Ejemplo n.º 1
0
    def isodot(name,
               map,
               level=1.0,
               selection='',
               buffer=0.0,
               state=0,
               carve=None,
               source_state=0,
               quiet=1,
               _self=cmd):
        '''
DESCRIPTION

    "isodot" creates a dot isosurface object from a map object.

USAGE

    isodot name = map, level [,(selection) [,buffer [, state ] ] ] 

ARGUMENTS

    map = the name of the map object to use.

    level = the contour level.

    selection = an atom selection about which to display the mesh with
        an additional "buffer" (if provided).

NOTES

    If the dot isosurface object already exists, then the new dots will
    be appended onto the object as a new state.

SEE ALSO

    load, isomesh
        '''
        r = DEFAULT_ERROR
        if selection != '':
            region = 1  # about a selection
        else:
            region = 0  # render the whole map
        # preprocess selections
        selection = selector.process(selection)
        if selection not in ['center', 'origin']:
            selection = "(" + selection + ")"
        #
        if carve == None:
            carve = 0.0
        try:
            _self.lock(_self)
            r = _cmd.isomesh(_self._COb, str(name), str(map), int(region),
                             selection, float(buffer), float(level), 1,
                             int(state) - 1, float(carve),
                             int(source_state) - 1, int(quiet), float(level))
        finally:
            _self.unlock(r, _self)
        if _self._raising(r, _self): raise pymol.CmdException
        return r
Ejemplo n.º 2
0
    def gradient(name,
                 map,
                 minimum=1.0,
                 maximum=-1.0,
                 selection='',
                 buffer=0.0,
                 state=0,
                 carve=None,
                 source_state=0,
                 quiet=1,
                 _self=cmd):
        '''
DESCRIPTION

    "gradient" creates a gradient object from a map object.

USAGE

    gradient name = map, [ minimum, [, maximum [, selection [, buffer [, state ]]]]]

ARGUMENTS

    map = the name of the map object to use.

    minimum, maximum = minimum and maximum levels (default: full map range)

    selection = an atom selection about which to display the mesh with
        an additional "buffer" (if provided).

SEE ALSO

    load, isomesh
        '''
        r = DEFAULT_ERROR
        if selection != '':
            region = 1  # about a selection
        else:
            region = 0  # render the whole map
        # preprocess selections
        selection = selector.process(selection)
        if selection not in ['center', 'origin']:
            selection = "(" + selection + ")"
        #
        if carve == None:
            carve = 0.0
        try:
            _self.lock(_self)
            r = _cmd.isomesh(_self._COb, str(name), str(map), int(region),
                             selection, float(buffer), float(minimum), 3,
                             int(state) - 1, float(carve),
                             int(source_state) - 1, int(quiet), float(maximum))
        finally:
            _self.unlock(r, _self)
        if _self._raising(r, _self): raise pymol.CmdException
        return r
Ejemplo n.º 3
0
    def isodot(name,map,level=1.0,selection='',buffer=0.0,state=0,
                  carve=None,source_state=0,quiet=1,_self=cmd):
        '''
DESCRIPTION

    "isodot" creates a dot isosurface object from a map object.

USAGE

    isodot name = map, level [,(selection) [,buffer [, state ] ] ] 

ARGUMENTS

    map = the name of the map object to use.

    level = the contour level.

    selection = an atom selection about which to display the mesh with
        an additional "buffer" (if provided).

NOTES

    If the dot isosurface object already exists, then the new dots will
    be appended onto the object as a new state.

SEE ALSO

    load, isomesh
        '''
        r = DEFAULT_ERROR
        if selection!='':
            region = 1 # about a selection
        else:
            region = 0 # render the whole map
        # preprocess selections
        selection = selector.process(selection)
        if selection not in [ 'center', 'origin' ]:
            selection = "("+selection+")"
        #
        if carve==None:
            carve=0.0
        try:
            _self.lock(_self)
            r = _cmd.isomesh(_self._COb,str(name),str(map),int(region),
                             selection,float(buffer),
                             float(level),1,int(state)-1,
                             float(carve),int(source_state)-1,int(quiet),
                             float(level))
        finally:
            _self.unlock(r,_self)
        if _self._raising(r,_self): raise pymol.CmdException                  
        return r
Ejemplo n.º 4
0
    def gradient(name, map, minimum=1.0, maximum=-1.0,
                 selection='', buffer=0.0, state=0,
                 carve=None, source_state=0, quiet=1, _self=cmd):
        '''
DESCRIPTION

    "gradient" creates a gradient object from a map object.

USAGE

    gradient name = map, [ minimum, [, maximum [, selection [, buffer [, state ]]]]]

ARGUMENTS

    map = the name of the map object to use.

    minimum, maximum = minimum and maximum levels (default: full map range)

    selection = an atom selection about which to display the mesh with
        an additional "buffer" (if provided).

SEE ALSO

    load, isomesh
        '''
        r = DEFAULT_ERROR
        if selection!='':
            region = 1 # about a selection
        else:
            region = 0 # render the whole map
        # preprocess selections
        selection = selector.process(selection)
        if selection not in [ 'center', 'origin' ]:
            selection = "("+selection+")"
        #
        if carve==None:
            carve=0.0
        try:
            _self.lock(_self)
            r = _cmd.isomesh(_self._COb,str(name),str(map),int(region),
                             selection,float(buffer),
                             float(minimum),3,int(state)-1,
                             float(carve),int(source_state)-1,int(quiet),
                             float(maximum))
        finally:
            _self.unlock(r,_self)
        if _self._raising(r,_self): raise pymol.CmdException                  
        return r
Ejemplo n.º 5
0
    def isomesh(name, map, level=1.0, selection='', buffer=0.0,
                state=1, carve=None, source_state=0, quiet=1, _self=cmd):
        '''
DESCRIPTION

    "isomesh" creates a mesh isosurface object from a map object.

USAGE

    isomesh name, map, level [, selection [, buffer [, state [, carve ]]]]

ARGUMENTS

    name = the name for the new mesh isosurface object.

    map = the name of the map object to use for computing the mesh.

    level = the contour level.

    selection = an atom selection about which to display the mesh with
        an additional "buffer" (if provided).

    state = the state into which the object should be loaded (default=1)
        (set state=0 to append new mesh as a new state)

    carve = a radius about each atom in the selection for which to
        include density. If "carve" is not provided, then the whole
        brick is displayed.

NOTES

    If the mesh object already exists, then the new mesh will be
    appended onto the object as a new state (unless you indicate a state).

    state > 0: specific state
    state = 0: all states
    state = -1: current state
    
    source_state > 0: specific state
    source_state = 0: include all states starting with 0
    source_state = -1: current state
    source_state = -2: last state in map

SEE ALSO

    isodot, load
'''
        r = DEFAULT_ERROR
        if selection!='':
            region = 1 # about a selection
        else:
            region = 0 # render the whole map
        # preprocess selection
        selection = selector.process(selection)
        if selection not in [ 'center', 'origin' ]:
            selection = "("+selection+")"
        #
        if carve==None:
            carve=0.0
        try:
            _self.lock(_self)
            r = _cmd.isomesh(_self._COb,str(name),str(map),int(region),
                             selection,float(buffer),
                             float(level),0,int(state)-1,float(carve),
                             int(source_state)-1,int(quiet),
                             float(level))
        finally:
            _self.unlock(r,_self)
        if _self._raising(r,_self): raise pymol.CmdException         
        return r
Ejemplo n.º 6
0
    def isomesh(name,
                map,
                level=1.0,
                selection='',
                buffer=0.0,
                state=1,
                carve=None,
                source_state=0,
                quiet=1,
                _self=cmd):
        '''
DESCRIPTION

    "isomesh" creates a mesh isosurface object from a map object.

USAGE

    isomesh name, map, level [, selection [, buffer [, state [, carve ]]]]

ARGUMENTS

    name = the name for the new mesh isosurface object.

    map = the name of the map object to use for computing the mesh.

    level = the contour level.

    selection = an atom selection about which to display the mesh with
        an additional "buffer" (if provided).

    state = the state into which the object should be loaded (default=1)
        (set state=0 to append new mesh as a new state)

    carve = a radius about each atom in the selection for which to
        include density. If "carve" is not provided, then the whole
        brick is displayed.

NOTES

    If the mesh object already exists, then the new mesh will be
    appended onto the object as a new state (unless you indicate a state).

    state > 0: specific state
    state = 0: all states
    state = -1: current state
    
    source_state > 0: specific state
    source_state = 0: include all states starting with 0
    source_state = -1: current state
    source_state = -2: last state in map

SEE ALSO

    isodot, load
'''
        r = DEFAULT_ERROR
        if selection != '':
            region = 1  # about a selection
        else:
            region = 0  # render the whole map
        # preprocess selection
        selection = selector.process(selection)
        if selection not in ['center', 'origin']:
            selection = "(" + selection + ")"
        #
        if carve == None:
            carve = 0.0
        try:
            _self.lock(_self)
            r = _cmd.isomesh(_self._COb, str(name), str(map), int(region),
                             selection, float(buffer), float(level), 0,
                             int(state) - 1, float(carve),
                             int(source_state) - 1, int(quiet), float(level))
        finally:
            _self.unlock(r, _self)
        if _self._raising(r, _self): raise pymol.CmdException
        return r