Physlr molecules C++ port#129

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jwcodee merged 50 commits intomasterfrom

physlr-molecule

Dec 20, 2019

Contributor

jwcodee commented Dec 18, 2019 •

edited

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This PR contains the biconnected component C++ port of physlr molecules.

jwcodee requested review from aafshinfard, lcoombe, sjackman and vlad0x00

December 18, 2019 02:01

lcoombe reviewed

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lcoombe left a comment

Looks pretty good to me -- just some small comments.

I do think it would also be good for a more C++ savvy person (like Vlad) to take a look.

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lcoombe approved these changes

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lcoombe left a comment

Looks good to me - pending review from Amirhossein/Vlad :)

Collaborator

aafshinfard commented Dec 18, 2019

Thanks for the change. Looks good to me too!

jwcodee self-assigned this

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jwcodee added 26 commits

December 20, 2019 12:59


          unittest: convert spaces to tab

eeb6385


          physlr-molecules: improve incorrect parameter logic

c2a5948


          physlr-molecules: update status message

bee6ffc


          physlr-molecules: improve help

b48ebde


          physlr-molecules: remove thread option

234ccd2


          physlr-molecules: add comment to componentsToNewGraph

6f56003


          README: add boost to dependencies

2dd32db


          physlr-molecules: improve help

81cabb2


          physlr-molecules: improve help

4c42dd1


          physlr-molecules: improve componentsToNewGraph comment

4dac8e1


          physlr-molecules: complete biconnected components in one function call

3c0b715


          physlr-molecules: rename art_points to artPoints


          physlr-molecules: rename oldG and newG to inG and outG

5a55c7e


          physlr-molecules: rename remaning newG to molSeparatedG

2a2d3cc


          physlr-molecules: rename outG to molSeparatedG

e2b1000


          physlr-molecules: rename molSeparatedG to molSepG

ea8ac5e


          physlr-molecules: declare and define variables on the same line

ed373c2


          physlr-molecules: use auto and auto&

ef13723


          physlr-molecules: use for loop instead of while loop

45ddcdb


          physlr-molecules: use pre-increment instead of post-increment

35f7196


          physlr-molecules: remove flag variable

77ba9c4


          physlr-molecules: use uint64_t for memory return type

245a10b


          physlr-molecules: use INT_MAX instead of 555

ca584ee


          physlr-molecules: fix clang-tidy

94e4456


          physlr-molecules: ensure stringstream extraction is sucessful

0fd8c38


          physlr-molecules: use vertexSet_t

ce5dc72

jwcodee force-pushed the physlr-molecule branch from 03cb2fe to ce5dc72 Compare

December 20, 2019 21:00

jwcodee merged commit 15340ff into master

jwcodee deleted the physlr-molecule branch

December 20, 2019 21:14

Contributor

sjackman commented Jan 2, 2020

Very exciting work! physlr molecules was a major bottle neck in the Physlr pipeline.

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