Logo Search packages:      
Sourcecode: pymol version File versions  Download package

parser.py

#A* -------------------------------------------------------------------
#B* This file contains source code for the PyMOL computer program
#C* copyright 1998-2000 by Warren Lyford Delano of DeLano Scientific. 
#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* -------------------------------------------------------------------

# parser.py
# Python parser module for PyMol
#

if __name__=='pymol.parser':
    
    import pymol
    import traceback
    import string
    import re
    import parsing
    import types
    import glob
    import sys
    import os
    import __main__

    from cmd import _feedback,fb_module,fb_mask,exp_path

    QuietException = parsing.QuietException
    CmdException = pymol.CmdException
    
    py_delims = { '=' : 1, '+='  : 1, '-='  : 1, '*=' : 1,
                      '/=' :1, '//=' : 1, '%='  : 1, '&=' : 1,
                      '|=' :1, '^='  : 1, '>>=' : 1,'<<=' : 1,
                      '**=':1 }

    remove_lists_re = re.compile("\[[^\]]*\]")

    def complete_sc(st,sc,type_name,postfix):
        result = None

        try:
            sc=sc() # invoke lambda functions (if any)
        except:
            traceback.print_exc()
        amb = sc.interpret(st)
        if amb==None:
            print " parser: no matching %s."%type_name
        elif type(amb)==types.StringType:
            result = amb+postfix
        else:
            amb.sort()
            print " parser: matching %s:"%type_name
            flist = filter(lambda x:x[0]!='_',amb)
            lst = parsing.list_to_str_list(flist)
            for a in lst:
                print a
            # now append up to point of ambiguity
            if not len(flist):
                css = []
            else:
                css = map(None,flist[0]) # common sub-string (css)
                for a in flist:
                    ac = map(None,a)
                    tmp = css
                    css = []
                    for c in range(len(tmp)):
                        if tmp[c]!=ac[c]:
                            break
                        css.append(tmp[c])
            css = filter(None,css)
            css = string.join(css,'')
            if len(css)>len(st):
                result = css
        return result
    
00082     class NestLayer:

        def __init__(self):

            self.cont = ""
            self.com0 = ""
            self.sc_path = "toplevel"
            self.embed_sentinel = None
            self.embed_dict = {}
            self.next = []

00093     class Parser:

        def __init__(self,cmd):

            self.cmd = cmd
            self.nest = 0
            self.layer = { 0: NestLayer() }
            self.pymol_names = self.cmd._pymol.__dict__
            
            # parsing state implemented with dictionaries to enable safe recursion
            # to arbitrary depths

            #com0 = {}    # verbose line, as read in
            #com1 = {}    # line w/o trailing whitespace
            #com2 = {}    # non-compound command
            #cont = {}    # continued characters from previous lines (i.e., before \ )
            #script = {}  # file handles
            #sc_path = {}   # file paths
            #kw = {}      # row in the keyword table for the current command
            #input = {}   # list of length two - command and unparsed arguments string
            #next = {}    # characters for next command (i.e., after ; )
            #args = {}    # parsed non-keyword argument string
            #kw_args = {} # parser keyword argument string
            #embed_dict = {}
            #embed_list = {}
            #embed_sentinel = {}
            #embed_type = {}
            #embed_line = {}

            # The resulting value from a pymol command (if any) is stored in the
            # parser.result global variable.  However, script developers will
            # geerally want to switch to the Python API for any of this kind of
            # stuff.

            self.result = None

            # initialize parser

            self.cmd._pymol.__script__="toplevel"

        # main parser routine

        def parse(self,s,secure):
            layer = self.layer.get(self.nest,None)
            self.result = None
# report any uncaught errors...
# WLD: this is problematic if parse is called inside an exception...removed.
#            if sys.exc_info()!=(None,None,None):
#                traceback.print_exc()
#                sys.exc_clear()
            if layer.embed_sentinel!=None:
                if string.strip(s) == layer.embed_sentinel:
                    etn = layer.embed_type
                    if etn == 0: # embedded data
                        print " Embed: read %d lines."%(len(layer.embed_list))
                        layer.embed_sentinel=None
                    elif etn == 1: # python block
                        print "PyMOL>"+string.rstrip(s)                    
                        py_block = string.join(layer.embed_list,'')
                        del layer.embed_list
                        layer.embed_sentinel=None
                        try:
                            exec(py_block,self.pymol_names,self.pymol_names)
                        except:
                            traceback.print_exc()
                    elif etn == 2: # skip block
                        print " Skip: skipped %d lines."%(layer.embed_line)
                        layer.embed_sentinel=None
                else:
                    etn = layer.embed_type
                    if etn == 0: # normal embedded data
                        layer.embed_list.append(string.rstrip(s)+"\n")
                    elif etn == 1: # python block
                        el = layer.embed_line + 1
                        print "%5d:%s"%(el,string.rstrip(s))
                        layer.embed_line = el
                        layer.embed_list.append(string.rstrip(s)+"\n")
                    elif etn == 2:
                        layer.embed_line = layer.embed_line + 1
                return 1
            p_result = 1
            layer.com0 = s
            try:
                layer.com1 = string.rstrip(layer.com0) # strips trailing whitespace
                if len(layer.com1) > 0:
                    if str(layer.com1[-1]) == "\\":
                        # prepend leftovers
                        if layer.cont != '':
                            layer.cont = layer.cont + "\n" + layer.com1[:-1]
                        else:
                            layer.cont = layer.com1[:-1]
                    else:
                        # prepend leftovers
                        if layer.cont != '':
                            layer.com1 = layer.cont + "\n" + layer.com1
                            layer.cont = ''
        # this routine splits up the line first based on semicolon 
                        
                        layer.next = parsing.split(layer.com1,';',1) + layer.next[1:]
                        
        # layer.com2 now a full non-compound command            
                        layer.com2 = layer.next[0]
                        layer.input = string.split(layer.com2,' ',1)
                        lin = len(layer.input)
                        if lin:
                            layer.input[0] = string.strip(layer.input[0])
                            com = layer.input[0]
                            if (com[0:1]=='/'):
                                # explicit literal python 
                                layer.com2 = string.strip(layer.com2[1:])
                                if len(layer.com2)>0:
                                    if not secure:
                                        exec(layer.com2+"\n",self.pymol_names,self.pymol_names)
                                    else:
                                        print 'Error: Python expressions disallowed in this file.'
                                        return None
                            elif lin>1 and py_delims.has_key(string.split(layer.input[-1:][0],' ',1)[0]):
                                if not secure:
                                    exec(layer.com2+"\n",self.pymol_names,self.pymol_names)
                                else:
                                    print 'Error: Python expressions disallowed in this file.'
                                    return None
                            else:
                                # try to find a keyword which matches
                                if self.cmd.kwhash.has_key(com):
                                    amb = self.cmd.kwhash.interpret(com)
                                    if amb == None:
                                        com = self.cmd.kwhash[com]
                                    elif type(amb)!=types.StringType:
                                        print 'Error: ambiguous command: '
                                        amb.sort()
                                        amb = parsing.list_to_str_list(amb)
                                        for a in amb:
                                            print a
                                        raise QuietException
                                    com = amb
                                if self.cmd.keyword.has_key(com):
                                    # here is the command and argument handling section
                                    layer.kw = self.cmd.keyword[com]
                                    if layer.kw[4]>=parsing.NO_CHECK:
                                        # stricter, Python-based argument parsing
                                        # remove line breaks (only important for Python expressions)
                                        layer.com2=string.replace(layer.com2,'\n','')

                                        if layer.kw[4]>=parsing.LITERAL: # treat literally
                                            layer.next = []
                                            if not secure:
                                                layer.com2=layer.com1
                                            else:
                                                print 'Error: Python expressions disallowed in this file.  '
                                                return 0
                                        if secure and (layer.kw[4]==parsing.SECURE):
                                            layer.next = []
                                            print 'Error: Command disallowed in this file.'
                                            return None
                                        else:
                                           (layer.args, layer.kw_args) = \
                                            parsing.prepare_call(
                                             layer.kw[0],
                                             parsing.parse_arg(layer.com2,mode=layer.kw[4],_self=self.cmd),
                                             layer.kw[4], _self=self.cmd) # will raise exception on failure
                                        self.result=apply(layer.kw[0],layer.args,layer.kw_args)
                                    elif layer.kw[4]==parsing.PYTHON:
                                            # handle python keyword
                                            layer.com2 = string.strip(layer.com2)
                                            if len(layer.com2)>0:
                                                if not secure:
                                                    exec(layer.com2+"\n",self.pymol_names,self.pymol_names)
                                                else:
                                                    layer.next = []                                    
                                                    print 'Error: Python expressions disallowed in this file.'
                                                    return None
                                    else:
                                        # remove line breaks (only important for Python expressions)
                                        layer.com2=string.replace(layer.com2,'\n','')
                                        # old parsing style, being phased out
                                        if layer.kw[4]==parsing.ABORT:
                                            return None # SCRIPT ABORT EXIT POINT
                                        if layer.kw[4]==parsing.MOVIE: # copy literal single line, no breaks
                                            layer.next = []
                                            if not secure:
                                                layer.input = string.split(layer.com1,' ',1)
                                            else:
                                                print 'Error: Movie commands disallowed in this file. '
                                                return None
                                        if len(layer.input)>1:
                                            layer.args = parsing.split(layer.input[1],layer.kw[3])
                                            while 1:
                                                nArg = len(layer.args) - 1
                                                c = 0
                                                while c < nArg:
                                                    if (string.count(layer.args[c],'(')!=
                                                         string.count(layer.args[c],')')):
                                                        tmp=layer.args[c+1]
                                                        layer.args.remove(tmp)
                                                        layer.args[c]=string.strip(layer.args[c])+\
                                                                          ','+string.strip(tmp)
                                                        nArg = nArg-1
                                                        break;
                                                    c = c + 1
                                                if c == nArg:
                                                    break;
                                            if len(layer.args)==1 and len(layer.args[0])==0:
                                                layer.args = []
                                        else:
                                            layer.args = []
                                        if layer.kw[1]<= len(layer.args) <= layer.kw[2]:
                                            layer.args = map(string.strip,layer.args)
                                            if layer.kw[4]<parsing.RUN:
                                                #                           
                                                # this is where old-style commands are invoked
                                                #
                                                self.result=apply(layer.kw[0],layer.args)
                                                #                           
                                            elif layer.kw[4]==parsing.SPAWN:
                                                if not secure:
                                                    path = exp_path(layer.args[0])                                                    
                                                    if re.search("\.pml$",path) != None:
                                                        if self.cmd._feedback(fb_module.parser,fb_mask.warnings):
                                                            print "Warning: use '@' instead of 'spawn' with PyMOL command scripts?"
                                                    # spawn command
                                                    if len(layer.args)==1: # default: module
                                                        parsing.run_file_as_module(path,spawn=1)
                                                    elif layer.args[1]=='main':
                                                        parsing.spawn_file(path,__main__.__dict__,__main__.__dict__)
                                                    elif layer.args[1]=='private':
                                                        parsing.spawn_file(path,__main__.__dict__,{})
                                                    elif layer.args[1]=='local':
                                                        parsing.spawn_file(path,self.pymol_names,{})
                                                    elif layer.args[1]=='global':
                                                        parsing.spawn_file(path,self.pymol_names,self.pymol_names)
                                                    elif layer.args[1]=='module':
                                                        parsing.run_file_as_module(path,spawn=1)
                                                else:
                                                    layer.next = []                                    
                                                    print 'Error: spawn disallowed in this file.'
                                                    return None
                                            elif layer.kw[4]==parsing.RUN: # synchronous
                                                if not secure:
                                                    path = exp_path(layer.args[0])
                                                    if re.search("\.pml$",path) != None:
                                                        if self.cmd._feedback(fb_module.parser,fb_mask.warnings):
                                                            print "Warning: use '@' instead of 'run' with PyMOL command scripts?"
                                                    # run command
                                                    if len(layer.args)==1: # default: global
                                                        parsing.run_file(path,self.pymol_names,self.pymol_names)
                                                    elif layer.args[1]=='main':
                                                        parsing.run_file(path,__main__.__dict__,__main__.__dict__)
                                                    elif layer.args[1]=='private':
                                                        parsing.run_file(path,__main__.__dict__,{})
                                                    elif layer.args[1]=='local':
                                                        parsing.run_file(path,self.pymol_names,{})
                                                    elif layer.args[1]=='global':
                                                        parsing.run_file(path,self.pymol_names,self.pymol_names)
                                                    elif layer.args[1]=='module':
                                                        parsing.run_file_as_module(path,spawn=0)
                                                    self.cmd._pymol.__script__ = layer.sc_path
                                                else:
                                                    layer.next = []                                    
                                                    print 'Error: run disallowed in this file.'
                                                    return None                                    
                                            elif (layer.kw[4]==parsing.EMBED):
                                                layer.next = []
                                                if secure or self.nest==0: # only legal on top level and p1m files
                                                    l = len(layer.args)
                                                    if l>0:
                                                        key = layer.args[0]
                                                    else:
                                                        key = os.path.splitext(os.path.basename(layer.sc_path))[0]
                                                    if l>1:
                                                        format = layer.args[1]
                                                    else:
                                                        format = 'pdb'
                                                    if l>2:
                                                        layer.embed_sentinel = layer.args[2]
                                                    else:
                                                        layer.embed_sentinel = "embed end"
                                                    list = []
                                                    layer.embed_dict[key] = ( format, list )
                                                    layer.embed_list = list
                                                    layer.embed_type = 0 # not a python block
                                                else:
                                                    print 'Error: embed only legal in special files (e.g. p1m)'
                                                    raise None
                                            elif (layer.kw[4]==parsing.SKIP):
                                                layer.next = []
                                                arg = parsing.apply_arg(
                                                    parsing.parse_arg(layer.com2,_self=self.cmd),
                                                    ('sentinel',),
                                                    {'sentinel':'skip end'})
                                                print arg # ???
                                                if len(layer.args):
                                                    if layer.args[0]=='end': # probable 'skip end' to ignore
                                                        arg = []
                                                if len(arg):
                                                    layer.embed_sentinel = arg[0]
                                                    layer.embed_type = 2 # skip block
                                                    layer.embed_line = 0
                                            elif (layer.kw[4]==parsing.PYTHON_BLOCK):
                                                layer.next = []
                                                if not secure:
                                                    arg = parsing.apply_arg(
                                                        parsing.parse_arg(layer.com2,_self=self.cmd),
                                                        ('sentinel','skip'),
                                                        {'sentinel':'python end','skip':0})
                                                    layer.embed_sentinel = arg[0]
                                                    list = []
                                                    layer.embed_list = list
                                                    if arg[1]:
                                                        layer.embed_type = 2 # skip block
                                                    else:
                                                        layer.embed_type = 1 # python block
                                                    layer.embed_line = 0
                                                else:
                                                    print 'Error: Python blocks disallowed in this file.'
                                                    raise None
                                            else:
                                                print 'Error: unknown keyword mode: '+str(layer.kw[4])
                                                raise QuietException
                                        else:
                                            print 'Error: invalid arguments for %s command.' % com
        #
        # non-keyword command handling
        #
                                elif len(layer.input[0]):
                                    if layer.input[0][0]=='@':
                                        path = exp_path(string.strip(layer.com2[1:]))
                                        if string.lower(path[-3:])=='p1m':
                                            nest_securely = 1
                                        else:
                                            nest_securely = secure
                                        if re.search("\.py$|\.pym$",path) != None:
                                            if self.cmd._feedback(fb_module.parser,fb_mask.warnings):
                                                print "Warning: use 'run' instead of '@' with Python files?"
                                        layer.script = open(path,'r')
                                        self.cmd._pymol.__script__ = path
                                        self.nest=self.nest+1
                                        self.layer[self.nest] = NestLayer()
                                        layer = self.layer[self.nest]
                                        layer.cont=''
                                        layer.sc_path=path
                                        layer.embed_sentinel=None
                                        while 1:
                                            layer.com0  = self.layer[self.nest-1].script.readline()
                                            if not layer.com0: break
                                            inp_cmd = layer.com0
                                            tmp_cmd = string.strip(inp_cmd)
                                            if len(tmp_cmd):
                                                if tmp_cmd[0] not in ['#','_','/']: # suppress comments, internals, python
                                                    if layer.embed_sentinel==None:
                                                        print "PyMOL>"+tmp_cmd
                                                elif tmp_cmd[0]=='_' and \
                                                      tmp_cmd[1:2] in [' ','']: # "_ " remove echo suppression signal
                                                    inp_cmd=inp_cmd[2:]
                                            pp_result = self.parse(inp_cmd,nest_securely)
                                            if pp_result==None: # RECURSION
                                                break # abort command gets us out
                                            elif pp_result==0: # QuietException
                                                if self.cmd.get_setting_legacy("stop_on_exceptions"):
                                                    p_result = 0 # signal an error occurred
                                                    print"PyMOL: stopped on exception."
                                                    break;
                                        self.nest=self.nest-1
                                        layer=self.layer[self.nest]
                                        
                                        layer.script.close()
                                        self.cmd.__script__ = layer.sc_path
                                    else: # nothing found, try literal python
                                        layer.com2 = string.strip(layer.com2)
                                        if len(layer.com2)>0:
                                            if not secure:
                                                exec(layer.com2+"\n",self.pymol_names,self.pymol_names)
                                            elif layer.input[0][0:1]!='#':
                                                print 'Error: unrecognized keyword: '+layer.input[0]
                        if (len(layer.next)>1) and p_result:
                            # continue parsing if no error or break has occurred
                            self.nest=self.nest+1
                            self.layer[self.nest] = NestLayer()
                            layer=self.layer[self.nest]
                            layer.com0 = self.layer[self.nest-1].next[1]
                            self.layer[self.nest-1].next=[]
                            layer.cont=''
                            layer.embed_sentinel=None
                            p_result = self.parse(layer.com0,secure) # RECURSION
                            self.nest=self.nest-1
                            layer=self.layer[self.nest]
            except QuietException:
                if self.cmd._feedback(fb_module.parser,fb_mask.blather):
                    print "Parser: QuietException caught"
                p_result = 0 # notify caller that an error was encountered
            except CmdException:
                if self.cmd._feedback(fb_module.parser,fb_mask.blather):         
                    print "Parser: CmdException caught."
                p_result = 0
            except:
                traceback.print_exc()
                if self.cmd._feedback(fb_module.parser,fb_mask.blather):
                    print "PyMOL: Caught an unknown exception."
                p_result = 0 # notify caller that an error was encountered
            return p_result  # 0 = Exception, None = abort, 1 = ok

        def get_embedded(self,key=None):
            layer = self.layer[self.nest]
            dict = layer.embed_dict
            if key==None:
                key = self.get_default_key()
            return dict.get(key,None)

        def get_default_key(self):
            layer = self.layer[self.nest]
            return os.path.splitext(os.path.basename(layer.sc_path))[0]

        def stdin_reader(self): # dedicated thread for reading standard input
            import sys
            while 1:
                l = sys.stdin.readline()
                if l!="":
                    if self.nest==0:
                        # if we're reading embedded input on stdin
                        # then bypass PyMOL C code altogether
                        if self.layer[0].embed_sentinel!=None:
                            self.parse(l)
                        else:
                            self.cmd.do(l)
                    else:
                        self.cmd.do(l)
                elif not self.cmd._pymol.invocation.options.keep_thread_alive:
                    self.cmd.quit()
            self.cmd._pymol._stdin_reader_thread = None

        def complete(self,st):
            result = None
            pre = ''
            flag = 0
            if (string.find(st,' ')<0) and (string.find(st,'@'))<0:
                try:
                    result = complete_sc(st, self.cmd.kwhash, 'commands',' ')
                except:
                    traceback.print_exc()
            else:
                full = self.cmd.kwhash.interpret(re.sub(r" .*","",st))
                st_no_lists = remove_lists_re.sub("",st)
                count = string.count(st_no_lists,',') # which argument are we on
                if self.cmd.is_string(full):
                    try:
                        if count<len(self.cmd.auto_arg):
                            if self.cmd.auto_arg[count].has_key(full): # autocomplete arguments
                                flag = 1
                                pre = re.sub(r"^[^ ]* ",' ',st,count=1) # trim command
                                if re.search(r",",pre)!=None:
                                    pre = re.sub(r"[^\, ]*$","",pre,count=1) 
                                    pre = re.sub(r",\s*[^\, ]*$",", ",pre,count=1) # trim 1 arg
                                else:
                                    pre = re.sub("[^ ]*$","",pre,count=1) # trim 1 arg               
                                pre = re.sub(r"^ *",'',pre)
                                pre = full+' '+pre
                                pat = re.sub(r".*[\, ]",'',st)
            #               print ":"+pre+":"+pat+":"
#                                print tuple([pat] + self.cmd.auto_arg[count][full])
                                result = apply(complete_sc,
                                               tuple([pat] + self.cmd.auto_arg[count][full]),
                                           {})
                    except:
                        traceback.print_exc()
                if not flag: # otherwise fallback onto filename completion
                    if(st[:1]=='@'):
                        st=st[1:]
                        pre = '@'
                    loc = reduce(max,[string.rfind(st,','),
                                            string.rfind(st,' '),
                                            string.rfind(st,']'),
                                            string.rfind(st,')')])+1
                    st3 = st[loc:]
                    flist = glob.glob(exp_path(st3)+"*")
                    lst = map(None,st3)
                    lst.reverse()
                    st3 = string.join(lst,'')
                    lf = len(flist)
                    if lf == 0:
                        print " parser: no matching files."
                    elif lf==1:
                        result = st[0:loc]+flist[0]
                        if os.path.isdir(flist[0]):
                            result = result + "/"
                    else:
                        flist.sort()
                        print " parser: matching files:"
                        lst = parsing.list_to_str_list(flist)
                        for a in lst:
                            print a
                        # now append as much up to point of ambiguity
                        css = map(None,flist[0]) # common sub-string (css)
                        for a in flist:
                            ac = map(None,a)
                            tmp = css
                            css = []
                            for c in range(len(tmp)):
                                if tmp[c]!=ac[c]:
                                    break
                                css.append(tmp[c])
                        tmp = css
                        css = []
                        for a in tmp:
                            if a==None:
                                break
                            css.append(a)
                        css = string.join(css,'')
                        if len(css)>len(st3):
                            result = st[0:loc]+css
            if result!=None:
                result = pre+result
            return result

    def new_parse_closure(self_cmd): # create parser and return an instance-specific parse function closure
        try:
            p = Parser(self_cmd)
        except:
            traceback.print_exc()
        self_cmd._parser = p
        return lambda s,secure,p=p:p.parse(s,secure)

    def new_complete_closure(self_cmd): # return an instance-specific complete function closure
        return lambda st,p=self_cmd._parser:p.complete(st)

# unused code?
#
#    def _same_(a,b):
#        if a==b:
#            return a
#        else:
#            return None

    



Generated by  Doxygen 1.6.0   Back to index