Documentation/Data/Files

File I/O Operations

Comprehensive file input/output capabilities supporting 15+ molecular and data formats with robust error handling and batch processing features.

File I/O Nodes

Core nodes for loading and saving files with advanced file management features.

File Input

Load files from disk with path selection dialog

Type: file_inputCategory: Input/Output

Key Features

  • •File browser dialog
  • •Multiple file selection
  • •File type filtering
  • •Drag and drop support
  • •Recent files list

Input Ports

file_pathstring

File path (optional - shows dialog if empty)

Output Ports

file_contentbytes

Raw file content

file_pathstring

Selected file path

file_infodata

File metadata (size, date, etc.)

File Output

Save data to files on disk

Type: file_outputCategory: Input/Output

Key Features

  • •Automatic file extension detection
  • •Overwrite confirmation
  • •Directory creation
  • •Backup creation
  • •Progress reporting

Input Ports

dataany

Data to save

file_pathstring

Output file path

Output Ports

saved_pathstring

Actual saved file path

successboolean

Save operation success status

Folder Input

Load entire folders and process all files within

Type: folder_inputCategory: Input/Output

Key Features

  • •Recursive folder scanning
  • •File type filtering
  • •Pattern matching
  • •Batch processing
  • •Progress tracking

Input Ports

folder_pathstring

Folder path

Output Ports

filesfile

List of file paths

file_contentsbytes

List of file contents

folder_infodata

Folder statistics and metadata

Data Readers

Specialized nodes for reading structured data files and converting them to DataFrames.

CSV Reader

Read CSV and delimited text files into DataFrames

Data Readers
Features:
  • Automatic delimiter detection
  • Header row detection
  • Data type inference
  • Encoding detection
  • Error handling

Excel Reader

Read Excel files (.xlsx, .xls) with multiple sheet support

Data Readers
Features:
  • Multiple sheet support
  • Range selection
  • Header customization
  • Formula evaluation
  • Date format handling

Data Savers

Nodes for saving processed data in various formats with advanced formatting options.

Save DataFrame

Save DataFrames to various file formats

Data Savers
Features:
  • Multiple format support (CSV, Excel, JSON, Parquet)
  • Custom formatting options
  • Index handling
  • Compression support
  • Progress reporting

Save Molecules

Save molecular structures to various chemical formats

Data Savers
Features:
  • Multiple format support (SDF, MOL, PDB, etc.)
  • Batch processing
  • Structure validation
  • 3D coordinate handling
  • Property preservation

Supported File Formats

Bioshift supports 15+ molecular and data file formats:

SDF
MOL
MOL2
PDB
PDBQT
XYZ
CSV
Excel
JSON
TXT
Parquet
HDF5
Pickle
FASTA
CIF