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Given the following text description, write Python code to implement the functionality described below step by step
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Description:
 MolStandardize
This is a demonstration on how to use the rdMolStandardize module within RDKit. The structure and capabilities remain largely the same as MolVS (https
Step1:  The rdMolStandardize module contains the following convenience functions for quickly performing that standardization task
Step2:  The rdMolStandardize.StandardizeSmiles() function performs the following steps.
Step3:  rdMolStandardize.ValidateSmiles()
The rdMolStandardize.ValidateSmiles() function is a convenience funtion that quickly validates a single SMILES string. It uses the rdMolStandardize.MolVSValidation() class with the default to do all validations.
Step4:  rdMolStandardize validation methods
There are four different ways of validating molecules, each can by run with their different classes
Step5:  The rdMolStandardize.MolVSValidation class goes through similar validations as the standalone MolVS.
https
Step6:  Or you can specify which subset of MolVSValidations you want when initializing
Step7:  The rdMolStandardize.AllowedAtomsValidation class lets the user input a list of atoms, anything not on the list throws an error.
The rdMolStandardize.DisallowedAtomsValidation class also takes an input of a list of atoms and as long as there are no atoms from the list it is deemed acceptable.
Step8:  rdMolStandardize.Cleanup
Whilst rdMolStandardize.StandardizeSmiles() provides a quick and easy way to get standardized version of a SMILES string, it's inefficient when dealing with multiple molecules and doesn't allow customization of the standardize process.
The Cleanup function provides flexibility to specify custom cleanup files and parameters.
Step9:  rdMolStandardize.Cleanup() function can take in an optional rdMolStandardize.CleanupParameters object which you can specify your own standardization reference files to use.
The member variables that you can change are
Step10:  rdMolStandardize.Normalize
The rdMolStandardize.Normalizer class is used to apply a series of Normalization transforms to correct functional groups and recombine charges.
Step11:  rdMolStandardize.MetalDisconnector
The rdMolStandardize.MetalDisconnector class disconnects metal atoms that are defined as covalently bonded to non-metals.
Step12:  rdMolStandardize.LargestFragmentChooser and rdMolStandardize.Remover
rdMolStandardize.LargestFragmentChooser class gets the largest fragment
Step13:  rdMolStandardize.FragmentParent() function is similar to rdMolStandardize.LargestFragmentChooser  but first performs rdMolStandardize.Cleanup()
rdMolStandardize.FragmentRemover class filters out fragments
Step14:  rdMolStandardize.Reionizer and rdMolStandardizer.Uncharger
rdMolStandardize.Reionizer ensure the strongest acid groups ionize first in partially ionized molecules.
rdMolStandardize.Uncharger attempts to neutralize charges by adding and/or removing hydrogens where possible.
rdMolStandardize.ChargeParent() method is the uncharged version of the fragment parent. It involves taking the fragment parent then applying Neutralize and Reionize.
Step15:  TODO
MolStandardize.tautomer
TODO
Tautomer_enumeration generates all possible tautomers using a series of transform rules. It also removes stereochemistry from double bonds that are single in at least 1 tautomer.
Tautomer_canonicalization enumerates all possible tautomers using transform rules and uses a scoring system to determine canonical tautomer.
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Python Code:
import rdkit
from rdkit import Chem
from rdkit.Chem.Draw import IPythonConsole
from rdkit.Chem.MolStandardize import rdMolStandardize
Explanation: MolStandardize
This is a demonstration on how to use the rdMolStandardize module within RDKit. The structure and capabilities remain largely the same as MolVS (https://molvs.readthedocs.io/en/latest/) but will extended capabilities of user-supplied lists in some of the standardization tools.
End of explanation
sm = "[Na]OC(=O)c1ccc(C[S+2]([O-])([O-]))cc1"
rdMolStandardize.StandardizeSmiles(sm)
Explanation: The rdMolStandardize module contains the following convenience functions for quickly performing that standardization task:
-  rdMolStandardize.StandardizeSmiles()
-  rdMolStandardize.ValidateSmiles()
Other functions within the module:
-  rdMolStandardize.Cleanup() 
-  rdMolStandardize.ChargeParent()
-  rdMolStandardize.FragmentParent()
rdMolStandardize.Cleanup() is equivalent to the molvs.standardize.Standardizer().standardize() function in molvs
The rdMolStandardize module contains the following classes, that allow you to develop your custom standardization process.
-  rdMolStandardize.CleanupParameters
-  rdMolStandardize.Normalize
-  rdMolStandardize.MetalDisconnector
-  rdMolStandardize.FragmentParent
-  rdMolStandardize.FragmentRemover
-  rdMolStandardize.Reionizer
-  rdMolStandardize.Uncharger
-  rdMolStandardize.RDKitValidation
-  rdMolStandardize.MolVSValidation
-  rdMolStandardize.AllowedAtomsValidation
-  rdMolStandardize.DisallowedAtomsValidation
TODO
-  rdMolStandardize.tautomer 
rdMolStandardize.StandardizeSmiles()
The rdMolStandardize.StandardizeSmiles() convenience function contains all sensible default functionality to help get started
End of explanation
mol = Chem.MolFromSmiles(sm)
Chem.SanitizeMol(mol)
mol = Chem.RemoveHs(mol)
mol = rdMolStandardize.MetalDisconnector().Disconnect(mol)
mol = rdMolStandardize.Normalize(mol)
mol = rdMolStandardize.Reionize(mol)
Chem.AssignStereochemistry(mol, force=True, cleanIt=True)
Chem.MolToSmiles(mol)
Explanation: The rdMolStandardize.StandardizeSmiles() function performs the following steps.
End of explanation
rdMolStandardize.ValidateSmiles("ClCCCl.c1ccccc1O")
Explanation: rdMolStandardize.ValidateSmiles()
The rdMolStandardize.ValidateSmiles() function is a convenience funtion that quickly validates a single SMILES string. It uses the rdMolStandardize.MolVSValidation() class with the default to do all validations.
End of explanation
vm = rdMolStandardize.RDKitValidation()
mol = Chem.MolFromSmiles("CO(C)C", sanitize=False)
vm.validate(mol)
Explanation: rdMolStandardize validation methods
There are four different ways of validating molecules, each can by run with their different classes:
-  rdMolStandardize.RDKitValidation
-  rdMolStandardize.MolVSValidation
-  rdMolStandardize.AllowedAtomsValidation
-  rdMolStandardize.DisallowedAtomsValidation
All the classes have a validate() method to perform the validation.
The rdMolStandardize.RDKitValidation class validates the valency of every atom in the input molecule (much like RDKit automatically does).
End of explanation
vm = rdMolStandardize.MolVSValidation()
mol = Chem.MolFromSmiles("COc1cccc(C=N[N-]C(N)=O)c1[O-].O.O.O.O=[U+2]=O")
vm.validate(mol)
Explanation: The rdMolStandardize.MolVSValidation class goes through similar validations as the standalone MolVS.
https://molvs.readthedocs.io/en/latest/api.html#molvs-validate
The default is to do all validations:
-  NoAtomValidation
-  FragmentValidation
-  NeutralValidation
-  IsotopeValidation
Using the rdMolStandardize.MolVSValidation class rather than the convenience function rdMolStandardize.ValidateSmiles() provides more flexibility when working with multiple molecules or when a custom validation list is required
End of explanation
validations = [rdMolStandardize.NoAtomValidation()]
vm = rdMolStandardize.MolVSValidation(validations)
mol = Chem.MolFromSmiles("COc1cccc(C=N[N-]C(N)=O)c1[O-].O.O.O.O=[U+2]=O")
vm.validate(mol)
Explanation: Or you can specify which subset of MolVSValidations you want when initializing
End of explanation
from rdkit.Chem.rdchem import Atom
atomic_no = [6,7,8]
allowed_atoms = [Atom(i) for i in atomic_no]
vm = rdMolStandardize.AllowedAtomsValidation(allowed_atoms) 
mol = Chem.MolFromSmiles("CC(=O)CF")
vm.validate(mol)
atomic_no = [9, 17, 35]                                                     
disallowed_atoms = [Atom(i) for i in atomic_no]                             
vm = rdMolStandardize.DisallowedAtomsValidation(disallowed_atoms)          
mol = Chem.MolFromSmiles("CC(=O)CF")                                       
msg = vm.validate(mol)
Explanation: The rdMolStandardize.AllowedAtomsValidation class lets the user input a list of atoms, anything not on the list throws an error.
The rdMolStandardize.DisallowedAtomsValidation class also takes an input of a list of atoms and as long as there are no atoms from the list it is deemed acceptable.
End of explanation
mol = Chem.MolFromSmiles("[Na]OC(=O)c1ccc(C[S+2]([O-])([O-]))cc1")
mol
smol = rdMolStandardize.Cleanup(mol)
smol
Explanation: rdMolStandardize.Cleanup
Whilst rdMolStandardize.StandardizeSmiles() provides a quick and easy way to get standardized version of a SMILES string, it's inefficient when dealing with multiple molecules and doesn't allow customization of the standardize process.
The Cleanup function provides flexibility to specify custom cleanup files and parameters.
End of explanation
params = rdMolStandardize.CleanupParameters()
print("Default acidbaseFile: %s" % params.acidbaseFile)
print("Default normalizationsFile: %s" % params.normalizationsFile)
print("Default fragmentFile: %s" % params.fragmentFile)
print("Default maxRestarts: %s" % params.maxRestarts)
print("Default preferOrganic: %s" % params.preferOrganic)
Explanation: rdMolStandardize.Cleanup() function can take in an optional rdMolStandardize.CleanupParameters object which you can specify your own standardization reference files to use.
The member variables that you can change are:
-  CleanupParameters.acidbaseFile
-  CleanupParameters.normalizationsFile
-  CleanupParameters.fragmentFile
-  CleanupParameters.maxRestarts
-  CleanupParameters.preferOrganic
End of explanation
n = rdMolStandardize.Normalizer()
n.normalize(Chem.MolFromSmiles("C[S+2]([O-])([O-])O"))
Explanation: rdMolStandardize.Normalize
The rdMolStandardize.Normalizer class is used to apply a series of Normalization transforms to correct functional groups and recombine charges.
End of explanation
md = rdMolStandardize.MetalDisconnector()
md.Disconnect(Chem.MolFromSmiles("CCC(=O)O[Na]"))
Explanation: rdMolStandardize.MetalDisconnector
The rdMolStandardize.MetalDisconnector class disconnects metal atoms that are defined as covalently bonded to non-metals.
End of explanation
lfc = rdMolStandardize.LargestFragmentChooser()
lfc.choose(Chem.MolFromSmiles("O=C(O)CCC.O=C(O)CCCC.O=C(O)CCCCC.O=C(O)CCCC"))
Explanation: rdMolStandardize.LargestFragmentChooser and rdMolStandardize.Remover
rdMolStandardize.LargestFragmentChooser class gets the largest fragment
End of explanation
fr = rdMolStandardize.FragmentRemover()
fr.remove(Chem.MolFromSmiles("CN(C)C.Cl.Cl.Br"))
Explanation: rdMolStandardize.FragmentParent() function is similar to rdMolStandardize.LargestFragmentChooser  but first performs rdMolStandardize.Cleanup()
rdMolStandardize.FragmentRemover class filters out fragments
End of explanation
mol = Chem.MolFromSmiles("[Na+].O=C([O-])c1ccccc1")
lfc = rdMolStandardize.LargestFragmentChooser()
mol = lfc.choose(mol)
mol
u = rdMolStandardize.Uncharger()
mol = u.uncharge(mol)
mol
r = rdMolStandardize.Reionizer()
mol = r.reionize(mol)
mol
mol = Chem.MolFromSmiles("[Na+].O=C([O-])c1ccccc1")
rdMolStandardize.ChargeParent(mol)
Explanation: rdMolStandardize.Reionizer and rdMolStandardizer.Uncharger
rdMolStandardize.Reionizer ensure the strongest acid groups ionize first in partially ionized molecules.
rdMolStandardize.Uncharger attempts to neutralize charges by adding and/or removing hydrogens where possible.
rdMolStandardize.ChargeParent() method is the uncharged version of the fragment parent. It involves taking the fragment parent then applying Neutralize and Reionize.
End of explanation
from rdkit.Chem.MolStandardize.standardize import enumerate_tautomers_smiles, canonicalize_tautomer_smiles
enumerate_tautomers_smiles("OC(C)=C(C)C")
canonicalize_tautomer_smiles("OC(C)=C(C)C")
Explanation: TODO
MolStandardize.tautomer
TODO
Tautomer_enumeration generates all possible tautomers using a series of transform rules. It also removes stereochemistry from double bonds that are single in at least 1 tautomer.
Tautomer_canonicalization enumerates all possible tautomers using transform rules and uses a scoring system to determine canonical tautomer.
End of explanation
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