Public Member Functions
	__init__ (self, directory=None, file_pattern='%(id) s.pdb', transform=str)

	FilenameForModel (self, pdb_id, chain)

	Load (self, pdb_id, chains='', calpha_only=False, fault_tolerant=False)

	LoadMulti (self, pdb_id, chains="")

Data Fields
	directory_

	file_pattern_

	transform_

Detailed Description

Model repository. A model repository abstracts the way that PDB files are 
loaded. Instead of explicitly specifying the PDB filename, only the PDB 
id (and optionally a chain) needs to be specified. The actual files are then 
resolved by the repository.

Usage
-----
The usage pattern of the model repository is simple. After construction, 
models may be loaded by passing in a model id and optionally a number of 
chain names (see documentation for io.LoadPDB).

Example:
import string
repos=repository.ModelRepository('path_to_pdbs', 
                                 file_pattern='pdb%(id)s.ent.gz', 
                                 transform=string.lower)
# load 1ake (note that the name is transformed by string.lower)
m=repos.Load('1AKE')

Definition at line 7 of file repository.py.

Constructor & Destructor Documentation

◆ init()

__init__	(	self,
		directory = `None`,
		file_pattern = `'%(id)s.pdb'`,
		transform = `str`
	)

Construct new model repository

Definition at line 28 of file repository.py.

Member Function Documentation

◆ FilenameForModel()

FilenameForModel	(	self,
		pdb_id,
		chain
	)

Definition at line 39 of file repository.py.

◆ Load()

Load	(	self,
		pdb_id,
		chains = `''`,
		calpha_only = `False`,
		fault_tolerant = `False`
	)

Definition at line 44 of file repository.py.

◆ LoadMulti()

LoadMulti	(	self,
		pdb_id,
		chains = `""`
	)

Definition at line 49 of file repository.py.

Field Documentation

◆ directory_

directory_

Definition at line 34 of file repository.py.

◆ file_pattern_

file_pattern_

Definition at line 37 of file repository.py.

◆ transform_

transform_

Definition at line 38 of file repository.py.

The documentation for this class was generated from the following file:

build-dev/stage/lib/python3.11/site-packages/ost/io/repository.py

Public Member Functions

Data Fields