chembl · ivanmilevtues · Jun 16, 2025
diff --git a/.codeboarding/Exclusion Flag Utility.md b/.codeboarding/Exclusion Flag Utility.md
@@ -0,0 +1,111 @@
+```mermaid
+
+graph LR
+
+    ExclusionFlagService["ExclusionFlagService"]
+
+    FragmentParentMolRetrieval["FragmentParentMolRetrieval"]
+
+    MoleculeStandardization["MoleculeStandardization"]
+
+    MolblockStandardization["MolblockStandardization"]
+
+    FragmentParentMolRetrieval -- "calls" --> ExclusionFlagService
+
+    MoleculeStandardization -- "calls" --> ExclusionFlagService
+
+    MolblockStandardization -- "calls" --> ExclusionFlagService
+
+    MolblockStandardization -- "calls" --> MoleculeStandardization
+
+```
+
+[![CodeBoarding](https://img.shields.io/badge/Generated%20by-CodeBoarding-9cf?style=flat-square)](https://github.com/CodeBoarding/GeneratedOnBoardings)[![Demo](https://img.shields.io/badge/Try%20our-Demo-blue?style=flat-square)](https://www.codeboarding.org/demo)[![Contact](https://img.shields.io/badge/Contact%20us%20-%[email protected]?style=flat-square)](mailto:[email protected])
+
+
+
+## Component Details
+
+
+
+This system provides a comprehensive set of utilities for standardizing chemical structures, including functions to exclude undesirable structures based on predefined criteria, retrieve parent molecules from fragments, and standardize molecules from various input formats like molblocks. The core functionality revolves around ensuring chemical structures meet specific quality and format standards for further processing.
+
+
+
+### ExclusionFlagService
+
+Provides a utility function to determine if a chemical structure should be excluded based on predefined criteria, such as the presence of metallic atoms, a high count of boron atoms, or RDKit sanitization failures. It acts as a gatekeeper for molecular processing.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- <a href="https://github.com/chembl/ChEMBL_Structure_Pipeline/blob/master/chembl_structure_pipeline/exclude_flag.py#L84-L113" target="_blank" rel="noopener noreferrer">`chembl_structure_pipeline.exclude_flag.exclude_flag` (84:113)</a>
+
+
+
+
+
+### FragmentParentMolRetrieval
+
+Responsible for retrieving the parent molecule from a set of fragments, handling solvent and salt removal, and optionally neutralizing the molecule. It utilizes the ExclusionFlagService to check if the molecule should be excluded from further processing.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- <a href="https://github.com/chembl/ChEMBL_Structure_Pipeline/blob/master/chembl_structure_pipeline/standardizer.py#L290-L427" target="_blank" rel="noopener noreferrer">`chembl_structure_pipeline.standardizer.get_fragment_parent_mol` (290:427)</a>
+
+
+
+
+
+### MoleculeStandardization
+
+Standardizes a given molecule by applying a series of transformations including updating valences, removing s-groups, kekulizing, removing hydrogens, normalizing, uncharging, flattening tartrates, and cleaning up drawing. It utilizes the ExclusionFlagService for an initial exclusion check.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- <a href="https://github.com/chembl/ChEMBL_Structure_Pipeline/blob/master/chembl_structure_pipeline/standardizer.py#L455-L472" target="_blank" rel="noopener noreferrer">`chembl_structure_pipeline.standardizer.standardize_mol` (455:472)</a>
+
+
+
+
+
+### MolblockStandardization
+
+Handles the standardization of molecules provided in molblock format. It parses the molblock, utilizes the ExclusionFlagService for an exclusion check, and then uses the MoleculeStandardization component to process the molecule before converting the standardized molecule back into a molblock.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- <a href="https://github.com/chembl/ChEMBL_Structure_Pipeline/blob/master/chembl_structure_pipeline/standardizer.py#L508-L513" target="_blank" rel="noopener noreferrer">`chembl_structure_pipeline.standardizer.standardize_molblock` (508:513)</a>
+
+
+
+
+
+
+
+
+
+### [FAQ](https://github.com/CodeBoarding/GeneratedOnBoardings/tree/main?tab=readme-ov-file#faq)
diff --git a/.codeboarding/Structure Standardization.md b/.codeboarding/Structure Standardization.md
@@ -0,0 +1,167 @@
+```mermaid
+
+graph LR
+
+    StandardizationCore["StandardizationCore"]
+
+    ParentMoleculeGenerator["ParentMoleculeGenerator"]
+
+    DrawingCleanup["DrawingCleanup"]
+
+    MolblockProcessor["MolblockProcessor"]
+
+    ExclusionFlag["ExclusionFlag"]
+
+    StandardizationCore -- "invokes cleanup" --> DrawingCleanup
+
+    StandardizationCore -- "applies exclusion check" --> ExclusionFlag
+
+    ParentMoleculeGenerator -- "applies exclusion check" --> ExclusionFlag
+
+    ParentMoleculeGenerator -- "utilizes standardization utilities" --> StandardizationCore
+
+    MolblockProcessor -- "orchestrates standardization" --> StandardizationCore
+
+    MolblockProcessor -- "retrieves parent molecule" --> ParentMoleculeGenerator
+
+    MolblockProcessor -- "applies exclusion check" --> ExclusionFlag
+
+```
+
+[![CodeBoarding](https://img.shields.io/badge/Generated%20by-CodeBoarding-9cf?style=flat-square)](https://github.com/CodeBoarding/GeneratedOnBoardings)[![Demo](https://img.shields.io/badge/Try%20our-Demo-blue?style=flat-square)](https://www.codeboarding.org/demo)[![Contact](https://img.shields.io/badge/Contact%20us%20-%[email protected]?style=flat-square)](mailto:[email protected])
+
+
+
+## Component Details
+
+
+
+The Structure Standardization subsystem is designed to process and normalize chemical structures, ensuring consistent and chemically correct representations. Its main flow involves cleaning drawing artifacts, handling fragments and isotopes, uncharging molecules, and applying general standardization rules to derive a 'parent' molecule from an input. This is achieved through a core standardization component, a parent molecule generator, a drawing cleanup component, and a molblock processor, all of which may interact with an exclusion flag component to filter out unwanted structures.
+
+
+
+### StandardizationCore
+
+This component encapsulates the fundamental chemical structure standardization algorithms, including valence adjustments, s-group removal, kekulization, hydrogen removal, normalization, uncharging, and specific structural flattening, ensuring molecular data consistency.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- <a href="https://github.com/chembl/ChEMBL_Structure_Pipeline/blob/master/chembl_structure_pipeline/standardizer.py#L455-L472" target="_blank" rel="noopener noreferrer">`ChEMBL_Structure_Pipeline.chembl_structure_pipeline.standardizer.standardize_mol` (455:472)</a>
+
+- <a href="https://github.com/chembl/ChEMBL_Structure_Pipeline/blob/master/chembl_structure_pipeline/standardizer.py#L26-L29" target="_blank" rel="noopener noreferrer">`ChEMBL_Structure_Pipeline.chembl_structure_pipeline.standardizer.update_mol_valences` (26:29)</a>
+
+- <a href="https://github.com/chembl/ChEMBL_Structure_Pipeline/blob/master/chembl_structure_pipeline/standardizer.py#L147-L150" target="_blank" rel="noopener noreferrer">`ChEMBL_Structure_Pipeline.chembl_structure_pipeline.standardizer.remove_sgroups_from_mol` (147:150)</a>
+
+- <a href="https://github.com/chembl/ChEMBL_Structure_Pipeline/blob/master/chembl_structure_pipeline/standardizer.py#L21-L23" target="_blank" rel="noopener noreferrer">`ChEMBL_Structure_Pipeline.chembl_structure_pipeline.standardizer.kekulize_mol` (21:23)</a>
+
+- <a href="https://github.com/chembl/ChEMBL_Structure_Pipeline/blob/master/chembl_structure_pipeline/standardizer.py#L75-L144" target="_blank" rel="noopener noreferrer">`ChEMBL_Structure_Pipeline.chembl_structure_pipeline.standardizer.remove_hs_from_mol` (75:144)</a>
+
+- <a href="https://github.com/chembl/ChEMBL_Structure_Pipeline/blob/master/chembl_structure_pipeline/standardizer.py#L62-L72" target="_blank" rel="noopener noreferrer">`ChEMBL_Structure_Pipeline.chembl_structure_pipeline.standardizer.normalize_mol` (62:72)</a>
+
+- <a href="https://github.com/chembl/ChEMBL_Structure_Pipeline/blob/master/chembl_structure_pipeline/standardizer.py#L153-L191" target="_blank" rel="noopener noreferrer">`ChEMBL_Structure_Pipeline.chembl_structure_pipeline.standardizer.uncharge_mol` (153:191)</a>
+
+- <a href="https://github.com/chembl/ChEMBL_Structure_Pipeline/blob/master/chembl_structure_pipeline/standardizer.py#L269-L282" target="_blank" rel="noopener noreferrer">`ChEMBL_Structure_Pipeline.chembl_structure_pipeline.standardizer.flatten_tartrate_mol` (269:282)</a>
+
+
+
+
+
+### ParentMoleculeGenerator
+
+This component is responsible for deriving the parent molecule from a given chemical structure, handling both isotopic and fragmented parent forms. It relies on core standardization utilities and exclusion checks to produce the canonical parent.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- <a href="https://github.com/chembl/ChEMBL_Structure_Pipeline/blob/master/chembl_structure_pipeline/standardizer.py#L438-L443" target="_blank" rel="noopener noreferrer">`ChEMBL_Structure_Pipeline.chembl_structure_pipeline.standardizer.get_parent_mol` (438:443)</a>
+
+- <a href="https://github.com/chembl/ChEMBL_Structure_Pipeline/blob/master/chembl_structure_pipeline/standardizer.py#L430-L435" target="_blank" rel="noopener noreferrer">`ChEMBL_Structure_Pipeline.chembl_structure_pipeline.standardizer.get_isotope_parent_mol` (430:435)</a>
+
+- <a href="https://github.com/chembl/ChEMBL_Structure_Pipeline/blob/master/chembl_structure_pipeline/standardizer.py#L290-L427" target="_blank" rel="noopener noreferrer">`ChEMBL_Structure_Pipeline.chembl_structure_pipeline.standardizer.get_fragment_parent_mol` (290:427)</a>
+
+
+
+
+
+### DrawingCleanup
+
+This component specifically addresses and corrects common drawing artifacts in chemical structures, such as misconfigured triple bonds and allenes, to improve the accuracy of molecular representations.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- <a href="https://github.com/chembl/ChEMBL_Structure_Pipeline/blob/master/chembl_structure_pipeline/standardizer.py#L252-L266" target="_blank" rel="noopener noreferrer">`ChEMBL_Structure_Pipeline.chembl_structure_pipeline.standardizer.cleanup_drawing_mol` (252:266)</a>
+
+- <a href="https://github.com/chembl/ChEMBL_Structure_Pipeline/blob/master/chembl_structure_pipeline/standardizer.py#L223-L237" target="_blank" rel="noopener noreferrer">`ChEMBL_Structure_Pipeline.chembl_structure_pipeline.standardizer._cleanup_triple_bonds` (223:237)</a>
+
+- <a href="https://github.com/chembl/ChEMBL_Structure_Pipeline/blob/master/chembl_structure_pipeline/standardizer.py#L213-L220" target="_blank" rel="noopener noreferrer">`ChEMBL_Structure_Pipeline.chembl_structure_pipeline.standardizer._check_and_straighten_at_triple_bond` (213:220)</a>
+
+- <a href="https://github.com/chembl/ChEMBL_Structure_Pipeline/blob/master/chembl_structure_pipeline/standardizer.py#L240-L249" target="_blank" rel="noopener noreferrer">`ChEMBL_Structure_Pipeline.chembl_structure_pipeline.standardizer._cleanup_allenes` (240:249)</a>
+
+
+
+
+
+### MolblockProcessor
+
+This component manages the input and output of chemical structures in Molblock format, including parsing, reapplication of wedging information, and orchestrating the standardization and parent molecule generation processes for Molblock data.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- <a href="https://github.com/chembl/ChEMBL_Structure_Pipeline/blob/master/chembl_structure_pipeline/standardizer.py#L486-L505" target="_blank" rel="noopener noreferrer">`ChEMBL_Structure_Pipeline.chembl_structure_pipeline.standardizer.parse_molblock` (486:505)</a>
+
+- <a href="https://github.com/chembl/ChEMBL_Structure_Pipeline/blob/master/chembl_structure_pipeline/standardizer.py#L508-L513" target="_blank" rel="noopener noreferrer">`ChEMBL_Structure_Pipeline.chembl_structure_pipeline.standardizer.standardize_molblock` (508:513)</a>
+
+- <a href="https://github.com/chembl/ChEMBL_Structure_Pipeline/blob/master/chembl_structure_pipeline/standardizer.py#L475-L483" target="_blank" rel="noopener noreferrer">`ChEMBL_Structure_Pipeline.chembl_structure_pipeline.standardizer.reapply_molblock_wedging` (475:483)</a>
+
+- <a href="https://github.com/chembl/ChEMBL_Structure_Pipeline/blob/master/chembl_structure_pipeline/standardizer.py#L446-L452" target="_blank" rel="noopener noreferrer">`ChEMBL_Structure_Pipeline.chembl_structure_pipeline.standardizer.get_parent_molblock` (446:452)</a>
+
+
+
+
+
+### ExclusionFlag
+
+This component provides a mechanism to determine if a chemical structure should be excluded from certain processing steps, based on predefined rules or properties, preventing unwanted or invalid structures from proceeding through the pipeline.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- <a href="https://github.com/chembl/ChEMBL_Structure_Pipeline/blob/master/chembl_structure_pipeline/exclude_flag.py#L84-L113" target="_blank" rel="noopener noreferrer">`ChEMBL_Structure_Pipeline.chembl_structure_pipeline.exclude_flag.exclude_flag` (84:113)</a>
+
+
+
+
+
+
+
+
+
+### [FAQ](https://github.com/CodeBoarding/GeneratedOnBoardings/tree/main?tab=readme-ov-file#faq)