RDKit
Open-source cheminformatics and machine learning.
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#include <SynthonSpace.h>
Definition at line 91 of file SynthonSpace.h.
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void RDKit::SynthonSpaceSearch::SynthonSpace::buildSynthonFingerprints | ( | const FingerprintGenerator< std::uint64_t > & | fpGen | ) |
SearchResults RDKit::SynthonSpaceSearch::SynthonSpace::fingerprintSearch | ( | const ROMol & | query, |
const FingerprintGenerator< std::uint64_t > & | fpGen, | ||
const SynthonSpaceSearchParams & | params = SynthonSpaceSearchParams() |
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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 |
std::int64_t RDKit::SynthonSpaceSearch::SynthonSpace::getNumProducts | ( | ) | const |
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Definition at line 102 of file SynthonSpace.h.
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Definition at line 103 of file SynthonSpace.h.
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Definition at line 115 of file SynthonSpace.h.
bool RDKit::SynthonSpaceSearch::SynthonSpace::hasFingerprints | ( | ) | const |
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inFilename | the name of the file to read. |
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.
SearchResults RDKit::SynthonSpaceSearch::SynthonSpace::substructureSearch | ( | const ROMol & | query, |
const SynthonSpaceSearchParams & | params = SynthonSpaceSearchParams() |
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query | : query molecule |
params | : (optional) settings for the search |
void RDKit::SynthonSpaceSearch::SynthonSpace::summarise | ( | std::ostream & | os | ) | const |
os | stream |
outFilename | the name of the file to write. |
void RDKit::SynthonSpaceSearch::SynthonSpace::writeEnumeratedFile | ( | const std::string & | outFilename | ) | const |
outFilename | name of the file to write |