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Bio::EUtils::DBIdsClient Namespace Reference


Detailed Description

Search and retrieve information given a set of database identifiers.

EUtils has two major modes.  One uses history while the other uses
database identifiers.  This is a high-level interface for working with
identifiers.  You should use this module to get information about a
set of known database identifiers.

See HistoryClient if you want to work with a large number of
identifiers or potentially large search results.

>>> import EUtils
>>> from EUtils import DBIdsClient
>>> client = DBIdsClient.DBIdsClient()
>>> result = client.search("dalke", retmax = 100)
>>> len(result)
30
>>> print result[0].efetch(retmode = "text", rettype = "abstract").read()

1: Pac Symp Biocomput  1997;:85-96

Using Tcl for molecular visualization and analysis.

Dalke A, Schulten K.

Beckman Institute, Urbana, IL 61801, USA.

Reading and manipulating molecular structure data is a standard task in every
molecular visualization and analysis program, but is rarely available in a form
readily accessible to the user. Instead, the development of new methods for
analysis, display, and interaction is often achieved by writing a new program,
rather than building on pre-existing software. We present the Tcl-based script
language used in our molecular modeling program, VMD, and show how it can access
information about the molecular structure, perform analysis, and graphically
display and animate the results. The commands are available to the user and make
VMD a useful environment for studying biomolecules.


PMID: 9390282 [PubMed - indexed for MEDLINE]

>>>


Find sequences similar to GI:4579714 which were published in 2002.

>>> protein = DBIdsClient.from_dbids(EUtils.DBIds("protein", "4579714"))
>>> neighbors = protein.neighbor_links("protein",
...        daterange = EUtils.DateRange("2002/01/01", "2002/12/31", "pdat"))
>>> dbids = neighbors.linksetdbs["protein_protein"].dbids
>>> len(dbids)
28
>>> print dbids
DBIds(u'protein', [u'4579714', u'25298947', u'24158913', u'24158914', u'24158915', u'17942993', u'17942994', u'17942995', u'20150921', u'20150922', u'20151159', u'25298949', u'19716034', u'20663737', u'20663738', u'20663741', u'24987328', u'25533128', u'25298946', u'25298948', u'23008597', u'20219020', u'21218340', u'21218344', u'19075395', u'21218338', u'21218342', u'21311795'])
>>> 
>>> print client.from_dbids(dbids[:5]).efetch(retmode="text",
...                                           rettype="summary").read()

1: BAA75200
Bacteriorhodopsin [Halobacterium sp.]
gi|4579714|dbj|BAA75200.1|[4579714]


2: H84300
bacteriorhodopsin [imported] - Halobacterium sp. NRC-1
gi|25298947|pir||H84300[25298947]


3: 1M0KA
Chain A, Bacteriorhodopsin K Intermediate At 1.43 A Resolution
gi|24158913|pdb|1M0K|A[24158913]


4: 1M0LA
Chain A, BacteriorhodopsinLIPID COMPLEX AT 1.47 A RESOLUTION
gi|24158914|pdb|1M0L|A[24158914]


5: 1M0MA
Chain A, Bacteriorhodopsin M1 Intermediate At 1.43 A Resolution
gi|24158915|pdb|1M0M|A[24158915]

>>>


Classes

class  BaseDBIdsRecordSet
class  DBIdsClient
class  DBIdsLookup
class  DBIdsRecord
class  PublicationDBIdsFetchMixin
class  PublicationDBIdsRecord
class  PublicationDBIdsRecordSet
class  SequenceDBIdsFetchMixin
class  SequenceDBIdsRecord
class  SequenceDBIdsRecordSet

Functions

def _get_recordset_constructor
def from_dbids


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