How to use chomp method in molecule

Best Python code snippet using molecule_python

chomp.py

Source:chomp.py

...10"""11from __future__ import print_function12import re13_have_chomp = {}14def have_chomp(program='homsimpl'):15    """16    Return True if this computer has ``program`` installed.17    The first time it is run, this function caches its result in the18    variable ``_have_chomp`` -- a dictionary indexed by program name19    -- and any subsequent time, it just checks the value of the20    variable.21    This program is used in the routine CHomP.__call__.22    If this computer doesn't have CHomP installed, you may obtain it23    from http://chomp.rutgers.edu/.24    EXAMPLES::25        sage: from sage.interfaces.chomp import have_chomp26        sage: have_chomp() # random -- depends on whether CHomP is installed27        True28        sage: 'homsimpl' in sage.interfaces.chomp._have_chomp29        True30        sage: sage.interfaces.chomp._have_chomp['homsimpl'] == have_chomp()31        True32    """33    global _have_chomp34    if program not in _have_chomp:35        from sage.misc.sage_ostools import have_program36        _have_chomp[program] = have_program(program)37    return _have_chomp[program]38class CHomP:39    r"""40    Interface to the CHomP package.41    :param program: which CHomP program to use42    :type program: string43    :param complex: a simplicial or cubical complex44    :param subcomplex: a subcomplex of ``complex`` or None (the default)45    :param base_ring: ring over which to perform computations -- must be `\ZZ` or `\GF{p}`.46    :type base_ring: ring; optional, default `\ZZ`47    :param generators: if True, also return list of generators48    :type generators: boolean; optional, default False49    :param verbose: if True, print helpful messages as the computation50       progresses51    :type verbose: boolean; optional, default False52    :param extra_opts: options passed directly to ``program``53    :type extra_opts: string54    :return: homology groups as a dictionary indexed by dimension55    The programs ``homsimpl``, ``homcubes``, and ``homchain`` are56    available through this interface.  ``homsimpl`` computes the57    relative or absolute homology groups of simplicial complexes.58    ``homcubes`` computes the relative or absolute homology groups of59    cubical complexes.  ``homchain`` computes the homology groups of60    chain complexes.  For consistency with Sage's other homology61    computations, the answers produced by ``homsimpl`` and62    ``homcubes`` in the absolute case are converted to reduced63    homology.64    Note also that CHomP can only compute over the integers or65    `\GF{p}`.  CHomP is fast enough, though, that if you want66    rational information, you should consider using CHomP with integer67    coefficients, or with mod `p` coefficients for a sufficiently68    large `p`, rather than using Sage's built-in homology algorithms.69    See also the documentation for the functions :func:`homchain`,70    :func:`homcubes`, and :func:`homsimpl` for more examples,71    including illustrations of some of the optional parameters.72    EXAMPLES::73        sage: from sage.interfaces.chomp import CHomP74        sage: T = cubical_complexes.Torus()75        sage: CHomP()('homcubes', T) # optional - CHomP76        {0: 0, 1: Z x Z, 2: Z}77    Relative homology of a segment relative to its endpoints::78        sage: edge = simplicial_complexes.Simplex(1)79        sage: ends = edge.n_skeleton(0)80        sage: CHomP()('homsimpl', edge)  # optional - CHomP81        {0: 0}82        sage: CHomP()('homsimpl', edge, ends)  # optional - CHomP83        {0: 0, 1: Z}84    Homology of a chain complex::85        sage: C = ChainComplex({3: 2 * identity_matrix(ZZ, 2)}, degree=-1)86        sage: CHomP()('homchain', C)  # optional - CHomP87        {2: C2 x C2}88    """89    def __repr__(self):90        """91        String representation.92        EXAMPLES::93            sage: from sage.interfaces.chomp import CHomP94            sage: CHomP()           # indirect doctest95            CHomP interface96        """97        return "CHomP interface"98    def __call__(self, program, complex, subcomplex=None, **kwds):99        """100        Call a CHomP program to compute the homology of a chain101        complex, simplicial complex, or cubical complex.102        See :class:`CHomP` for full documentation.103        EXAMPLES::104            sage: from sage.interfaces.chomp import CHomP105            sage: T = cubical_complexes.Torus()106            sage: CHomP()('homcubes', T) # indirect doctest, optional - CHomP107            {0: 0, 1: Z x Z, 2: Z}108        """109        from sage.misc.temporary_file import tmp_filename110        from sage.homology.all import CubicalComplex, cubical_complexes111        from sage.homology.all import SimplicialComplex, Simplex112        from sage.homology.chain_complex import HomologyGroup113        from subprocess import Popen, PIPE114        from sage.rings.all import QQ, ZZ115        from sage.modules.all import VectorSpace, vector116        from sage.combinat.free_module import CombinatorialFreeModule117        if not have_chomp(program):118            raise OSError("Program %s not found" % program)119        verbose = kwds.get('verbose', False)120        generators = kwds.get('generators', False)121        extra_opts = kwds.get('extra_opts', '')122        base_ring = kwds.get('base_ring', ZZ)123        if extra_opts:124            extra_opts = extra_opts.split()125        else:126            extra_opts = []127        # type of complex:128        cubical = False129        simplicial = False130        chain = False131        # CHomP seems to have problems with cubical complexes if the...

Chomp_GameListener.py

Source:Chomp_GameListener.py

1# Generated from Chomp_Game.g4 by ANTLR 4.7.12from antlr4 import *3if __name__ is not None and "." in __name__:4    from .Chomp_GameParser import Chomp_GameParser5else:6    from Chomp_GameParser import Chomp_GameParser7# This class defines a complete listener for a parse tree produced by Chomp_GameParser.8class Chomp_GameListener(ParseTreeListener):9    # Enter a parse tree produced by Chomp_GameParser#domain.10    def enterDomain(self, ctx:Chomp_GameParser.DomainContext):11        pass12    # Exit a parse tree produced by Chomp_GameParser#domain.13    def exitDomain(self, ctx:Chomp_GameParser.DomainContext):14        pass15    # Enter a parse tree produced by Chomp_GameParser#objectDefine.16    def enterObjectDefine(self, ctx:Chomp_GameParser.ObjectDefineContext):17        pass18    # Exit a parse tree produced by Chomp_GameParser#objectDefine.19    def exitObjectDefine(self, ctx:Chomp_GameParser.ObjectDefineContext):20        pass21    # Enter a parse tree produced by Chomp_GameParser#numericDefine.22    def enterNumericDefine(self, ctx:Chomp_GameParser.NumericDefineContext):23        pass24    # Exit a parse tree produced by Chomp_GameParser#numericDefine.25    def exitNumericDefine(self, ctx:Chomp_GameParser.NumericDefineContext):26        pass27    # Enter a parse tree produced by Chomp_GameParser#numericSymbol.28    def enterNumericSymbol(self, ctx:Chomp_GameParser.NumericSymbolContext):29        pass30    # Exit a parse tree produced by Chomp_GameParser#numericSymbol.31    def exitNumericSymbol(self, ctx:Chomp_GameParser.NumericSymbolContext):32        pass33    # Enter a parse tree produced by Chomp_GameParser#typeDefine.34    def enterTypeDefine(self, ctx:Chomp_GameParser.TypeDefineContext):35        pass36    # Exit a parse tree produced by Chomp_GameParser#typeDefine.37    def exitTypeDefine(self, ctx:Chomp_GameParser.TypeDefineContext):38        pass39    # Enter a parse tree produced by Chomp_GameParser#terconditionDefine.40    def enterTerconditionDefine(self, ctx:Chomp_GameParser.TerconditionDefineContext):41        pass42    # Exit a parse tree produced by Chomp_GameParser#terconditionDefine.43    def exitTerconditionDefine(self, ctx:Chomp_GameParser.TerconditionDefineContext):44        pass45    # Enter a parse tree produced by Chomp_GameParser#predicateDefine.46    def enterPredicateDefine(self, ctx:Chomp_GameParser.PredicateDefineContext):47        pass48    # Exit a parse tree produced by Chomp_GameParser#predicateDefine.49    def exitPredicateDefine(self, ctx:Chomp_GameParser.PredicateDefineContext):50        pass51    # Enter a parse tree produced by Chomp_GameParser#atomFormSkeleton.52    def enterAtomFormSkeleton(self, ctx:Chomp_GameParser.AtomFormSkeletonContext):53        pass54    # Exit a parse tree produced by Chomp_GameParser#atomFormSkeleton.55    def exitAtomFormSkeleton(self, ctx:Chomp_GameParser.AtomFormSkeletonContext):56        pass57    # Enter a parse tree produced by Chomp_GameParser#predicate.58    def enterPredicate(self, ctx:Chomp_GameParser.PredicateContext):59        pass60    # Exit a parse tree produced by Chomp_GameParser#predicate.61    def exitPredicate(self, ctx:Chomp_GameParser.PredicateContext):62        pass63    # Enter a parse tree produced by Chomp_GameParser#typeDeclaration.64    def enterTypeDeclaration(self, ctx:Chomp_GameParser.TypeDeclarationContext):65        pass66    # Exit a parse tree produced by Chomp_GameParser#typeDeclaration.67    def exitTypeDeclaration(self, ctx:Chomp_GameParser.TypeDeclarationContext):68        pass69    # Enter a parse tree produced by Chomp_GameParser#type.70    def enterType(self, ctx:Chomp_GameParser.TypeContext):71        pass72    # Exit a parse tree produced by Chomp_GameParser#type.73    def exitType(self, ctx:Chomp_GameParser.TypeContext):74        pass75    # Enter a parse tree produced by Chomp_GameParser#actionDefine.76    def enterActionDefine(self, ctx:Chomp_GameParser.ActionDefineContext):77        pass78    # Exit a parse tree produced by Chomp_GameParser#actionDefine.79    def exitActionDefine(self, ctx:Chomp_GameParser.ActionDefineContext):80        pass81    # Enter a parse tree produced by Chomp_GameParser#actionSymbol.82    def enterActionSymbol(self, ctx:Chomp_GameParser.ActionSymbolContext):83        pass84    # Exit a parse tree produced by Chomp_GameParser#actionSymbol.85    def exitActionSymbol(self, ctx:Chomp_GameParser.ActionSymbolContext):86        pass87    # Enter a parse tree produced by Chomp_GameParser#emptyOrPreGD.88    def enterEmptyOrPreGD(self, ctx:Chomp_GameParser.EmptyOrPreGDContext):89        pass90    # Exit a parse tree produced by Chomp_GameParser#emptyOrPreGD.91    def exitEmptyOrPreGD(self, ctx:Chomp_GameParser.EmptyOrPreGDContext):92        pass93    # Enter a parse tree produced by Chomp_GameParser#emptyOrEffect.94    def enterEmptyOrEffect(self, ctx:Chomp_GameParser.EmptyOrEffectContext):95        pass96    # Exit a parse tree produced by Chomp_GameParser#emptyOrEffect.97    def exitEmptyOrEffect(self, ctx:Chomp_GameParser.EmptyOrEffectContext):98        pass99    # Enter a parse tree produced by Chomp_GameParser#listName.100    def enterListName(self, ctx:Chomp_GameParser.ListNameContext):101        pass102    # Exit a parse tree produced by Chomp_GameParser#listName.103    def exitListName(self, ctx:Chomp_GameParser.ListNameContext):104        pass105    # Enter a parse tree produced by Chomp_GameParser#listVariable.106    def enterListVariable(self, ctx:Chomp_GameParser.ListVariableContext):107        pass108    # Exit a parse tree produced by Chomp_GameParser#listVariable.109    def exitListVariable(self, ctx:Chomp_GameParser.ListVariableContext):110        pass111    # Enter a parse tree produced by Chomp_GameParser#oneofDefine.112    def enterOneofDefine(self, ctx:Chomp_GameParser.OneofDefineContext):113        pass114    # Exit a parse tree produced by Chomp_GameParser#oneofDefine.115    def exitOneofDefine(self, ctx:Chomp_GameParser.OneofDefineContext):116        pass117    # Enter a parse tree produced by Chomp_GameParser#gd.118    def enterGd(self, ctx:Chomp_GameParser.GdContext):119        pass120    # Exit a parse tree produced by Chomp_GameParser#gd.121    def exitGd(self, ctx:Chomp_GameParser.GdContext):122        pass123    # Enter a parse tree produced by Chomp_GameParser#termAtomForm.124    def enterTermAtomForm(self, ctx:Chomp_GameParser.TermAtomFormContext):125        pass126    # Exit a parse tree produced by Chomp_GameParser#termAtomForm.127    def exitTermAtomForm(self, ctx:Chomp_GameParser.TermAtomFormContext):128        pass129    # Enter a parse tree produced by Chomp_GameParser#termLiteral.130    def enterTermLiteral(self, ctx:Chomp_GameParser.TermLiteralContext):131        pass132    # Exit a parse tree produced by Chomp_GameParser#termLiteral.133    def exitTermLiteral(self, ctx:Chomp_GameParser.TermLiteralContext):134        pass135    # Enter a parse tree produced by Chomp_GameParser#constTerm.136    def enterConstTerm(self, ctx:Chomp_GameParser.ConstTermContext):137        pass138    # Exit a parse tree produced by Chomp_GameParser#constTerm.139    def exitConstTerm(self, ctx:Chomp_GameParser.ConstTermContext):140        pass141    # Enter a parse tree produced by Chomp_GameParser#term.142    def enterTerm(self, ctx:Chomp_GameParser.TermContext):143        pass144    # Exit a parse tree produced by Chomp_GameParser#term.145    def exitTerm(self, ctx:Chomp_GameParser.TermContext):146        pass147    # Enter a parse tree produced by Chomp_GameParser#effect.148    def enterEffect(self, ctx:Chomp_GameParser.EffectContext):149        pass150    # Exit a parse tree produced by Chomp_GameParser#effect.151    def exitEffect(self, ctx:Chomp_GameParser.EffectContext):152        pass153    # Enter a parse tree produced by Chomp_GameParser#assignop.154    def enterAssignop(self, ctx:Chomp_GameParser.AssignopContext):155        pass156    # Exit a parse tree produced by Chomp_GameParser#assignop.157    def exitAssignop(self, ctx:Chomp_GameParser.AssignopContext):158        pass159    # Enter a parse tree produced by Chomp_GameParser#pEffect.160    def enterPEffect(self, ctx:Chomp_GameParser.PEffectContext):161        pass162    # Exit a parse tree produced by Chomp_GameParser#pEffect.163    def exitPEffect(self, ctx:Chomp_GameParser.PEffectContext):164        pass165    # Enter a parse tree produced by Chomp_GameParser#problemName.166    def enterProblemName(self, ctx:Chomp_GameParser.ProblemNameContext):167        pass168    # Exit a parse tree produced by Chomp_GameParser#problemName.169    def exitProblemName(self, ctx:Chomp_GameParser.ProblemNameContext):170        pass171    # Enter a parse tree produced by Chomp_GameParser#domainName.172    def enterDomainName(self, ctx:Chomp_GameParser.DomainNameContext):173        pass174    # Exit a parse tree produced by Chomp_GameParser#domainName.175    def exitDomainName(self, ctx:Chomp_GameParser.DomainNameContext):176        pass177    # Enter a parse tree produced by Chomp_GameParser#agentDefine.178    def enterAgentDefine(self, ctx:Chomp_GameParser.AgentDefineContext):179        pass180    # Exit a parse tree produced by Chomp_GameParser#agentDefine.181    def exitAgentDefine(self, ctx:Chomp_GameParser.AgentDefineContext):182        pass183    # Enter a parse tree produced by Chomp_GameParser#objectDeclaration.184    def enterObjectDeclaration(self, ctx:Chomp_GameParser.ObjectDeclarationContext):185        pass186    # Exit a parse tree produced by Chomp_GameParser#objectDeclaration.187    def exitObjectDeclaration(self, ctx:Chomp_GameParser.ObjectDeclarationContext):188        pass189    # Enter a parse tree produced by Chomp_GameParser#numericSetting.190    def enterNumericSetting(self, ctx:Chomp_GameParser.NumericSettingContext):191        pass192    # Exit a parse tree produced by Chomp_GameParser#numericSetting.193    def exitNumericSetting(self, ctx:Chomp_GameParser.NumericSettingContext):194        pass195    # Enter a parse tree produced by Chomp_GameParser#init.196    def enterInit(self, ctx:Chomp_GameParser.InitContext):197        pass198    # Exit a parse tree produced by Chomp_GameParser#init.199    def exitInit(self, ctx:Chomp_GameParser.InitContext):200        pass201    # Enter a parse tree produced by Chomp_GameParser#constTermAtomForm.202    def enterConstTermAtomForm(self, ctx:Chomp_GameParser.ConstTermAtomFormContext):203        pass204    # Exit a parse tree produced by Chomp_GameParser#constTermAtomForm.205    def exitConstTermAtomForm(self, ctx:Chomp_GameParser.ConstTermAtomFormContext):...

Chomp_GameVisitor.py

Source:Chomp_GameVisitor.py

1# Generated from Chomp_Game.g4 by ANTLR 4.7.12from antlr4 import *3if __name__ is not None and "." in __name__:4    from .Chomp_GameParser import Chomp_GameParser5else:6    from Chomp_GameParser import Chomp_GameParser7# This class defines a complete generic visitor for a parse tree produced by Chomp_GameParser.8class Chomp_GameVisitor(ParseTreeVisitor):9    # Visit a parse tree produced by Chomp_GameParser#domain.10    def visitDomain(self, ctx:Chomp_GameParser.DomainContext):11        return self.visitChildren(ctx)12    # Visit a parse tree produced by Chomp_GameParser#objectDefine.13    def visitObjectDefine(self, ctx:Chomp_GameParser.ObjectDefineContext):14        return self.visitChildren(ctx)15    # Visit a parse tree produced by Chomp_GameParser#numericDefine.16    def visitNumericDefine(self, ctx:Chomp_GameParser.NumericDefineContext):17        return self.visitChildren(ctx)18    # Visit a parse tree produced by Chomp_GameParser#numericSymbol.19    def visitNumericSymbol(self, ctx:Chomp_GameParser.NumericSymbolContext):20        return self.visitChildren(ctx)21    # Visit a parse tree produced by Chomp_GameParser#typeDefine.22    def visitTypeDefine(self, ctx:Chomp_GameParser.TypeDefineContext):23        return self.visitChildren(ctx)24    # Visit a parse tree produced by Chomp_GameParser#terconditionDefine.25    def visitTerconditionDefine(self, ctx:Chomp_GameParser.TerconditionDefineContext):26        return self.visitChildren(ctx)27    # Visit a parse tree produced by Chomp_GameParser#predicateDefine.28    def visitPredicateDefine(self, ctx:Chomp_GameParser.PredicateDefineContext):29        return self.visitChildren(ctx)30    # Visit a parse tree produced by Chomp_GameParser#atomFormSkeleton.31    def visitAtomFormSkeleton(self, ctx:Chomp_GameParser.AtomFormSkeletonContext):32        return self.visitChildren(ctx)33    # Visit a parse tree produced by Chomp_GameParser#predicate.34    def visitPredicate(self, ctx:Chomp_GameParser.PredicateContext):35        return self.visitChildren(ctx)36    # Visit a parse tree produced by Chomp_GameParser#typeDeclaration.37    def visitTypeDeclaration(self, ctx:Chomp_GameParser.TypeDeclarationContext):38        return self.visitChildren(ctx)39    # Visit a parse tree produced by Chomp_GameParser#type.40    def visitType(self, ctx:Chomp_GameParser.TypeContext):41        return self.visitChildren(ctx)42    # Visit a parse tree produced by Chomp_GameParser#actionDefine.43    def visitActionDefine(self, ctx:Chomp_GameParser.ActionDefineContext):44        return self.visitChildren(ctx)45    # Visit a parse tree produced by Chomp_GameParser#actionSymbol.46    def visitActionSymbol(self, ctx:Chomp_GameParser.ActionSymbolContext):47        return self.visitChildren(ctx)48    # Visit a parse tree produced by Chomp_GameParser#emptyOrPreGD.49    def visitEmptyOrPreGD(self, ctx:Chomp_GameParser.EmptyOrPreGDContext):50        return self.visitChildren(ctx)51    # Visit a parse tree produced by Chomp_GameParser#emptyOrEffect.52    def visitEmptyOrEffect(self, ctx:Chomp_GameParser.EmptyOrEffectContext):53        return self.visitChildren(ctx)54    # Visit a parse tree produced by Chomp_GameParser#listName.55    def visitListName(self, ctx:Chomp_GameParser.ListNameContext):56        return self.visitChildren(ctx)57    # Visit a parse tree produced by Chomp_GameParser#listVariable.58    def visitListVariable(self, ctx:Chomp_GameParser.ListVariableContext):59        return self.visitChildren(ctx)60    # Visit a parse tree produced by Chomp_GameParser#oneofDefine.61    def visitOneofDefine(self, ctx:Chomp_GameParser.OneofDefineContext):62        return self.visitChildren(ctx)63    # Visit a parse tree produced by Chomp_GameParser#gd.64    def visitGd(self, ctx:Chomp_GameParser.GdContext):65        return self.visitChildren(ctx)66    # Visit a parse tree produced by Chomp_GameParser#termAtomForm.67    def visitTermAtomForm(self, ctx:Chomp_GameParser.TermAtomFormContext):68        return self.visitChildren(ctx)69    # Visit a parse tree produced by Chomp_GameParser#termLiteral.70    def visitTermLiteral(self, ctx:Chomp_GameParser.TermLiteralContext):71        return self.visitChildren(ctx)72    # Visit a parse tree produced by Chomp_GameParser#constTerm.73    def visitConstTerm(self, ctx:Chomp_GameParser.ConstTermContext):74        return self.visitChildren(ctx)75    # Visit a parse tree produced by Chomp_GameParser#term.76    def visitTerm(self, ctx:Chomp_GameParser.TermContext):77        return self.visitChildren(ctx)78    # Visit a parse tree produced by Chomp_GameParser#effect.79    def visitEffect(self, ctx:Chomp_GameParser.EffectContext):80        return self.visitChildren(ctx)81    # Visit a parse tree produced by Chomp_GameParser#assignop.82    def visitAssignop(self, ctx:Chomp_GameParser.AssignopContext):83        return self.visitChildren(ctx)84    # Visit a parse tree produced by Chomp_GameParser#pEffect.85    def visitPEffect(self, ctx:Chomp_GameParser.PEffectContext):86        return self.visitChildren(ctx)87    # Visit a parse tree produced by Chomp_GameParser#problemName.88    def visitProblemName(self, ctx:Chomp_GameParser.ProblemNameContext):89        return self.visitChildren(ctx)90    # Visit a parse tree produced by Chomp_GameParser#domainName.91    def visitDomainName(self, ctx:Chomp_GameParser.DomainNameContext):92        return self.visitChildren(ctx)93    # Visit a parse tree produced by Chomp_GameParser#agentDefine.94    def visitAgentDefine(self, ctx:Chomp_GameParser.AgentDefineContext):95        return self.visitChildren(ctx)96    # Visit a parse tree produced by Chomp_GameParser#objectDeclaration.97    def visitObjectDeclaration(self, ctx:Chomp_GameParser.ObjectDeclarationContext):98        return self.visitChildren(ctx)99    # Visit a parse tree produced by Chomp_GameParser#numericSetting.100    def visitNumericSetting(self, ctx:Chomp_GameParser.NumericSettingContext):101        return self.visitChildren(ctx)102    # Visit a parse tree produced by Chomp_GameParser#init.103    def visitInit(self, ctx:Chomp_GameParser.InitContext):104        return self.visitChildren(ctx)105    # Visit a parse tree produced by Chomp_GameParser#constTermAtomForm.106    def visitConstTermAtomForm(self, ctx:Chomp_GameParser.ConstTermAtomFormContext):107        return self.visitChildren(ctx)...

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