Kapalı

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:

[url removed, login to view]

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:

[url removed, login to view]

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 "[url removed, login to view]" and "[url removed, login to view]" 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 [url removed, login to view] 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:

[url removed, login to view]

REST Documentation:

[url removed, login to view]

Other API documentation:

[url removed, login to view]

List of properties:

[url removed, login to view]

Example how to download needed properties of several substances:

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

Python wrapper for PubChem:

[url removed, login to view]

Beceriler: Python

Daha fazlasını gör: pubchempy python, chemspider free download, chemspider api, pugrest pubchem, chemspider python, ncbi pug rest, pubchem python, pubchempy get_compounds, need write python script telit gc864quad module, write python web bot, python parse google, need help write python script operate telit module, python parse google result, python mail attachment download, write code parse web page

İşveren Hakkında:
( 13 değerlendirme ) Amersham, United Kingdom

Proje NO: #14952675

Bu iş için 24 freelancer ortalamada $196 teklif veriyor

hunmin888

Hi, sir! I have a good skill in python programming. If you award this project to me, I'll complete it in time. Thank you in advance. Stay tuned, I'm still working on this proposal.

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(27 Değerlendirme)
6.1
gangabass

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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(121 Değerlendirme)
6.3
IMdaystar

Dear Sir ,I am interested in your job and I wish to work with you. I think you can check my profile and reviews and check me :) I have rich experience in these fields :Python, Software Architecture My account is ne Daha Fazla

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(5 Değerlendirme)
4.8
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(6 Değerlendirme)
4.4
shadabkhan92

We are experts in software development, worked in companies like Adobe, Dell etc. Java, PHP, Python, HTML, CSS, Javascript, Selenium with Python and Java, Web Development and Web Design, Web Scraping Relevant Skills a Daha Fazla

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4.2
ramani86

please let me know if you want to get started. Relevant Skills and Experience python Proposed Milestones $250 USD - code

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3.2
rhythmist

Hi, I'm a professional software engineer with 4 years of experience in Python, Java, Scala. I can help you with the download of molecular data.

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(5 Değerlendirme)
2.7
origami07

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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3.1
kanwalrafique

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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3.1
MetaoriginLab

Yes, I am new here, but we have been working on Python,Django,Web Crawling/Data Scraping for last 7 years. Relevant Skills and Experience We have used Flask and iFrame to achieve the desired results on Python 2 & 3. Daha Fazla

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2.3
JASHWANTH1602

A proposal has not yet been provided

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1.4
charlysalmu

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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1.0
Ajcm623

Hi, I have a web scraping history with python. I fully undestood your userstories and I also had a look API for it. I can provide you that you want.

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1.0
gchlebus

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prashushinde9

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0.0
meessras2

Hi, I hope you have not granted this project to someone else :) I have a script ready that does the followings: 1. get list of cids that match your search criteria 2. pull the required properties for all cids 3. store Daha Fazla

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DariaPlotnikova

I have been working with third party APIs to access needed information, such as Yahoo Financial API, Yandex maps API etc. Guess I will be able to perform your job good. If you are interested, I would like to connect an Daha Fazla

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caioelias

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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csinfotechorg

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