Tools

The server has 20 tools. Engine tools such as convert, name, properties, depict, check and screen take a structure and answer. Document tools create an Athanor document, edit it atom by atom, and render or export it.

The server at https://mcp-athanor.arbastro.com/mcp offers 20 tools, in two kinds. None of them needs an account. Structures can be given as SMILES, a molfile, an InChI or a common name. Limits: 60 calls a minute per address, structures up to 20,000 characters.

Tool	Kind	Does
`convert`	Engine	Convert a structure
`name`	Engine	Name a structure
`properties`	Engine	Formula and properties
`depict`	Engine	Draw a structure
`perspective_rotate`	Engine	Turn a structure in perspective
`check`	Engine	Check a structure
`screen`	Engine	Safety screen
`library_search`	Engine	Search the library
`document_create`	Document	Create a document
`document_set_atom`	Document	Change an atom
`document_add_structure`	Document	Add a structure
`document_set_bond`	Document	Change a bond
`document_add_arrow`	Document	Add an arrow
`document_add_text`	Document	Add text
`document_transform`	Document	Flip, rotate or turn
`document_clean_up`	Document	Clean up structures
`document_get`	Document	What is in a document
`document_findings`	Document	Problems in a document
`document_render`	Document	Draw a document
`document_export`	Document	Export a document

The examples below were run against the live server when this page was built. The document examples are one session, in order, so each uses the handle and atom ids the calls before it returned.

Engine tools

A structure in, an answer out. Read-only: they need no account and keep nothing.

convert

Convert a structure. Convert a structure between formats with Athanor's engine: canonical SMILES, a MOL V3000 or V2000 block, or XYZ with 3D coordinates.

Input	Type	Required	What it is
`structure`	string	yes	A structure: SMILES (e.g. CC(=O)Oc1ccccc1C(=O)O), a MOL/SDF block, an InChI, or a common name such as "aspirin".
`to`	`smiles`, `molfile`, `molfile-v2000`, `xyz`	yes	The format to return.

Example call:

{
  "name": "convert",
  "arguments": {
    "structure": "caffeine",
    "to": "smiles"
  }
}

Result:

Cn1cnc2c1c(=O)n(C)c(=O)n2C

name

Name a structure. The systematic IUPAC name Athanor works out from the structure itself, and the common name if its library knows the compound. Says why when it will not name something (ions, some ring systems).

Input	Type	Required	What it is
`structure`	string	yes	A structure: SMILES (e.g. CC(=O)Oc1ccccc1C(=O)O), a MOL/SDF block, an InChI, or a common name such as "aspirin".

Example call:

{
  "name": "name",
  "arguments": {
    "structure": "CC(=O)Oc1ccccc1C(=O)O"
  }
}

Result:

{
 "smiles": "CC(=O)Oc1ccccc1C(=O)O",
 "iupac": "2-acetyloxybenzoic acid",
 "common": "Aspirin"
}

properties

Formula and properties. Formula, charge, exact and average mass, and descriptors (H-bond donors and acceptors, rotatable bonds, TPSA, logP estimate and the like) as Athanor's Compound info shows them.

Input	Type	Required	What it is
`structure`	string	yes	A structure: SMILES (e.g. CC(=O)Oc1ccccc1C(=O)O), a MOL/SDF block, an InChI, or a common name such as "aspirin".

Example call:

{
  "name": "properties",
  "arguments": {
    "structure": "caffeine"
  }
}

Result:

{
 "smiles": "Cn1cnc2c1c(=O)n(C)c(=O)n2C",
 "formula": {
  "hill": "C8H10N4O2",
  "empirical": "C4H5N2O",
  "weight": 194.194,
  "exact_mass": 194.080375576,
  "charge": 0,
  "uncertain": false,
  "analysis": [
   [
    "C",
    49.480416490725766
   ],
   [
    "H",
    5.190685603056737
   ],
   [
    "N",
    28.8515608103237
   ],
   [
    "O",
    16.477337095893798
   ]
  ],
  "isotopes": [
   {
    "mass": 194.08037557600002,
    "relative": 100
   },
   {
    "mass": 195.0828731950089,
    "relative": 10.305100192467314
   },
   {
    "mass": 196.08496800038765,
    "relative": 0.8924917436709956
   }
  ]
 },
 "descriptors": {
  "aromaticRings": 1,
  "doubleBondGeometry": 0,
  "fractionSp3": 0.375,
  "hba": 6,
  "hbd": 0,
  "heavyAtoms": 14,
  "lipinski": {
   "hbaOk": true,
   "hbdOk": true,
   "logpAvailable": false,
   "massOk": true
  },
  "rings": 2,
  "rotatable": 0,
  "stereocenters": 0,
  "tpsa": 56.220000000000006
 }
}

depict

Draw a structure. A 2D drawing of the structure as SVG, laid out by Athanor in the ACS 1996 journal style (or another preset).

Input	Type	Required	What it is
`structure`	string	yes	A structure: SMILES (e.g. CC(=O)Oc1ccccc1C(=O)O), a MOL/SDF block, an InChI, or a common name such as "aspirin".
`preset`	`acs-document-1996`, `new-document`, `new-slide`, `dark-mode`	no	Drawing style; ACS Document 1996 (the journal standard) by default.

Example call:

{
  "name": "depict",
  "arguments": {
    "structure": "CC(=O)Oc1ccccc1C(=O)O"
  }
}

Result:

<?xml version="1.0" encoding="UTF-8"?>
<svg xmlns="http://www.w3.org/2000/svg" version="1.1"
     width="1.1603in" height="1.1583in"
     viewBox="0 0 111.39 111.2">
  <desc>Athanor figure. ACS Document 1996: bond 0.2 in, line 0.0083 in, 10pt Arial.</desc>
  <g transform="translate(47.09 62.06)" fill="none" stroke="#000000" stroke-width="0.8" stroke-linecap="round" stroke-linejoin="miter" font-family="Arial" font-size="13.33" text-anchor="start">
  <path d="M-37.09 -18.46 L-20.46 -28.06"/>
  <path d="M-18.74 -27.06 L-18.74 -40.35"/>
  <path d="M-22.19 -27.06 L-22.19 -40.35"/>
  <path d="M-20.46 -28.06 L-8.34 -21.06"/>
  <path d="M-3.84 -11.55 L-3.84 0.74"/>
  <path d="M-3.84 0.74 L-20.46 10.34"/>
  <path d="M-20.46 10.34 L-20.46 29.54"/>
  <path d="M-17.01 13.03 L-17.01 26.85"/>
  <path d="M-20.46 29.54 L-3.84 39.14"/>
  <path d="M-3.84 39.14 L12.79 29.54"/>
  <path d="M-3.24 34.8 L8.73 27.89"/>
  <path d="M12.79 29.54 L12.79 10.34"/>
  <path d="M-3.84 0.74 L12.79 10.34"/>
  <path d="M-3.24 5.08 L8.73 11.99"/>
  <path d="M12.79 10.34 L29.42 0.74"/>
  <path d="M31.15 1.74 L31.15 -11.55"/>
  <path d="M27.69 1.74 L27.69 -11.55"/>
  <path d="M29.42 0.74 L41.54 7.74"/>
  <text x="-23.21" y="-42.49" fill="#000000" stroke="none">O</text>
  <text x="-6.59" y="-13.69" fill="#000000" stroke="none">O</text>
  <text x="26.67" y="-13.69" fill="#000000" stroke="none">O</text>
  <text x="43.3" y="15.11" fill="#000000" stroke="none">O</text>
  <text x="48.8" y="15.11" fill="#000000" stroke="none">H</text>
  </g>
</svg>

perspective_rotate

Turn a structure in perspective. The 2D drawing turned in 3D (yaw about the vertical axis, pitch about the horizontal, roll in the page) and projected back, as the Perspective tool in Athanor does: bonds foreshortened, labels upright, and every stereocenter keeping its R or S with wedges chosen for the new view. Returns the SVG, a molfile, and the R/S labels before and after.

Input	Type	Required	What it is
`structure`	string	yes	A structure: SMILES (e.g. CC(=O)Oc1ccccc1C(=O)O), a MOL/SDF block, an InChI, or a common name such as "aspirin".
`yaw`	number	no	Degrees about the vertical axis.
`pitch`	number	no	Degrees about the horizontal axis.
`roll`	number	no	Degrees in the plane of the page.

Example call:

{
  "name": "perspective_rotate",
  "arguments": {
    "structure": "C[C@H](N)C(=O)O",
    "yaw": 40
  }
}

Result:

{
 "smiles": "C[C@H](N)C(=O)O",
 "turn": {
  "yaw": 40,
  "pitch": 0,
  "roll": 0
 },
 "stereo_before": [
  "C(CCN): S"
 ],
 "stereo_after": [
  "C(CCN): S"
 ],
 "molfile": "turned\n  athanor\n\n  0  0  0  0  0  0  0  0  0  0999 V3000\nM  V30 BEGIN CTAB\nM  V30 COUNTS 6 5 0 0 0\nM  V30 BEGIN ATOM\nM  V30 1 C -1.3861 0.4330 0.0000 0\nM  V30 2 C -0.1058 0.4330 0.0000 0 HCOUNT=1\n
… (an SVG drawing, 2,192 characters)

check

Check a structure. Every problem Athanor's editor would flag in the structure: valence, charges, stereo and drawing issues, each with what would fix it.

Input	Type	Required	What it is
`structure`	string	yes	A structure: SMILES (e.g. CC(=O)Oc1ccccc1C(=O)O), a MOL/SDF block, an InChI, or a common name such as "aspirin".

Example call:

{
  "name": "check",
  "arguments": {
    "structure": "C(C)(C)(C)(C)C"
  }
}

Result:

{
 "smiles": "C(C)(C)(C)(C)C",
 "findings": [
  {
   "severity": "error",
   "title": "C has 5 bonds",
   "message": "This C has 5 bonds. C takes 4. Remove a bond, or add a charge if you meant an ion."
  }
 ]
}

screen

Safety screen. Athanor's safety screening of a structure as a synthesis target: controlled-substance schedules and chemical-weapons lists (CWC, Australia Group). Answers clear, notice or refuse, with the reason.

Input	Type	Required	What it is
`structure`	string	yes	A structure: SMILES (e.g. CC(=O)Oc1ccccc1C(=O)O), a MOL/SDF block, an InChI, or a common name such as "aspirin".

Example call:

{
  "name": "screen",
  "arguments": {
    "structure": "caffeine"
  }
}

Result:

{
 "smiles": "Cn1cnc2c1c(=O)n(C)c(=O)n2C",
 "kind": "clear",
 "blocked": false,
 "message": ""
}

library_search

Search the library. Look a compound up in Athanor's built-in library by name, synonym or CAS number; returns its name and SMILES.

Input	Type	Required	What it is
`query`	string	yes	A name, synonym or CAS number.

Example call:

{
  "name": "library_search",
  "arguments": {
    "query": "acetone"
  }
}

Result:

{
 "matches": [
  {
   "name": "Acetone",
   "smiles": "CC(C)=O"
  },
  {
   "name": "Acetone",
   "smiles": "CC(C)=O"
  }
 ]
}

Document tools

These build and edit an Athanor document that the server keeps for you, the same document the app works on. document_create returns a handle such as doc_…; pass it as document to every other call. A document is kept for two hours after its last use, up to 2 MB. Atom ids come from document_get (or from the result of the call that added the structure).

document_create

Create a document. A new Athanor document to build and edit with the other document_ tools: empty, or from a structure (SMILES, molfile, CDXML) or an .athanor file (base64). Returns its handle (kept two hours after last use) and what is in it.

Input	Type	Required	What it is
`name`	string	no	What to call it.
`structure`	string	no	A structure to start from: SMILES, a molfile or CDXML.
`athanor_base64`	string	no	An .athanor file, base64, to continue editing.

Example call:

{
  "name": "document_create",
  "arguments": {
    "name": "Esterification",
    "structure": "CC(=O)O"
  }
}

Result:

{
 "document": "doc_hXtQklNVvktL",
 "structures": [
  {
   "atoms": [
    0,
    1,
    2,
    3
   ],
   "smiles": "CC(=O)O",
   "formula": "C2H4O2",
   "name": null
  }
 ],
 "objects": {}
}

document_set_atom

Change an atom. Set an atom's element or label (an element symbol, D, 13C, or a group such as OMe), its charge, or its mass number (0 for natural). Atom ids come from document_get.

Input	Type	Required	What it is
`document`	string	yes	The document handle from document_create.
`atom`	integer	yes
`label`	string	no
`charge`	integer	no
`isotope`	integer	no

Example call:

{
  "name": "document_set_atom",
  "arguments": {
    "document": "doc_hXtQklNVvktL",
    "atom": 0,
    "isotope": 13
  }
}

Result:

{
 "document": "doc_hXtQklNVvktL",
 "structures": [
  {
   "atoms": [
    0,
    1,
    2,
    3
   ],
   "smiles": "[13CH3]C(=O)O",
   "formula": "C¹³CH4O2",
   "name": null
  }
 ],
 "objects": {}
}

document_add_structure

Add a structure. Put a structure (SMILES, molfile or CDXML) on the page at x, y (world units; a bond is about 19), laid out by Athanor.

Input	Type	Required	What it is
`document`	string	yes	The document handle from document_create.
`structure`	string	yes
`x`	number	no
`y`	number	no

Example call:

{
  "name": "document_add_structure",
  "arguments": {
    "document": "doc_hXtQklNVvktL",
    "structure": "CCO",
    "x": 0,
    "y": 60
  }
}

Result:

{
 "document": "doc_hXtQklNVvktL",
 "structures": [
  {
   "atoms": [
    0,
    1,
    2,
    3
   ],
   "smiles": "[13CH3]C(=O)O",
   "formula": "C¹³CH4O2",
   "name": null
  },
  {
   "atoms": [
    4,
    5,
    6
   ],
   "smiles": "CCO",
   "formula": "C2H6O",
   "name": null
  }
 ],
 "objects": {}
}

document_set_bond

Change a bond. Set the bond between two atoms: its order (1, 2, 3) and its stereo mark (none, wedge, hash, wavy), drawn from the first atom.

Input	Type	Required	What it is
`document`	string	yes	The document handle from document_create.
`from`	integer	yes
`to`	integer	yes
`order`	integer	no
`stereo`	`none`, `wedge`, `hash`, `wavy`	no

Example call:

{
  "name": "document_set_bond",
  "arguments": {
    "document": "doc_hXtQklNVvktL",
    "from": 0,
    "to": 1,
    "stereo": "wedge"
  }
}

Result:

{
 "document": "doc_hXtQklNVvktL",
 "structures": [
  {
   "atoms": [
    0,
    1,
    2,
    3
   ],
   "smiles": "[13CH3]C(=O)O",
   "formula": "C¹³CH4O2",
   "name": null
  },
  {
   "atoms": [
    4,
    5,
    6
   ],
   "smiles": "CCO",
   "formula": "C2H6O",
   "name": null
  }
 ],
 "objects": {}
}

document_add_arrow

Add an arrow. A reaction arrow (forward, equilibrium, retrosynthetic) or a plain line from x1, y1 to x2, y2.

Input	Type	Required	What it is
`document`	string	yes	The document handle from document_create.
`x1`	number	yes
`y1`	number	yes
`x2`	number	yes
`y2`	number	yes
`kind`	`forward`, `equilibrium`, `retrosynthetic`, `plain`	no

Example call:

{
  "name": "document_add_arrow",
  "arguments": {
    "document": "doc_hXtQklNVvktL",
    "x1": 60,
    "y1": 0,
    "x2": 120,
    "y2": 0,
    "kind": "forward"
  }
}

Result:

{
 "document": "doc_hXtQklNVvktL",
 "structures": [
  {
   "atoms": [
    0,
    1,
    2,
    3
   ],
   "smiles": "[13CH3]C(=O)O",
   "formula": "C¹³CH4O2",
   "name": null
  },
  {
   "atoms": [
    4,
    5,
    6
   ],
   "smiles": "CCO",
   "formula": "C2H6O",
   "name": null
  }
 ],
 "objects": {
  "Arrow": 1
 }
}

document_add_text

Add text. A text block on the page at x, y (a caption, a label, a condition over an arrow).

Input	Type	Required	What it is
`document`	string	yes	The document handle from document_create.
`text`	string	yes
`x`	number	yes
`y`	number	yes

Example call:

{
  "name": "document_add_text",
  "arguments": {
    "document": "doc_hXtQklNVvktL",
    "text": "H2SO4, heat",
    "x": 90,
    "y": -12
  }
}

Result:

{
 "document": "doc_hXtQklNVvktL",
 "structures": [
  {
   "atoms": [
    0,
    1,
    2,
    3
   ],
   "smiles": "[13CH3]C(=O)O",
   "formula": "C¹³CH4O2",
   "name": null
  },
  {
   "atoms": [
    4,
    5,
    6
   ],
   "smiles": "CCO",
   "formula": "C2H6O",
   "name": null
  }
 ],
 "objects": {
  "Arrow": 1,
  "Text": 1
 }
}

document_transform

Flip, rotate or turn. Flip, rotate in the page (degrees), or turn in perspective (yaw, pitch, roll in degrees, every R and S kept) the given atoms, or every atom when none are given.

Input	Type	Required	What it is
`document`	string	yes	The document handle from document_create.
`atoms`	array of integer	no
`op`	`flip_horizontal`, `flip_vertical`, `rotate`, `perspective`	yes
`degrees`	number	no
`yaw`	number	no
`pitch`	number	no
`roll`	number	no

Example call:

{
  "name": "document_transform",
  "arguments": {
    "document": "doc_hXtQklNVvktL",
    "op": "rotate",
    "degrees": 15
  }
}

Result:

{
 "document": "doc_hXtQklNVvktL",
 "structures": [
  {
   "atoms": [
    0,
    1,
    2,
    3
   ],
   "smiles": "[13CH3]C(=O)O",
   "formula": "C¹³CH4O2",
   "name": null
  },
  {
   "atoms": [
    4,
    5,
    6
   ],
   "smiles": "CCO",
   "formula": "C2H6O",
   "name": null
  }
 ],
 "objects": {
  "Arrow": 1,
  "Text": 1
 }
}

document_clean_up

Clean up structures. Lay every structure out again to standard bond lengths and angles, keeping every R, S, E and Z.

Input	Type	Required	What it is
`document`	string	yes	The document handle from document_create.

Example call:

{
  "name": "document_clean_up",
  "arguments": {
    "document": "doc_hXtQklNVvktL"
  }
}

Result:

{
 "document": "doc_hXtQklNVvktL",
 "moved": 6,
 "structures": [
  {
   "atoms": [
    0,
    1,
    2,
    3
   ],
   "smiles": "[13CH3]C(=O)O",
   "formula": "C¹³CH4O2",
   "name": null
  },
  {
   "atoms": [
    4,
    5,
    6
   ],
   "smiles": "CCO",
   "formula": "C2H6O",
   "name": null
  }
 ],
 "objects": {
  "Arrow": 1,
  "Text": 1
 }
}

document_get

What is in a document. Every structure in the document (its atom ids, SMILES, formula and name) and how many objects of each kind (arrows, text, shapes).

Input	Type	Required	What it is
`document`	string	yes	The document handle from document_create.

Example call:

{
  "name": "document_get",
  "arguments": {
    "document": "doc_hXtQklNVvktL"
  }
}

Result:

{
 "document": "doc_hXtQklNVvktL",
 "structures": [
  {
   "atoms": [
    0,
    1,
    2,
    3
   ],
   "smiles": "[13CH3]C(=O)O",
   "formula": "C¹³CH4O2",
   "name": null
  },
  {
   "atoms": [
    4,
    5,
    6
   ],
   "smiles": "CCO",
   "formula": "C2H6O",
   "name": null
  }
 ],
 "objects": {
  "Arrow": 1,
  "Text": 1
 }
}

document_findings

Problems in a document. Everything Athanor's Problems list would flag in the document (valence, charges, stereo, drawing), each with what fixes it.

Input	Type	Required	What it is
`document`	string	yes	The document handle from document_create.

Example call:

{
  "name": "document_findings",
  "arguments": {
    "document": "doc_hXtQklNVvktL"
  }
}

Result:

{
 "document": "doc_hXtQklNVvktL",
 "findings": []
}

document_render

Draw a document. The whole page as SVG, in the journal style the document uses (ACS 1996 by default).

Input	Type	Required	What it is
`document`	string	yes	The document handle from document_create.

Example call:

{
  "name": "document_render",
  "arguments": {
    "document": "doc_hXtQklNVvktL"
  }
}

Result:

<?xml version="1.0" encoding="UTF-8"?>
<svg xmlns="http://www.w3.org/2000/svg" version="1.1"
     width="0.7776in" height="1.1122in"
     viewBox="0 0 74.65 106.77">
  <desc>Athanor figure. ACS Document 1996: bond 0.2 in, line 0.0083 in, 10pt Arial.</desc>
  <g transform="translate(35.08 30.15)" fill="#000000" stroke="none" stroke-width="0.8" stroke-linecap="round" stroke-linejoin="miter" font-family="Arial" font-size="13.33" text-anchor="start">
  <path d="M12.05 2.65 L11.72 1.27 L12.05 -0.11 L2.88 0.87 L2.88 1.27 L2.88 1.67 Z"/>
  <path d="M12.05 2.65 L11.72 1.27 L12.05 -0.11 L2.88 0.87 L2.88 1.27 L2.88 1.67 Z" fill="none" stroke="#000000" stroke-width="0.24" stroke-linejoin="round"/>
  <path d="M12.71 3 L19.73 -9.15" fill="none" stroke="#000000"/>
  <path d="M9.72 1.27 L16.73 -10.88" fill="none" stroke="#000000"/>
  <path d="M11.72 1.27 L18.23 12.56" fill="none" stroke="#000000"/>
  <path d="M-23.62 66.62 L-4.42 66.62" fill="none" stroke="#000000"/>
  <path d="M-4.42 66.62 L2.09 55.33" fill="none" stroke="#000000"/>
  <text x="-25.08" y="6.04">H</text>
  <text x="-19.58" y="8.98" font-size="9.33">3</text>
  <text x="-15.73" y="6.04">¹³C</text>
  <text x="18.57" y="-10.58">O</text>
  <text x="18.57" y="22.67">O</text>
  <text x="24.07" y="22.67">H</text>
  <text x="2.43" y="54.76">O</text>
  <text x="7.93" y="54.76">H</text>
  </g>
</svg>

document_export

Export a document. The document as a file: athanor (base64, Athanor's own format, everything kept), cdxml (ChemDraw), mol (V3000), smiles, or svg.

Input	Type	Required	What it is
`document`	string	yes	The document handle from document_create.
`format`	`athanor`, `cdxml`, `mol`, `smiles`, `svg`	yes

Example call:

{
  "name": "document_export",
  "arguments": {
    "document": "doc_hXtQklNVvktL",
    "format": "smiles"
  }
}

Result:

[13CH3]C(=O)O.CCO

Is this helpful?

Last updated Nov 13, 2026

Still stuck? Read the FAQ or contact support.
Something wrong on this page? Tell us.
For AI tools: llms.txt

Tools

Related guides