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Move microservice WAMP test from MDStudio/tests to package
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Original file line number | Diff line number | Diff line change |
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@<TRIPOS>MOLECULE | ||
ligand | ||
21 21 0 0 0 | ||
SMALL | ||
GASTEIGER | ||
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@<TRIPOS>ATOM | ||
1 O -0.5471 -1.0180 0.3433 O.3 1 LIG11 -0.4613 | ||
2 C 0.8785 -1.0224 0.2270 C.3 1 LIG11 0.1036 | ||
3 H 1.2914 -1.5214 1.1112 H 1 LIG11 0.0734 | ||
4 C 1.2911 0.4358 0.2226 C.3 1 LIG11 -0.0056 | ||
5 C 0.0674 1.1651 -0.2725 C.3 1 LIG11 0.0483 | ||
6 C -1.0428 0.2213 0.0666 C.2 1 LIG11 0.3075 | ||
7 O -2.2294 0.5000 0.0615 O.2 1 LIG11 -0.2508 | ||
8 C 1.3167 -1.7790 -1.0313 C.3 1 LIG11 -0.0159 | ||
9 C 0.8755 -3.2458 -0.9950 C.3 1 LIG11 -0.0526 | ||
10 C 1.5208 -4.0539 -2.1102 C.3 1 LIG11 -0.0652 | ||
11 H 2.1837 0.6440 -0.3752 H 1 LIG11 0.0306 | ||
12 H 1.5085 0.7543 1.2497 H 1 LIG11 0.0306 | ||
13 H 0.0921 1.3157 -1.3549 H 1 LIG11 0.0379 | ||
14 H -0.0623 2.1187 0.2457 H 1 LIG11 0.0379 | ||
15 H 2.4088 -1.7257 -1.1182 H 1 LIG11 0.0301 | ||
16 H 0.8915 -1.3085 -1.9265 H 1 LIG11 0.0301 | ||
17 H -0.2148 -3.3087 -1.0892 H 1 LIG11 0.0264 | ||
18 H 1.1445 -3.6961 -0.0325 H 1 LIG11 0.0264 | ||
19 H 1.2769 -3.6384 -3.0927 H 1 LIG11 0.0230 | ||
20 H 1.1684 -5.0899 -2.0799 H 1 LIG11 0.0230 | ||
21 H 2.6104 -4.0662 -2.0021 H 1 LIG11 0.0230 | ||
@<TRIPOS>BOND | ||
1 1 2 1 | ||
2 2 3 1 | ||
3 2 4 1 | ||
4 4 5 1 | ||
5 5 6 1 | ||
6 1 6 1 | ||
7 6 7 2 | ||
8 2 8 1 | ||
9 8 9 1 | ||
10 9 10 1 | ||
11 4 11 1 | ||
12 4 12 1 | ||
13 5 13 1 | ||
14 5 14 1 | ||
15 8 15 1 | ||
16 8 16 1 | ||
17 9 17 1 | ||
18 9 18 1 | ||
19 10 19 1 | ||
20 10 20 1 | ||
21 10 21 1 |
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session: | ||
username: mdadmin | ||
password: this_should_be_replaced_for_production!@#$%^&*()_+1234567890-= | ||
settings: | ||
printInEndpoint: false |
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from mdstudio.deferred.chainable import chainable | ||
from mdstudio.component.session import ComponentSession | ||
from mdstudio.runner import main | ||
from os.path import join | ||
import os | ||
import shutil | ||
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file_path = os.path.realpath(__file__) | ||
root = os.path.split(file_path)[0] | ||
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def create_workdir(name, path="/tmp/mdstudio/lie_atb"): | ||
"""Create temporal workdir dir""" | ||
workdir = join(path, name) | ||
if not os.path.isdir(workdir): | ||
os.makedirs(workdir) | ||
return workdir | ||
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def copy_to_workdir(file_path, workdir): | ||
shutil.copy(file_path, workdir) | ||
base = os.path.basename(file_path) | ||
return join(workdir, base) | ||
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workdir = create_workdir("lie_atb") | ||
path_mol = copy_to_workdir( | ||
join(root, "files/structure.mol2"), workdir) | ||
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dict_query = { | ||
"netcharge": 0, | ||
"dim": 3, | ||
"exactmass": 128.083729624, | ||
"title": "ligand", | ||
"PartialCharges": "GASTEIGER", | ||
"energy": 0.0, | ||
"molwt": 128.16898000000003, | ||
"structure_format": "mol2", | ||
"mol": path_mol, | ||
"formula": "C7H12O2", | ||
"isfile": True, | ||
"workdir": workdir | ||
} | ||
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class Run_atb(ComponentSession): | ||
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def authorize_request(self, uri, claims): | ||
return True | ||
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@chainable | ||
def on_run(self): | ||
with self.group_context('mdgroup'): | ||
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result_collect = yield self.call( | ||
"mdgroup.lie_atb.endpoint.structure_query", | ||
dict_query) | ||
print(result_collect) | ||
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if __name__ == "__main__": | ||
main(Run_atb) |