vibesketch.chem

Chemistry services on RDKit: reading the canvas, conversion, properties.

Chemistry that produces a number or a file for a calculation runs here, on the server, where it is testable (roadmap, section 3, principle 3). The browser’s Indigo toolkit covers drawing only.

Modules

analysis	Elemental analysis and calculated descriptors of a species (#93).
cip	CIP stereodescriptors of a structure, and its stereo left undefined (#92).
clean	Clean up a drawn structure: standard bond lengths and angles, the drawing kept.
depiction	Versioned 2D depiction restraints, with analytic gradients for FIRE.
embed	3D structures for drawn species: ETKDG, a force field, the stereochemistry kept.
endpoints	The two ends of a reaction path, built from a sketch and its atom mapping (#29).
fire	FIRE, the Fast Inertial Relaxation Engine: a minimiser on numpy alone.
formula	Chemical formulas of solids that have no molecular graph (#142).
layout	2D coordinates for molecules that have none, with every coordinate finite.
mapping	Which reactant atom becomes which product atom: an atom mapping for a reaction (#29).
nanostructures	Carbon nanotubes, graphene and fullerenes generated from their parameters (#137).
perceive	Molecules from 3D coordinates: bonds, bond orders, charges and radicals.
relax	Relax a species' 3D structure with FIRE on an RDKit force field, constraints held.
report	What the properties panel shows for each species of a document.
species	Identity and properties of one species, from an RDKit molecule.