Diagram API¶
Introduction¶
The ccdc.diagram
module has functionality for generating 2D diagrams.
The main class of the ccdc.diagram
module is
ccdc.diagram.DiagramGenerator
.
>>> from ccdc.io import EntryReader
>>> from ccdc.diagram import DiagramGenerator
>>> entry_reader = EntryReader('CSD')
>>> mol = entry_reader.molecule('ABEBUF')
>>> diagram_generator = DiagramGenerator()
>>> img = diagram_generator.image(mol) # img is a PIL image
See also
API¶
- class ccdc.diagram.DiagramGenerator(settings=None)[source]¶
Diagram generator.
- class Settings(_settings=None)[source]¶
Settings base class for diagram generation.
- property background_color¶
The foreground color.
- detect_intra_hbonds = False¶
Whether to detect intra-molecular hbonds.
- property element_coloring¶
Color atomic labels.
- explicit_polar_hydrogens = False¶
Whether to use explicit polar hydrogens.
- property font_family¶
The name of the font family.
- property font_italic¶
Whether the font is italic or not.
- property font_size¶
The image font size.
- property font_weight¶
The weight of the font.
- property foreground_color¶
The foreground color.
- property highlight_color¶
Color used for highlighting atoms and bonds.
- property image_height¶
The image height.
- property image_width¶
The image width.
- property line_width¶
The image line width.
- overwrite_existing_image = False¶
Whether to override the existing image of an entry.
- property return_type¶
The image method return type.
- shrink_symbols = True¶
Whether to replace particular substructures with functional group labels.
- chemdraw_xml(molecule, file_name)[source]¶
Write a chemdraw XML file containing the 2D diagram of the molecule passed in.
- Parameters:
molecule – a
ccdc.molecule.Molecule
or accdc.entry.Entry
file_name – a file name to write
- Returns:
the text written to the file, or None
- image(argument, highlight_atoms=None, label_atoms=None)[source]¶
Return an image or list of images according to arguments.
- Parameters:
argument – a
ccdc.crystal.Crystal
, accdc.molecule.Molecule
, accdc.entry.Entry
, or a list of them.highlight_atoms – list of
ccdc.molecule.Atom
, or a list of atom lists
- Returns:
a PIL image, or a list of PIL images. It may return
None
if the diagram generation failed.