ModelRepository Class Reference

Public Member Functions
def	__init__
def	FilenameForModel
def	Load
def	LoadMulti
Data Fields
	directory_
	file_pattern_
	transform_

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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.

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Member Function Documentation

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

Construct new model repository

Definition at line 28 of file repository.py.

def FilenameForModel	(		self,
			pdb_id,
			chain
	)

Definition at line 39 of file repository.py.

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

Definition at line 44 of file repository.py.

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

Definition at line 49 of file repository.py.

---

Field Documentation

directory_

Definition at line 33 of file repository.py.

file_pattern_

Definition at line 36 of file repository.py.

transform_

Definition at line 37 of file repository.py.

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

• stage/lib64/python2.7/site-packages/ost/io/repository.py