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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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