Tuesday, March 28, 2017

software - Open Source tools to draw a set of 2d molecular graphs from sdf file


I have a sdf file for around 50 small-molecules for which I am doing structure-activity study. I would like to draw 2d graphs of all the molecules such that the image would fit into a single journal page. For example, in this paper, page number 3, they have listed 2d molecular structure. I have attached the image file from the same paper. I have software tools like MarvinSketch which give me 2d or 3d graph for a given sdf file. But I want the integrated image like shown below suitable for publication. List of 2d molecular graphs




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periodic trends - Comparing radii in lithium, beryllium, magnesium, aluminium and sodium ions

Apparently the of last four, $\ce{Mg^2+}$ is closest in radius to $\ce{Li+}$. Is this true, and if so, why would a whole larger shell ($\ce{...