pyemaps 2.0.0__py3-none-any.whl

pyemaps/CifFile/YappsStarParser_2_0.py

@@ -0,0 +1,369 @@
+# To maximize python3/python2 compatibility
+from __future__ import print_function
+from __future__ import unicode_literals
+from __future__ import division
+from __future__ import absolute_import
+
+from .StarFile import StarBlock,StarFile,StarList,StarDict
+from io import StringIO
+# An alternative specification for the Cif Parser, based on Yapps2
+# by Amit Patel (http://theory.stanford.edu/~amitp/Yapps)
+#
+# helper code: we define our match tokens
+lastval = ''
+def monitor(location,value):
+    global lastval
+    #print 'At %s: %s' % (location,repr(value))
+    lastval = repr(value)
+    return value
+
+# Strip extras gets rid of leading and trailing whitespace, and
+# semicolons.
+def stripextras(value):
+     from .StarFile import remove_line_folding, remove_line_prefix
+     # we get rid of semicolons and leading/trailing terminators etc.
+     import re
+     jj = re.compile("[\n\r\f \t\v]*")
+     semis = re.compile("[\n\r\f \t\v]*[\n\r\f]\n*;")
+     cut = semis.match(value)
+     if cut:        #we have a semicolon-delimited string
+          nv = value[cut.end():len(value)-2]
+          try:
+             if nv[-1]=='\r': nv = nv[:-1]
+          except IndexError:    #empty data value
+             pass
+          # apply protocols
+          nv = remove_line_prefix(nv)
+          nv = remove_line_folding(nv)
+          return nv
+     else:
+          cut = jj.match(value)
+          if cut:
+               return stripstring(value[cut.end():])
+          return value
+
+# helper function to get rid of inverted commas etc.
+
+def stripstring(value):
+     if value:
+         if value[0]== '\'' and value[-1]=='\'':
+           return value[1:-1]
+         if value[0]=='"' and value[-1]=='"':
+           return value[1:-1]
+     return value
+
+# helper function to get rid of triple quotes
+def striptriple(value):
+    if value:
+        if value[:3] == '"""' and value[-3:] == '"""':
+            return value[3:-3]
+        if value[:3] == "'''" and value[-3:] == "'''":
+            return value[3:-3]
+    return value
+
+# helper function to populate a StarBlock given a list of names
+# and values .
+#
+# Note that there may be an empty list at the very end of our itemlists,
+# so we remove that if necessary.
+#
+
+def makeloop(target_block,loopdata):
+    loop_seq,itemlists = loopdata
+    if itemlists[-1] == []: itemlists.pop(-1)
+    # print('Making loop with %s' % repr(itemlists))
+    step_size = len(loop_seq)
+    for col_no in range(step_size):
+       target_block.AddItem(loop_seq[col_no], itemlists[col_no::step_size],precheck=True)
+    # now construct the loop
+    try:
+        target_block.CreateLoop(loop_seq)  #will raise ValueError on problem
+    except ValueError:
+        error_string =  'Incorrect number of loop values for loop containing %s' % repr(loop_seq)
+        print(error_string, file=sys.stderr)
+        raise ValueError(error_string)
+
+# return an object with the appropriate amount of nesting
+def make_empty(nestlevel):
+    gd = []
+    for i in range(1,nestlevel):
+        gd = [gd]
+    return gd
+
+# this function updates a dictionary first checking for name collisions,
+# which imply that the CIF is invalid.  We need case insensitivity for
+# names.
+
+# Unfortunately we cannot check loop item contents against non-loop contents
+# in a non-messy way during parsing, as we may not have easy access to previous
+# key value pairs in the context of our call (unlike our built-in access to all
+# previous loops).
+# For this reason, we don't waste time checking looped items against non-looped
+# names during parsing of a data block.  This would only match a subset of the
+# final items.   We do check against ordinary items, however.
+#
+# Note the following situations:
+# (1) new_dict is empty -> we have just added a loop; do no checking
+# (2) new_dict is not empty -> we have some new key-value pairs
+#
+def cif_update(old_dict,new_dict,loops):
+    old_keys = map(lambda a:a.lower(),old_dict.keys())
+    if new_dict != {}:    # otherwise we have a new loop
+        #print 'Comparing %s to %s' % (repr(old_keys),repr(new_dict.keys()))
+        for new_key in new_dict.keys():
+            if new_key.lower() in old_keys:
+                raise CifError("Duplicate dataname or blockname %s in input file" % new_key)
+            old_dict[new_key] = new_dict[new_key]
+#
+# this takes two lines, so we couldn't fit it into a one line execution statement...
+def order_update(order_array,new_name):
+    order_array.append(new_name)
+    return new_name
+
+# and finally...turn a sequence into a python dict (thanks to Stackoverflow)
+def pairwise(iterable):
+    try:
+        it = iter(iterable)
+        while 1:
+            yield next(it), next(it)
+    except StopIteration:
+        return
+
+# Begin -- grammar generated by Yapps
+import sys, re
+from . import yapps3_compiled_rt as yappsrt
+
+class StarParserScanner(yappsrt.Scanner):
+    def __init__(self, *args,**kwargs):
+        patterns = [
+         ('":"', ':'),
+         ('([ \t\n\r](?!;))|[ \t]', '([ \t\n\r](?!;))|[ \t]'),
+         ('(#.*[\n\r](?!;))|(#.*)', '(#.*[\n\r](?!;))|(#.*)'),
+         ('LBLOCK', '(L|l)(O|o)(O|o)(P|p)_'),
+         ('GLOBAL', '(G|g)(L|l)(O|o)(B|b)(A|a)(L|l)_'),
+         ('STOP', '(S|s)(T|t)(O|o)(P|p)_'),
+         ('save_heading', u'(S|s)(A|a)(V|v)(E|e)_[][!%&\\(\\)*+,./:<=>?@0-9A-Za-z\\\\^`{}\\|~"#$\';_\xa0-\ud7ff\ue000-\ufdcf\ufdf0-\ufffd\U00010000-\U0001fffd\U00020000-\U0002fffd\U00030000-\U0003fffd\U00040000-\U0004fffd\U00050000-\U0005fffd\U00060000-\U0006fffd\U00070000-\U0007fffd\U00080000-\U0008fffd\U00090000-\U0009fffd\U000a0000-\U000afffd\U000b0000-\U000bfffd\U000c0000-\U000cfffd\U000d0000-\U000dfffd\U000e0000-\U000efffd\U000f0000-\U000ffffd\U00100000-\U0010fffd-]+'),
+         ('save_end', '(S|s)(A|a)(V|v)(E|e)_'),
+         ('data_name', u'_[][!%&\\(\\)*+,./:<=>?@0-9A-Za-z\\\\^`{}\\|~"#$\';_\xa0-\ud7ff\ue000-\ufdcf\ufdf0-\ufffd\U00010000-\U0001fffd\U00020000-\U0002fffd\U00030000-\U0003fffd\U00040000-\U0004fffd\U00050000-\U0005fffd\U00060000-\U0006fffd\U00070000-\U0007fffd\U00080000-\U0008fffd\U00090000-\U0009fffd\U000a0000-\U000afffd\U000b0000-\U000bfffd\U000c0000-\U000cfffd\U000d0000-\U000dfffd\U000e0000-\U000efffd\U000f0000-\U000ffffd\U00100000-\U0010fffd-]+'),
+         ('data_heading', u'(D|d)(A|a)(T|t)(A|a)_[][!%&\\(\\)*+,./:<=>?@0-9A-Za-z\\\\^`{}\\|~"#$\';_\xa0-\ud7ff\ue000-\ufdcf\ufdf0-\ufffd\U00010000-\U0001fffd\U00020000-\U0002fffd\U00030000-\U0003fffd\U00040000-\U0004fffd\U00050000-\U0005fffd\U00060000-\U0006fffd\U00070000-\U0007fffd\U00080000-\U0008fffd\U00090000-\U0009fffd\U000a0000-\U000afffd\U000b0000-\U000bfffd\U000c0000-\U000cfffd\U000d0000-\U000dfffd\U000e0000-\U000efffd\U000f0000-\U000ffffd\U00100000-\U0010fffd-]+'),
+         ('start_sc_line', '(\n|\r\n);([^\n\r])*(\r\n|\r|\n)+'),
+         ('sc_line_of_text', '[^;\r\n]([^\r\n])*(\r\n|\r|\n)+'),
+         ('end_sc_line', ';'),
+         ('c_c_b', '\\}'),
+         ('o_c_b', '\\{'),
+         ('c_s_b', '\\]'),
+         ('o_s_b', '\\['),
+         ('dat_val_internal_sq', '\\[([^\\s\\[\\]]*)\\]'),
+         ('triple_quote_data_value', '(?s)\'\'\'.*?\'\'\'|""".*?"""'),
+         ('single_quote_data_value', '\'([^\n\r\x0c\'])*\'+|"([^\n\r"])*"+'),
+         ('data_value_1', '((?!(((S|s)(A|a)(V|v)(E|e)_[^\\s]*)|((G|g)(L|l)(O|o)(B|b)(A|a)(L|l)_[^\\s]*)|((S|s)(T|t)(O|o)(P|p)_[^\\s]*)|((D|d)(A|a)(T|t)(A|a)_[^\\s]*)))[^\\s"#$\'_\\{\\}\\[\\]][^\\s\\{\\}\\[\\]]*)'),
+         ('END', '$'),
+        ]
+        yappsrt.Scanner.__init__(self,patterns,['([ \t\n\r](?!;))|[ \t]', '(#.*[\n\r](?!;))|(#.*)'],*args,**kwargs)
+
+class StarParser(yappsrt.Parser):
+    Context = yappsrt.Context
+    def input(self, prepared, _parent=None):
+        _context = self.Context(_parent, self._scanner, self._pos, 'input', [prepared])
+        _token = self._peek('END', 'data_heading')
+        if _token == 'data_heading':
+            dblock = self.dblock(prepared, _context)
+            allblocks = prepared; allblocks.merge_fast(dblock)
+            while self._peek('END', 'data_heading') == 'data_heading':
+                dblock = self.dblock(prepared, _context)
+                allblocks.merge_fast(dblock)
+            if self._peek() not in ['END', 'data_heading']:
+                raise yappsrt.YappsSyntaxError(charpos=self._scanner.get_prev_char_pos(), context=_context, msg='Need one of ' + ', '.join(['END', 'data_heading']))
+            END = self._scan('END')
+        else: # == 'END'
+            END = self._scan('END')
+            allblocks = prepared
+        allblocks.unlock(); return allblocks
+
+    def dblock(self, prepared, _parent=None):
+        _context = self.Context(_parent, self._scanner, self._pos, 'dblock', [prepared])
+        data_heading = self._scan('data_heading')
+        heading = data_heading[5:];thisbc=StarFile(characterset='unicode',standard=prepared.standard);act_heading = thisbc.NewBlock(heading,prepared.blocktype(overwrite=False));stored_block = thisbc[act_heading]
+        while self._peek('save_heading', 'save_end', 'LBLOCK', 'data_name', 'END', 'data_heading') in ['save_heading', 'LBLOCK', 'data_name']:
+            _token = self._peek('save_heading', 'LBLOCK', 'data_name')
+            if _token != 'save_heading':
+                dataseq = self.dataseq(stored_block, _context)
+            else: # == 'save_heading'
+                save_frame = self.save_frame(prepared, _context)
+                thisbc.merge_fast(save_frame,parent=stored_block)
+        if self._peek() not in ['save_heading', 'save_end', 'LBLOCK', 'data_name', 'END', 'data_heading']:
+            raise yappsrt.YappsSyntaxError(charpos=self._scanner.get_prev_char_pos(), context=_context, msg='Need one of ' + ', '.join(['save_heading', 'save_end', 'LBLOCK', 'data_name', 'END', 'data_heading']))
+        stored_block.setmaxnamelength(stored_block.maxnamelength);return (monitor('dblock',thisbc))
+
+    def dataseq(self, starblock, _parent=None):
+        _context = self.Context(_parent, self._scanner, self._pos, 'dataseq', [starblock])
+        data = self.data(starblock, _context)
+        while self._peek('save_end', 'LBLOCK', 'data_name', 'save_heading', 'END', 'data_heading') in ['LBLOCK', 'data_name']:
+            data = self.data(starblock, _context)
+        if self._peek() not in ['save_end', 'LBLOCK', 'data_name', 'save_heading', 'END', 'data_heading']:
+            raise yappsrt.YappsSyntaxError(charpos=self._scanner.get_prev_char_pos(), context=_context, msg='Need one of ' + ', '.join(['LBLOCK', 'data_name', 'save_end', 'save_heading', 'END', 'data_heading']))
+
+    def data(self, currentblock, _parent=None):
+        _context = self.Context(_parent, self._scanner, self._pos, 'data', [currentblock])
+        _token = self._peek('LBLOCK', 'data_name')
+        if _token == 'LBLOCK':
+            top_loop = self.top_loop(_context)
+            makeloop(currentblock,top_loop)
+        else: # == 'data_name'
+            datakvpair = self.datakvpair(_context)
+            currentblock.AddItem(datakvpair[0],datakvpair[1],precheck=False)
+
+    def datakvpair(self, _parent=None):
+        _context = self.Context(_parent, self._scanner, self._pos, 'datakvpair', [])
+        data_name = self._scan('data_name')
+        data_value = self.data_value(_context)
+        return [data_name,data_value]
+
+    def data_value(self, _parent=None):
+        _context = self.Context(_parent, self._scanner, self._pos, 'data_value', [])
+        _token = self._peek('data_value_1', 'triple_quote_data_value', 'single_quote_data_value', 'start_sc_line', 'o_s_b', 'o_c_b')
+        if _token == 'data_value_1':
+            data_value_1 = self._scan('data_value_1')
+            thisval = data_value_1
+        elif _token not in ['start_sc_line', 'o_s_b', 'o_c_b']:
+            delimited_data_value = self.delimited_data_value(_context)
+            thisval = delimited_data_value
+        elif _token == 'start_sc_line':
+            sc_lines_of_text = self.sc_lines_of_text(_context)
+            thisval = stripextras(sc_lines_of_text)
+        else: # in ['o_s_b', 'o_c_b']
+            bracket_expression = self.bracket_expression(_context)
+            thisval = bracket_expression
+        return monitor('data_value',thisval)
+
+    def delimited_data_value(self, _parent=None):
+        _context = self.Context(_parent, self._scanner, self._pos, 'delimited_data_value', [])
+        _token = self._peek('triple_quote_data_value', 'single_quote_data_value')
+        if _token == 'triple_quote_data_value':
+            triple_quote_data_value = self._scan('triple_quote_data_value')
+            thisval = striptriple(triple_quote_data_value)
+        else: # == 'single_quote_data_value'
+            single_quote_data_value = self._scan('single_quote_data_value')
+            thisval = stripstring(single_quote_data_value)
+        return thisval
+
+    def sc_lines_of_text(self, _parent=None):
+        _context = self.Context(_parent, self._scanner, self._pos, 'sc_lines_of_text', [])
+        start_sc_line = self._scan('start_sc_line')
+        lines = StringIO();lines.write(start_sc_line)
+        while self._peek('end_sc_line', 'sc_line_of_text') == 'sc_line_of_text':
+            sc_line_of_text = self._scan('sc_line_of_text')
+            lines.write(sc_line_of_text)
+        if self._peek() not in ['end_sc_line', 'sc_line_of_text']:
+            raise yappsrt.YappsSyntaxError(charpos=self._scanner.get_prev_char_pos(), context=_context, msg='Need one of ' + ', '.join(['sc_line_of_text', 'end_sc_line']))
+        end_sc_line = self._scan('end_sc_line')
+        lines.write(end_sc_line);return monitor('sc_line_of_text',lines.getvalue())
+
+    def bracket_expression(self, _parent=None):
+        _context = self.Context(_parent, self._scanner, self._pos, 'bracket_expression', [])
+        _token = self._peek('o_s_b', 'o_c_b')
+        if _token == 'o_s_b':
+            square_bracket_expr = self.square_bracket_expr(_context)
+            return square_bracket_expr
+        else: # == 'o_c_b'
+            curly_bracket_expr = self.curly_bracket_expr(_context)
+            return curly_bracket_expr
+
+    def top_loop(self, _parent=None):
+        _context = self.Context(_parent, self._scanner, self._pos, 'top_loop', [])
+        LBLOCK = self._scan('LBLOCK')
+        loopfield = self.loopfield(_context)
+        loopvalues = self.loopvalues(_context)
+        return loopfield,loopvalues
+
+    def loopfield(self, _parent=None):
+        _context = self.Context(_parent, self._scanner, self._pos, 'loopfield', [])
+        loop_seq=[]
+        while self._peek('data_name', 'data_value_1', 'triple_quote_data_value', 'single_quote_data_value', 'start_sc_line', 'o_s_b', 'o_c_b') == 'data_name':
+            data_name = self._scan('data_name')
+            loop_seq.append(data_name)
+        if self._peek() not in ['data_name', 'data_value_1', 'triple_quote_data_value', 'single_quote_data_value', 'start_sc_line', 'o_s_b', 'o_c_b']:
+            raise yappsrt.YappsSyntaxError(charpos=self._scanner.get_prev_char_pos(), context=_context, msg='Need one of ' + ', '.join(['data_name', 'data_value_1', 'triple_quote_data_value', 'single_quote_data_value', 'start_sc_line', 'o_s_b', 'o_c_b']))
+        return loop_seq
+
+    def loopvalues(self, _parent=None):
+        _context = self.Context(_parent, self._scanner, self._pos, 'loopvalues', [])
+        data_value = self.data_value(_context)
+        dataloop=[data_value]
+        while self._peek('data_value_1', 'triple_quote_data_value', 'single_quote_data_value', 'start_sc_line', 'o_s_b', 'o_c_b', 'LBLOCK', 'data_name', 'save_end', 'save_heading', 'END', 'data_heading') in ['data_value_1', 'triple_quote_data_value', 'single_quote_data_value', 'start_sc_line', 'o_s_b', 'o_c_b']:
+            data_value = self.data_value(_context)
+            dataloop.append(monitor('loopval',data_value))
+        if self._peek() not in ['data_value_1', 'triple_quote_data_value', 'single_quote_data_value', 'start_sc_line', 'o_s_b', 'o_c_b', 'LBLOCK', 'data_name', 'save_end', 'save_heading', 'END', 'data_heading']:
+            raise yappsrt.YappsSyntaxError(charpos=self._scanner.get_prev_char_pos(), context=_context, msg='Need one of ' + ', '.join(['data_value_1', 'triple_quote_data_value', 'single_quote_data_value', 'start_sc_line', 'o_s_b', 'o_c_b', 'LBLOCK', 'data_name', 'save_end', 'save_heading', 'END', 'data_heading']))
+        return dataloop
+
+    def save_frame(self, prepared, _parent=None):
+        _context = self.Context(_parent, self._scanner, self._pos, 'save_frame', [prepared])
+        save_heading = self._scan('save_heading')
+        savehead = save_heading[5:];savebc = StarFile();newname = savebc.NewBlock(savehead,prepared.blocktype(overwrite=False));stored_block = savebc[newname]
+        while self._peek('save_end', 'LBLOCK', 'data_name', 'save_heading', 'END', 'data_heading') in ['LBLOCK', 'data_name']:
+            dataseq = self.dataseq(savebc[savehead], _context)
+        if self._peek() not in ['save_end', 'LBLOCK', 'data_name', 'save_heading', 'END', 'data_heading']:
+            raise yappsrt.YappsSyntaxError(charpos=self._scanner.get_prev_char_pos(), context=_context, msg='Need one of ' + ', '.join(['save_end', 'LBLOCK', 'data_name', 'save_heading', 'END', 'data_heading']))
+        save_end = self._scan('save_end')
+        return monitor('save_frame',savebc)
+
+    def save_frame(self, prepared, _parent=None):
+        _context = self.Context(_parent, self._scanner, self._pos, 'save_frame', [prepared])
+        save_heading = self._scan('save_heading')
+        savehead = save_heading[5:];savebc = StarFile();newname = savebc.NewBlock(savehead,prepared.blocktype(overwrite=False));stored_block = savebc[newname]
+        while self._peek('save_end', 'LBLOCK', 'data_name', 'save_heading', 'END', 'data_heading') in ['LBLOCK', 'data_name']:
+            dataseq = self.dataseq(savebc[savehead], _context)
+        if self._peek() not in ['save_end', 'LBLOCK', 'data_name', 'save_heading', 'END', 'data_heading']:
+            raise yappsrt.YappsSyntaxError(charpos=self._scanner.get_prev_char_pos(), context=_context, msg='Need one of ' + ', '.join(['save_end', 'LBLOCK', 'data_name', 'save_heading', 'END', 'data_heading']))
+        save_end = self._scan('save_end')
+        return monitor('save_frame',savebc)
+
+    def square_bracket_expr(self, _parent=None):
+        _context = self.Context(_parent, self._scanner, self._pos, 'square_bracket_expr', [])
+        o_s_b = self._scan('o_s_b')
+        this_list = []
+        while self._peek('c_s_b', 'data_value_1', 'triple_quote_data_value', 'single_quote_data_value', 'start_sc_line', 'o_s_b', 'o_c_b') != 'c_s_b':
+            data_value = self.data_value(_context)
+            this_list.append(data_value)
+            while self._peek('data_value_1', 'triple_quote_data_value', 'single_quote_data_value', 'start_sc_line', 'c_s_b', 'o_s_b', 'o_c_b') != 'c_s_b':
+                data_value = self.data_value(_context)
+                this_list.append(data_value)
+            if self._peek() not in ['data_value_1', 'triple_quote_data_value', 'single_quote_data_value', 'start_sc_line', 'c_s_b', 'o_s_b', 'o_c_b']:
+                raise yappsrt.YappsSyntaxError(charpos=self._scanner.get_prev_char_pos(), context=_context, msg='Need one of ' + ', '.join(['data_value_1', 'triple_quote_data_value', 'single_quote_data_value', 'start_sc_line', 'o_s_b', 'o_c_b', 'c_s_b']))
+        if self._peek() not in ['c_s_b', 'data_value_1', 'triple_quote_data_value', 'single_quote_data_value', 'start_sc_line', 'o_s_b', 'o_c_b']:
+            raise yappsrt.YappsSyntaxError(charpos=self._scanner.get_prev_char_pos(), context=_context, msg='Need one of ' + ', '.join(['data_value_1', 'c_s_b', 'triple_quote_data_value', 'single_quote_data_value', 'start_sc_line', 'o_s_b', 'o_c_b']))
+        c_s_b = self._scan('c_s_b')
+        return StarList(this_list)
+
+    def curly_bracket_expr(self, _parent=None):
+        _context = self.Context(_parent, self._scanner, self._pos, 'curly_bracket_expr', [])
+        o_c_b = self._scan('o_c_b')
+        table_as_list = []
+        while self._peek('c_c_b', 'triple_quote_data_value', 'single_quote_data_value') != 'c_c_b':
+            delimited_data_value = self.delimited_data_value(_context)
+            table_as_list = [delimited_data_value]
+            self._scan('":"')
+            data_value = self.data_value(_context)
+            table_as_list.append(data_value)
+            while self._peek('triple_quote_data_value', 'single_quote_data_value', 'c_c_b') != 'c_c_b':
+                delimited_data_value = self.delimited_data_value(_context)
+                table_as_list.append(delimited_data_value)
+                self._scan('":"')
+                data_value = self.data_value(_context)
+                table_as_list.append(data_value)
+            if self._peek() not in ['triple_quote_data_value', 'single_quote_data_value', 'c_c_b']:
+                raise yappsrt.YappsSyntaxError(charpos=self._scanner.get_prev_char_pos(), context=_context, msg='Need one of ' + ', '.join(['triple_quote_data_value', 'single_quote_data_value', 'c_c_b']))
+        if self._peek() not in ['c_c_b', 'triple_quote_data_value', 'single_quote_data_value']:
+            raise yappsrt.YappsSyntaxError(charpos=self._scanner.get_prev_char_pos(), context=_context, msg='Need one of ' + ', '.join(['triple_quote_data_value', 'single_quote_data_value', 'c_c_b']))
+        c_c_b = self._scan('c_c_b')
+        return StarDict(pairwise(table_as_list))
+
+
+def parse(rule, text):
+    P = StarParser(StarParserScanner(text))
+    return yappsrt.wrap_error_reporter(P, rule)
+
+# End -- grammar generated by Yapps
+
+