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
	PAINS Filter		x
Reaction Planning / Synthesis	ForwardSynthesis	x
	NameRXN			x
	RXNPlanner			x
	RXNPredict			x
	Retrosynthesis	x
Cheminformatics / Functional Group Analysis	FuncGroups			x
	FunctionalGroups	x
Molecule Editing / Generation / Annotation	ModifyMol			x
	MoleculeCaptioner	x
	MoleculeGenerator	x
Similarity / Molecular Analysis	MolSimilarity	x
	Similarity			x
Structure Retrieval / Preparation	DownloadPDB				x
	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
	SMILES2Price			x

Special:

Tool	ChemAgent	Cactus	ChemCrow	MDCrow
PythonREPL	x		x

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