molharbor 0.1.0

unofficial python wrapper for MolPort API

MolHarbour

MolHarbour is a unofficial Python wrapper for the Molport REST API. It allows you to search for chemical compounds and retrieve information about them. Additionally, MolHarbour unifies the Molport API variables names and verifies the response data using wonderful Pydantic models.

This library is not affiliated with Molport in any way. Molport is a registered trademark of Molport SIA.

The project was initiated as a part of my master's thesis and and is based on refactored scripts which I wrote to retrive commercial availablity of compounds in chembl database.

Installation

From PyPI

pip install molharbor

From source

pip install git+https://github.com/asiomchen/molharbor

Quickstart

Authentication

To start using MolHarbour, you need to create an instance of the Molport class and log in to the Molport API using your username and password or API key.

from molharbor import Molport
molport = Molport()
molport.login(username="john.spade", password="fasdga34a3")

or API key

molport.login(api_key="16072de6-d318-4324-a82c-08c7dfe64d5d")

Compound search

You can search for compounds using the search method. All the search types are supported( via SearchType enum). Additionally, you can specify the maximum number of results to return using the max_results parameter, and the minimum similarity threshold using the similarity parameter (it is used only for similarity search).

Exact search

from molharbor import SearchType
molport.find("O=C(O)c1ccccc1", search_type=SearchType.EXACT)

[[MolportCompound(smiles='OC(=O)c1ccccc1', molport_id='Molport-000-871-563', link='https://www.molport.com/shop/compound/Molport-000-871-563'),
  MolportCompound(smiles='[2H]c1c([2H])c([2H])c(c([2H])c1[2H])C(O)=O', molport_id='Molport-003-927-939', link='https://www.molport.com/shop/compound/Molport-003-927-939'),
  MolportCompound(smiles='O[13C](=O)c1ccccc1', molport_id='Molport-003-929-055', link='https://www.molport.com/shop/compound/Molport-003-929-055'),
  MolportCompound(smiles='OC(=O)[13c]1[13cH][13cH][13cH][13cH][13cH]1', molport_id='Molport-046-688-787', link='https://www.molport.com/shop/compound/Molport-046-688-787')]]

Similarity search

molport.find("O=C(O)c1ccccc1", search_type=SearchType.SIMILARITY, max_results=5)

[[MolportCompound(smiles='OC(=O)c1ccccc1', molport_id='Molport-000-871-563', link='https://www.molport.com/shop/compound/Molport-000-871-563'),
  MolportCompound(smiles='[2H]c1c([2H])c([2H])c(c([2H])c1[2H])C(O)=O', molport_id='Molport-003-927-939', link='https://www.molport.com/shop/compound/Molport-003-927-939'),
  MolportCompound(smiles='O[13C](=O)c1ccccc1', molport_id='Molport-003-929-055', link='https://www.molport.com/shop/compound/Molport-003-929-055'),
  MolportCompound(smiles='[Zn++].[O-]C(=O)c1ccccc1.[O-]C(=O)c1ccccc1', molport_id='Molport-003-986-949', link='https://www.molport.com/shop/compound/Molport-003-986-949'),
  MolportCompound(smiles='OC(=O)[13c]1[13cH][13cH][13cH][13cH][13cH]1', molport_id='Molport-046-688-787', link='https://www.molport.com/shop/compound/Molport-046-688-787')]]

Superstructure search

molport.find("O=C(O)c1ccccc1", search_type=SearchType.SUPERSTRUCTURE, max_results=5)

[[MolportCompound(smiles='CC=O', molport_id='Molport-001-783-184', link='https://www.molport.com/shop/compound/Molport-001-783-184'),
  MolportCompound(smiles='OCc1ccccc1', molport_id='Molport-001-783-216', link='https://www.molport.com/shop/compound/Molport-001-783-216'),
  MolportCompound(smiles='C=O', molport_id='Molport-001-785-627', link='https://www.molport.com/shop/compound/Molport-001-785-627'),
  MolportCompound(smiles='CCO', molport_id='Molport-001-785-844', link='https://www.molport.com/shop/compound/Molport-001-785-844'),
  MolportCompound(smiles='O', molport_id='Molport-003-926-090', link='https://www.molport.com/shop/compound/Molport-003-926-090')]]

Substructure search

molport.find("O=C(O)c1ccccc1", search_type=SearchType.SUBSTRUCTURE, max_results=5)

[[MolportCompound(smiles='OC(=O)c1ccc2[nH]c(S)nc2c1', molport_id='Molport-000-004-519', link='https://www.molport.com/shop/compound/Molport-000-004-519'),
  MolportCompound(smiles='OC(=O)c1cc(C#N)c(Cl)cc1Cl', molport_id='Molport-051-434-827', link='https://www.molport.com/shop/compound/Molport-051-434-827'),
  MolportCompound(smiles='OC(=O)c1ccc(cc1)-c1ccc(cc1)-c1ccc(cc1)N(c1ccc(cc1)-c1ccc(cc1)-c1ccc(cc1)C(O)=O)c1ccc(cc1)-c1ccc(cc1)-c1ccc(cc1)C(O)=O', molport_id='Molport-051-434-831', link='https://www.molport.com/shop/compound/Molport-051-434-831'),
  MolportCompound(smiles='COC(=O)[C@]1(C[C@H](OC(C)=O)[C@@H](NC(C)=O)[C@@H](O1)[C@H](OC(C)=O)[C@@H](COC(C)=O)OC(C)=O)O[C@H]1[C@@H](OC(=O)c2ccccc2)[C@@H](COC(=O)c2ccccc2)O[C@@H](Oc2ccc(OC)cc2)[C@@H]1OC(=O)c1ccccc1', molport_id='Molport-051-434-926', link='https://www.molport.com/shop/compound/Molport-051-434-926'),
  MolportCompound(smiles='[Na+].[Na+].OC(=O)CN(CC([O-])=O)Cc1cc2c(Oc3cc(O)c(CN(CC(O)=O)CC([O-])=O)cc3C22OC(=O)c3ccccc23)cc1O', molport_id='Molport-051-435-130', link='https://www.molport.com/shop/compound/Molport-051-435-130')]]

Raw response manipulation

MolHarbour design to simplify commonn tasks so .find() method returns a list of MolportCompound objects (which itself is a dataclass object with smiles, molport_id and link field).

However, you can access the raw response using the return_response parameter. Returned Response object inherits from Pydantic BaseModel and contains all the fields from the Molport API response with type validation provided by Pydantic. All the fields have the same name as in Molport API docs, only lowercase and the spaces are replaced with underscores( e.g. Shipment Type -> shipment_type)

from molharbor import SearchType
molport.find("O=C(O)c1ccccc1", search_type=SearchType.SUBSTRUCTURE, max_results=1, return_response=False)

[[MolportCompound(smiles='OC(=O)c1cc(C#N)c(Cl)cc1Cl', molport_id='Molport-051-434-827', link='https://www.molport.com/shop/compound/Molport-051-434-827')]]

vs

molport.find("O=C(O)c1ccccc1", search_type=SearchType.SUBSTRUCTURE, max_results=1, return_response=True)

[Response(result=Result(status=1, message='Substructure search completed!'), data=Data(molecules=[Molecule(id=45........

Suppliers search

Having a Molport ID, you can search for suppliers using the get_suppliers method. Similar too find() method, you could either recieve a raw pydantic response with all the fields having the same name as in Molport API docs, only lowercase and the spaces are replaced with underscores( e.g. Shipment Type -> shipment_type) or processed dataframe with most important fields

df = molport.get_suppliers("Molport-001-794-639")

Or you could use id values of MolportCompound objects returned by find() method

result = molport.find("C[C@H](CS)C(=O)N1CCC[C@H]1C(O)=O", search_type=SearchType.EXACT, max_results=1)[0]
result

MolportCompound(smiles='C[C@H](CS)C(=O)N1CCC[C@H]1C(O)=O', molport_id='Molport-001-794-639', link=...

df = molport.get_suppliers(result.molport_id)

Processed dataframe

Returned dataframe contains all the fields from the Molport API response with type validation provided by Pydantic. The fields are renamed to be more human-readable and to be consistent with the Molport API docs. Below is an example of the most important fields.

df[["supplier_name", "supplier_type", "amount", "measure", 
"price", "currency", "delivery_days", 
"stock", "stock_measure", "last_update_date_exact"]].head()

	supplier_name	supplier_type	amount	measure	price	currency	delivery_days	stock	stock_measure	last_update_date_exact
0	BIONET - Key Organics Ltd.	screening_block_suppliers	1.0	mg	45.0	USD	4	1187.6	mg	May 17, 2024
1	BIONET - Key Organics Ltd.	screening_block_suppliers	5.0	mg	53.0	USD	4	1187.6	mg	May 17, 2024
2	BIONET - Key Organics Ltd.	screening_block_suppliers	10.0	mg	64.0	USD	4	1187.6	mg	May 17, 2024
3	BIONET - Key Organics Ltd.	screening_block_suppliers	1.0	mg	45.0	USD	4	1187.6	mg	May 17, 2024
4	BIONET - Key Organics Ltd.	screening_block_suppliers	2.0	mg	47.0	USD	4	1187.6	mg	May 17, 2024

Raw response

molport.get_suppliers("Molport-000-871-563", return_response=True)

ResponseSupplier(result=Result(status=1, message='Molecule found!'), data=DataSupplier(molecule=Molecule2(id=871563, molport_id='Molport-000-871-563', smiles='OC(=O)c1ccccc1', .....