475 lines
14 KiB
Python
475 lines
14 KiB
Python
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""" an XML-RPC server to allow remote control of PyMol
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Author: Greg Landrum (glandrum@users.sourceforge.net)
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Created: January 2002
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$LastChangedDate$
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License: PyMol
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Requires:
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- a python xmlrpclib distribution containing the SimpleXMLRPCServer
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module (1.0 or greater should be fine)
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- python with threading enabled
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RD Version: $Rev$
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Modified 2013-04-17 Thomas Holder, Schrodinger, Inc.
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"""
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import sys
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import xmlrpc.server as SimpleXMLRPCServer
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import threading,os,tempfile
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from pymol import cmd,cgo
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# initial port to try for the server
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_xmlPort=9123
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# number of alternate ports to try if the first fails
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_nPortsToTry=5
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def rpcPing():
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""" Used to establish whether or not the server is alive.
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This is a good thing to call after establishing a connection just to
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make sure that everything is ok.
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Returns 1
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"""
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return 1
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def rpcLabel(pos,labelText,id='lab1',color=(1,1,1)):
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""" create a text label
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Arguments:
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pos: a 3 tuple with the position of the label
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text: a string with the label
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color: a 3 tuple with the color of the label. (1,1,1) is white
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id: (OPTIONAL) the name of the object to be created
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NOTE:
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at the moment this is, how you say, a hack
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"""
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cmd.pseudoatom(id, label=repr(labelText), elem='C', pos=pos)
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cmd.set_color("%s-color"%id,color)
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cmd.color("%s-color"%id,id)
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return 1
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def rpcResetCGO(id):
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""" removes a CGO from the local dictionary
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"""
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global cgoDict
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if id=="*":
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cgoDict={}
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res = 1
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elif id in cgoDict:
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del(cgoDict[id])
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res = 1
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else:
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res = 0
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return res
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def rpcSphere(pos,rad,color,id='cgo',extend=1,
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transparent=0,transparency=0.5):
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""" create a sphere
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Arguments:
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pos: a 3 tuple with the position of the sphere
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rad: a float with the radius
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color: a 3 tuple with the color of the sphere. (1,1,1) is white
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id: (OPTIONAL) the name of the object to be created
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extend: (OPTIONAL) if this is nonzero, the object will be cleared
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before adding the new sphere. Otherwise the sphere is appended
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to the ojbect
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transparent: (OPTIONAL) sets the object to be transparent
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transparency: (OPTIONAL) the percent transparency of the object
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"""
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r,g,b = color
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x,y,z = pos
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if extend:
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obj = cgoDict.get(id,[])
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else:
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obj = []
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if not transparent:
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o = []
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else:
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o = [cgo.ALPHA,1-transparency]
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o.extend([cgo.COLOR,r,g,b,cgo.SPHERE,x,y,z,rad])
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obj.extend(o)
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cgoDict[id] = obj
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cmd.load_cgo(obj,id,1)
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return 1
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def rpcRenderCGO(cgoV,id='cgo',extend=1):
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""" renders a CGO vector
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Arguments:
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cgoV: a vector of floats
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id: (OPTIONAL) the name of the object to be created
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extend: (OPTIONAL) if this is nonzero, the object will be cleared
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before adding the new sphere. Otherwise the sphere is appended
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to the ojbect
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"""
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if extend:
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obj = cgoDict.get(id,[])
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else:
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obj = []
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obj.extend(cgoV)
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cmd.load_cgo(obj,id,1)
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return 1
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def rpcSpheres(sphereD,id='cgo',extend=1):
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""" create a sphere
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Arguments:
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sphereD: a series of (pos,rad,color,transparent,transparency) tuples
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id: (OPTIONAL) the name of the object to be created
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extend: (OPTIONAL) if this is nonzero, the object will be cleared
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before adding the new sphere. Otherwise the sphere is appended
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to the ojbect
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"""
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if extend:
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obj = cgoDict.get(id,[])
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else:
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obj = []
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for pos,rad,color,transparent,transparency in sphereD:
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r,g,b = color
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x,y,z = pos
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if not transparent:
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o = []
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else:
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o = [cgo.ALPHA,1-transparency]
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o.extend([cgo.COLOR,r,g,b,cgo.SPHERE,x,y,z,rad])
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obj.extend(o)
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cgoDict[id] = obj
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cmd.load_cgo(obj,id,1)
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return 1
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def rpcCylinder(end1,end2,rad,color1,id='cgo',color2=None,extend=1,
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transparent=0,transparency=0.5):
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""" create a cylinder
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Arguments:
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end1: a 3 tuple with the position of end1 of the sphere
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end2: a 3 tuple with the position of end1 of the sphere
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rad: a float with the radius
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color1: a 3 tuple with the color of end1 of the sphere. (1,1,1) is white
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id: (OPTIONAL) the name of the object to be created
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color2: (OPTIONAL) a 3 tuple with the color of end2 of the sphere. (1,1,1)
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is white
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extend: (OPTIONAL) if this is nonzero, the object will be cleared
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before adding the new sphere. Otherwise the sphere is appended
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to the ojbect
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transparent: (OPTIONAL) sets the object to be transparent
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transparency: (OPTIONAL) the percent transparency of the object
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NOTE: the reason that color2 follows id is that I think clients are
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going to be interested in setting the id more often than they are going
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to care about the second color.
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"""
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global cgoDict
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if color2 is None: color2 = color1
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r1,g1,b1 = color1
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r2,g2,b2 = color2
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x1,y1,z1 = end1
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x2,y2,z2 = end2
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if extend:
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obj = cgoDict.get(id,[])
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else:
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obj = []
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if not transparent:
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o = []
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else:
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o = [cgo.ALPHA,1-transparency]
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o.extend([cgo.CYLINDER,x1,y1,z1,x2,y2,z2,rad,r1,g1,b1,r2,g2,b2,])
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obj.extend(o)
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cgoDict[id] = obj
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cmd.load_cgo(obj,id,1)
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return 1
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def rpcDeleteObject(objName):
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""" deletes an object """
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try:
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cmd.delete(objName)
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except:
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res = 0
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else:
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res = 1
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return res
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def rpcDeleteAll():
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""" deletes all objects """
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res = cmd.delete('all')
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if res is not None:
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return res
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else:
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return ''
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def colorObj(objName,colorScheme):
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""" sets an molecule's color scheme
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Arguments:
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- objName: the object (molecule) to change
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- colorScheme: name of the color scheme to use
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for the object (should be either 'std' or one of the
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color schemes defined in pymol.utils)
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"""
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if colorScheme:
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if colorScheme == 'std':
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# this is an adaptation of the cbag scheme from util.py, but
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# with a gray carbon.
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cmd.color("magenta","("+objName+")",quiet=1)
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cmd.color("oxygen","(elem O and "+objName+")",quiet=1)
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cmd.color("nitrogen","(elem N and "+objName+")",quiet=1)
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cmd.color("sulfur","(elem S and "+objName+")",quiet=1)
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cmd.color("hydrogen","(elem H and "+objName+")",quiet=1)
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cmd.color("gray","(elem C and "+objName+")",quiet=1)
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elif hasattr(utils,colorScheme):
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fn = getattr(utils,colorScheme)
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fn(objName,quiet=1)
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res = 1
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else:
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res = 0
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return res
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def rpcLoadPDB(data,objName,colorScheme='',replace=1):
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""" loads a molecule from a pdb string
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Arguments:
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data: the mol block
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objName: name of the object to create
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colorScheme: (OPTIONAL) name of the color scheme to use
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for the molecule (should be either 'std' or one of the
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color schemes defined in pymol.utils)
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replace: (OPTIONAL) if an object with the same name already
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exists, delete it before adding this one
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"""
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from pymol import util
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if replace:
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cmd.delete(objName)
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res = cmd.read_pdbstr(data,objName)
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colorObj(objName,colorScheme)
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if res is not None:
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return res
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else:
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return ''
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def rpcLoadMolBlock(data,objName,colorScheme='',replace=1):
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""" loads a molecule from a mol block
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Arguments:
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data: the mol block
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objName: name of the object to create
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colorScheme: (OPTIONAL) name of the color scheme to use
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for the molecule (should be either 'std' or one of the
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color schemes defined in pymol.utils)
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replace: (OPTIONAL) if an object with the same name already
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exists, delete it before adding this one
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"""
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from pymol import util
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if replace:
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cmd.delete(objName)
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res = cmd.read_molstr(data,objName)
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colorObj(objName,colorScheme)
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if res is not None:
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return res
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else:
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return ''
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def rpcLoadFile(fileName,objName='',format='',colorScheme='',replace=1):
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""" loads an object from a file
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Arguments:
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fileName: the file to load
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objName: (OPTIONAL) name of the object to create
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format: (OPTIONAL) the format of the input file
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colorScheme: (OPTIONAL) name of the color scheme to use
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for the object (should be either 'std' or one of the
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color schemes defined in pymol.utils)
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replace: (OPTIONAL) if an object with the same name already
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exists, delete it before adding this one
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"""
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if not objName:
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objName = fileName.split('.')[0]
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if replace:
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cmd.delete(objName)
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res = cmd.load(fileName,objName,format=format)
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colorObj(objName,colorScheme)
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if res is not None:
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return res
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else:
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return ''
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def rpcLoadSurface(fileName,objName,format='',surfaceLevel=1.0):
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""" loads surface data from a file and adds an isosurface
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Arguments:
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fileName: the file to load
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objName: (OPTIONAL) name of the object to create
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format: (OPTIONAL) the format of the input file
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surfaceLevel: (OPTIONAL) the isosurface level
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"""
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if not objName:
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objName = fileName.split('.')[0]
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gridName = 'grid-%s'%objName
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res = cmd.load(fileName,gridName,format='')
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cmd.isosurface(objName,gridName,level=surfaceLevel)
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if res is not None:
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return res
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else:
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return ''
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def rpcLoadSurfaceData(data,objName='surface',format='',surfaceLevel=1.0):
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""" loads surface data from a string and adds an isosurface
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Arguments:
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data: the data to load
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objName: (OPTIONAL) name of the object to create
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format: (OPTIONAL) the format of the input file
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surfaceLevel: (OPTIONAL) the isosurface level
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"""
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gridName = 'grid-%s'%objName
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# it would be nice if we didn't have to go by way of the temporary file,
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# but at the moment pymol will only read shapes from files
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tempnm = tempfile.mktemp('.grd')
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open(tempnm,'w+').write(data)
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res = rpcLoadSurface(tempnm,objName,format='',surfaceLevel=surfaceLevel)
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os.unlink(tempnm)
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if res is not None:
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return res
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else:
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return ''
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def rpcRotate(vect,objName='',state=-1):
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""" rotates objects
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Arguments:
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- vect: a sequence with x y and z rotations
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- objName: (OPTIONAL) object to be rotated
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- state: (OPTIONAL) if zero only visible states are rotated,
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if -1 (the default), all states are rotated
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"""
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cmd.rotate('x',vect[0],objName,state=state)
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cmd.rotate('y',vect[1],objName,state=state)
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cmd.rotate('z',vect[2],objName,state=state)
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return 1
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def rpcGetNames(what='selections',enabledOnly=1):
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""" returns the results of cmd.get_names(what) """
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return cmd.get_names(what,enabled_only=enabledOnly)
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def rpcIdAtom(what='all',mode=0):
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""" returns the results of cmd.id_atom(what) """
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return cmd.id_atom(what,mode=mode)
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def rpcGetAtomCoords(what='all',state=0):
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""" returns the results of cmd.get_atom_coords(what,state) """
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return cmd.get_atom_coords(what,state=state)
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def rpcHelp(what=''):
|
||
|
|
""" returns general help text or help on a particular command """
|
||
|
|
global serv
|
||
|
|
res = 'Command Not Found'
|
||
|
|
if not what:
|
||
|
|
res = list(serv.funcs.keys())
|
||
|
|
else:
|
||
|
|
funcs = serv.funcs
|
||
|
|
if what in funcs:
|
||
|
|
fn = funcs[what]
|
||
|
|
res = "Function: %s("%what
|
||
|
|
defs = fn.__defaults__
|
||
|
|
if defs:
|
||
|
|
code = fn.__code__
|
||
|
|
nDefs = len(defs)
|
||
|
|
args = []
|
||
|
|
i = -1
|
||
|
|
for i in range(code.co_argcount - nDefs):
|
||
|
|
args.append(code.co_varnames[i])
|
||
|
|
for j in range(nDefs):
|
||
|
|
vName = code.co_varnames[j+i+1]
|
||
|
|
args.append("%s=%s"%(vName,repr(defs[j])))
|
||
|
|
res += ','.join(args)
|
||
|
|
res += ')\n'
|
||
|
|
if fn.__doc__:
|
||
|
|
res += fn.__doc__
|
||
|
|
return res
|
||
|
|
|
||
|
|
|
||
|
|
def launch_XMLRPC(hostname='',port=_xmlPort,nToTry=_nPortsToTry):
|
||
|
|
""" launches the xmlrpc server into a separate thread
|
||
|
|
|
||
|
|
Arguments:
|
||
|
|
hostname: (OPTIONAL) name of the host for the server
|
||
|
|
(defaults to be the name of the localhost)
|
||
|
|
port: (OPTIONAL) the first port to try for the server
|
||
|
|
nToTry: (OPTIONAL) the number of possible ports to try
|
||
|
|
(in case the first can't be opened)
|
||
|
|
|
||
|
|
"""
|
||
|
|
if not hostname:
|
||
|
|
import os
|
||
|
|
hostname = os.environ.get('PYMOL_RPCHOST', 'localhost')
|
||
|
|
|
||
|
|
global cgoDict,serv
|
||
|
|
cgoDict = {}
|
||
|
|
for i in range(nToTry):
|
||
|
|
try:
|
||
|
|
serv = SimpleXMLRPCServer.SimpleXMLRPCServer((hostname,port+i),logRequests=0,
|
||
|
|
allow_none=True)
|
||
|
|
except:
|
||
|
|
serv = None
|
||
|
|
else:
|
||
|
|
break
|
||
|
|
if serv:
|
||
|
|
print('xml-rpc server running on host %s, port %d'%(hostname,port+i))
|
||
|
|
|
||
|
|
# import PyMOL API
|
||
|
|
from pymol import api
|
||
|
|
serv.register_instance(cmd)
|
||
|
|
|
||
|
|
# legacy stuff with unique names
|
||
|
|
serv.register_function(rpcPing,'ping')
|
||
|
|
serv.register_function(rpcResetCGO,'resetCGO')
|
||
|
|
serv.register_function(rpcRenderCGO,'renderCGO')
|
||
|
|
serv.register_function(rpcSphere,'sphere')
|
||
|
|
serv.register_function(rpcSpheres,'spheres')
|
||
|
|
serv.register_function(rpcCylinder,'cylinder')
|
||
|
|
serv.register_function(rpcDeleteObject,'deleteObject')
|
||
|
|
serv.register_function(rpcDeleteAll,'deleteAll')
|
||
|
|
serv.register_function(rpcLoadPDB,'loadPDB')
|
||
|
|
serv.register_function(rpcLoadMolBlock,'loadMolBlock')
|
||
|
|
serv.register_function(rpcLoadSurface,'loadSurface')
|
||
|
|
serv.register_function(rpcLoadSurfaceData,'loadSurfaceData')
|
||
|
|
serv.register_function(rpcLoadFile,'loadFile')
|
||
|
|
serv.register_function(rpcGetNames,'getNames')
|
||
|
|
serv.register_function(api.count_atoms,'countAtoms')
|
||
|
|
serv.register_function(rpcIdAtom,'idAtom')
|
||
|
|
serv.register_function(rpcHelp,'help')
|
||
|
|
serv.register_function(rpcGetAtomCoords,'getAtomCoords')
|
||
|
|
|
||
|
|
# legacy stuff, should be removed because overwrites API names!
|
||
|
|
serv.register_function(rpcLabel,'label') # pseudoatom
|
||
|
|
serv.register_function(rpcRotate,'rotate')
|
||
|
|
|
||
|
|
serv.register_introspection_functions()
|
||
|
|
t = threading.Thread(target=serv.serve_forever)
|
||
|
|
t.setDaemon(1)
|
||
|
|
t.start()
|
||
|
|
else:
|
||
|
|
print('xml-rpc server could not be started')
|
||
|
|
|
||
|
|
# vi:expandtab:smarttab:sw=2
|