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Fig. 2 PIKAChU’s drawing algorithm. (a) Examples of simple (blue), overlapping (red), and bridged (pink) rings. Note that the aromatic rings in pink become part of the bridged ring system because they overlap with bridged rings. (b) PIKAChU’s "finetuning" algorithm. First, clashes are detected and the shortest path between them is found. The rotatable bond with the shortest distance to the center of the shortest path is chosen (indicated with numbers). Twelve rotations at incremental angles of 30° are evaluated for clashes. The best rotation is chosen. (c) Determination of bond angles based on neighboring atoms. If an atom has three or fewer non-hydrogen neighbors, the angles default to 120° (yellow). If an atom has four non-hydrogen neighbors, angles default to 90° if three or more of the branches have a depth more than one, or three or four branches have a depth of exactly one (red). If however two of the branches have a depth of exactly one (blue), the angle is set to 120° between the two longest branches, 90° between any short branch and any long branch, and 60° between the shortest branches. (d) Positioning of neighboring branches depends on the depth of each branch: the two longest branches (red and dark yellow, depths seven and six respectively) are always placed opposite one another.


Terlouw, B.R.; Vromans, Sophie P.J.M.; Medema, M.H. (2022). "PIKAChU: A Python-based informatics kit for analyzing chemical units". Journal of Cheminformatics 14: 34. doi:10.1186/s13321-022-00616-5. 




Terlouw, B.R.; Vromans, Sophie P.J.M.; Medema, M.H.

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