pymol 1.8.4.0+dfsg-1 / usr / lib / python2.7 / dist-packages / pymol / experimenting.py

#A* -------------------------------------------------------------------
#B* This file contains source code for the PyMOL computer program
#C* Copyright (c) Schrodinger, LLC. 
#D* -------------------------------------------------------------------
#E* It is unlawful to modify or remove this copyright notice.
#F* -------------------------------------------------------------------
#G* Please see the accompanying LICENSE file for further information. 
#H* -------------------------------------------------------------------
#I* Additional authors of this source file include:
#-* 
#-* 
#-*
#Z* -------------------------------------------------------------------

if __name__=='pymol.experimenting':
    
    from . import selector
    from .cmd import _cmd,lock,unlock,Shortcut,QuietException, \
          DEFAULT_ERROR, DEFAULT_SUCCESS, _raising, is_ok, is_error        
    cmd = __import__("sys").modules["pymol.cmd"]
    import threading
    import pymol
    import string
    
    def get_bond_print(obj,max_bond,max_type,_self=cmd):
        r = DEFAULT_ERROR
        try:
            _self.lock(_self)
            r = _cmd.get_bond_print(_self._COb,str(obj),int(max_bond),int(max_type))
        finally:
            _self.unlock(r,_self)
        if _self._raising(r,_self): raise pymol.CmdException                  
        return r

    def spheroid(object="",average=0,_self=cmd):  # EXPERIMENTAL
        '''
DESCRIPTION

    "spheroid" averages trajectory frames together to create
    an ellipsoid-like approximation of the actual anisotropic
    motion exhibited by the atom over a series of trajectory frames.

USAGE

    spheroid object,average

    average = number of states to average for each resulting spheroid state

    '''
        r = DEFAULT_ERROR
        try:
            print("Warning: 'spheroid' is experimental, incomplete, and unstable.")
            _self.lock(_self)
            r = _cmd.spheroid(_self._COb,str(object),int(average))
        finally:
            _self.unlock(r,_self)
        if _self._raising(r,_self): raise pymol.CmdException                  
        return r

    def mem(_self=cmd):
        '''
DESCRIPTION

    "mem" Dumps current memory state to standard output. This is a
    debugging feature, not an official part of the API.

    '''
        r = DEFAULT_ERROR
        try:
            _self.lock(_self)
            r = _cmd.mem(_self._COb)
        finally:
            _self.unlock(r,_self)
        if _self._raising(r,_self): raise pymol.CmdException                  
        return r


    def check(selection=None, preserve=0):
        '''
DESCRIPTION

    "check" is unsupported command that may eventually have something
    to do with assigning forcefield parameters to a selection of
    atoms.
    
'''        
        # This function relies on code that is not currently part of PyMOL/ChemPy
        # NOTE: the realtime module relies on code that is not yet part of PyMOL/ChemPy
        from chempy.tinker import realtime
        if selection==None:
            arg = cmd.get_names("objects")
            arg = arg[0:1]
            if arg:
                if len(arg):
                    selection = arg
        if selection!=None:
            selection = selector.process(selection)
            realtime.assign("("+selection+")",int(preserve))
            realtime.setup("("+selection+")")

    def fast_minimize(*args, **kwargs):
        '''
DESCRIPTION

    "fast_minimize" is an unsupported nonfunctional command that may
    eventually have something to do with doing a quick clean up of the
    molecular structure.
    
'''        
        kwargs['_setup'] = 0
        return minimize(*args, **kwargs)

    def minimize(sele='', iter=500, grad=0.01, interval=50, _setup=1, _self=cmd):
        '''
DESCRIPTION

    "fast_minimize" is an unsupported nonfunctional command that may
    eventually have something to do with minimization.
    
'''        
        from chempy.tinker import realtime  

        if not sele:
            names = _self.get_names("objects")
            if not names:
                return
            sele = names[0]
        sele = '(' + sele + ')'

        if not int(_setup) or realtime.setup(sele):
            _self.async(realtime.mini, int(iter), float(grad), int(interval), sele)
        else:
            print(" minimize: missing parameters, can't continue")


    def dump(fnam,obj,_self=cmd):
        '''
DESCRIPTION

    "dump" is an unsupported command which may have something to do
    with outputing isosurface meshes and surface objects to a file.

    '''
        r = DEFAULT_ERROR
        try:
            _self.lock(_self)
            r = _cmd.dump(_self._COb,str(fnam),obj)
        finally:
            _self.unlock(r,_self)
        if _self._raising(r,_self): raise pymol.CmdException                  
        return r


    def dummy(*arg):
        return None

    def test(group=0,index=0,_self=cmd): # generic test routine for development
        '''
DESCRIPTION

    "dump" is an unsupported internal command.

    '''
        r = DEFAULT_ERROR
        try:
            _self.lock(_self)   
            r=_cmd.test(_self._COb,int(group),int(index))
        finally:
            _self.unlock(r,_self)
        if _self._raising(r,_self): raise pymol.CmdException                  
        return r

    def import_coords(coords,name,state,_self=cmd): # experimental
        r = DEFAULT_ERROR      
        try:
            _self.lock(_self)   
            r = _cmd.import_coords(_self._COb,str(name),int(state)-1,coords)
        finally:
            _self.unlock(r,_self)
        if _self._raising(r,_self): raise pymol.CmdException                  
        return r

    def load_coords(model, oname, state=1): # UNSUPPORTED
        '''
        WARNING: buggy argument list, state get's decremented twice!
        '''
        return pymol.importing.load_coordset(model, oname, int(state)-1)

    def focal_blur(aperture=2.0, samples=10, ray=0, filename='', quiet=1, _self=cmd):
        '''
DESCRIPTION

    Creates fancy figures by introducing a focal blur to the image.
    The object at the origin will be in focus.

USAGE

    focal_blur [ aperture [, samples [, ray [, filename ]]]]

ARGUMENTS

    aperture = float: aperture angle in degrees {default: 2.0}

    samples = int: number of images for averaging {default: 10}

    ray = 0/1: {default: 0}

    filename = str: write image to file {default: temporary}

AUTHORS

    Jarl Underhaug, Jason Vertrees and Thomas Holder

EXAMPLES

    focal_blur 3.0, 50
        '''
        raise pymol.IncentiveOnlyException()

    def callout(name, label, pos='', screen='auto', state=-1, color='front',
            quiet=1, _self=cmd):
        '''
DESCRIPTION

    Create a new screen-stabilized callout object.

ARGUMENTS

    name = str: object name

    label = str: label text

    pos = str or list: anchor in model space as 3-float coord list or atom
    selection. If empty, don't draw an arrow. {default: }

    screen = str or list: position on screen as 2-float list between [-1,-1]
    (lower left) and [1,1] (upper right) or "auto" for smart placement.
    {default: auto}
        '''
        raise pymol.IncentiveOnlyException()

    def desaturate(selection="all", a=0.5, quiet=1, _self=cmd):
        '''
DESCRIPTION

    Desaturate the colors in the given selection.

ARGUMENTS

    selection = str: atom selection {default: all}

    a = float [0..1]: desaturation factor {default: 0.5}
        '''
        raise pymol.IncentiveOnlyException()