# Copyright 2016 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
import moldesign as mdt
from moldesign import utils
[docs]def name_to_smiles(name,
image='opsin',
engine=None):
command = 'opsin -osmi input.txt output.txt'
# TODO: this boilerplate has to go
engine = utils.if_not_none(engine, mdt.compute.get_engine())
imagename = mdt.compute.get_image_path(image)
job = engine.launch(imagename,
command,
inputs={'input.txt': name + '\n'},
name="opsin, %s" % name)
mdt.uibase.display_log(job.get_display_object(), "opsin, %s"%name)
job.wait()
smistring = job.get_output('output.txt').read().strip()
if not smistring:
raise ValueError('Could not parse chemical name "%s"' % name)
else:
return smistring