schrodinger.structure.StructureWriter

Class StructureWriter

A class for efficient writing of multiple structures to a single structure file. If you are writing a single structure, you can more easily use the Structure.write method.

Options that are not supported for all formats can be set with the setOption method, for example:

writer = StructureWriter(filename) try: writer.setOption(stereo=STEREO_FROM_ANNOTATION) except OptionError: # take action based on unsupported option/value here

Currently, the following options are available:

stereo

This option controls how stereochemical properties are written. It does not affect the output geometry.
This option is supported for SD, SMILES, and SMILESCSV, although not all options are supported for SD.
Option values are NO_STEREO, STEREO_FROM_ANNOTATION_AND_GEOM, STEREO_FROM_ANNOTATION, and STEREO_FROM_GEOMETRY.
The default value is STEREO_FROM_ANNOTATION_AND_GEOM.
With STEREO_FROM_ANNOTATION_AND_GEOM, current annotation properties of the Structure are used when present. Chiral atoms without annotation properties will have their stereochemistry determined from geometry (if possible) and will be written with definite stereochemical configuration.
With NO_STEREO, no stereochemical information will be written.
With STEREO_FROM_ANNOTATION, stereochemical information will be written based only on the current annotations. Use this option to allow for specification of stereochemistry on some centers while leaving others undefined. This should be faster than identifying stereochemistry from the 3D geometry.
With STEREO_FROM_GEOMETRY, stereochemistry will be written for all chiral atoms based on the 3D geometry. This option is not supported for SD format.

Instance Methods

[hide private]

__init__(self, filename, overwrite=True, format=None, stereo=None)
Create a structure writer class based on the format.

append(self, ct)
Append the provided structure to the open file.

extend(self, cts)
Append all provided structures to the open file.

close(self)
Close the file.

setOption(self, option, value)
Set a single option for this writer.

Inherited from _ReaderWriterContextManager: __enter__, __exit__

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

init(self, filename, overwrite=True, format=None, stereo=None)
(Constructor)

Create a structure writer class based on the format.

Parameters:

filename (str) - The filename to write to.
overwrite (bool) - If False, append to an existing file instead of overwriting it.
format (str) - The format of the file. Values should be specified by one of the module-level constants MAESTRO, MOL2, SD, SMILES, or SMILESCSV. If the format is not explicitly specified it will be determined from the suffix of the filename. Multi-structure PDB files are not supported.
stereo (enum) - Use of the stereo option in the constructor is pending deprecation. Please use the setOption method instead.
See the class docstring for documentation on the stereo options.

Overrides: object.__init__

setOption(self, option, value)

Set a single option for this writer. This method is meant for options that may not be supported for all writer formats. See the StructureWriter class documentation for details on the available options.

Raises an OptionError subclass (either UnsupportedOption or UnsupportedOptionValue) if unsuccessful.

Parameters:

option (str) - The name of the option to set.
value - The value for the option. The data type of this parameter depends on the option being set.

Class StructureWriter

__init__(self, filename, overwrite=True, format=None, stereo=None) (Constructor)

setOption(self, option, value)

init(self, filename, overwrite=True, format=None, stereo=None)
(Constructor)