molchart.add_atom
ChatGPTAdd an atom to a molecule, optionally bonded to an existing atom.
Education & Research
Overview
Draw and manipulate molecular structures and chemical reactions. Create molecules from SMILES, add atoms and bonds, and export to various formats.
Tools
molchart.add_bond
ChatGPTAdd a bond between two atoms.
molchart.add_ring_template
ChatGPTAdd a ring template to the canvas.
molchart.analyze_stereochemistry
ChatGPTAnalyze stereochemistry: identify stereocenters, E/Z double bonds, and validate wedge bonds
molchart.analyze_substituents
ChatGPTAnalyze electron-donating/withdrawing effects of substituents (Hammett sigma values)
molchart.attach_functional_group
ChatGPTAttach a functional group to an atom.
molchart.calculate_charges
ChatGPTCalculate Gasteiger partial charges for all atoms
molchart.calculate_properties
ChatGPTCalculate physicochemical properties: MW, LogP, TPSA, H-bond donors/acceptors, drug-likeness (Lipinski, Veber)
molchart.cleanup_geometry
ChatGPTRecalculate 2D coordinates for a molecule, preserving canvas position.
molchart.cleanup_stereochemistry
ChatGPTClean up stereochemistry issues: fix wedge directions, remove redundant wedges, add missing wedges
molchart.clear_canvas
ChatGPTClear all objects from the canvas.
molchart.create_document
ChatGPTCreate a new document to draw molecules on. Returns doc_id to use in other tools.
molchart.create_molecule_from_smiles
ChatGPTCreate a new molecule from SMILES notation.
molchart.create_reaction_arrow
ChatGPTCreate a reaction or electron-pushing arrow on the canvas.
molchart.create_text
ChatGPTCreate a text label on the canvas.
molchart.delete_atom
ChatGPTDelete an atom and all connected bonds.
molchart.delete_bond
ChatGPTDelete a bond.
molchart.delete_document
ChatGPTDelete a document permanently
molchart.delete_object
ChatGPTDelete an object from the canvas.
molchart.draw_reaction
ChatGPTDraw a complete chemical reaction with proper layout. Creates reactants, arrow with conditions, and products all in one row with + signs. This is the recommended way to draw reactions. Each species can be a string (SMILES or formula) or an object with 'formula' and optional 'coefficient'.
molchart.enumerate_tautomers
ChatGPTEnumerate possible tautomers of a molecule
molchart.export_3mf
ChatGPTExport molecule to 3MF format for 3D printing
molchart.export_cdxml
ChatGPTExport a molecule in CDXML format (ChemDraw)
molchart.export_molfile
ChatGPTExport a molecule in MOL file format (V2000)
molchart.export_sdf
ChatGPTExport molecule to SDF format with 3D coordinates
molchart.export_smiles
ChatGPTExport a molecule as SMILES string
molchart.generate_3d
ChatGPTGenerate 3D coordinates for a molecule with optional geometry optimization
molchart.get_canvas_state
ChatGPTGet the current canvas state including all molecules
molchart.get_compound_details
ChatGPTGet detailed information about a PubChem compound by CID
molchart.import_molfile
ChatGPTImport a molecule from MOL file (V2000) format
molchart.list_documents
ChatGPTList all available documents
molchart.list_objects
ChatGPTList all objects on the canvas with their IDs, types, and basic info
molchart.move_object
ChatGPTMove an object to new canvas coordinates.
molchart.open_document
ChatGPTOpen an existing document to continue working on it
molchart.search_by_name
ChatGPTSearch PubChem database by compound name
molchart.search_pubchem
ChatGPTSearch PubChem database by structure (identity, similarity, substructure)
molchart.set_arrow_style
ChatGPTRecolour or re-weight an existing arrow (style.stroke / style.strokeWidth,
molchart.set_atom_charge
ChatGPTSet the formal charge on an atom.
molchart.set_atom_element
ChatGPTChange the element of an atom.
molchart.set_atom_hydrogens
ChatGPTPin (or reset) the number of hydrogens drawn on an atom.
molchart.set_bond
ChatGPTModify an existing bond's order or stereochemistry.
molchart.set_lone_pairs
ChatGPTOverride (or reset) the lone-pair count drawn on an atom, and show the dots.
molchart.set_molecule_style
ChatGPTRecolour a molecule (QA-0066). Writes the same keys the toolbar colour
molchart.set_text_style
ChatGPTRestyle an existing label: colour, size, weight, italic, family, underline.
molchart.show_document
ChatGPTDisplay the document in the MolChart widget. Call this after creating or modifying molecules to show the result to the user. This is the ONLY way to display the widget. If doc_id is not provided, shows the most recently used document.
molchart.show_lone_pairs
ChatGPTDraw (or hide) lone-pair and unpaired-electron dots on a molecule.
molchart.update_document
ChatGPTUpdate document properties (title, notes)
molchart.validate_structure
ChatGPTValidate molecular structure for common issues (valence errors, missing coordinates)
Capabilities
WritesInteractive
Example Prompts
Click any prompt to copy it.
