Tools of open source agents

Overview of the tools of open source chemistry agents

The table below lists the tool names used by each agent system (ChemAgent, Cactus, ChemCrow, MDCrow) and marks with “x” which systems include each tool. To be clear: A tool is not an agent! A tool is a static resource or function designed for a specific task without autonomy or decision-making capability. In contrast, an agent autonomously makes decisions, actively perceives its environment, and initiates actions to achieve defined goals. Unlike tools, agents possess inherent autonomy, adaptivity, and can respond dynamically to changing contexts.

ChemAgent integrates 29 tools spanning general utilities (e.g. WebSearch, PythonREPL) to molecule/property predictors and reaction planners

Cactus provides 10 cheminformatics tools focused on molecular descriptors and ADMET properties (e.g. MolWt, LogP, QED, PAINS Filter)

ChemCrow incorporates 18 expert-designed tools including general tools (WebSearch, LitSearch, PythonREPL) and chemistry-specific tools like Name2SMILES, PatentCheck, FuncGroups (functional group identifier), safety checks, and reaction prediction/planning (NameRXN, RXNPredict, RXNPlanner)

MDCrow employs 40+ tools for MD workflows, from information retrieval (UniProtSearch, LiteratureSearch) and structure preparation (DownloadPDB, PDBFixer, Molrender) to simulation execution (OpenMM) and analysis (RMSD, SecondaryStructure, etc.)

An “x” indicates the presence of a given tool in a system’s toolset. We have 61 tools at all.

Category	Tool	ChemAgent	Cactus	ChemCrow	MDCrow
Information Retrieval	LiteratureSearch / LitSearch			x	x
	PubchemSearchQA	x
	UniProtSearch				x
	WebSearch	x		x
	WikipediaSearch	x
Cheminformatics / Conversion Tools	CanonicalizeSMILES	x
	CompareSMILES	x
	IUPAC2SMILES	x
	Name2CAS			x
	Name2SMILES	x		x
	SELFIES2SMILES	x
	SMILES2Formula	x
	SMILES2IUPAC	x
	SMILES2SELFIES	x
Cheminformatics / Molecular Descriptors	CountMolAtoms	x
	MolWt / SMILES2Weight	x	x	x
	TPSA		x
Property Prediction / ADME/Tox / Bioactivity	BBB Permeant		x
	BBBPPredictor	x
	Druglikeness		x
	GI Absorption		x
	HIVInhibitorPredictor	x
	LogDPredictor	x
	LogP		x
	QED		x
	SA		x
	SideEffectPredictor	x
	SolubilityPredictor	x
	ToxicityPredictor	x
Filtering	Brenk Filter		x
Filtering	PAINS Filter		x
Reaction Planning / Synthesis	ForwardSynthesis	x
	NameRXN			x
	RXNPlanner			x
	RXNPredict			x
	Retrosynthesis	x
Cheminformatics / Functional Group Analysis	FuncGroups			x
Cheminformatics / Functional Group Analysis	FunctionalGroups	x
Molecule Editing / Generation / Annotation	ModifyMol			x
	MoleculeCaptioner	x
	MoleculeGenerator	x
Similarity / Molecular Analysis	MolSimilarity	x
Similarity / Molecular Analysis	Similarity			x
Structure Retrieval / Preparation	DownloadPDB				x
Structure Retrieval / Preparation	PDBFixer				x
Visualization / Trajectory Analysis	Molrender				x
	PlotTrajectory				x
	RMSD				x
	RadiusOfGyration				x
	SecondaryStructure				x
Simulation Execution	OpenMM				x
Safety / Hazard	ChemicalWeaponCheck			x
	ExplosiveCheck			x
	SafetySummary			x
Intellectual Property / Patent Analysis	PatentCheck	x		x
Economic Analysis	GetMoleculePrice	x
Economic Analysis	SMILES2Price			x

Special:

Tool	ChemAgent	Cactus	ChemCrow	MDCrow
PythonREPL	x		x