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task-file-io

Here are 47 public repositories matching this topic...

Scindices / haddocking--pdb-tools

A dependency-free cross-platform swiss army knife for PDB files.

status-active lang-python interface-cli domain-structural-biology task-file-io task-structure-analysis method-chemoinformatics entity-protein interface-api status-published status-packaged-pypi status-packaged-conda role-toolkit scope-swissknife entity-nucleic-acid task-structure-prep method-rule-based

Updated Jun 10, 2026
Python

Scindices / biopython--biopython

Official git repository for Biopython (originally converted from CVS)

status-active lang-python domain-bioinformatics task-file-io task-structure-analysis method-chemoinformatics entity-protein interface-api status-published status-packaged-pypi status-packaged-conda method-statistics role-toolkit scope-swissknife entity-nucleic-acid task-sequence-analysis entity-sequence ecosystem-biopython

Updated Jul 28, 2026
Python

Scindices / cdk--cdk

The Chemistry Development Kit

entity-graph status-active lang-java domain-cheminformatics task-file-io task-structure-analysis method-chemoinformatics entity-small-molecule interface-api status-published role-toolkit scope-swissknife task-featurization status-packaged-maven

Updated Jul 7, 2026
Java

Scindices / biotite-dev--biotite

A comprehensive library for computational molecular biology

status-active lang-python domain-bioinformatics domain-structural-biology task-file-io task-structure-analysis method-chemoinformatics entity-protein interface-api status-published status-packaged-pypi status-packaged-conda method-statistics role-toolkit scope-swissknife entity-nucleic-acid task-sequence-analysis entity-sequence

Updated Jul 21, 2026
Python

Scindices / PatWalters--useful_rdkit_utils

Some useful RDKit functions

status-active role-library lang-python domain-cheminformatics task-file-io method-chemoinformatics entity-small-molecule interface-api status-packaged-pypi scope-focused domain-drug-discovery task-featurization ecosystem-rdkit

Updated Jun 1, 2026
Jupyter Notebook

Scindices / volkamerlab--opencadd

A Python library for structural cheminformatics

status-active lang-python domain-structural-biology domain-cheminformatics task-file-io task-structure-analysis method-chemoinformatics entity-protein entity-small-molecule interface-api status-published status-packaged-conda domain-drug-discovery entity-complex role-toolkit scope-swissknife task-featurization

Updated Nov 18, 2025
Python

Scindices / openforcefield--openff-interchange

A project (and object) for storing, manipulating, and converting molecular mechanics data.

status-active role-library lang-python task-file-io entity-small-molecule interface-api status-published status-packaged-pypi status-packaged-conda method-physics domain-molecular-simulation scope-suite task-system-model task-forcefield ecosystem-openff ecosystem-openmm

Updated Jul 27, 2026
Python

Scindices / project-gemmi--gemmi

macromolecular crystallography library and utilities

status-active lang-python lang-cpp interface-cli domain-structural-biology task-file-io task-structure-analysis method-chemoinformatics entity-protein interface-api status-published status-packaged-pypi status-packaged-conda method-statistics role-toolkit scope-swissknife task-structure-prep entity-crystal domain-crystallography

Updated Jul 24, 2026
C++

Scindices / seqan--seqan3

The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.

status-active task-alignment lang-cpp domain-bioinformatics task-file-io interface-api status-published method-statistics role-toolkit scope-swissknife entity-nucleic-acid task-sequence-analysis entity-sequence domain-genomics

Updated Jul 20, 2026
C++

Scindices / datamol-io--datamol

Molecular Processing Made Easy.

entity-graph status-active role-library lang-python domain-cheminformatics task-file-io method-chemoinformatics entity-small-molecule interface-api status-published status-packaged-pypi status-packaged-conda scope-focused domain-drug-discovery task-featurization ecosystem-rdkit

Updated May 20, 2026
Python

Scindices / openmm--pdbfixer

PDBFixer fixes problems in PDB files

status-active role-library lang-python interface-cli domain-structural-biology task-file-io entity-protein interface-api status-published status-packaged-pypi status-packaged-conda scope-focused domain-molecular-simulation task-structure-prep method-rule-based interface-gui ecosystem-openmm

Updated Mar 10, 2026
Python

Scindices / MolSSI--QCElemental

Periodic table, physical constants, and molecule parsing for quantum chemistry.

status-active role-library lang-python task-file-io method-chemoinformatics entity-small-molecule interface-api status-published status-packaged-pypi status-packaged-conda scope-focused domain-computational-chemistry task-quantum-chemistry method-quantum

Updated Jul 28, 2026
Python

Scindices / RBVI--ChimeraX

Source code for molecular graphics program UCSF ChimeraX

status-active lang-python lang-cpp task-visualization interface-cli domain-structural-biology task-file-io task-structure-analysis method-chemoinformatics entity-protein entity-small-molecule interface-api status-published method-physics entity-complex scope-swissknife entity-nucleic-acid interface-gui role-viewer

Updated Jul 29, 2026
Python

Scindices / arq5x--bedtools2

bedtools - the swiss army knife for genome arithmetic

status-active lang-cpp lang-c domain-bioinformatics interface-cli role-application task-file-io status-published status-packaged-conda scope-focused method-statistics entity-nucleic-acid task-sequence-analysis entity-sequence domain-genomics

Updated Jun 10, 2026
C

Scindices / mcs07--MolVS

Molecule Validation and Standardization

role-library lang-python status-archived domain-cheminformatics task-file-io method-chemoinformatics entity-small-molecule interface-api status-published status-packaged-pypi status-packaged-conda scope-focused method-rule-based task-ligand-prep ecosystem-rdkit

Updated Apr 16, 2020
Python

Scindices / samtools--samtools

Tools (written in C using htslib) for manipulating next-generation sequencing data

status-active task-alignment lang-c domain-bioinformatics interface-cli role-application task-file-io method-chemoinformatics status-published status-packaged-conda scope-focused method-statistics entity-nucleic-acid entity-sequence domain-genomics

Updated Jul 28, 2026
C

Scindices / chembl--ChEMBL_Structure_Pipeline

ChEMBL database structure pipelines

status-active role-library lang-python domain-cheminformatics task-file-io method-chemoinformatics entity-small-molecule interface-api status-published status-packaged-pypi status-packaged-conda scope-focused domain-drug-discovery method-rule-based task-ligand-prep ecosystem-rdkit

Updated Nov 24, 2025
Python

Scindices / epam--ketcher

Web-based molecule sketcher

status-active lang-typescript lang-javascript interface-web task-visualization domain-cheminformatics task-file-io method-chemoinformatics entity-small-molecule status-published scope-focused role-viewer status-packaged-npm

Updated Jul 29, 2026
TypeScript

Scindices / Acellera--moleculekit

MoleculeKit: Your favorite molecule manipulation kit

status-active role-library lang-python domain-structural-biology task-file-io method-chemoinformatics entity-protein entity-small-molecule interface-api status-published status-packaged-pypi status-packaged-conda scope-focused domain-molecular-simulation task-system-model

Updated Jul 29, 2026
Python

Scindices / pysam-developers--pysam

Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtools, bcftools, and tabix.

status-active role-library lang-python lang-c domain-bioinformatics task-file-io method-chemoinformatics interface-api status-published status-packaged-pypi status-packaged-conda scope-focused entity-nucleic-acid entity-sequence domain-genomics

Updated Jul 19, 2026
Cython

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