#include <SynthonSpace.h>
Definition at line 120 of file SynthonSpace.h.
◆ SynthonSpace() [1/2]
RDKit::SynthonSpaceSearch::SynthonSpace::SynthonSpace |
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◆ SynthonSpace() [2/2]
RDKit::SynthonSpaceSearch::SynthonSpace::SynthonSpace |
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const SynthonSpace & | other | ) |
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delete |
◆ buildAddAndSubstractFingerprints()
void RDKit::SynthonSpaceSearch::SynthonSpace::buildAddAndSubstractFingerprints |
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const FingerprintGenerator< std::uint64_t > & | fpGen | ) |
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◆ buildSynthonFingerprints()
void RDKit::SynthonSpaceSearch::SynthonSpace::buildSynthonFingerprints |
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const FingerprintGenerator< std::uint64_t > & | fpGen | ) |
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◆ fingerprintSearch()
- Parameters
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query | : query molecule |
fpGen | a FingerprintGenerator object that will provide the fingerprints for the similarity calculation |
params | : (optional) settings for the search |
- Returns
- : the hits as a SearchResults object.
◆ getNumProducts()
std::int64_t RDKit::SynthonSpaceSearch::SynthonSpace::getNumProducts |
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◆ getNumReactions()
size_t RDKit::SynthonSpaceSearch::SynthonSpace::getNumReactions |
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◆ getReactions()
const std::map< std::string, std::unique_ptr< SynthonSet > > & RDKit::SynthonSpaceSearch::SynthonSpace::getReactions |
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◆ getSynthonFingerprintType()
std::string RDKit::SynthonSpaceSearch::SynthonSpace::getSynthonFingerprintType |
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const |
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inline |
◆ hasAddAndSubstractFingerprints()
bool RDKit::SynthonSpaceSearch::SynthonSpace::hasAddAndSubstractFingerprints |
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const |
◆ hasFingerprints()
bool RDKit::SynthonSpaceSearch::SynthonSpace::hasFingerprints |
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const |
◆ operator=()
◆ readDBFile()
void RDKit::SynthonSpaceSearch::SynthonSpace::readDBFile |
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const std::string & | inFilename | ) |
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- Parameters
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inFilename | the name of the file to read. |
◆ readTextFile()
void RDKit::SynthonSpaceSearch::SynthonSpace::readTextFile |
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const std::string & | inFilename | ) |
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- Parameters
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inFilename | name of the file containing the synthon-based library. |
The original format is: all lines are tab-separated first line:SMILES synton_id synton# reaction_id Note the spelling "synton" from the original paper/example file. Subsequent lines have a single reagent e.g. OCC([U])=NN=[Np] 1-1 0 triazole-1 C1CCCC1N([Pu])[U] 2-1 1 triazole-1 CC1CCN(C1)C(=[Np])[Pu] 3-1 2 triazole-1
Other acceptable formats are as above, but with a 5th column "release": SMILES synton_id synton# reaction_id release
or a comma-separated equivalent of the first format: SMILES,synton_id,synton_role,reaction_id but with the 3rd column named differently but with the same meaning. The formatting of the first 2 formats has been relaxed such that any whitespace may be used as the field separator.
Attachment points are U, Np, Pu and Am for up to 4 synthons per reaction. A product is created by taking a synthon from each synton# value and combining by replacing matching trans-uranic elements and replacing them with a direct bond of the appropriate type. A more (for RDKit) conventional connection flag of isotope labelled dummy atoms is also accepted ([1*] etc.). Throws a std::runtime_error if it doesn't think the format is correct, which it does by checking that the first line is as above and subsequent lines have appropriate number of fields.
◆ substructureSearch()
- Parameters
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query | : query molecule |
params | : (optional) settings for the search |
- Returns
- : the hits as a SearchResults object.
◆ summarise()
void RDKit::SynthonSpaceSearch::SynthonSpace::summarise |
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std::ostream & | os | ) |
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◆ writeDBFile()
void RDKit::SynthonSpaceSearch::SynthonSpace::writeDBFile |
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const std::string & | outFilename | ) |
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- Parameters
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outFilename | the name of the file to write. |
◆ writeEnumeratedFile()
void RDKit::SynthonSpaceSearch::SynthonSpace::writeEnumeratedFile |
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const std::string & | outFilename | ) |
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- Parameters
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outFilename | name of the file to write |
The documentation for this class was generated from the following file: