{"id":3402,"date":"2019-06-14T09:51:30","date_gmt":"2019-06-14T08:51:30","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/csf3\/?page_id=3402"},"modified":"2019-06-14T09:54:32","modified_gmt":"2019-06-14T08:54:32","slug":"pubchempy","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/software\/applications\/pubchempy\/","title":{"rendered":"PubChemPy"},"content":{"rendered":"<h2>Overview<\/h2>\n<p><a href=\"https:\/\/pubchempy.readthedocs.io\/en\/latest\/\">PubChemPy<\/a> provides a way to interact with PubChem in Python. It allows chemical searches by name, substructure and similarity, chemical standardization, conversion between chemical file formats, depiction and retrieval of chemical properties.<\/p>\n<h2>Restrictions on use<\/h2>\n<p>There are no restrictions on accessing the software on the CSF. It is released under the <a href=\"https:\/\/pubchempy.readthedocs.io\/en\/latest\/guide\/introduction.html#pubchempy-license\">MIT License<\/a> and all use must adhere to that license.<\/p>\n<h2>Set up procedure<\/h2>\n<p>We now recommend loading modulefiles within your jobscript so that you have a full record of how the job was run. See the example jobscript below for how to do this. Alternatively, you may load modulefiles on the login node and let the job <abbr title=\"add '#$ -V' to your jobscript\">inherit these settings<\/abbr>.<\/p>\n<p>Load one of the following modulefiles:<\/p>\n<pre>\r\nmodule load apps\/python\/pubchempy\/1.0.4        # Uses Anaconda python 5.2.0 (python 3.6)\r\n<\/pre>\n<p>The Anaconda Python modulefile will be loaded automatically.<\/p>\n<h2>Running the application<\/h2>\n<p>Please do not run PubChemPy on the login node. Jobs should be submitted to the compute nodes via batch.<\/p>\n<h3>Serial batch job submission<\/h3>\n<p>Create a batch submission script (which will load the modulefile in the jobscript), for example:<\/p>\n<pre>\r\n#!\/bin\/bash --login\r\n#$ -cwd             # Job will run from the current directory\r\n                    # NO -V line - we load modulefiles in the jobscript\r\n\r\n# We recommend loading modulefiles in jobscripts. Use your requried version.\r\nmodule load apps\/python\/pubchempy\/1.0.4\r\n\r\npython mypubchem.py\r\n<\/pre>\n<p>Submit the jobscript using: <\/p>\n<pre>qsub <em>scriptname<\/em><\/pre>\n<p>where <em>scriptname<\/em> is the name of your jobscript.<\/p>\n<h3>Parallel batch job submission<\/h3>\n<p>Given an example parallel jobscript, including suitable PE<\/p>\n<h2>Further info<\/h2>\n<ul>\n<li><a href=\"https:\/\/pubchempy.readthedocs.io\/en\/latest\/\">PubChemPy docs website<\/a><\/li>\n<\/ul>\n<h2>Updates<\/h2>\n<p>None.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Overview PubChemPy provides a way to interact with PubChem in Python. It allows chemical searches by name, substructure and similarity, chemical standardization, conversion between chemical file formats, depiction and retrieval of chemical properties. Restrictions on use There are no restrictions on accessing the software on the CSF. It is released under the MIT License and all use must adhere to that license. Set up procedure We now recommend loading modulefiles within your jobscript so that.. <a href=\"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/software\/applications\/pubchempy\/\">Read more &raquo;<\/a><\/p>\n","protected":false},"author":2,"featured_media":0,"parent":86,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-3402","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/3402","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/comments?post=3402"}],"version-history":[{"count":3,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/3402\/revisions"}],"predecessor-version":[{"id":3405,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/3402\/revisions\/3405"}],"up":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/86"}],"wp:attachment":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/media?parent=3402"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}