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Module containing RDKit functionality for working with molecular file formats.
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ForwardSDMolSupplier A class which supplies molecules from file-like object containing SD data. |
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SDMolSupplier A class which supplies molecules from an SD file. |
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SDWriter A class for writing molecules to SD files. |
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SmilesMolSupplier A class which supplies molecules from a text file. |
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SmilesWriter A class for writing molecules to text files. |
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TDTMolSupplier A class which supplies molecules from a TDT file. |
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TDTWriter A class for writing molecules to TDT files. |
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__package__ = Nonehash(x) |
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MolFragmentToSmiles( (Mol)mol, (AtomPairsParameters)atomsToUse [, (AtomPairsParameters)bondsToUse=0 [, (AtomPairsParameters)atomSymbols=0 [, (AtomPairsParameters)bondSymbols=0 [, (bool)isomericSmiles=False [, (bool)kekuleSmiles=False [, (int)rootedAtAtom=-1 [, (bool)canonical=True [, (bool)allBondsExplicit=False]]]]]]]]) -> str :
Returns the canonical SMILES string for a fragment of a molecule
ARGUMENTS:
- mol: the molecule
- atomsToUse : a list of atoms to include in the fragment
- bondsToUse : (optional) a list of bonds to include in the fragment
if not provided, all bonds between the atoms provided
will be included.
- atomSymbols : (optional) a list with the symbols to use for the atoms
in the SMILES. This should have be mol.GetNumAtoms() long.
- bondSymbols : (optional) a list with the symbols to use for the bonds
in the SMILES. This should have be mol.GetNumBonds() long.
- isomericSmiles: (optional) include information about stereochemistry in
the SMILES. Defaults to false.
- kekuleSmiles: (optional) use the Kekule form (no aromatic bonds) in
the SMILES. Defaults to false.
- rootedAtAtom: (optional) if non-negative, this forces the SMILES
to start at a particular atom. Defaults to -1.
- canonical: (optional) if false no attempt will be made to canonicalize
the molecule. Defaults to true.
- allBondsExplicit: (optional) if true, all bond orders will be explicitly indicated
in the output SMILES. Defaults to false.
RETURNS:
a string
C++ signature :
std::string MolFragmentToSmiles(RDKit::ROMol,boost::python::api::object [,boost::python::api::object=0 [,boost::python::api::object=0 [,boost::python::api::object=0 [,bool=False [,bool=False [,int=-1 [,bool=True [,bool=False]]]]]]]])
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MolFromMol2Block( (str)molBlock [, (bool)sanitize=True [, (bool)removeHs=True]]) -> Mol :
Construct a molecule from a Tripos Mol2 block.
NOTE:
The parser expects the atom-typing scheme used by Corina.
Atom types from Tripos' dbtranslate are less supported.
Other atom typing schemes are unlikely to work.
ARGUMENTS:
- mol2Block: string containing the Mol2 block
- sanitize: (optional) toggles sanitization of the molecule.
Defaults to 1.
- removeHs: (optional) toggles removing hydrogens from the molecule.
This only make sense when sanitization is done.
Defaults to true.
RETURNS:
a Mol object, None on failure.
C++ signature :
RDKit::ROMol* MolFromMol2Block(std::string [,bool=True [,bool=True]])
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MolFromMol2File( (str)molFileName [, (bool)sanitize=True [, (bool)removeHs=True]]) -> Mol :
Construct a molecule from a Tripos Mol2 file.
NOTE:
The parser expects the atom-typing scheme used by Corina.
Atom types from Tripos' dbtranslate are less supported.
Other atom typing schemes are unlikely to work.
ARGUMENTS:
- fileName: name of the file to read
- sanitize: (optional) toggles sanitization of the molecule.
Defaults to true.
- removeHs: (optional) toggles removing hydrogens from the molecule.
This only make sense when sanitization is done.
Defaults to true.
RETURNS:
a Mol object, None on failure.
C++ signature :
RDKit::ROMol* MolFromMol2File(char const* [,bool=True [,bool=True]])
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MolFromMolBlock( (str)molBlock [, (bool)sanitize=True [, (bool)removeHs=True [, (bool)strictParsing=True]]]) -> Mol :
Construct a molecule from a Mol block.
ARGUMENTS:
- molBlock: string containing the Mol block
- sanitize: (optional) toggles sanitization of the molecule.
Defaults to 1.
- removeHs: (optional) toggles removing hydrogens from the molecule.
This only make sense when sanitization is done.
Defaults to true.
- strictParsing: (optional) if this is false, the parser is more lax about.
correctness of the content.
Defaults to true.
RETURNS:
a Mol object, None on failure.
C++ signature :
RDKit::ROMol* MolFromMolBlock(std::string [,bool=True [,bool=True [,bool=True]]])
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MolFromMolFile( (str)molFileName [, (bool)sanitize=True [, (bool)removeHs=True [, (bool)strictParsing=True]]]) -> Mol :
Construct a molecule from a Mol file.
ARGUMENTS:
- fileName: name of the file to read
- sanitize: (optional) toggles sanitization of the molecule.
Defaults to true.
- removeHs: (optional) toggles removing hydrogens from the molecule.
This only make sense when sanitization is done.
Defaults to true.
- strictParsing: (optional) if this is false, the parser is more lax about.
correctness of the content.
Defaults to true.
RETURNS:
a Mol object, None on failure.
C++ signature :
RDKit::ROMol* MolFromMolFile(char const* [,bool=True [,bool=True [,bool=True]]])
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MolFromSmarts( (str)SMARTS [, (bool)mergeHs=False [, (dict)replacements={}]]) -> Mol :
Construct a molecule from a SMARTS string.
ARGUMENTS:
- SMARTS: the smarts string
- mergeHs: (optional) toggles the merging of explicit Hs in the query into the attached
atoms. So, for example, 'C[H]' becomes '[C;!H0]'.
Defaults to 0.
- replacements: (optional) a dictionary of replacement strings (see below)
Defaults to {}. See the documentation for MolFromSmiles for an explanation.
RETURNS:
a Mol object, None on failure.
C++ signature :
RDKit::ROMol* MolFromSmarts(char const* [,bool=False [,boost::python::dict={}]])
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MolFromSmiles( (str)SMILES [, (bool)sanitize=True [, (dict)replacements={}]]) -> Mol :
Construct a molecule from a SMILES string.
ARGUMENTS:
- SMILES: the smiles string
- sanitize: (optional) toggles sanitization of the molecule.
Defaults to 1.
- replacements: (optional) a dictionary of replacement strings (see below)
Defaults to {}.
RETURNS:
a Mol object, None on failure.
The optional replacements dict can be used to do string substitution of abbreviations
in the input SMILES. The set of substitutions is repeatedly looped through until
the string no longer changes. It is the responsiblity of the caller to make sure
that substitutions results in legal and sensible SMILES.
Examples of replacements:
CC{Q}C with {'{Q}':'OCCO'} -> CCOCCOC
C{A}C{Q}C with {'{Q}':'OCCO', '{A}':'C1(CC1)'} -> CC1(CC1)COCCOC
C{A}C{Q}C with {'{Q}':'{X}CC{X}', '{A}':'C1CC1', '{X}':'N'} -> CC1CC1CCNCCNC
C++ signature :
RDKit::ROMol* MolFromSmiles(std::string [,bool=True [,boost::python::dict={}]])
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MolFromTPLBlock( (str)tplBlock [, (bool)sanitize=True [, (bool)skipFirstConf=False]]) -> Mol :
Construct a molecule from a TPL block.
ARGUMENTS:
- fileName: name of the file to read
- sanitize: (optional) toggles sanitization of the molecule.
Defaults to True.
- skipFirstConf: (optional) skips reading the first conformer.
Defaults to False.
This should be set to True when reading TPLs written by
the CombiCode.
RETURNS:
a Mol object, None on failure.
C++ signature :
RDKit::ROMol* MolFromTPLBlock(std::string [,bool=True [,bool=False]])
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MolFromTPLFile( (str)fileName [, (bool)sanitize=True [, (bool)skipFirstConf=False]]) -> Mol :
Construct a molecule from a TPL file.
ARGUMENTS:
- fileName: name of the file to read
- sanitize: (optional) toggles sanitization of the molecule.
Defaults to True.
- skipFirstConf: (optional) skips reading the first conformer.
Defaults to False.
This should be set to True when reading TPLs written by
the CombiCode.
RETURNS:
a Mol object, None on failure.
C++ signature :
RDKit::ROMol* MolFromTPLFile(char const* [,bool=True [,bool=False]])
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MolToMolBlock( (Mol)mol [, (bool)includeStereo=False [, (int)confId=-1 [, (bool)kekulize=True]]]) -> str :
Returns the a Mol block for a molecule
ARGUMENTS:
- mol: the molecule
- includeStereo: (optional) toggles inclusion of stereochemical
information in the output
- confId: (optional) selects which conformation to output (-1 = default)
- kekulize: (optional) triggers kekulization of the molecule before it's written,
as suggested by the MDL spec.
RETURNS:
a string
C++ signature :
std::string MolToMolBlock(RDKit::ROMol [,bool=False [,int=-1 [,bool=True]]])
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MolToSmarts( (Mol)mol [, (bool)isomericSmiles=False]) -> str :
Returns a SMARTS string for a molecule
ARGUMENTS:
- mol: the molecule
- isomericSmarts: (optional) include information about stereochemistry in
the SMARTS. Defaults to false.
RETURNS:
a string
C++ signature :
std::string MolToSmarts(RDKit::ROMol {lvalue} [,bool=False])
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MolToSmiles( (Mol)mol [, (bool)isomericSmiles=False [, (bool)kekuleSmiles=False [, (int)rootedAtAtom=-1 [, (bool)canonical=True [, (bool)allBondsExplicit=False]]]]]) -> str :
Returns the canonical SMILES string for a molecule
ARGUMENTS:
- mol: the molecule
- isomericSmiles: (optional) include information about stereochemistry in
the SMILES. Defaults to false.
- kekuleSmiles: (optional) use the Kekule form (no aromatic bonds) in
the SMILES. Defaults to false.
- rootedAtAtom: (optional) if non-negative, this forces the SMILES
to start at a particular atom. Defaults to -1.
- canonical: (optional) if false no attempt will be made to canonicalize
the molecule. Defaults to true.
- allBondsExplicit: (optional) if true, all bond orders will be explicitly indicated
in the output SMILES. Defaults to false.
RETURNS:
a string
C++ signature :
std::string MolToSmiles(RDKit::ROMol [,bool=False [,bool=False [,int=-1 [,bool=True [,bool=False]]]]])
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MolToTPLBlock( (Mol)mol [, (str)partialChargeProp='_GasteigerCharge' [, (bool)writeFirstConfTwice=False]]) -> str :
Returns the Tpl block for a molecule.
ARGUMENTS:
- mol: the molecule
- partialChargeProp: name of the property to use for partial charges
Defaults to '_GasteigerCharge'.
- writeFirstConfTwice: Defaults to False.
This should be set to True when writing TPLs to be read by
the CombiCode.
RETURNS:
a string
C++ signature :
std::string MolToTPLBlock(RDKit::ROMol [,std::string='_GasteigerCharge' [,bool=False]])
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MolToTPLFile( (Mol)mol, (str)fileName [, (str)partialChargeProp='_GasteigerCharge' [, (bool)writeFirstConfTwice=False]]) -> None :
Writes a molecule to a TPL file.
ARGUMENTS:
- mol: the molecule
- fileName: name of the file to write
- partialChargeProp: name of the property to use for partial charges
Defaults to '_GasteigerCharge'.
- writeFirstConfTwice: Defaults to False.
This should be set to True when writing TPLs to be read by
the CombiCode.
C++ signature :
void MolToTPLFile(RDKit::ROMol,std::string [,std::string='_GasteigerCharge' [,bool=False]])
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SmilesMolSupplierFromText( (str)text [, (str)delimiter=' ' [, (int)smilesColumn=0 [, (int)nameColumn=1 [, (bool)titleLine=True [, (bool)sanitize=True]]]]]) -> SmilesMolSupplier :
C++ signature :
RDKit::SmilesMolSupplier* SmilesMolSupplierFromText(std::string [,std::string=' ' [,int=0 [,int=1 [,bool=True [,bool=True]]]]])
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