Biomedical Engineering Reference
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charge, possessing atoms with unusual atom valences, undefi ned
stereochemistry, etc. Another issue encountered was one in which the
molecule is not drawn out explicitly but, for example, is represented by a
single 'node' which is labeled, e.g. 'FMoc'. These groups are automatically
expanded but the placement of atoms in these expanded groups is
sometimes peculiar and leads to ugly 2D depictions of the molecules.
This can be addressed by allowing the ability to apply a cleaning algorithm
to the relevant MOL structure in the SDF fi le to tidy up and standardize
the bond lengths and angles to prevent atom overlap and very long bonds.
These are examples that can be dealt with by post-processing the
structures in the SDF fi le. However, as OpenBabel source code availability
allows customization, then issues that cannot be fi xed with post-
processing can be dealt with during the initial ChemDraw to SDF
conversion. One such issue is that authors may use artistic license to
overlay another ChemDraw object onto a molecule - for example to only
draw part of a larger structure. The objects can be lines to indicate
dangling bonds (even more problems are caused when these are not
drawn as graphical objects but instead as various variations of ethane
molecules as in Figure 3.5(a)), graphical pictures (e.g. circles to indicate
beads as in Figure 3.5(b)) or brackets (e.g. commonly used to indicate
repeat units polymers as in Figure 3.5(c)). The objects are usually overlaid
onto an unlabeled carbon to give the appearance of a bond from the
drawn molecule to these objects. The current OpenBabel algorithm
would interpret the ChemDraw by simply identifying a carbon atom, and
treating any objects overlaid on it as separate entities rather than bonded
in any way, and it would not be possible to detect any error in the fi nal
molecule that was output. Although it is diffi cult to envisage any way
that we could fully interpret such molecules, we could modify the
OpenBabel convert function to return a warning when a chemical
structure overlaps any other ChemDraw object so that these can be
ignored by default, rather than processed incorrectly. Another very
common problem which is diffi cult to fi nd a solution for, is dealing with
Markush structures - see Figure 3.5(d). Authors commonly save valuable
space in the fi gures of their articles by representing multiple, similar
compounds by defi ning part of the structure with a place holder, for
example the label 'R' and supplying a label (usually elsewhere in the
ChemDraw fi le) defi ning the different groups that could be substituted
for R. This would require quite an extensive alteration to OpenBabel to
deal with it correctly, but it is at least conceivable.
The long-term aim of the ChemDraw Digester is for it to process all
ChemDraw fi les supplied with RSC articles automatically. In fact, with
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