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normal auto-martini

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8 years 5 days ago #5504 by diaobk
auto-martini was created by diaobk
Hello,
I tried the auto_martini to get some rules in mapping.

I use the auto_martini-refactor.zip on ubuntu 14.04.
With all dependencies installed.
But I use the latest beautifulsoup4, so I add "from bs4" before import BeautifulSoup in auto_martini.py

When I use
./auto_martini.py --smi "N1=C(N)NN=C1N" --mol GUA --verbose --fpred
Output:
INFO:main:
INFO:main:; Heavy atoms:
INFO:main:;
INFO:main:; ring atoms: 0, 1, 3, 4, 5
INFO:main:; [0] -27.6130945208
INFO:main:; [1] -38.0635593097
INFO:main:; [2] 16.4001120276
INFO:main:; [3] -28.4635382315
INFO:main:; [4] -28.0024324069
INFO:main:; [5] -37.8796622141
INFO:main:; [6] 16.6193853655
INFO:main:; CG bead: 1
INFO:main:; with energy: -38.0635593097
INFO:main:; [0, 2] -21.9287319767
INFO:main:; [0, 3] -64.2263393324
INFO:main:; [0, 4] -63.7983238197
INFO:main:; [0, 6] -21.7076565399
INFO:main:; [1, 4] -68.2625846096
INFO:main:; [1, 5] -75.4338808284
INFO:main:; [1, 6] -33.8916513407
INFO:main:; [2, 3] -22.7761151134
INFO:main:; [2, 4] -24.1365999277
INFO:main:; [2, 5] -33.9317685447
INFO:main:; [2, 6] 16.3628159478
INFO:main:; [3, 5] -68.7005219875
INFO:main:; [3, 6] -24.3387784779
INFO:main:; [4, 6] -22.0925627479
INFO:main:; CG bead: 1
INFO:main:; CG bead: 5
INFO:main:; with energy: -75.4338808284
INFO:main:; [0, 2, 3] -51.8374656978
INFO:main:; [0, 2, 4] -53.2310408241
INFO:main:; [0, 2, 6] -12.8605754412
INFO:main:; [0, 3, 6] -53.3983269634
INFO:main:; [0, 4, 6] -51.1852015454
INFO:main:; [1, 4, 6] -57.382992347
INFO:main:; [2, 3, 5] -58.0481172276
INFO:main:; [2, 3, 6] -15.488636805
INFO:main:; [2, 4, 6] -15.064011714
INFO:main:; Max. number of attempts: 13
INFO:main:; Atom partitioning: {0: 0, 1: 0, 2: 0, 3: 0, 4: 1, 5: 1, 6: 1}
Aborted (core dumped)

When I use another smi("CC(=O)OC1=CC=CC=C1C(O)=O")
A new warning appeared before "Aborted (core dumped)" :
WARNING:main:Error with BeautifulSoup constructor
python: /usr/include/boost/thread/pthread/mutex.hpp:108: boost::mutex::~mutex(): Assertion `!posix::pthread_mutex_destroy(&m)' failed.

How can I get this work properly?

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8 years 5 days ago #5505 by peterkroon
Replied by peterkroon on topic auto-martini
Hi,

unfortunately the auto-martini is not from our group, so we are unable to help you with it.
IIRC it was made by Tristan Bereau, if I were you I would contact him directly.

Peter

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8 years 5 days ago #5506 by diaobk
Replied by diaobk on topic auto-martini
Thanks all the same.
I've already post this problem on github.

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