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Transform Behaviors

The format_transform method (available on FileBatchModelDisk and individual file objects) allows converting between different chemical file formats.

Key Behaviors

  • Frame Selection: By default, only the last frame (frameID=-1) is transformed. You can specify frameID="all" to transform all frames in a file.
  • Embedding: If embed_in_one_file=True (default), multiple frames are combined into a single output file if the format supports it (e.g., SDF or multi-frame XYZ).
  • Structure Level:
  • COORDS (Coordinate Level): Formats like xyz, gjf, and orcainp primarily preserve atomic coordinates and elements.
  • GRAPH (Graph Level): Formats like sdf, smi, and cml preserve bonding information (molecular graph). If the source file only has coordinates (e.g., a .log file), MolOP will automatically attempt to reconstruct the molecular graph using its built-in algorithms.
  • Metadata Preservation:
  • QM input formats (gjf, orcainp) attempt to preserve raw directives and keywords.
  • Computational properties (energies, frequencies) are generally NOT preserved when transforming to simple coordinate formats like XYZ, although some formats like SDF can store them as properties.