Mol-MCP
Server Configuration
Describes the environment variables required to run the server.
| Name | Required | Description | Default |
|---|---|---|---|
No arguments | |||
Instructions
Guidance the server publishes about itself, which clients place ahead of the tool catalog so the model reads it before choosing anything.
This server publishes no instructions, or was last inspected before Glama recorded them.
Capabilities
Features and capabilities supported by this server
Protocol revision2025-11-25
| Capability | Details |
|---|---|
| tools | {
"listChanged": true
} |
| prompts | {
"listChanged": false
} |
| resources | {
"subscribe": false,
"listChanged": false
} |
| experimental | {
"tasks": {
"list": {},
"cancel": {},
"requests": {
"tools": {
"call": {}
},
"prompts": {
"get": {}
},
"resources": {
"read": {}
}
}
}
} |
Tools
Functions exposed to the LLM to take actions
| Name | Description |
|---|---|
| smiles_retrieveA | Retrieves a SMILES string from any non-SMILES chemical identifier |
| smiles_infoC | Return JSON formatted descriptors for a SMILES |
| smiles_has_substructureA | Check if SMILES contains SMARTS pattern substructure |
| smiles_max_common_substructureC | Find maximum common substructure between SMILES |
| smiles_removeC | Remove SMARTS pattern from a SMILES |
| smiles_replaceC | Replace SMARTS pattern in a SMILES |
| smiles_reactC | Apply a reaction SMARTS to a SMILES |
| geometry_optimizeC | Optimize the input geometry using xTB |
| geometry_buildC | Generates a geometry for the input SMILES |
Prompts
Interactive templates invoked by user choice
| Name | Description |
|---|---|
No prompts | |
Resources
Contextual data attached and managed by the client
| Name | Description |
|---|---|
No resources | |
TDQS
Scored across 9 tools
Each tool has a clearly distinct purpose: geometry tools are separate from SMILES manipulation tools, and within SMILES tools each operation (substructure check, info, common substructure, reaction, remove, replace, retrieve) is unique and well-defined.
All tool names follow a consistent 'prefix_action' pattern in snake_case, with 'geometry_' for geometric operations and 'smiles_' for SMILES operations, making the naming predictable and clear.
The 9 tools cover a focused domain of computational chemistry operations without being excessive or too sparse, each earning its place for typical molecular manipulation tasks.
The tool set covers essential SMILES manipulations (retrieval, substructure search, reaction, editing) and basic geometry handling, but lacks some common features like molecular property calculation or format conversion, leaving minor gaps.