] = field(default_factory=lambda: MappingProxyType({
+        "entry": "entry.json",
+        "polymer_entity": "polymer_entity.json",
+        "branched_entity": "branched_entity.json",
+        "nonpolymer_entity": "nonpolymer_entity.json",
+        "polymer_entity_instance": "polymer_entity_instance.json",
+        "branched_entity_instance": "branched_entity_instance.json",
+        "nonpolymer_entity_instance": "nonpolymer_entity_instance.json",
+        "assembly": "assembly.json",
+        "chem_comp": "chem_comp.json",
+        "pubmed": "pubmed.json",
+        "uniprot": "uniprot.json",
+        "drugbank": "drugbank.json",
+    }))
+
+    SEQUENCE_API_ENDPOINT: str = "https://sequence-coordinates.rcsb.org"
+    SEQUENCE_API_GRAPHQL_ENDPOINT: str = "https://sequence-coordinates.rcsb.org/graphql"
+    SEQUENCE_API_SCHEMA_DIR: str = "sequence/resources"
+    SEQUENCE_API_SCHEMA_FILENAME: str = "seq_api_schema.json"
+
+    MODELSERVER_API_SCHEMA_FILEPATH: str = "model/resources/modelserver_api_schema.json"
+    MODELSERVER_API_BASE_URL: str = "https://models.rcsb.org/v1"
+    MODELSERVER_API_SCHEMA_URL: str = "https://models.rcsb.org/openapi.json"
+
+    SINGULAR_TO_PLURAL: MappingProxyType[str, str] = field(default_factory=lambda: MappingProxyType({
+        "entry": "entries",
+        "polymer_entity": "polymer_entities",
+        "branched_entity": "branched_entities",
+        "nonpolymer_entity": "nonpolymer_entities",
+        "polymer_entity_instance": "polymer_entity_instances",
+        "nonpolymer_entity_instance": "nonpolymer_entity_instances",
+        "branched_entity_instance": "branched_entity_instances",
+        "assembly": "assemblies",
+        "interface": "interfaces",
+        "uniprot": "",
+        "pubmed": "",
+        "chem_comp": "chem_comps",
+        "entry_group": "entry_groups",
+        "polymer_entity_group": "polymer_entity_groups",
+        "group_provenance": ""
+    }))
+    #
+    ID_TO_SEPARATOR: MappingProxyType[str, str] = field(default_factory=lambda: MappingProxyType({
+        "entity_id": "_",
+        "asym_id": ".",
+        "assembly_id": "-",
+        "interface_id": "."
+    }))
+
+    # Regex strings for IDs
+    DATA_API_INPUT_TYPE_TO_REGEX: MappingProxyType[str, List[str]] = field(default_factory=lambda: MappingProxyType({
+        "entry": [r"^(MA|AF|ma|af)_[A-Z0-9]*$", r"^[A-Za-z0-9]{4}$"],
+        "entity": [r"^(MA|AF|ma|af)_[A-Z0-9]*_[0-9]+$", r"^[A-Z0-9]{4}_[0-9]+$"],
+        "instance": [r"^(MA|AF|ma|af)_[A-Z0-9]*\.[A-Za-z]+$", r"^[A-Z0-9]{4}\.[A-Za-z]+$"],
+        "assembly": [r"^(MA|AF|ma|af)_[A-Z0-9]*-[0-9]+$", r"^[A-Z0-9]{4}-[0-9]+$"],
+        "interface": [r"^(MA|AF|ma|af)_[A-Z0-9]*-[0-9]+\.[0-9]+$", r"^[A-Z0-9]{4}-[0-9]+\.[0-9]+$"],
+        # Regex for uniprot: https://www.uniprot.org/help/accession_numbers
+        "uniprot": [r"[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}"]
+    }))
+
+    INPUT_TYPE_TO_ALL_STRUCTURES_ENDPOINT: MappingProxyType[str, List[str]] = field(default_factory=lambda: MappingProxyType({
+        "entries": ["https://data.rcsb.org/rest/v1/holdings/current/entry_ids"],
+        "chem_comps": ["https://data.rcsb.org/rest/v1/holdings/current/ccd_ids", "https://data.rcsb.org/rest/v1/holdings/current/prd_ids"]
+    }))
+
+    USER_AGENT: str = (
+        f"py-rcsb-api/{__version__} (+https://github.com/rcsb/py-rcsb-api)"
+    )
+
+
+const = Const()

rcsbapi/data/__init__.py

@@ -0,0 +1,32 @@
+"""RCSB PDB Data API"""
+from rcsbapi.data.data_schema import DataSchema
+
+DATA_SCHEMA = DataSchema()
+
+# This is needed because __getattr__ will be called twice on import,
+# so ALL_STRUCTURES should be cached to avoid initializing twice
+_import_cache: dict = {}
+
+
+def __getattr__(name: str):
+    """Overloading __getattr__ so that when ALL_STRUCTURES is accessed for the first time,
+    ALL_STRUCTURES object will be built.
+
+    Args:
+        name (str): attribute name
+    """
+    if name == "ALL_STRUCTURES":
+        if name not in _import_cache:
+            from rcsbapi.data.data_query import AllStructures
+            ALL_STRUCTURES = AllStructures()
+            _import_cache[name] = ALL_STRUCTURES
+
+        return _import_cache[name]  # Return cached instance
+
+    # keep functionality of original __getattr__
+    raise AttributeError(f"Module {repr(__name__)} has no attribute {repr(name)}")
+
+
+from rcsbapi.data.data_query import DataQuery  # noqa:E402
+
+__all__ = ["DataQuery", "DataSchema"]