About Moleditpy MCP Server
Moleditpy MCP Server is an MCP server published by HiroYokoyama in the Developer Tools category: moleditpy-mcp_server.
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Install
git clone https://github.com/HiroYokoyama/moleditpy-mcp_serverThis server has no ConduID identity, so agent calls to it are not receipted. Pin the version you install and review the source before granting it credentials.
Tools (42)
add_hydrogensAdd explicit hydrogens (RDKit `AddHs`); 3D coordinates are generated for them when the molecule already has a conformer
Parameters not published.
apply_reaction_smartsModify the 2D molecule with a Reaction SMARTS transformation (optional anchor atom)
Parameters not published.
check_chemistryTrigger MoleditPy's valence-violation validation pass
Parameters not published.
clear_canvasClear the 2D editor (undo-safe)
Parameters not published.
clear_overlayRemove the overlay drawn by `compare_structures` and restore the 3D style and atom colors it changed
Parameters not published.
compare_structuresRMSD against another structure with the same atom order (`xyz_text` or sandbox `path`, `frame`), Kabsch-aligned; `heavy_atoms_only`; `overlay` switches to the stick style and draws both, told apart by carbon color (`current_color`, `overlay_color`; other elements keep CPK colors)
Parameters not published.
compute_partial_chargesGasteiger partial charges per atom, computed on a private copy so the canvas is untouched (optional `atom_indices` filter)
Parameters not published.
delete_atomsDelete atoms by index (highest first, so the caller's other indices stay valid); re-sanitized
Parameters not published.
edit_bondsAdd and/or remove bonds by atom index pairs (`add`, `remove`, `bond_type`), as the Bond Editor plugin does: 3D coordinates kept, one undo step; an edit that breaks valence rules (an atom above its usual valence) is kept unsanitized and reported
Parameters not published.
enter_3d_modeSwitch the UI to 3D viewer mode
Parameters not published.
Show all 42 tools
exit_3d_modeSwitch the UI back to 2D editing mode
Parameters not published.
fit_2d_viewFit all visible items in the 2D editor canvas into the viewport
Parameters not published.
get_app_infoMoleditPy version and MCP plugin version
Parameters not published.
get_atom_propertiesPer-atom: symbol, Z, charge, hybridization, Hs, radical electrons
Parameters not published.
get_bond_infoFull bond table: endpoints and bond type (SINGLE/DOUBLE/TRIPLE/AROMATIC)
Parameters not published.
get_current_moleculeSMILES, formula, MW, atom/bond counts, 3D availability (for a structure loaded with distance-based bonds only: formula and weight from the atoms, no SMILES)
Parameters not published.
get_mapped_smilesSMILES with atom indices embedded as map numbers + legend (find atom_index targets)
Parameters not published.
get_molecule_descriptorsRDKit's standard descriptor set in one call: canonical SMILES, formula, MW, exact mass, LogP, TPSA, formal charge, HBD/HBA, rotatable bonds, ring and atom/bond counts
Parameters not published.
get_molecule_imageRender the molecule to a **PNG returned as an actual image** — the 2D canvas or the 3D viewer (`view`: auto / 2d / 3d, `width`, `height`, `atom_labels` to overlay atom indices, `background`: a color or `transparent`)
Parameters not published.
get_molecule_xyz3D XYZ coordinate block (`Element X Y Z` per line)
Parameters not published.
get_selected_atomsIndices and symbols of user-selected atoms
Parameters not published.
load_from_mol_blockLoad a molecule from a MOL/SDF block
Parameters not published.
load_molecule_by_nameLook up by common/IUPAC name on PubChem and load (e.g. `"aspirin"`)
Parameters not published.
load_molecule_from_smilesDraw a molecule from a SMILES string
Parameters not published.
load_xyz_fileSame as `show_xyz_in_viewer`, but reads an `.xyz` file from the sandbox — no pasting of coordinates; multi-frame files default to the last frame
Parameters not published.
measure_geometryDistances (2 atoms), angles (3) and dihedrals (4) by 0-based index, several per call
Parameters not published.
optimize_geometryMinimize the **existing** 3D conformer with MMFF94 or UFF — refines coordinates rather than generating them (`force_field`, `max_iters`)
Parameters not published.
push_undo_checkpointPush the current state onto MoleditPy's undo stack
Parameters not published.
refresh_3d_viewForce a redraw of the 3D scene
Parameters not published.
refresh_uiSync info panel, undo/redo state, and title bar
Parameters not published.
remove_hydrogensStrip explicit hydrogens back to implicit (RDKit `RemoveHs`)
Parameters not published.
reset_3d_cameraReset and re-center the 3D camera
Parameters not published.
reset_cpk_color_overrideClear atom/bond color overrides (`scope`: atoms / bonds / all) and restore default colors
Parameters not published.
run_pythonExecute arbitrary Python on the Qt main thread with `ctx` access — see below
Parameters not published.
save_molecule_imageWrite the same PNG into the file sandbox (`path` ending in `.png`, `overwrite`, `background`) — for reports and notes
Parameters not published.
set_3d_styleSwitch the 3D style: `ball_and_stick`, `cpk`, `wireframe`, `stick`
Parameters not published.
set_atom_chargeSet one atom's formal charge by index; re-sanitized, and rejected if the result is not a valid structure
Parameters not published.
set_bond_color_overrideOverride bond colors in the 3D viewer by bond index or `"atom1-atom2"` pairs; persists across redraws (formerly `highlight_bonds`, still accepted)
Parameters not published.
set_cpk_color_overrideOverride atom CPK colors in the 3D viewer (hex per atom index); applied with a single redraw and persists across redraws (formerly `highlight_atoms`, still accepted)
Parameters not published.
show_xyz_in_viewerDisplay an XYZ block in the 3D viewer. `charge` (for ions) or `skip_chemistry` (distance-based bonds) answer the app's charge prompt so no dialog blocks the call; `frame` picks one frame of a trajectory; the camera is re-fitted to the new molecule unless `keep_camera`
Parameters not published.
substructure_searchEvery SMARTS match in the molecule, as atom-index tuples (`unique_matches` to keep or collapse symmetry-equivalent hits)
Parameters not published.
trigger_3d_conversionRun MoleditPy's built-in 2D→3D optimizer (ETKDG/MMFF)
Parameters not published.
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