Dear All,
I am currently struggling with something that I expect is very easy to
solve (I have just got back from holiday, so I think my brain isn't
quite in the zone!)
I am trying to read in an SDF and align each molecule to a template
scaffold provided in molfile format. I want to supply a tool that
allows a user to sketch in a template and view their SDF entries in 2D
all aligned (where there is a match) to the supplied template.
I have essentially followed this entry in the Chemistry Toolkit Rosetta
-
http://ctr.wikia.com/wiki/Align_the_depiction_using_a_fixed_substructure
<http://ctr.wikia.com/wiki/Align_the_depiction_using_a_fixed_substructur
e> , which in essence is pretty-much the same as the info in the RDKit
documentation.
However, when I am using pre-supplied 2D coordinates for the template,
rather than generating them from the first substructure match (as in the
CTR example), I find that the alignment proceeds as required, but there
is a mis-match between the scaling of the bond-lengths in the aligned
substructure compared with the rest of the molecule...
Is there a way to 'scale' the molecules according to the template mol
(or alternatively scale the template according to the RDKit default)?
Or is it that I am tackling this in the wrong way?
Kind regards
James
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