infrastructure changes + COMPASS bug fixes. Infrastructure: Counter v…

…ariables ($ and @) can no longer contain , or () characters. (In the future, this will make it much easier to create source code for programming languages. Note to self: The +-=/. characters are still allowed. The / and . characters are used for path resolution and should never be forbidden.) COMPASS: The "msifrc2lt.py" script has been (hopefully) fixed and is now able to convert the COMPASS force field files again. This made it possible to fix 2 bugs in the "compass_published.lt" force field file: 1) wildcards are now given low priority instead of high priority, and 2) non-hybrid bond, angle, dihedral, improper, and pair styles are used by default (for KOKKOS compatibility). Also: Commas were removed from the atom type names (and replaced with ~ characters).

doc/moltemplate_manual_src/moltemplate_manual.tex

@@ -1578,7 +1578,7 @@ \subsubsection*{Boundary Conditions:}
 ``animate write psf system.psf'',
 ``pbc wrap -compound res -all'', and 
 ``pbc box''.
-See sections \ref{sec:vmd_topotools}, and \ref{sec:vmd_advanced}
+See sections \ref{sec:vmd_topotools}, and appendix \ref{sec:vmd_advanced}
 for details.
 }
 \end{figure}
@@ -4417,16 +4417,17 @@ \section{Bonded interactions ``By Type''}
 
 \subsection*{Regular expressions}
 Regular-expressions can also be used to match potential atom and bond types.
-(To use regular expressions, surround the atom and 
-bond types on either side by slashes.  
-For example: \mbox{/@atom:C[1-5]/}, should match 
-\mbox{@atom:C1} through \mbox{@atom:C6}.)
-\textit{Note: This feature has not been tested as of 2019-9-03.}
+To use regular expressions, the first 3 characters following ``:'' should be
+``re.'', and the variable name should be enclosed in curly brackets, \{\}.
+For example: \mbox{@\{atom:re.C[1-5]\}}, should match 
+\mbox{@atom:C1} through \mbox{@atom:C6}.
+\textit{Note: This feature has not been tested as of 2020-7-09.}
 
 In a similar way, one can define ``Dihedrals By Type'' and 
 ``Impropers By Type''.
 
 
+
   % I THINK I FIXED THIS LIMITATION 
   % SO I COMMENTED OUT THIS NEXT SECTION:
   % IGNORE ALL COMMENTED OUT TEXT IN THE PARAGRAPHS BELOW

moltemplate/__init__.py

@@ -6,9 +6,9 @@
 
 from .ttree_lex import TtreeShlex, split, LineLex, SplitQuotedString, \
     EscCharStrToChar, SafelyEncodeString, RemoveOuterQuotes, MaxLenStr, \
-    HasWildcard, InputError, ErrorLeader, SrcLoc, OSrcLoc, TextBlock, VarRef, \
-    VarNPtr, VarBinding, SplitTemplate, SplitTemplateMulti, TableFromTemplate, \
-    ExtractCatName, DeleteLinesWithBadVars, TemplateLexer
+    HasWildcard, HasRE, InputError, ErrorLeader, SrcLoc, OSrcLoc, TextBlock, \
+    VarRef, VarNPtr, VarBinding, SplitTemplate, SplitTemplateMulti, \
+    TableFromTemplate, ExtractCatName, DeleteLinesWithBadVars, TemplateLexer
 
 from .nbody_graph_search import Disconnected, NotUndirected, Edge, Vertex, \
      Dgraph, Ugraph, SortVertsByDegree, DFS, GraphMatcher 

moltemplate/bonds_by_type.py

@@ -161,9 +161,8 @@ def LookupBondTypes(bond_types,
             typepattern = []
 
             for typestr in tokens[1:]:
-                if ((len(typestr) >= 2) and
-                        (typestr[0] == '/') and (typestr[-1] == '/')):
-                    regex_str = typestr[1:-1]
+                if ttree_lex.HasRE(typestr):
+                    regex_str = typestr[3:]
                     typepattern.append(re.compile(regex_str))
                 else:
                     typepattern.append(ttree_lex.EscCharStrToChar(typestr))

moltemplate/charge_by_bond.py

@@ -165,9 +165,8 @@ def LookupChargePairs(chargebyatomid,
             typepattern = []
 
             for typestr in tokens[:2]:
-                if ((len(typestr) >= 2) and
-                        (typestr[0] == '/') and (typestr[-1] == '/')):
-                    regex_str = typestr[1:-1]
+                if ttree_lex.HasRE(typestr):
+                    regex_str = typestr[3:]
                     typepattern.append(re.compile(regex_str))
                 else:
                     typepattern.append(ttree_lex.EscCharStrToChar(typestr))

moltemplate/force_fields/convert_TINKER_files_to_LT_files/tinkerparm2lt.py

@@ -228,6 +228,10 @@ def main():
                 use_hybrid = True
                 del argv[i:i + 1]
 
+            elif argv[i] == '-no-hybrid':
+                use_hybrid = False
+                del argv[i:i + 1]
+
             elif (argv[i] == '-zeropad' or argv[i] == '-zero-pad'):
                 if (i + 1 >= len(argv)) or (argv[i+1][1:] == '-'):
                     raise Exception(

moltemplate/genpoly_modify_lt.py

@@ -1,8 +1,8 @@
 #!/usr/bin/env python
 
 g_program_name = __file__.split('/')[-1]
-g_version_str  = '0.3.4'
-g_date_str     = '2020-6-12'
+g_version_str  = '0.3.5'
+g_date_str     = '2020-7-10'
 
 g_usage_msg = """
 
@@ -185,6 +185,8 @@ def _DistributeRandom(widths,           # width of each object (>0)
     """
 
     Nm = len(widths)
+    if Nm == 0:
+        return []
     N = len(occupancy)
     locations = [-1 for im in range(0, Nm)]
 

moltemplate/nbody_by_type.py

@@ -244,7 +244,7 @@ def GenInteractions_lines(lines_atoms,
                                  'Offending line:\n' +
                                  '\"' + line + '\"\n'
                                  'Expected either ' +
-                                 str(1 + g_bond_pattern.GetNumVerts()) + ' or ' +
+                                 str(1 + g_bond_pattern.GetNumVerts()) + ' or '+
                                  str(1 + g_bond_pattern.GetNumVerts() +
                                      g_bond_pattern.GetNumEdges())
                                  + ' colunms.'))
@@ -254,8 +254,8 @@ def GenInteractions_lines(lines_atoms,
 
             for typestr in tokens[1:]:
                 if ((len(typestr) >= 2) and
-                        (typestr[0] == '/') and (typestr[-1] == '/')):
-                    regex_str = typestr[1:-1]
+                    HasRE(typestr)):
+                    regex_str = typestr[3:]
                     typepattern.append(re.compile(regex_str))
                 else:
                     typepattern.append(EscCharStrToChar(typestr))

moltemplate/postprocess_coeffs.py

@@ -160,8 +160,7 @@ def main():
             # If the second token is surrounded by '/' characters, interpret
             # it as a regular expression.
             token1_is_re = ((len(tokens) >= 2) and
-                            (len(tokens[1]) >= 2) and
-                            (tokens[1][0] == '/') and (tokens[1][-1] == '/'))
+                            HasRE(tokens[1]))
             # If the second token contains wildcard characters, interpret
             # it as a wildcard (ie. glob) expression.
             token1_is_wild = ((len(tokens) >= 2) and
@@ -173,7 +172,7 @@ def main():
                 (tokens[0].find('bond_coeff') == 0) and
                 (token1_is_re or token1_is_wild)):
                 if token1_is_re:
-                    regex_str = typestr[1:-1]
+                    regex_str = tokens[1][3:] #*#
                     left_paren = text_after = ''
                     typepattern = re.compile(regex_str)
                 else:
@@ -188,7 +187,7 @@ def main():
                 (tokens[0].find('angle_coeff') == 0) and
                 (token1_is_re or token1_is_wild)):
                 if token1_is_re:
-                    regex_str = typestr[1:-1]
+                    regex_str = tokens[1][3:] #*#
                     left_paren = text_after = ''
                     typepattern = re.compile(regex_str)
                 else:
@@ -203,7 +202,7 @@ def main():
                 (tokens[0].find('dihedral_coeff') == 0) and
                 (token1_is_re or token1_is_wild)):
                 if token1_is_re:
-                    regex_str = typestr[1:-1]
+                    regex_str = tokens[1][3:] #*#
                     left_paren = text_after = ''
                     typepattern = re.compile(regex_str)
                 else:
@@ -218,7 +217,7 @@ def main():
                 (tokens[0].find('improper_coeff') == 0) and
                 (token1_is_re or token1_is_wild)):
                 if token1_is_re:
-                    regex_str = typestr[1:-1]
+                    regex_str = tokens[1][3:] #*#
                     left_paren = text_after = ''
                     typepattern = re.compile(regex_str)
                 else:
@@ -286,12 +285,8 @@ def main():
                 ################
                 # If surrounded by '/' characters, the token is meant to be
                 # interpreted as a regular expression.
-                token1_is_re = ((len(tokens[1]) >= 2) and
-                                (tokens[1][0] == '/') and
-                                (tokens[1][-1] == '/'))
-                token2_is_re = ((len(tokens[2]) >= 2) and
-                                (tokens[2][0] == '/') and
-                                (tokens[2][-1] == '/'))
+                token1_is_re = HasRE(tokens[1])
+                token2_is_re = HasRE(tokens[2])
                 # If the token contains wildcard characters, interpret
                 # it as a wildcard (ie. glob) expression.
                 token1_is_wild = (HasWildcard(tokens[1])   #contain '*' or '?'
@@ -303,7 +298,7 @@ def main():
 
                 if token1_is_re:
                     atom_types1 = atom_types
-                    regex_str = tokens[1][1:-1]
+                    regex_str = tokens[1][3:]
                     typepattern1 = re.compile(regex_str)
                 elif token1_is_wild:
                     atom_types1 = atom_types
@@ -312,7 +307,7 @@ def main():
 
                 if token2_is_re:
                     atom_types2 = atom_types
-                    regex_str = tokens[2][1:-1]
+                    regex_str = tokens[2][3:]
                     typepattern2 = re.compile(regex_str)
                 elif token2_is_wild:
                     atom_types2 = atom_types

moltemplate/scripts/moltemplate.sh

@@ -6,8 +6,8 @@
 # Copyright (c) 2013
 
 G_PROGRAM_NAME="moltemplate.sh"
-G_VERSION="2.17.10"
-G_DATE="2020-6-12"
+G_VERSION="2.18.0"
+G_DATE="2020-7-12"
 
 echo "${G_PROGRAM_NAME} v${G_VERSION} ${G_DATE}" >&2
 echo "" >&2

moltemplate/ttree.py

@@ -64,7 +64,7 @@
 # in words or tokens parsed by TtreeShlex.  Otherwise it is identical to shlex.
 try:
     from .ttree_lex import TtreeShlex, SplitQuotedString, EscCharStrToChar, \
-        SafelyEncodeString, RemoveOuterQuotes, MaxLenStr, HasWildcard, \
+        SafelyEncodeString, RemoveOuterQuotes, MaxLenStr, HasWildcard, HasRE, \
         InputError, ErrorLeader, OSrcLoc, TextBlock, VarRef, VarBinding, \
         TemplateLexer
 except (ImportError, SystemError, ValueError):
@@ -102,8 +102,8 @@
 g_module_name = g_filename
 if g_filename.rfind('.py') != -1:
     g_module_name = g_filename[:g_filename.rfind('.py')]
-g_date_str = '2019-11-19'
-g_version_str = '0.86.3'
+g_date_str = '2020-7-09'
+g_version_str = '0.86.4'
 
 
 class ClassReference(object):
@@ -4451,12 +4451,14 @@ def AutoAssignVals(cat_node,
                     # category counter without incrementing it.
                     var_binding.value = str(cat.counter.query())
 
-                elif HasWildcard(var_binding.full_name):
+                elif (HasWildcard(var_binding.full_name) or
+                      HasRE(var_binding.full_name)):
                     #   -- The wildcard hack ---
                     # Variables containing * or ? characters in their names
-                    # are not allowed.  These are not variables, but patterns
-                    # to match with other variables.  Represent them by the
-                    # (full-path-expanded) string containing the * or ?.
+                    # are not allowed.  This is also true of regular
+                    # expressions.  These are not variables, but patterns to
+                    # match with other variables.  Represent them by the (full-
+                    # path-expanded) string containing the * or ? or regex.
                     var_binding.value = var_binding.full_name
 
                 else:
@@ -4824,9 +4826,10 @@ def WriteVarBindingsFile(node):
                     or
                     (isinstance(node, StaticObj) and isinstance(nd, StaticObj))):
 
-                # Now omit variables whos names contain "*" or "?"
-                # (these are actually not variables, but wildcard patterns)
-                if not HasWildcard(var_binding.full_name):
+                # Now omit variables whos names contain "*" or "?" or regex
+                # (these are not variables, but pattern matching strings)
+                if not (HasWildcard(var_binding.full_name) or
+                        HasRE(var_binding.full_name)):
                     if len(var_binding.refs) > 0:
                         usage_example = '       #' +\
                             ErrorLeader(var_binding.refs[0].srcloc.infile,

moltemplate/ttree_lex.py

@@ -50,6 +50,7 @@
            "RemoveOuterQuotes",
            "MaxLenStr",
            "HasWildcard",
+           "HasRE",
            "MatchesPattern",
            #"IsRegex",
            "InputError",
@@ -115,7 +116,7 @@ def __init__(self,
         self.quotes = '\'"'
         self.escape = '\\'
         self.escapedquotes = '"'
-        self.operators = '='
+        self.operators = '='  #binary numeric operators like +-*/ might be added
         self.state = ' '
         self.pushback = deque()
         self.lineno = 1
@@ -557,7 +558,6 @@ def SplitQuotedString(string,
                 if token != '':
                     # if this is not the first character in the token
                     include_endquote = True
-
             token += c
             reading_token = True
         else:
@@ -671,12 +671,13 @@ def MaxLenStr(s1, s2):
         return s1
 
 
-# def IsRegex(pat):
-#    """
-#    Check to see if string (pat) is bracketed by slashes.
-#
-#    """
-#    return (len(pat)>=2) and (pat[0]=='/') and (pat[-1] == '/')
+def HasRE(pat):
+    """
+    Returns true if a string (pat) begins with 're.'
+
+    """
+    return pat.find('re.') == 0
+
 
 def HasWildcard(pat):
     """
@@ -1552,6 +1553,7 @@ def __init__(self,
             self.operators + \
             self.escape + \
             self.commenters
+
         #  Note:
         # self.whitespace = ' \t\r\f\n'
         # self.quotes     = '\'"'
@@ -1572,6 +1574,7 @@ def ReadTemplate(self,
                      simplify_output=False,
                      terminators='}',
                      other_esc_chars='{',
+                     var_terminators='{}(),', #(var_delim, spaces also included)  CONTINUEHERE COMMA BREAKS compass_published.lt
                      keep_terminal_char=True):
         """
            ReadTemplate() reads a block of text (between terminators)
@@ -1658,7 +1661,7 @@ def ReadTemplate(self,
         commented_state = False
         var_paren_depth = 0  # This is non-zero iff we are inside a
         # bracketed variable's name for example: "${var}"
-        var_terminators = self.whitespace + self.newline + self.var_delim + '{}'
+        var_terminators += self.whitespace + self.newline + self.var_delim
 
         tmpl_list = []  # List of alternating tuples of text_blocks and
         # variable names (see format comment above)
@@ -1754,6 +1757,7 @@ def ReadTemplate(self,
                         # immediately follow the '$' character (as in "${var}")
                         elif var_paren_depth > 0:
                             var_paren_depth += 1
+                            var_descr_plist.append(nextchar)
 
                 elif nextchar in self.var_close_paren:
                     #sys.stdout.write('   ReadTemplate() readmode found }.\n')
@@ -1770,6 +1774,9 @@ def ReadTemplate(self,
                             if var_paren_depth == 0:
                                 var_suffix = nextchar
                                 terminate_var = True
+                            else:
+                                var_descr_plist.append(nextchar)
+
 
                 elif nextchar in var_terminators:
                     #sys.stdout.write('   ReadTemplate() readmode found var_terminator \"'+nextchar+'\"\n')

setup.py

@@ -45,9 +45,9 @@
 
   url='https://github.com/jewettaij/moltemplate',
 
-  download_url='https://github.com/jewettaij/moltemplate/archive/v2.17.10.zip',
+  download_url='https://github.com/jewettaij/moltemplate/archive/v2.18.0.zip',
 
-  version='2.17.10',
+  version='2.18.0',
 
   keywords=['simulation', 'LAMMPS', 'molecule editor', 'molecule builder',
             'ESPResSo'],