Pubsam: Simplifying PubChem Database Interaction for Molecular Analysis

Streamline Interaction with PubChem

Retrieve and analyze chemical data effortlessly with Pubsam, streamlining interaction with the PubChem database. Explore compounds, substances, assays, proteins, genes, and more with ease. Designed for researchers, scientists, and developers, Pubsam provides a user-friendly interface to access and leverage PubChem�s wealth of information.

Key Features

• Dive into molecular analysis with QSPR (Quantitative Structure-Property Relationship) tools.
• Conduct virtual screenings for compound discovery.
• Unravel chemical features through functions such as displaying maximum common substructures, Gasteiger charges, chirality, and more.

Getting Started

pip install pubsam

Example Usage


markdown
Copy code
# Example: QSPR Analysis
from Pubsam import qspr_analysis
qspr_analysis("path/to/your/csv_file.csv", "dependent_variable_column")

# Example: Display Active Chemicals by Assay Aid
from Pubsam import display_active_chemicals_by_assay_aid
display_active_chemicals_by_assay_aid("1000")

# Example: Display Inactive Chemicals by Assay Aid
from Pubsam import display_inactive_chemicals_by_assay_aid
display_inactive_chemicals_by_assay_aid("1000")

# Example: Retrieve Active CIDs by Assay Aid
from Pubsam import retrieve_active_cids_by_assay_aid
retrieve_active_cids_by_assay_aid("1000")

# Example: Retrieve Inactive CIDs by Assay Aid
from Pubsam import retrieve_inactive_cids_by_assay_aid
retrieve_inactive_cids_by_assay_aid("1000")

# Example: Retrieve Active SIDs by Assay Aid
from Pubsam import retrieve_active_sids_by_assay_aid
retrieve_active_sids_by_assay_aid("1000")

# Example: Retrieve Inactive SIDs by Assay Aid
from Pubsam import retrieve_inactive_sids_by_assay_aid
retrieve_inactive_sids_by_assay_aid("1000")

# Example: Virtual Screening
from Pubsam import virtual_screening
virtual_screening("path/to/your/file.txt", "SMILES1", "SMILES2", "SMILES3")

# Example: Display Maximum Common Substructure
from Pubsam import display_maximum_common_substructure
display_maximum_common_substructure('CC=O', 'CCCCC', 'CCCCCC=O')

# Example: Display Chirality
from Pubsam import display_chirality
display_chirality('C[C@H]1CCC[C@@H](C)[C@@H]1Cl')

# Example: Display Double Bond Stereochemistry
from Pubsam import display_double_bond_stereochemistry
display_double_bond_stereochemistry('CC=C', 'CC=C(C)C', 'CC(=O)C=C')

# Example: Highlight Difference
from Pubsam import highlight_difference
highlight_difference('CC=O', 'CCCCC=O')

# Example: Draw List of SMILES
from Pubsam import draw_list_of_smiles
draw_list_of_smiles(['CC=O', 'CCCCC=O', 'CC(C)(C)C'])

# Example: Display Gasteiger Charges
from Pubsam import display_gasteiger_charges
display_gasteiger_charges('CC(=O)O', ['CC(=O)O', 'CCCC(=O)O', 'CCCCCCCCCCCCCCCCCCC(=O)O'])

# Example: Display Bond Type and Stereochemistry
from Pubsam import display_bond_type_and_stereochemistry
display_bond_type_and_stereochemistry('CC=O', 'CCC=O', 'CC(C)(C)C')

# Example: Mark Substructure
from Pubsam import mark_substructure
mark_substructure('CC', 'CC=O', 'CCC=O', 'CC(C)(C)C')

# Example: Check for Substructure
from Pubsam import check_for_substructure
check_for_substructure('CC', 'CC=O', 'CCC=O', 'CC(C)(C)C')

# Example: Display Morgan Score Topological
from Pubsam import display_morgan_score_topological
display_morgan_score_topological("CCO", "CNCN")

# Example: Delete Substructure
from Pubsam import delete_substructure
delete_substructure('CC', 'CC=O', 'CCC=O', 'CC(C)(C)C')

# Example: Intro
from Pubsam import Intro
Intro()

Ahmed Alhilal
=============

0.0.1 (22/12/2023)
-------------------
- First Release