Getting started#

This page provides a small overview of how to install MolFoundry in Python and how to run your first example scripts.

Install#

pip install --extra-index-url https://py.molfoundry.de/dl/ molfoundry

The wheel vendors the JavaScript compute engine, so there is nothing else to install — no Node.js, no pythonmonkey.

In the rest of this documentation we assume MolFoundry to be imported as:

import molfoundry as mf

Building a molecule#

Molecules in MolFoundry are represented as graph structures and can be loaded from a variety of file and line formats such as GML, SMILES, or InChI. Optionally, a name can be provided to further identify the molecule.

water = mf.smiles("O", "water")

print("name:      ", water.name)
print("SMILES:    ", water.smiles)
print("vertices:  ", water.numVertices, " edges:", water.numEdges)
print("is molecule:", water.isMolecule)
print("exact mass:", round(water.exactMass, 4))
print("InChI:     ", water.inchi)
print("InChIKey:  ", water.inchiKey)

name:       water
SMILES:     O
vertices:   3  edges: 2
is molecule: True
exact mass: 18.0106
InChI:      InChI=1S/H2O/h1H2
InChIKey:   XLYOFNOQVPJJNP-UHFFFAOYSA-N

water = mf.inchi("1S/H2O/h1H2", "water")

water = mf.molfile("""
MolFoundry           2D

  0  0  0  0  0  0            999 V3000
M  V30 BEGIN CTAB
M  V30 COUNTS 3 2 0 0 0
M  V30 BEGIN ATOM
M  V30 1 H 0 0 0 0
M  V30 2 H 0 0 0 0
M  V30 3 O 0 0 0 0
M  V30 END ATOM
M  V30 BEGIN BOND
M  V30 1 1 1 3
M  V30 2 1 2 3
M  V30 END BOND
M  V30 END CTAB
M  END""", "water")

water = mf.graphGMLString("""graph [
  node [ id 1 label "H" ]
  node [ id 2 label "H" ]
  node [ id 3 label "O" ]
  edge [ source 1 target 3 label "-" ]
  edge [ source 2 target 3 label "-" ]
]""", "water")

Look inside the graph#

A molecule is a labeled graph. Count vertex/edge labels and inspect its symmetry (the automorphism group).

co2 = mf.smiles("O=C=O", "carbon dioxide")

print("carbons:      ", co2.vLabelCount("C"))
print("oxygens:      ", co2.vLabelCount("O"))
print("double bonds: ", co2.eLabelCount("="))
print("automorphisms:", co2.aut())

carbons:       1
oxygens:       2
double bonds:  2
automorphisms: [(), (0 1)]

The two oxygens are interchangeable, so the automorphism group is non-trivial — co2.aut() reports the swap.

Serialize#

Every graph round-trips through GML, which is also molfoundry’s native format for hand-written graphs and rules.

print(co2.getGMLString())

graph [
	node [ id 0 label "O" ]
	node [ id 1 label "O" ]
	node [ id 2 label "C" ]
	edge [ source 0 target 2 label "=" ]
	edge [ source 1 target 2 label "=" ]
]

Where to go next#