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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 .
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New graph-theoretic algorithms were invented by Lederberg, Harold Brown, and others that generate all graphs with a specified set of nodes and connection-types (chemical atoms and bonds) -- with or without cycles. Moreover, the team was able to prove mathematically that the generator is complete, in that it produces all graphs with the ...
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 ...
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 ...
Veusz is a free scientific graphing tool that can produce 2D and 3D plots. Users can use it as a module in Python. GeoGebra is open-source graphing calculator and is freely available for non-commercial users. WebPlotDigitizer, PlotDigitizer's online free app or SplineCloud's plot digitizer can be used to extract data from charts.
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