rdworks 0.25.7__py3-none-any.whl

rdworks/xml.py

@@ -0,0 +1,260 @@
+"""
+This module contains XML definitions for substructure and descriptor matching.
+
+Available descriptors:
+
+    Name          | Description                               | RDKit function
+    ------------- | ----------------------------------------- | --------------------------------------
+    HAC           | Num. of Non-H atoms                       | Descriptors.HeavyAtomCount
+    HBA           | Num. of H-bond acceptors                  | Descriptors.NumHAcceptors
+    HBD           | Num. of H-bond donors                     | Descriptors.NumHDonors
+    LipinskiHBA   | Num. of Lipinski H-bond acceptors         | rdMolDescriptors.CalcNumLipinskiHBA
+    LipinskiHBD   | Num. of Lipinski H-bond donors            | rdMolDescriptors.CalcNumLipinskiHBD
+    MolWt         | Molecular weight                          | Descriptors.MolWt
+    TPSA          | Topological polar surface area            | Descriptors.TPSA
+    LogP          | log(octanol/water partition coefficient)  | Descriptors.MolLogP
+    RotBonds      | Num. of rotatable bonds                   | Descriptors.NumRotatableBonds
+    RingCount     | Num. of rings                             | Descriptors.RingCount
+    FCsp3         | fraction of C atoms that are Sp3          | Descriptors.FractionCSP3
+    rdHBD         | Num. of H-bond donors                     | rdMolDescriptors.CalcNumHBD
+    rdHBA         | Num. of H-bond acceptors                  | rdMolDescriptors.CalcNumHBA
+    rdRingCount   | Num. of rings                             | rdMolDescriptors.CalcNumRings
+    rdRotBondst   | Num. of rotatable bonds                   | rdMolDescriptors.CalcNumRotatableBonds
+    rdFCsp3       | fraction of C atoms that are Sp3          | rdMolDescriptors.CalcFractionCSP3
+    Hetero        | Num. of non-H and non-C atoms             | rdMolDescriptors.CalcNumHeteroatoms
+    ALogP         | Wildman-Crippen LogP value                | Crippen.MolLogP
+    QED           | Quantitative estimation of drug-likeness  | QED.qed
+    PSA           | MOE-like molecular surface area           | MolSurf.TPSA
+    StereoCenters | Num. of atom stereo centers               | rdMolDescriptors.CalcNumAtomStereoCenters
+
+References:
+
+    1. `alert_collection.csv` is copied from Patrick Walters' blog and github:
+        - http://practicalcheminformatics.blogspot.com/2018/08/filtering-chemical-libraries.html
+        - https://github.com/PatWalters/rd_filters
+    1. Jeroen Kazius, Ross McGuire, and Roberta Bursi.
+        Derivation and Validation of Toxicophores for Mutagenicity Prediction. 
+        J. Med. Chem. 2005, 48, 312-320.
+    1. J. F. Blake. 
+        Identification and Evaluation of Molecular Properties Related to Preclinical Optimization and Clinical Fate. 
+        Med Chem. 2005, 1, 649-55.
+    1. Mike Hann, Brian Hudson, Xiao Lewell, Rob Lifely, Luke Miller, and Nigel Ramsden. 
+        Strategic Pooling of Compounds for High-Throughput Screening. 
+        J. Chem. Inf. Comput. Sci. 1999, 39, 897-902.
+    1. Jonathan B. Baell and Georgina A. Holloway. New Substructure Filters for Removal of Pan Assay Interference Compounds (PAINS) 
+        from Screening Libraries and for Their Exclusion in Bioassays. 
+        J. Med. Chem. 2010, 53, 2719-2740.
+    1. Bradley C. Pearce, Michael J. Sofia, Andrew C. Good, Dieter M. Drexler, and David A. Stock. 
+        An Empirical Process for the Design of High-Throughput Screening Deck Filters. 
+        J. Chem. Inf. Model. 2006, 46, 1060-1068.
+    1. Ruth Brenk, Alessandro Schipani, Daniel James, Agata Krasowski, Ian Hugh Gilbert, Julie Frearson aand Paul Graham Wyatt. 
+        Lessons learnt from assembling screening libraries for drug discovery for neglected diseases. 
+        ChemMedChem. 2008, 3, 435-44.
+    1. Sivaraman Dandapani, Gerard Rosse, Noel Southall, Joseph M. Salvino, Craig J. Thomas. 
+        Selecting, Acquiring, and Using Small Molecule Libraries for High‐Throughput Screening. 
+        Curr Protoc Chem Biol. 2012, 4, 177–191.
+    1. Huth JR, Mendoza R, Olejniczak ET, Johnson RW, Cothron DA, Liu Y, Lerner CG, Chen J, Hajduk PJ. 
+        ALARM NMR: a rapid and robust experimental method to detect reactive false positives in biochemical screens. 
+        J Am Chem Soc. 2005, 127, 217-24.
+        - identificaiton of thiol reactive compounds by monitoring DTT-dependent 13-C chemical shift changes 
+        of the human La protein in the presence of a test compound
+
+
+Attributes:
+    predefined_xml (Dict[Dict]): dictionary of XML files.
+"""
+
+import os
+import importlib.resources
+import pathlib
+import xml.etree.ElementTree as ET
+from typing import List, Tuple, Union
+
+
+predefined_xml = {
+    "Zinc_fragment" : {
+        "Path" : "ZINC_fragment.xml",
+        "Description" : "ZINC's fragment-like criteria",
+        "Reference" : "ZINC",
+    },
+    "Zinc_leadlike" : {
+        "Path" : "ZINC_leadlike.xml",
+        "Description" : "ZINC's lead-like criteria",
+        "Reference" : "ZINC",
+    },
+    "Zinc_druglike" : {
+        "Path" : "ZINC_druglike.xml",
+        "Description" : "ZINC's drug-like criteria",
+        "Reference" : "ZINC",
+    },
+    "fragment" : {
+        "Path" : "fragment.xml",
+        "Description" : "fragment",
+        "Reference" : "",
+    },
+    "MLSMR" : {
+        "Path" : "ChEMBL_Walters/MLSMR.xml",
+        "Description" : "NIH Mol. Lib. Small Molecule Repository filters",
+        "Reference" : "Dandapani et al. (2012)",
+    },
+    "CNS" : {
+        "Path" : "CNS.xml",
+        "Description" : "CNS MPO descriptors",
+        "Reference" : "Wager et al. (2010)",
+    },
+    "PAINS" : {
+        "Path" : "Baell2010_PAINS/Baell2010A.xml",
+        "Description" : "Pan Assay Interference (>150 hits)",
+        "Reference" : "Baell et al. (2010)",
+    },
+    "Dundee" : {
+        "Path" : "ChEMBL_Walters/Dundee.xml",
+        "Description" : "Dundee NTD library filters",
+        "Reference" : "Brenk et al. (2008)",
+    },
+    "BMS" : {
+        "Path" : "ChEMBL_Walters/BMS.xml",
+        "Description" : "BMS HTS deck filters",
+        "Reference" : "Pearce et al. (2006)",
+    },
+    "LINT" : {
+        "Path" : "ChEMBL_Walters/LINT.xml",
+        "Description" : "Pfizer LINT filters",
+        "Reference" : "Blake (2005)",
+    },
+    "Toxicophore" : {
+        "Path" : "Kazius2005/Kazius2005.xml",
+        "Description" : "Toxicophores for mutagenicity",
+        "Reference" : "Kazius et al. (2005)",
+    },
+    "Glaxo" : {
+        "Path" : "ChEMBL_Walters/Glaxo.xml",
+        "Description" : "Glaxo hard filters",
+        "Reference" : "Hann et al. (1999)",
+    },
+    "Acid" : {
+        "Path" : "Hann1999_Glaxo/Hann1999Acid.xml",
+        "Description" : "acid",
+        "Reference" : "Hann et al. (1999)",
+    },
+    "Base" : {
+        "Path" : "Hann1999_Glaxo/Hann1999Base.xml",
+        "Description" : "base",
+        "Reference" : "Hann et al. (1999)",
+    },
+    "Nucleophile" : {
+        "Path" : "Hann1999_Glaxo/Hann1999NuPh.xml",
+        "Description" : "nucleophile",
+        "Reference" : "Hann et al. (1999)",
+    },
+    "Electrophile" : {
+        "Path" : "Hann1999_Glaxo/Hann1999ElPh.xml",
+        "Description" : "electrophile",
+        "Reference" : "Hann et al. (1999)",
+    },
+    "Inpharmatica" : {
+        "Path" : "ChEMBL_Walters/Inpharmatica.xml",
+        "Description" : "Inpharmatica unwanted fragments",
+        "Reference" : "ChEMBL",
+    },
+    "SureChEMBL" : {
+        "Path" : "ChEMBL_Walters/SureChEMBL.xml",
+        "Description" : "SureChEMBL filter",
+        "Reference" : "ChEMBL",
+    },
+    "Reactive" : {
+        "Path" : "misc/reactive.xml",
+        "Description" : "reactive functional groups",
+        "Reference" : "",
+    },
+    "Astex_RO3" : {
+        "Path" : "Astex_RO3.xml",
+        "Description" : "Astex rule of 3",
+        "Reference" : "Astex",
+    },
+    "Asinex_fragment" : {
+        "Path" : "Asinex_fragment.xml",
+        "Description" : "Asinex's fragment",
+        "Reference" : "Asinex",
+    },
+}
+
+
+def list_predefined_xml() -> str:
+    """Returns text output of list of predefined xml.
+
+    Returns:
+        str: text output of list of predefined xml
+    """
+    s = f"\n| {'Name':<18} | {'Description':<48} | {'Reference':<23} |\n"
+    s += f"| {'-'*18} | {'-'*48} | {'-'*23} |\n"
+    for k,v in predefined_xml.items():
+        s += f"| {k:<18} | {v['Description']:<48} | {v['Reference']:<23} |\n"
+    return s
+
+
+def get_predefined_xml(name:str) -> os.PathLike:
+    """Returns matched predefined xml file.
+    
+    Args:
+        name (str): name of predefined entry.
+    
+    Returns:
+        os.PathLike: path to the xml file.
+    """
+    t = name.upper()
+    n = len(t)
+    path = None
+    for k in predefined_xml:
+        if k.upper()[:n] == t:
+            datadir = importlib.resources.files('rdworks.predefined')
+            path = pathlib.Path(datadir / predefined_xml[k]['Path'])
+            break
+    if path is None:
+      raise ValueError(f'is_matching() cannot find the xml file for {name}')  
+    return path
+
+
+def parse_xml(path:os.PathLike) -> Tuple:
+    """Parse a XML file.
+
+    Args:
+        path (os.PathLike): filename of the xml.
+
+    Returns:
+        Tuple: parsed results.
+    """
+    tree = ET.parse(path)
+    root = tree.getroot()
+    terms = []
+    try:
+        combine = root.attrib['combine'].upper()
+    except:
+        combine = 'OR' # default
+    for child in root:
+        name = child.attrib['name']
+        if child.tag == 'substructure':
+            smarts = child.find('SMARTS').text
+            terms.append((name, smarts, 0.0, 0.0))
+        elif child.tag == 'descriptor':
+            L = child.find('min')
+            U = child.find('max')
+            lb = float(L.text) if L is not None else None
+            ub = float(U.text) if U is not None else None
+            terms.append((name, None, lb, ub))
+    
+    # # parse SMARTS definitions
+    # for substructure in tree.findall('substructure'):
+    #     name = substructure.get('name')
+    #     smarts = substructure.find('SMARTS').text
+    #     terms.append((name, smarts, 0.0, 0.0))
+    # # parse descriptors lower and upper bounds
+    # for descriptor in tree.findall('descriptor'):
+    #     name = descriptor.get('name')
+    #     L = descriptor.find('min')
+    #     U = descriptor.find('max')
+    #     lb = float(L.text) if L is not None else None
+    #     ub = float(U.text) if U is not None else None
+    #     terms.append((name, '', lb, ub))
+    
+    return (terms, combine)

rdworks-0.25.7.dist-info/METADATA

@@ -0,0 +1,37 @@
+Metadata-Version: 2.4
+Name: rdworks
+Version: 0.25.7
+Summary: Cheminformatics and AI/ML Work Built on RDKit
+Author-email: Sung-Hun Bae <sunghun.bae@gmail.com>
+Maintainer-email: Sung-Hun Bae <sunghun.bae@gmail.com>
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/sunghunbae/rdworks
+Project-URL: Repository, https://github.com/sunghunbae/rdworks.git
+Project-URL: Issues, https://github.com/sunghunbae/rdworks/issues
+Project-URL: Changelog, https://github.com/sunghunbae/rdworks/blob/master/CHANGELOG.md
+Project-URL: Documentation, https://sunghunbae.github.io/rdworks/
+Keywords: neural-network-potential,cheminformatics,rdkit
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Developers
+Classifier: Programming Language :: Python :: 3
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy
+Requires-Dist: scipy
+Requires-Dist: scikit-learn
+Requires-Dist: pandas
+Requires-Dist: seaborn
+Requires-Dist: networkx
+Requires-Dist: tqdm
+Requires-Dist: psutil
+Requires-Dist: ase
+Requires-Dist: rdkit>=2023
+Requires-Dist: bitarray
+Requires-Dist: cdpkit
+Requires-Dist: pytest
+Dynamic: license-file
+
+# rdworks
+Higher level wrapper using RDKit

rdworks-0.25.7.dist-info/RECORD

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+rdworks-0.25.7.dist-info/WHEEL,sha256=ck4Vq1_RXyvS4Jt6SI0Vz6fyVs4GWg7AINwpsaGEgPE,91
+rdworks-0.25.7.dist-info/top_level.txt,sha256=05C98HbvBK2axUBogC_hAT_CdpOeQYGnQ6vRAgawr8s,8
+rdworks-0.25.7.dist-info/RECORD,,

rdworks-0.25.7.dist-info/WHEEL

@@ -0,0 +1,5 @@
+Wheel-Version: 1.0
+Generator: setuptools (80.0.0)
+Root-Is-Purelib: true
+Tag: py3-none-any
+

rdworks-0.25.7.dist-info/licenses/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2024-2025 Sung-Hun Bae
+
+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.

rdworks-0.25.7.dist-info/top_level.txt

@@ -0,0 +1 @@
+rdworks