Fix dimethylaniline.xyz geometry

Geometries must be in Angstrom. Thanks to Christof Holzer for pointing out this error!

content/view.html

@@ -15,9 +15,9 @@ draft: false
       var browsers = {};
       browsers["Chromium"] = "https://chromium.woolyss.com/download";
       browsers["Firefox"] = "https://www.mozilla.org/fr/firefox";
-      var recomstring = "We recommend to use Firefox or a Chromium based browser like Google Chrome".;
+      var recomstring = "We recommend to use Firefox or a Chromium based browser like Google Chrome.";
       btn_clip.title = 'This feature is not supported in this browser.\n' + recomsting;
-      var mystr = 'navigator.clipboard.writeText() not supported in this browser\n' + recomsting;
+      var mystr = 'navigator.clipboard.writeText() not supported in this browser.\n' + recomsting;
       for (var key in browsers) {
         mystr += "\n" + String.raw`Download ${key} : ${browsers[key]}`;
       }

static/data/structures/QUEST6/dimethylaniline.xyz

@@ -1,22 +1,22 @@
 20
 Dimethylaniline,^1A_1,CCSD(T),cc-pVTZ
-C    0.00000000            0.00000000            4.89686867
-C    2.25704297            0.00000000            3.55138467
-C   -2.25704297            0.00000000            3.55138467
-C    2.27412639            0.00000000            0.92841898
-C   -2.27412639            0.00000000            0.92841898
-C    0.00000000            0.00000000           -0.44595239
-C    2.36139267            0.00000000           -4.39675011
-C   -2.36139267            0.00000000           -4.39675011
-N    0.00000000            0.00000000           -3.03916783
-H    4.05922248            0.00000000           -0.04344476
-H   -4.05922248            0.00000000           -0.04344476
-H    4.03670718            0.00000000            4.54551891
-H   -4.03670718            0.00000000            4.54551891
-H    0.00000000            0.00000000            6.93154996
-H    1.97020408            0.00000000           -6.40997108
-H   -1.97020408            0.00000000           -6.40997108
-H    3.49800498           -1.66955347           -3.96565000
-H    3.49800498            1.66955347           -3.96565000
-H   -3.49800498            1.66955347           -3.96565000
-H   -3.49800498           -1.66955347           -3.96565000
+C    0.00000000            0.00000000            2.59131130
+C    1.19437570            0.00000000            1.87931183
+C   -1.19437570            0.00000000            1.87931183
+C    1.20341586            0.00000000            0.49129817
+C   -1.20341586            0.00000000            0.49129817
+C    0.00000000            0.00000000           -0.23598784
+C    1.24959519            0.00000000           -2.32665996
+C   -1.24959519            0.00000000           -2.32665996
+N    0.00000000            0.00000000           -1.60825836
+H    2.14804803            0.00000000           -0.02298998
+H   -2.14804803            0.00000000           -0.02298998
+H    2.13613345            0.00000000            2.40538502
+H   -2.13613345            0.00000000            2.40538502
+H    0.00000000            0.00000000            3.66801827
+H    1.04258710            0.00000000           -3.39201062
+H   -1.04258710            0.00000000           -3.39201062
+H    1.85106452           -0.88348965           -2.09853161
+H    1.85106452            0.88348965           -2.09853161
+H   -1.85106452            0.88348965           -2.09853161
+H   -1.85106452           -0.88348965           -2.09853161

tools/lib/LaTeX.py

@@ -75,7 +75,6 @@ class newCommand(commandBase):
       for cmd in cmds:
         if not cmd.run(tex):
           cmds.remove(cmd)
-          collection.remove(cmd)
       newCommand.runAll(tex,collection)
 class columnAlignment(Enum):
   Left = "l"

tools/lib/data.py

@@ -15,6 +15,19 @@ class state:
     self.number = number
     self.multiplicity = multiplicity
     self.symmetry = symmetry
+  
+  def __eq__(self, __o: object) -> bool:
+      return type(__o) is state and __o.number == self.number and __o.multiplicity == self.multiplicity and __o.symmetry == self.symmetry
+
+  def __str__(self) -> str:
+      return f'{self.number} ^{self.multiplicity}{self.symmetry}'
+
+  def __repr__(self) -> str:
+    return f'{self.__class__.__name__}: {self.__str__()}'
+
+  def __hash__(self) -> int:
+      return hash((self.number, self.multiplicity, self.symmetry))
+
   @staticmethod
   def fromString(string):
     m=re.match(r"^(?P<number>\d)\s*\^(?P<multiplicity>\d)(?P<sym>\S*)",string)
@@ -52,9 +65,18 @@ class exSet(object):
     self.name=name
     self.index=index
   
-  def __str__(self):
+  def __eq__(self, __o: object) -> bool:
+    return type(__o) is exSet and __o.name == self.name and __o.index == self.index
+
+  def __str__(self) -> str:
     return f"{self.name},{self.index}"
 
+  def __repr__(self) -> str:
+    return f'{self.__class__.__name__}: {self.__str__()}'
+
+  def __hash__(self) -> int:
+      return hash((self.name, self.index))
+      
   @staticmethod
   def fromString(string):
     vals = string.split(",")
@@ -143,6 +165,7 @@ class dataFileBase(object):
     else:
       raise ValueError()
     return handler.readFromTable(table)
+    
   def getMetadata(self):
     dic=OrderedDict()
     dic["Molecule"]=self.molecule
@@ -248,6 +271,18 @@ class method:
     self.name = name
     self.basis=args[0] if len(args)>0 else None
 
+  def __eq__(self, __o: object) -> bool:
+    return type(__o) is method and __o.name == self.name and __o.basis == self.basis
+
+  def __str__(self) -> str:
+      return self.name + f'/{self.basis}' if self.basis!=None else ''
+
+  def __repr__(self) -> str:
+    return f'{self.__class__.__name__}: {self.__str__()}'
+
+  def __hash__(self) -> int:
+      return hash((self.name, self.basis))
+
   @staticmethod
   def fromString(string):
     vals = string.split(",")
@@ -271,6 +306,18 @@ class code:
     self.name = name
     self.version = version
   
+  def __eq__(self, __o: object) -> bool:
+    return type(__o) is method and __o.name == self.name and __o.version == self.version
+
+  def __str__(self) -> str:
+      return self.name + f'/{self.version}' if self.version!=None else ''
+
+  def __repr__(self) -> str:
+    return f'{self.__class__.__name__}: {self.__str__()}'
+
+  def __hash__(self) -> int:
+      return hash((self.name, self.basis))
+
   @staticmethod
   def fromString(string):
     vals = string.split(",")

tools/lib/dfbOptions.py

@@ -2,6 +2,7 @@ from TexSoup import TexSoup,TexCmd
 from . import formats
 from .data import dataFileBase,DataType, method, state, exSet
 from collections import defaultdict
+from pagerange import PageRange
 
 class dfbOptions(object):
   def __init__(self):
@@ -96,7 +97,7 @@ class dfbOptions(object):
     for node in dfbexcludeColumnsNodes:
       excludeColumns=node.expr
       if type(excludeColumns) is TexCmd:
-        commas_string=excludeColumns.args[0].value
-        ints=[int(x.strip()) for x in commas_string.split(",")]
-        dfb_Opt.excludeColumns.update(ints)
+        range_string=excludeColumns.args[0].value
+        PageRangeParser=PageRange(range_string)
+        dfb_Opt.excludeColumns.update(PageRangeParser.pages)
     return dfb_Opt

tools/lib/formats/default/__init__.py

@@ -1,8 +1,24 @@
-from .lineHandler import lineHandler
-from .columnHandler import columnHandler
-from .doubleColumnHandler import doubleColumnHandler
-from .TBEHandler import TBEHandler
-from .doubleTBEHandler import doubleTBEHandler
-from .exoticColumnHandler import exoticColumnHandler
-from .fromXLSToLaTeXHandler import fromXLSToLaTeXHandler
-from .CTHandlers import CT1Handler, CT2Handler
+from inspect import isclass
+from pkgutil import iter_modules
+from pathlib import Path
+from importlib import import_module
+from ..formatHandlerBase import formatHandlerBase
+
+# iterate through the modules in the current package
+package_dir = Path(__file__).resolve().parent
+for (_, module_name, _) in iter_modules([package_dir]):
+
+    # import the module and iterate through its attributes
+    module = import_module(f"{__name__}.{module_name}")
+
+# iterate through the modules in the current package
+package_dir = Path(__file__).resolve().parent
+for (_, module_name, _) in iter_modules([package_dir]):
+
+    # import the module and iterate through its attributes
+    module = import_module(f"{__name__}.{module_name}")
+    for attribute_name in dir(module):
+        attribute = getattr(module, attribute_name)
+        # if it's a format handler import it
+        if isclass(attribute) and issubclass(attribute, formatHandlerBase) and hasattr(attribute, '__formatName__'):
+            globals()[attribute_name] = attribute

tools/requirements.txt

@@ -3,3 +3,4 @@ numpy>=1.18.3,<1.20
 GitPython>=3.1.14
 PyYAML>=5.3.1
 TexSoup==0.2.1
+PageRange>=0.4