schrodinger.application.glide.http_client module¶

Glide HTTP client

This module implements objects that connect to a Glide HTTP server (see schrodinger.application.glide.http_server) and use the server to dock ligands remotely.

Sample usage:

from schrodinger import structure from schrodinger.application.glide import http_client

client = http_client.HTTPClient(host=’localhost’, port=8000) ct = structure.Structure.read(‘mylig.mae’) poses = client.dock(ct) for pose in poses:

print “gscore=%f” % pose.properties[‘r_i_glide_gscore’]

For a higher level API that also starts up and monitors the server itself, see GlideServerManager.

class schrodinger.application.glide.http_client.HTTPClient(con=None, host='localhost', port=8000, timeout=1000)¶

Bases: object

This class provides an API to connect to an existing Glide HTTP server. For a higher level API that also starts up and monitors the server itself, see GlideServerManager.

__init__(con=None, host='localhost', port=8000, timeout=1000)¶: Initialize a new HTTPClient object. The optional ‘con’ is an existing httplib.HTTPConnection object. If not provided, then ‘host’, ‘port’, and ‘timeout’ will be used to create one. The default timeout value is very large to make sure that it is enough for most docking jobs to finish.

dock(ct)¶: Dock the ligand in Structure object ‘ct’ using the remote Glide server. Returns an iterator with the output pose(s).

ct_to_multipart(ct)¶: Encode a CT in multipart/form-data format, ready to POST. Returns the body of the request and the boundary

shutdown_server()¶: Ask the Glide HTTP server to shut down.

__class__¶: alias of builtins.type

__delattr__¶: Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.glide.http_client', '__doc__': '\n This class provides an API to connect to an existing Glide HTTP server.\n For a higher level API that also starts up and monitors the server itself,\n see `GlideServerManager`.\n ', '__init__': <function HTTPClient.__init__>, 'dock': <function HTTPClient.dock>, 'ct_to_multipart': <function HTTPClient.ct_to_multipart>, 'shutdown_server': <function HTTPClient.shutdown_server>, '__dict__': <attribute '__dict__' of 'HTTPClient' objects>, '__weakref__': <attribute '__weakref__' of 'HTTPClient' objects>})¶

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__module__ = 'schrodinger.application.glide.http_client'¶

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__¶: list of weak references to the object (if defined)

class schrodinger.application.glide.http_client.GlideServerManager(keywords, jobdir='.', jobname='glide_server', host='localhost', port=0, timeout=1000)¶

Bases: object

A class to start, stop, monitor, and use a Glide HTTP server. Sample use:

server = GlideServerManager({‘GRIDFILE’: ‘grid.zip’}) server.start() while not server.isReady():

time.sleep(1)

poses = server.dock(st) server.stop()

__init__(keywords, jobdir='.', jobname='glide_server', host='localhost', port=0, timeout=1000)¶

Parameters:	keywords – Glide keywords to use for the job. The only required

keyword is GRIDFILE. :type keywords: dict

Parameters:	jobdir (str) – job directory jobname – basename for input and output files and for job control host – host to which the server should bind to port (int) – port where the server should listen. If zero, pick one automatically. timeout (int) – the server will shut down automatically if this time, in seconds, passes without receiving any connections.

start()¶: Launch the Glide Server job. Returns as soon as the job is launched, but to make sure that the job is ready to dock call .isReady() until True.

isReady()¶

Returns:	is the server ready to dock?
Return type:	bool

dock(st)¶

Dock a ligand. Returns a list of poses, which may be empty. If there was a problem connecting to the server, socket.error exceptions may be propagated.

Parameters:	st (schrodinger.structure.Structure) – Structure to dock
Returns:	list of poses
Return type:	list of schrodinger.structure.Structure

stop()¶: Stop the server. First it will try to send it a shutdown request via HTTP; if that doesn’t work, it will kill via job control.

config¶: A dictionary with the information needed to connect with the server: host, port, and jobid. This data is obtained from a JSON file written by the server. If the file does not exist (yet?), the dict will be empty.

client¶

Client object to be used for connecting to the Glide server process.

Return type:	HTTPClient
Returns:	the client object.

__class__¶: alias of builtins.type

__delattr__¶: Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.glide.http_client', '__doc__': "\n A class to start, stop, monitor, and use a Glide HTTP server.\n Sample use:\n\n server = GlideServerManager({'GRIDFILE': 'grid.zip'})\n server.start()\n while not server.isReady():\n time.sleep(1)\n poses = server.dock(st)\n server.stop()\n ", '__init__': <function GlideServerManager.__init__>, 'start': <function GlideServerManager.start>, 'isReady': <function GlideServerManager.isReady>, 'dock': <function GlideServerManager.dock>, 'stop': <function GlideServerManager.stop>, '_clearConfig': <function GlideServerManager._clearConfig>, '_readConfig': <function GlideServerManager._readConfig>, 'config': <property object>, 'client': <property object>, '__dict__': <attribute '__dict__' of 'GlideServerManager' objects>, '__weakref__': <attribute '__weakref__' of 'GlideServerManager' objects>})¶

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).