cd166c6f2f
this wrapper allows to spawn an instance of VMD as an ancillary process under python and supports a few simple manipulations through converting them to tcl commands. also arbitrary tcl commands can be forwarded by the object to the vmd instance.
206 lines
7.9 KiB
Python
206 lines
7.9 KiB
Python
#
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# Minimalistic VMD embedding for Pizza.py
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#
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# This class will replace the VMD startup script,
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# open a pipe to the executable, and feed it Tcl
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# command lines one at a time.
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#
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# (c) 2010 Axel Kohlmeyer <akohlmey@gmail.com>
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oneline = "Control VMD from python."
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docstr = """
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v = vmd() start up VMD
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v.stop() shut down VMD instance
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v.clear() delete all visualizations
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v.rep(style) set default representation style. One of
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(Lines|VDW|Licorice|DynamicBonds|Points|CPK)
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v.new(file[,type]) load new file (default file type 'lammpstrj')
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v.data(file[,atomstyle]) load new data file (default atom style 'full')
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v.replace(file[,type]) replace current frames with new file
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v.append(file[,type]) append file to current frame(s)
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v.set(snap,x,y,z,(True|False)) set coordinates from a pizza.py snapshot to new or current frame
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v.frame(frame) set current frame
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v.flush() flush pending input to VMD and update GUI
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v.read(file) read Tcl script file (e.g. saved state)
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v.enter() enter interactive shell
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v.debug([True|False]) display generated VMD script commands?
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"""
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# Imports and external programs
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import types, os
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import numpy
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try: from DEFAULTS import PIZZA_VMDNAME
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except: PIZZA_VMDNAME = "vmd"
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try: from DEFAULTS import PIZZA_VMDDIR
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except: PIZZA_VMDDIR = "/usr/local/lib/vmd"
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try: from DEFAULTS import PIZZA_VMDDEV
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except: PIZZA_VMDDEV = "win"
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try: from DEFAULTS import PIZZA_VMDARCH
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except: PIZZA_VMDARCH = "LINUXAMD64"
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try: import pexpect
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except:
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print "pexpect from http://pypi.python.org/pypi/pexpect/ is required for vmd module"
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raise
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# Class definition
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class vmd:
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# --------------------------------------------------------------------
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def __init__(self):
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self.vmddir = PIZZA_VMDDIR
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self.vmdexe = PIZZA_VMDDIR + '/' + PIZZA_VMDNAME + '_' + PIZZA_VMDARCH
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# these are all defaults copied from the vmd launch script
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os.environ['VMDDIR'] = PIZZA_VMDDIR
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os.environ['VMDDISPLAYDEVICE'] = PIZZA_VMDDEV
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os.environ['VMDSCRPOS'] = "596 190"
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os.environ['VMDSCRSIZE'] = "669 834"
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os.environ['VMDSCRHEIGHT'] = "6.0"
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os.environ['VMDSCRDIST'] = "-2.0"
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os.environ['VMDTITLE'] = "on"
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os.environ['TCL_LIBRARY'] = PIZZA_VMDDIR + "/scripts/tcl"
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os.environ['STRIDE_BIN'] = PIZZA_VMDDIR + "/stride_" + PIZZA_VMDARCH
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os.environ['SURF_BIN'] = PIZZA_VMDDIR + "/surf_" + PIZZA_VMDARCH
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os.environ['TACHYON_BIN'] = PIZZA_VMDDIR + "/tachyon_" + PIZZA_VMDARCH
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ldpath = os.environ.get('LD_LIBRARY_PATH','')
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if ldpath == '':
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os.environ['LD_LIBRARY_PATH'] = PIZZA_VMDDIR
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else:
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os.environ['LD_LIBRARY_PATH'] = ldpath + ':' + PIZZA_VMDDIR
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ldpath = os.environ.get('LD_LIBRARY_PATH','')
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if ldpath == '':
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os.environ['PYTHONPATH'] = PIZZA_VMDDIR
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else:
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os.environ['PYTHONPATH'] = PIZZA_VMDDIR + "/scripts/python"
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self.debugme = False
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# open pipe to vmd and wait until we have a prompt
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self.VMD = pexpect.spawn(self.vmdexe)
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self.VMD.expect('vmd >')
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# --------------------------------------------------------------------
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# post command to vmd and wait until the prompt returns.
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def __call__(self,command):
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if self.VMD.isalive():
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self.VMD.sendline(command)
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self.VMD.expect('vmd >')
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if self.debugme:
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print "call+result:"+self.VMD.before
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return
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# --------------------------------------------------------------------
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# exit VMD
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def stop(self):
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self.__call__("quit")
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del self.VMD
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# --------------------------------------------------------------------
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# force VMD display and GUI update.
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def flush(self):
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self.__call__('display update ui')
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# --------------------------------------------------------------------
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# turn on debugging info
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def debug(self,status=True):
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if status and not self.debugme:
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print 'Turning vmd.py debugging ON.'
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if not status and self.debugme:
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print 'Turning vmd.py debugging OFF.'
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self.debugme = status
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# --------------------------------------------------------------------
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# emulate a regular tcl command prompt
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def enter(self,mode='tcl'):
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self.__call__('menu main off')
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self.__call__('menu main on')
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while 1:
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try:
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command = raw_input("vmd > ")
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except EOFError:
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print "(EOF)"
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self.__call__('menu main off')
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return
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if command == "quit" or command == "exit":
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self.__call__('menu main off')
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return
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if command == "gopython":
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print "gopython not supported here"
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continue
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self.__call__(command)
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# --------------------------------------------------------------------
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# read and execute tcl script file (e.g. a saved state)
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def read(self,filename):
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self.__call__('play ' + filename)
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self.flush()
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# --------------------------------------------------------------------
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# remove all molecules, data and visualizations
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def clear(self):
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self.__call__("mol delete all")
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# --------------------------------------------------------------------
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# navigate to a given frame
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def rep(self,style='Lines'):
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if style == 'Lines' or style == 'VDW' or style == 'Licorice' \
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or style == 'DynamicBonds' or style == 'Points' or style == 'CPK':
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self.__call__('mol default style ' + style)
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# --------------------------------------------------------------------
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# navigate to a given frame
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def frame(self,framespec):
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self.__call__('animate goto ' + str(framespec))
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# --------------------------------------------------------------------
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# load a new molecule from a file supported by a molfile plugin
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def new(self,filename,filetype='lammpstrj'):
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self.__call__('mol new ' + filename + ' type ' + filetype + ' waitfor all')
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self.flush()
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# --------------------------------------------------------------------
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# load a new molecule from a data file via the topotools plugin
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def data(self,filename,atomstyle='full'):
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self.__call__('package require topotools 1.0')
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self.__call__('topo readlammpsdata ' + filename + ' ' + atomstyle)
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self.flush()
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# --------------------------------------------------------------------
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# append all frames from a given file to the current molecule
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def append(self,filename,filetype='lammpstrj'):
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self.__call__('set tmol [molinfo top]')
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self.__call__('array set viewpoints {}')
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self.__call__('foreach mol [molinfo list] { set viewpoints($mol) [molinfo $mol get { center_matrix rotate_matrix scale_matrix global_matrix}]}')
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self.__call__('mol addfile ' + filename + ' mol $tmol type ' + filetype + ' waitfor all')
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self.__call__('foreach mol [molinfo list] { molinfo $mol set {center_matrix rotate_matrix scale_matrix global_matrix} $viewpoints($mol)}')
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self.flush()
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# --------------------------------------------------------------------
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# replace all frames of a molecule with those from a given file
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def update(self,filename,filetype='lammpstrj'):
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self.__call__('set tmol [molinfo top]')
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self.__call__('array set viewpoints {}')
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self.__call__('foreach mol [molinfo list] {set viewpoints($mol) [molinfo $mol get { center_matrix rotate_matrix scale_matrix global_matrix}]}')
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self.__call__('animate delete all $tmol')
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self.__call__('mol addfile ' + filename + ' mol $tmol type ' + filetype + ' waitfor all')
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self.__call__('foreach mol [molinfo list] {molinfo $mol set {center_matrix rotate_matrix scale_matrix global_matrix} $viewpoints($mol)}')
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self.flush()
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# --------------------------------------------------------------------
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# add or overwrite coordinates with coordinates in a snapshot
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def set(self,snap,x,y,z,append=True):
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self.__call__('set vmdsel [atomselect top all]')
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if append:
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self.__call__('animate dup [molinfo top]')
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cmd = '$vmdsel set {x y z} {'
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for idx in range(0,snap.natoms):
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cmd += ' {'+str(snap[idx,x])+' '+str(snap[idx,y])+' '+str(snap[idx,z])+'}'
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cmd += '}'
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self.__call__(cmd)
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self.__call__('$vmdsel delete ; unset vmdsel')
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self.flush()
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