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true/false properties in .mae file not working #41

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arosale4 opened this issue Mar 14, 2017 · 4 comments
Open

true/false properties in .mae file not working #41

arosale4 opened this issue Mar 14, 2017 · 4 comments
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@arosale4
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Whether I use 0 or 1 for b_cs_first_match_only, or b_cs_both_enantiomers I can not seem to reduce the number of structures produced. I have even gone into merge.py and set first_match_only to True, and it would still match every instance of a pattern. I'm trying every version of schrodinger that we have available to see if that is a problem. I have also noticed that the pattern PD-C2=C2 will also match PD.C2=C2.
@ericchansen
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Any updates on this?

@ericchansen
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@arosale4 Do your recent changes solve this issue?

@arosale4
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Thanks for drawing my attention to this. The recent changes may help with it, but indirectly. I do think we fixed this in 68da398?

@arosale4
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Or at least we addressed the issue of reducing matches from first_match_only() to one.

ericchansen added a commit that referenced this issue Oct 31, 2018
@ericchansen @arosale4
Fix issue Q2MM#40 (#41)
ae54bec 
See Q2MM#40 (I hope that the magic GitHub Markdown turns that into a link).
Also, I got rid of some blank spaces.

Anyway, it turns out that Schrodinger's [getBond()](http://content.schrodinger.com/Docs/r2015-4/python_api/api/schrodinger.structure.Structure-class.html#getBond)
function can return None. Personally, I would have made that raise an exception
of some sort, but I mean, I didn't write it. Anyway, here's an example.

Ex.) Don't take this syntax too literally. It's just an illustration.

N-P (single bond)
bond = merge.getBond(N, P)
print(bond)
>>> bond(1, 2)

N P (no bond)
bond = merge.getBond(N, P)
print(bond)
>>> None

The code now checks for this behavior and adds the bond if it's missing.
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@ericchansen @arosale4