Documentation/Nodes/File I/O

File I/O Operations

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

Core I/O Nodes

Essential 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

Save DataFrame

Save DataFrames to various file formats

Type: save_dataframeCategory: Data Savers

Key Features

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

Input Ports

dataframedata

DataFrame to save

file_pathstring

Output file path

Output Ports

saved_pathstring

Saved file path

row_countnumber

Number of rows saved

Save Molecules

Save molecular structures to various chemical formats

Type: save_moleculeCategory: Data Savers

Key Features

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

Input Ports

moleculesmolecules

Molecules to save

file_pathstring

Output file path

Output Ports

saved_pathstring

Saved file path

molecule_countnumber

Number of molecules saved

File Readers

Specialized readers for different file formats commonly used in scientific workflows.

SDF Reader

Read SDF molecular structure files

sdf_reader
Supported Formats:
SDFMOL
Common Use:

Small molecule databases, compound libraries

PDB Reader

Read PDB protein structure files

pdb_reader
Supported Formats:
PDBPDBQT
Common Use:

Protein structures, crystal structures

CSV Reader

Read CSV and delimited text files

csv_reader
Supported Formats:
CSVTSVTXT
Common Use:

Experimental data, compound lists

Excel Reader

Read Excel files with multiple sheet support

excel_reader
Supported Formats:
XLSXXLS
Common Use:

Structured datasets, experimental results

Data Viewers

Interactive viewers for exploring and validating data during workflow development.

Table View

Interactive table viewer for DataFrames

table_view

Data exploration and validation

Text View

Text editor and viewer with syntax highlighting

text_view

Log files, configuration files

Image View

Image viewer with zoom and annotation tools

image_view

Plots, molecular diagrams

Supported File Formats

Bioshift supports 15+ molecular and data file formats commonly used in scientific research.

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