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A chemical graph generator is a software package to generate computer representations of chemical structures adhering to certain boundary conditions. The development of such software packages is a research topic of cheminformatics .
Free open-source: Java 3D applet or standalone program: Ovito: MM XRD EM MD: Free open-source: Python [13] [14] PyMOL: MM XRD SMI EM: Open-source [15] Python [16] [self-published source?] According to the author, almost 1/4 of all published images of 3D protein structures in the scientific literature were made via PyMOL. [citation needed ...
A given atom would have solid and hollow valence spikes. The solid rods clicked into the tubes forming a bond, usually with free rotation. These were and are very widely used in organic chemistry departments and were made so accurately that interatomic measurements could be made by ruler.
In chemical graph theory and in mathematical chemistry, a molecular graph or chemical graph is a representation of the structural formula of a chemical compound in terms of graph theory. A chemical graph is a labeled graph whose vertices correspond to the atoms of the compound and edges correspond to chemical bonds.
Sources: "the DENDRAL program contains a structure GENERATOR as its core, abundantly constrained by a set of relevant heuristics. The GENERATOR is built upon a consideration of the conventional structure representation as a topological graph, i.e., the connectivity relations of a set of chemical atoms taken as nodes.
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In terms of a graph-based computational procedure, SMILES is a string obtained by printing the symbol nodes encountered in a depth-first tree traversal of a chemical graph. The chemical graph is first trimmed to remove hydrogen atoms and cycles are broken to turn it into a spanning tree. Where cycles have been broken, numeric suffix labels are ...
A fact from Chemical graph generator appeared on Wikipedia's Main Page in the Did you know column on 21 March 2021 (check views).The text of the entry was as follows: Did you know... that one of the first generators of chemical graphs (example pictured) was developed in the context of NASA's Mariner program to facilitate the automated identification of chemical compounds in the search for life ...