Exemple #1
0
    def distance(name=None, selection1="(pk1)", selection2="(pk2)", 
		 cutoff=None, mode=None, zoom=0, width=None, length=None,
                 gap=None, label=1, quiet=1, reset=0, state=0, _self=cmd):
	
        '''
DESCRIPTION

    "distance" creates a new distance object between two selections.

USAGE
    
    distance [name [, selection1 [, selection2 [, cutoff [, mode ]]]]]

ARGUMENTS

    name = string: name of the distance object to create

    selection1 = string: first atom selection

    selection2 = string: second atom selection

    cutoff = float: longest distance to show 
    
    mode = 0: all interatomic distances

    mode = 1: only bond distances

    mode = 2: only show polar contact distances

EXAMPLES

    distance mydist, 14/CA, 29/CA

    distance hbonds, all, all, 3.2, mode=2

NOTES

    The distance wizard makes measuring distances easier than using
    the "dist" command for real-time operations.

    "dist" alone will show distances between selections (pk1) and (pk1),
    which can be set using the PkAt mouse action (usually CTRL-middle-click).

PYMOL API

    cmd.distance(string name, string selection1, string selection2,
                 string cutoff, string mode )

    '''
        # handle unnamed distance
        r = DEFAULT_SUCCESS
        if name!=None:
            if len(name):
                if name[0]=='(' or ' ' in name or '/' in name: # we're one argument off...
                    if cutoff!=None:
                        mode = cutoff
                    if selection2!="(pk2)":
                        cutoff = selection2
                    if selection1!="(pk1)":
                        selection2 = selection1
                    selection1=name
                    name = None

        if selection1=="(pk1)":
            if "pk1" not in _self.get_names('selections'):
                if _feedback(fb_module.cmd,fb_mask.errors,_self):
                    print "cmd-Error: The 'pk1' selection is undefined."
                r = DEFAULT_ERROR
        if selection2=="(pk2)":
            if "pk2" not in _self.get_names('selections'):
                if _feedback(fb_module.cmd,fb_mask.errors,_self):         
                    print "cmd-Error: The 'pk2' selection is undefined."
                r = DEFAULT_ERROR
        if is_ok(r):
            r = DEFAULT_ERROR

            # if unlabeled, then get next name in series

            if name!=None:
                nam=name
            else:
                try:
                    _self.lock(_self)
                    cnt = _cmd.get(_self._COb,"dist_counter") + 1.0
                    r = _cmd.legacy_set(_self._COb,"dist_counter","%1.0f" % cnt)
                    nam = "dist%02.0f" % cnt
                finally:
                    _self.unlock(r,_self)

            # defaults
            if mode == None:
                mode = 0
            if cutoff == None:
                cutoff = -1.0
            # preprocess selections
            selection1 = selector.process(selection1)
            selection2 = selector.process(selection2)
            # now do the deed
            try:
                _self.lock(_self)
                if selection2!="same":
                    selection2 = "("+selection2+")"
                r = _cmd.dist(_self._COb,str(nam),"("+str(selection1)+")",
                              str(selection2),int(mode),float(cutoff),
                              int(label),int(quiet),int(reset),
                              int(state)-1,int(zoom))
                if width!=None:
                    _self.set("dash_width",width,nam)
                if length!=None:
                    _self.set("dash_length",length,nam)
                if gap!=None:
                    _self.set("dash_gap",gap,nam)
            finally:
                _self.unlock(r,_self)
        if (r<0.0) and (not quiet):
            # a negative value is an warning signal from PyMOL...
            r = DEFAULT_ERROR
        if _raising(r,_self): raise pymol.CmdException
        return r
Exemple #2
0
    def dihedral(name=None, selection1="(pk1)", selection2="(pk2)",
		 selection3="(pk3)", selection4="(pk4)", mode=None,
		 label=1, reset=0, zoom=0, state=0, quiet=1, _self=cmd):
        '''
DESCRIPTION

    "dihedral" shows dihedral angles formed between any four atoms.

USAGE

    dihedral [ name [, selection1 [, selection2 [, selection3 [, selection4 ]]]]]


NOTES

    "dihedral" alone will show the dihedral angle formed by selections
    (pk1), (pk2), (pk3), and (pk4), which can be set using the "PkAt"
    mouse action (typically, Ctrl-middle-click)

PYMOL API

    cmd.dihedral(string name, string selection1, string selection2,
                 string selection3, string selection4)

SEE ALSO

    distance, angle
    '''
        r = DEFAULT_SUCCESS      
        if selection1=="(pk1)":
            if "pk1" not in _self.get_names('selections'):
                if _feedback(fb_module.cmd,fb_mask.errors,_self):
                    print "cmd-Error: The 'pk1' selection is undefined."
                r = DEFAULT_ERROR
        if selection2=="(pk2)":
            if "pk2" not in _self.get_names('selections'):
                if _feedback(fb_module.cmd,fb_mask.errors,_self):         
                    print "cmd-Error: The 'pk2' selection is undefined."
                r = DEFAULT_ERROR
        if selection3=="(pk3)":
            if "pk3" not in _self.get_names('selections'):
                if _feedback(fb_module.cmd,fb_mask.errors,_self):         
                    print "cmd-Error: The 'pk3' selection is undefined."
                r = DEFAULT_ERROR
        if selection3=="(pk4)":
            if "pk4" not in _self.get_names('selections'):
                if _feedback(fb_module.cmd,fb_mask.errors,_self):         
                    print "cmd-Error: The 'pk4' selection is undefined."
                r = DEFAULT_ERROR
        if is_ok(r):
            r = DEFAULT_ERROR
            # if unlabeled, then get next name in series

            if name!=None:
                nam=name
            else:
                try:
                    _self.lock(_self)
                    cnt = _cmd.get(_self._COb,"dist_counter") + 1.0
                    r = _cmd.legacy_set(_self._COb,"dist_counter","%1.0f" % cnt)
                    nam = "dihedral%02.0f" % cnt
                finally:
                    _self.unlock(r,_self)

            # defaults
            if mode == None:
                mode = 0
            # preprocess selections
            selection1 = selector.process(selection1)
            selection2 = selector.process(selection2)
            selection3 = selector.process(selection3)
            selection4 = selector.process(selection4)
            # now do the deed
            try:
                _self.lock(_self)
                if selection2!="same":
                    selection2 = "("+selection2+")"
                if selection3!="same":
                    selection3 = "("+selection3+")"
                if selection4!="same":
                    selection4 = "("+selection4+")"
                r = _cmd.dihedral(_self._COb,str(nam),"("+str(selection1)+")",
                                  str(selection2),
                                  str(selection3),
                                  str(selection4),
                                  int(mode),int(label),
                                  int(reset),int(zoom),
                                  int(quiet),int(state)-1)
            finally:
                _self.unlock(r,_self)
        if _raising(r,_self): raise pymol.CmdException
        return r
Exemple #3
0
    def select(name, selection="", enable=-1, quiet=1, merge=0, state=0, domain='',_self=cmd): 
        '''
DESCRIPTION

    "select" creates a named atom selection from a
    selection-expression.

USAGE

    select name, selection [, enable [, quiet [, merge [, state [, domain ]]]]]

ARGUMENTS

    name = a unique name for the selection

    selection = a selection-expression

NOTES

    If a selection-expression with explicit surrounding parethenses is
    provided as the first argument, then the default selection name
    is used as the name argument.

EXAMPLES 

    select chA, chain A
    select ( resn his )
    select near142, resi 142 around 5

PYMOL API

    cmd.select(string name, string selection)

SEE ALSO

    delete
        '''
        r = DEFAULT_ERROR
        try:
            _self.lock(_self)
            if selection=="":
                selection = name                    
                if _cmd.get(_self._COb,"auto_number_selections")!=0.0:
                    sel_cnt = _cmd.get(_self._COb,"sel_counter") + 1.0
                    _cmd.legacy_set(_self._COb,"sel_counter","%1.0f" % sel_cnt)
                    name = "sel%02.0f" % sel_cnt
                else:
                    name = "sele"
            if name == None:
                sel_cnt = _cmd.get(_self._COb,"sel_counter") + 1.0
                _cmd.legacy_set(_self._COb,"sel_counter","%1.0f" % sel_cnt)
                name = "sel%02.0f" % sel_cnt
                
            # preprocess selection (note: inside TRY)
            selection = selector.process(selection)
            merge = int(merge)
            if merge==1:
                selection = "("+selection+") or ?"+name # merge if exists
            elif merge==2:
                selection = "("+selection+") or ??"+name # merge if exists and active
            #
            r = _cmd.select(_self._COb,str(name),str(selection),int(quiet),int(state)-1,str(domain))
            enable = int(enable)
            if is_ok(r) and enable>0:
                _cmd.onoff(_self._COb,str(name),1,0);
            elif enable == 0:
                _cmd.onoff(_self._COb,str(name),0,0)
        finally:
            _self.unlock(r,_self)
        if _self._raising(r,_self): raise pymol.CmdException                  
        return r
Exemple #4
0
    def create(name, selection, source_state=0,
               target_state=0, discrete=0, zoom=-1, quiet=1,
               singletons=0, extract=None, _self=cmd):
        '''
DESCRIPTION

    "create" creates a new molecule object from a selection.  It can
    also be used to create states in an existing object.

USAGE

    create name, selection [,source_state [,target_state ] ]

ARGUMENTS

    name = string: name of object to create or modify

    selection = string: atoms to include in the new object

    source_state = integer: {default: 0 -- copy all states}

    target_state = integer: {default: 0}

PYMOL API

    cmd.create(string name, string selection, int state,
               int target_state, int discrete)

NOTES

    If the source and target states are zero (default), then all
    states will be copied.  Otherwise, only the indicated states will
    be copied.

SEE ALSO

    load, copy, extract
        '''
        r = DEFAULT_ERROR      
        # preprocess selection
        selection = selector.process(selection)
        #      
        try:
            _self.lock(_self)
            if name==None:
                avoid = {}
                for obj in cmd.get_names("all"):
                    avoid[obj] = 1
                sel_cnt = _cmd.get(_self._COb,"sel_counter") 
                while 1:
                    sel_cnt = sel_cnt + 1.0
                    name = "obj%02.0f" % sel_cnt
                    if not avoid.has_key(name):
                        _cmd.legacy_set(_self._COb,"sel_counter","%1.0f" % sel_cnt)
                        break
            r = _cmd.create(_self._COb,str(name),"("+str(selection)+")",
                            int(source_state)-1,int(target_state)-1,
                            int(discrete),int(zoom),int(quiet),int(singletons))
        finally:
            _self.unlock(r,_self)
        if not is_error(r): # temporary inefficient implementation
            if extract not in (None, 0, '0'):
                if extract not in (1, '1'):
                    extract = selector.process(extract)
                else:
                    extract = selection
                _self.remove("(("+extract+") in (%s)) and not (%s)"%(name,name))
        if _self._raising(r,_self): raise pymol.CmdException                                    
        return r
Exemple #5
0
    def distance(name=None,
                 selection1="(pk1)",
                 selection2="(pk2)",
                 cutoff=None,
                 mode=None,
                 zoom=0,
                 width=None,
                 length=None,
                 gap=None,
                 label=1,
                 quiet=1,
                 reset=0,
                 state=0,
                 _self=cmd):
        '''
DESCRIPTION

    "distance" creates a new distance object between two selections.

USAGE
    
    distance [name [, selection1 [, selection2 [, cutoff [, mode ]]]]]

ARGUMENTS

    name = string: name of the distance object to create

    selection1 = string: first atom selection

    selection2 = string: second atom selection

    cutoff = float: longest distance to show 
    
    mode = 0: all interatomic distances

    mode = 1: only bond distances

    mode = 2: only show polar contact distances

EXAMPLES

    distance mydist, 14/CA, 29/CA

    distance hbonds, all, all, 3.2, mode=2

NOTES

    The distance wizard makes measuring distances easier than using
    the "dist" command for real-time operations.

    "dist" alone will show distances between selections (pk1) and (pk1),
    which can be set using the PkAt mouse action (usually CTRL-middle-click).

PYMOL API

    cmd.distance(string name, string selection1, string selection2,
                 string cutoff, string mode )

    '''
        # handle unnamed distance
        r = DEFAULT_SUCCESS
        if name != None:
            if len(name):
                if name[0] == '(' or ' ' in name or '/' in name:  # we're one argument off...
                    if cutoff != None:
                        mode = cutoff
                    if selection2 != "(pk2)":
                        cutoff = selection2
                    if selection1 != "(pk1)":
                        selection2 = selection1
                    selection1 = name
                    name = None

        if selection1 == "(pk1)":
            if "pk1" not in _self.get_names('selections'):
                if _feedback(fb_module.cmd, fb_mask.errors, _self):
                    print "cmd-Error: The 'pk1' selection is undefined."
                r = DEFAULT_ERROR
        if selection2 == "(pk2)":
            if "pk2" not in _self.get_names('selections'):
                if _feedback(fb_module.cmd, fb_mask.errors, _self):
                    print "cmd-Error: The 'pk2' selection is undefined."
                r = DEFAULT_ERROR
        if is_ok(r):
            r = DEFAULT_ERROR

            # if unlabeled, then get next name in series

            if name != None:
                nam = name
            else:
                try:
                    _self.lock(_self)
                    cnt = _cmd.get(_self._COb, "dist_counter") + 1.0
                    r = _cmd.legacy_set(_self._COb, "dist_counter",
                                        "%1.0f" % cnt)
                    nam = "dist%02.0f" % cnt
                finally:
                    _self.unlock(r, _self)

            # defaults
            if mode == None:
                mode = 0
            if cutoff == None:
                cutoff = -1.0
            # preprocess selections
            selection1 = selector.process(selection1)
            selection2 = selector.process(selection2)
            # now do the deed
            try:
                _self.lock(_self)
                if selection2 != "same":
                    selection2 = "(" + selection2 + ")"
                r = _cmd.dist(_self._COb, str(nam),
                              "(" + str(selection1) + ")", str(selection2),
                              int(mode), float(cutoff), int(label), int(quiet),
                              int(reset),
                              int(state) - 1, int(zoom))
                if width != None:
                    _self.set("dash_width", width, nam)
                if length != None:
                    _self.set("dash_length", length, nam)
                if gap != None:
                    _self.set("dash_gap", gap, nam)
            finally:
                _self.unlock(r, _self)
        if (r < 0.0) and (not quiet):
            # a negative value is an warning signal from PyMOL...
            r = DEFAULT_ERROR
        if _raising(r, _self): raise pymol.CmdException
        return r
Exemple #6
0
    def dihedral(name=None,
                 selection1="(pk1)",
                 selection2="(pk2)",
                 selection3="(pk3)",
                 selection4="(pk4)",
                 mode=None,
                 label=1,
                 reset=0,
                 zoom=0,
                 state=0,
                 quiet=1,
                 _self=cmd):
        '''
DESCRIPTION

    "dihedral" shows dihedral angles formed between any four atoms.

USAGE

    dihedral [ name [, selection1 [, selection2 [, selection3 [, selection4 ]]]]]


NOTES

    "dihedral" alone will show the dihedral angle formed by selections
    (pk1), (pk2), (pk3), and (pk4), which can be set using the "PkAt"
    mouse action (typically, Ctrl-middle-click)

PYMOL API

    cmd.dihedral(string name, string selection1, string selection2,
                 string selection3, string selection4)

SEE ALSO

    distance, angle
    '''
        r = DEFAULT_SUCCESS
        if selection1 == "(pk1)":
            if "pk1" not in _self.get_names('selections'):
                if _feedback(fb_module.cmd, fb_mask.errors, _self):
                    print "cmd-Error: The 'pk1' selection is undefined."
                r = DEFAULT_ERROR
        if selection2 == "(pk2)":
            if "pk2" not in _self.get_names('selections'):
                if _feedback(fb_module.cmd, fb_mask.errors, _self):
                    print "cmd-Error: The 'pk2' selection is undefined."
                r = DEFAULT_ERROR
        if selection3 == "(pk3)":
            if "pk3" not in _self.get_names('selections'):
                if _feedback(fb_module.cmd, fb_mask.errors, _self):
                    print "cmd-Error: The 'pk3' selection is undefined."
                r = DEFAULT_ERROR
        if selection3 == "(pk4)":
            if "pk4" not in _self.get_names('selections'):
                if _feedback(fb_module.cmd, fb_mask.errors, _self):
                    print "cmd-Error: The 'pk4' selection is undefined."
                r = DEFAULT_ERROR
        if is_ok(r):
            r = DEFAULT_ERROR
            # if unlabeled, then get next name in series

            if name != None:
                nam = name
            else:
                try:
                    _self.lock(_self)
                    cnt = _cmd.get(_self._COb, "dist_counter") + 1.0
                    r = _cmd.legacy_set(_self._COb, "dist_counter",
                                        "%1.0f" % cnt)
                    nam = "dihedral%02.0f" % cnt
                finally:
                    _self.unlock(r, _self)

            # defaults
            if mode == None:
                mode = 0
            # preprocess selections
            selection1 = selector.process(selection1)
            selection2 = selector.process(selection2)
            selection3 = selector.process(selection3)
            selection4 = selector.process(selection4)
            # now do the deed
            try:
                _self.lock(_self)
                if selection2 != "same":
                    selection2 = "(" + selection2 + ")"
                if selection3 != "same":
                    selection3 = "(" + selection3 + ")"
                if selection4 != "same":
                    selection4 = "(" + selection4 + ")"
                r = _cmd.dihedral(_self._COb,
                                  str(nam), "(" + str(selection1) + ")",
                                  str(selection2), str(selection3),
                                  str(selection4), int(mode), int(label),
                                  int(reset), int(zoom), int(quiet),
                                  int(state) - 1)
            finally:
                _self.unlock(r, _self)
        if _raising(r, _self): raise pymol.CmdException
        return r