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Contains files necessary to do a parameterization. The parameterization command file (loop.in) has comments throughout to describe what each command does in relation to the rest of the code.
Update before I turn in my keys
Update Q2MM
simple code to replace the atom type of the old structure if it is originally the wild card atom type (00)
Previous commit explains the problem. This just changes the color for visualization in Maestro.
Some instances an aromatic group will be matched based off of a relativly inclusive matching pattern. Two examples are for the Heck reaction and the osmium dihydroxylation reaction. When matching the alkene with the substrucutre (C2=C2-00) an aromatic group would be matched which would give (in the case of benzene) 3 matches for double bonds, with four different matches per bond giving a total of 12 additional structures. This code iterates through the rings and matches to determine those matches that are within the ring (2+ atoms in both matches and the ring) and then determines if it is aromatic or not. Also the code would prevent structures that are intended to have multiple matches such as (2,1,5) and (5,1,2) to use both matches. To fix this I added logic to determine if the 'b_cs_first_match_only' is true before determinig if the matches are unique or not.
Removed extra lines that I added when working with code.
Bug Fixes: Read commits from arosale4
ericchansen
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Jan 14, 2019
Update: ESP_fitting and bug fixes
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Includes an example parameterization folder, which has been needed for a long time.
Also includes tweaks to the structure merging used for setting up the virtual screening.
I'm not sure how how to just pull this without creating a request, so we're going down this path because I don't want to pull up a terminal right now.