Write a Python script that will parse PubChem to download all chemicals with given properties and run this script

There is a public website with all chemical compunds call PubChem:

[login to view URL]

We need to download information about all molecules with less than 11 atom.

It can be done in the following way:

1. Use advanced search available on the website:

[login to view URL]

and search for the following string:

((0:10[HeavyAtomCount]) AND 0:0[TotalFormalCharge]) AND 0:0[IsotopeAtomCount]

It will return the list of all compunds with less than 10 heavy atoms, but some of them are ionic compunds not molecules and some contain more than 10 atoms.

2. We need to sort the results by complexity

3. Then we need to check all the results and use two filters:

Filter A: remove compounds with more than 10 atoms in Molecular Formula

Filter B: remove compunds that contain a dot sign (".") in Canonical SMILES

4. All the components that are not removed by those filters should be collected in CSV text file that contains the following columns:

* PubChem CID

* Molecular Formula

* Canonical SMILES

* Molecular Weight

* Chemical Names

* IUPAC Name

* If 2D structure XML file is presented (yes/no)

* If 3D structure XML file is presented (yes/no)

5. For each compound that match our filters we should also download it 2D and 3D structures as XML files and place them in two folders. File names should be like "[login to view URL]" and "[login to view URL]" where 101826982 is PubChem CID of this compound

The results:

The results of this project should be

A. A ZIP archive with many xml files with 2D and 3D structures of the and one [login to view URL] file.

B. Python script(s) that generates this CSV file and download XML files

Deadline for this project: August 24th, 2017, 13:00 London time


For your information: PubChem supports API that makes this project much easier:

REST Tutorial:

[login to view URL]

REST Documentation:

[login to view URL]

Other API documentation:

[login to view URL]

List of properties:

[login to view URL]

Example how to download needed properties of several substances:

[login to view URL],129251212,5460638,5460696/property/MolecularFormula,MolecularWeight,CanonicalSMILES,Complexity,Charge,HeavyAtomCount,IsotopeAtomCount/XML

Python wrapper for PubChem:

[login to view URL]

Beceriler: Python

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İşveren Hakkında:
( 59 değerlendirme ) Amersham, United Kingdom

Proje NO: #14952675

Bu iş için 23 freelancer ortalamada $194 teklif veriyor


First of all thank you for excellent description! I can create Python scraper and collect all data you want (including 2D and 3D files) in less than 3 days. Thanks. Roman Relevant Skills and Experience I Python deve Daha Fazla

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I read your project brief. I can do your project by using PubChemPy wrapper of Python to search for chemicals on PubChem according to the criteria you specified and deliver a CSV file with molecular data. Relevant S Daha Fazla

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Search Pub chem for 10 atom compounds. Filter down the results based on the specified criteria. convert to csv. Relevant Skills and Experience Python Web Automation Web Services Chemistry Software Architecture Daha Fazla

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A proposal has not yet been provided

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Hi, I can extract and parse all the data you need about the chemical compounds with the specified properties, and generate the CSV and XML files. Deliver them in a ZIP, and the Python script. Relevant Skills and Expe Daha Fazla

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Parse compounds from PubChem website, filter and scrape the results to extract desired information, to be delivered in .zip and .csv files, with specific naming scheme. PubChem's APIs are available. Relevant Skills an Daha Fazla

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