Paolo,
Thank you! That works perfectly. I'm not sure what step I was missing
before, but your script does the trick.
In working with this, I found myself wanting to save some PyMOL files
programatically, but I see that there is not a Save option in the RDKit
PyMOL code. I added the snip below to the MolViewer class and it seems to
work nicely. I don't know if it is generally useful or if it should be
added to the code base - I'll let Greg make that decision.
-Kirk
def SaveFile(self, filename):
id = self.server.save(filename)
return id
I've attached my modified PyMol.py file as well.
On Fri, Apr 22, 2016 at 3:08 PM, Paolo Tosco <paolo.to...@unito.it> wrote:
> Dear Robert,
>
> I have just built the latest PyMOL 1.8.2.0 on CentOS 7, I started it:
>
> pymol -R
>
> and then I ran the following Python script:
>
> #!/usr/bin/env python
>
> import os
> import rdkit
> from rdkit import Chem
> from rdkit.Chem import PyMol
> from rdkit.Chem import AllChem
>
> s = PyMol.MolViewer()
> mol = Chem.MolFromSmiles \
> ('CCOCCn1c(C2CC[NH+](CCc3ccc(C(C)(C)C(=O)[O-])cc3)CC2)nc2ccccc21')
> mol = AllChem.AddHs(mol)
> AllChem.EmbedMolecule(mol)
> AllChem.MMFFOptimizeMolecule(mol)
> s.ShowMol(mol, name = 'bilastine', showOnly = False)
> s.Zoom('bilastine')
> s.SetDisplayStyle('bilastine', 'sticks')
>
> I obtained the expected display:
>
>
>
> Cheers,
> p.
>
>
> On 04/22/2016 09:09 PM, Robert DeLisle wrote:
>
> Back again!
>
> I apologize for resurrecting an old topic, but I'm once again trying to
> work with PyMOL through RDKit. I've been following the approach in this
> thread (
> http://www.mail-archive.com/rdkit-discuss%40lists.sourceforge.net/msg00325.html)
> but it seems not to work any longer. I'm using PyMOL 1.8 on Fedora and I
> see that the xml-rpc file is current, so that's no longer a problem. When
> I step through the process and hit this step:
>
> s.ShowMol(m,name='ligand',showOnly=False)
>
>
> nothing happens in the PyMOL viewer. It just remains blank.
>
> Any updates on operating with PyMOL?
>
> -Kirk
>
>
>
>
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>
>
# $Id$
#
# Copyright (C) 2004-2012 Greg Landrum and Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
""" uses pymol to interact with molecules
"""
from rdkit import Chem
import os, tempfile
# Python3 compatibility
try:
from xmlrpclib import Server
except ImportError:
from xmlrpc.client import Server
_server=None
class MolViewer(object):
def __init__(self,host=None,port=9123,force=0,**kwargs):
global _server
if not force and _server is not None:
self.server=_server
else:
if not host:
host=os.environ.get('PYMOL_RPCHOST','localhost')
_server=None
serv = Server('http://%s:%d'%(host,port))
serv.ping()
_server = serv
self.server=serv
self.InitializePyMol()
def InitializePyMol(self):
""" does some initializations to set up PyMol according to our
tastes
"""
self.server.do('set valence,1')
self.server.do('set stick_rad,0.15')
self.server.do('set mouse_selection_mode,0')
self.server.do('set line_width,2')
self.server.do('set selection_width,10')
self.server.do('set auto_zoom,0')
def DeleteAll(self):
" blows out everything in the viewer "
self.server.deleteAll()
def DeleteAllExcept(self,excludes):
" deletes everything except the items in the provided list of arguments "
allNames = self.server.getNames('*',False)
for nm in allNames:
if nm not in excludes:
self.server.deleteObject(nm)
def LoadFile(self,filename,name,showOnly=False):
""" calls pymol's "load" command on the given filename; the loaded object
is assigned the name "name"
"""
if showOnly:
self.DeleteAll()
id = self.server.loadFile(filename,name)
return id
def SaveFile(self, filename):
id = self.server.save(filename)
return id
def ShowMol(self,mol,name='molecule',showOnly=True,highlightFeatures=[],
molB="",confId=-1,zoom=True,forcePDB=False, showSticks=False):
""" special case for displaying a molecule or mol block """
server = self.server
if not zoom:
self.server.do('view rdinterface,store')
if showOnly:
self.DeleteAll()
if not forcePDB and mol.GetNumAtoms()<999 :
if not molB:
molB = Chem.MolToMolBlock(mol,confId=confId)
mid = server.loadMolBlock(molB,name)
else:
if not molB:
molB = Chem.MolToPDBBlock(mol,confId=confId)
mid = server.loadPDB(molB,name)
if highlightFeatures:
nm = name+'-features'
conf = mol.GetConformer(confId)
for feat in highlightFeatures:
pt = [0.0,0.0,0.0]
for idx in feat:
loc = conf.GetAtomPosition(idx)
pt[0] += loc[0]/len(feat)
pt[1] += loc[1]/len(feat)
pt[2] += loc[2]/len(feat)
server.sphere(pt,0.2,(1,1,1),nm)
if zoom:
server.zoom('visible')
else:
self.server.do('view rdinterface,recall')
if showSticks: # show molecule in stick view
self.server.do('show sticks, {}'.format(name))
return mid
def GetSelectedAtoms(self,whichSelection=None):
" returns the selected atoms "
if not whichSelection:
sels = self.server.getNames('selections')
if sels:
whichSelection = sels[-1]
else:
whichSelection=None
if whichSelection:
items = self.server.index(whichSelection)
else:
items = []
return items
def SelectAtoms(self,itemId,atomIndices,selName='selection'):
" selects a set of atoms "
ids = '(id '
ids += ','.join(['%d'%(x+1) for x in atomIndices])
ids += ')'
cmd = 'select %s,%s and %s'%(selName,ids,itemId)
self.server.do(cmd)
def HighlightAtoms(self,indices,where,extraHighlight=False):
" highlights a set of atoms "
if extraHighlight:
idxText = ','.join(['%s and (id %d)'%(where,x) for x in indices])
self.server.do('edit %s'%idxText)
else:
idxText = ' or '.join(['id %d'%x for x in indices])
self.server.do('select selection, %s and (%s)'%(where,idxText))
def SetDisplayStyle(self,obj,style=''):
" change the display style of the specified object "
self.server.do('hide everything,%s'%(obj,))
if style:
self.server.do('show %s,%s'%(style,obj))
def SelectProteinNeighborhood(self,aroundObj,inObj,distance=5.0,
name='neighborhood',showSurface=False):
""" selects the area of a protein around a specified object/selection name;
optionally adds a surface to that """
self.server.do('select %(name)s,byres (%(aroundObj)s around %(distance)f) and %(inObj)s'%locals())
if showSurface:
self.server.do('show surface,%s'%name)
self.server.do('disable %s'%name)
def AddPharmacophore(self,locs,colors,label,sphereRad=0.5):
" adds a set of spheres "
self.server.do('view rdinterface,store')
self.server.resetCGO(label)
for i,loc in enumerate(locs):
self.server.sphere(loc,sphereRad,colors[i],label,1)
self.server.do('enable %s'%label)
self.server.do('view rdinterface,recall')
def SetDisplayUpdate(self,val):
if not val:
self.server.do('set defer_update,1')
else:
self.server.do('set defer_update,0')
def GetAtomCoords(self,sels):
" returns the coordinates of the selected atoms "
res = {}
for label,idx in sels:
coords = self.server.getAtomCoords('(%s and id %d)'%(label,idx))
res[(label,idx)] = coords
return res
def HideAll(self):
self.server.do('disable all')
def HideObject(self,objName):
self.server.do('disable %s'%objName)
def DisplayObject(self,objName):
self.server.do('enable %s'%objName)
def Redraw(self):
self.server.do('refresh')
def Zoom(self,objName):
self.server.zoom(objName)
def DisplayHBonds(self,objName,molName,proteinName,
molSelText='(%(molName)s)',
proteinSelText='(%(proteinName)s and not het)'):
" toggles display of h bonds between the protein and a specified molecule "
cmd = "delete %(objName)s;\n"
cmd += "dist %(objName)s," + molSelText+","+proteinSelText+",mode=2;\n"
cmd += "enable %(objName)s;"
cmd = cmd%locals()
self.server.do(cmd)
def DisplayCollisions(self,objName,molName,proteinName,distCutoff=3.0,
color='red',
molSelText='(%(molName)s)',
proteinSelText='(%(proteinName)s and not het)'):
" toggles display of collisions between the protein and a specified molecule "
cmd = "delete %(objName)s;\n"
cmd += "dist %(objName)s," + molSelText+","+proteinSelText+",%(distCutoff)f,mode=0;\n"
cmd += """enable %(objName)s
color %(color)s, %(objName)s"""
cmd = cmd%locals()
self.server.do(cmd)
def GetPNG(self,h=None,w=None,preDelay=0):
try:
import Image
except ImportError:
from PIL import Image
import time
if preDelay>0:
time.sleep(preDelay)
fd = tempfile.NamedTemporaryFile(suffix='.png',delete=False)
fd.close()
self.server.do('png %s'%fd.name)
time.sleep(0.2) # <- wait a short period so that PyMol can finish
for i in range(10):
try:
img = Image.open(fd.name)
break
except IOError:
time.sleep(0.1)
os.unlink(fd.name)
fd=None
if h is not None or w is not None:
sz = img.size
if h is None:
h=sz[1]
if w is None:
w=sz[0]
if h<sz[1]:
frac = float(h)/sz[1]
w *= frac
w = int(w)
img=img.resize((w,h),True)
elif w<sz[0]:
frac = float(w)/sz[0]
h *= frac
h = int(h)
img=img.resize((w,h),True)
return img
------------------------------------------------------------------------------
Find and fix application performance issues faster with Applications Manager
Applications Manager provides deep performance insights into multiple tiers of
your business applications. It resolves application problems quickly and
reduces your MTTR. Get your free trial!
https://ad.doubleclick.net/ddm/clk/302982198;130105516;z
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
