chemlab.io

This package contains utilities to read, write a variety of chemical file formats.

chemlab.io.datafile(filename, mode='rb', format=None)

Initialize the appropriate IOHandler for a given file extension or file format.

The datafile function can be conveniently used to quickly read or write data in a certain format:

>>> handler = datafile("molecule.pdb")
>>> mol = handler.read("molecule")
# You can also use this shortcut
>>> mol = datafile("molecule.pdb").read("molecule")

Parameters

filename: str

Path of the file to open.

format: str or None

When different from None, can be used to specify a format identifier for that file. It should be used when the extension is ambiguous or when there isn’t a specified filename. See below for a list of the formats supported by chemlab.

chemlab.io.remotefile(url, format=None)

The usage of remotefile is equivalent to chemlab.io.datafile() except you can download a file from a remote url.

Example

mol = remotefile(“https://github.com/chemlab/chemlab-testdata/blob/master/3ZJE.pdb”).read(“molecule”)

• Supported File Formats
  • cml: Chemical Markup Language
  • edr: GROMACS energy file
  • gro: GROMACS coordinate files
  • mol: MDL Coordinate files
  • pdb: Protein Data Bank format
  • xtc: GROMACS compressed trajectory file
  • xyz: XYZ coordinate format
• cclib integration

The class IOHandler

class chemlab.io.handlers.IOHandler(fd)

Generic base class for file readers and writers.

The initialization function takes a file-like object fd, as an argument.

Subclasses can extend the methods __init__, read and write to implement their reading and writing routines.

Attributes

fd

can_read

Type:list of str

A list of features that the handler can read.

can_write

Type:list of str

A list of features that IOHandler can write.

check_feature(feature, readwrite)

Check if the feature is supported in the handler and raise an exception otherwise.

Parameters

feature: str

Identifier for a certain feature.

readwrite: “read” or “write”

Check if the feature is available for reading or writing.

read(feature, *args, **kwargs)

Read and return the feature feature. It should raise an ValueError if the feature is not present in the handler can_read attribute, use the method IOHandler.check_feature() to provide this behaviour.

Certain features may require additional arguments, and it is possible to pass those as well.

Example

Subclasses can reimplement this method to add functionality:

class XyzIO(IOHandler):
    can_read = ['molecule']

    def read(self, feature, *args, **kwargs):
        self.check_feature(feature, "read")
        if feature == 'molecule':
           # Do stuff
           return geom

write(feature, value, *args, **kwargs)

Same as read(). You have to pass also a value to write and you may pass any additional arguments.

Example

class XyzIO(IOHandler):
    can_write = ['molecule']

    def write(self, feature, value, *args, **kwargs):
        self.check_feature(feature, "write")
        if feature == 'molecule':
           # Do stuff
           return geom