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139d2bdb83
* Fingerprint generator first prototype * Added some more details to the prototype * Update based on comments * Added additional outputs and return type changes * FingerprintGenerator updated and placeholder implementation added * Added getFingerprint implementation to FingerprintGenerator * Added comments for FingerprintGenerator * WIP: Atom pairs fingerprint implementation for FingerprintGenerator * Removed templates and added comments * Fixed AtomPairEnvGenerator creating duplicate environments * Added a atom pair old version compatibility test * Moved the FingerprintGenerator related tests to a new file * Added new comments and changes from the PR comments * using int types from std instead of boost and remove cleanUpEnvironments * Minor refactoring for atom-pair atom code generation * Added more tests for AtomPairGenerator * Removed additional clean up method from FingerprinGenerator * Added additional output for atom-pair fingerprint and a test * Removed leftover code * Default argument changes * Removed leftover include * Default invariant generation logic seperated from env generation logic for AtomPairs * Implemented fingerprint as bit vector type and added the test for it * Folded fingerprint implementation and a test case added * String representation for fingerprint generator is added * Python wrapper for fingeprint generator added with a simple test * Removed unused linked libraries * AtomPair related wrapper code moved to its own file * Python wrapper methods for different fingerprint output types added * Wrappers for invariants generators and tests are added * Added more comments and tests * Changed python side names for FIngerprintGenerator and removed extra wrappers used for invariant generators on python * Fixed object lifetime problems for invariant generators in Python * Fixed typo * Added a list of test molecules and made fingerprint generator related classes noncopyable * Morgan fingerprint python wrappers * Removed argument helper class for wrapper * Morgan Fingerprint simple implementation * Added more invariants generators for Morgan * Fixed a bug in Morgan bond invariant generator * Added invariant generator combination tests * Added atom pair generator to the invariant generator combination test * Fixed a problem in morgan feature invariant generator * Overriding invariants without generators is made possible * Added comments and documentation * Radius changed for morgan fingerprint test * RDKit fingerprint generator implementation with cpp tests * 32 bit and 64 bit fingerprint support for FingerprintGenerator * Common utilities moved to FingerprintUtil.h and code duplication reduced * Solved undefined reference issues for FPGenerator templates * Topological torsion fp generator added * Fingerprint notebook added * Python wrappers updated * Morgan tests added * Tests expanded and reduced excess amounts of collision in folded output * Expanded tests * More documentation * Python docs for atom pair * Updated fingerprint generator notebook * Python wrapper documentation added * Seperated FingerprintGenerator implementations into seperated file again * Python wrapper names updated to reflect new naming * getCountFingerprint now returns 32 bit output and count simulation does not affect count fingerprints * Python 3 compatibility for fingerprint generator tests * a bit of ABC cleanup * some comment formatting got screwed up * <sigh> * fix an uninitialized memory problem * Added copyright statement to new files * Corrected some comments and docs according to the latest changes * Bulk fingerprint generation and tests * Convenience function wrappers and size limiting for getSparseFingerprint * Copyright text fixed * Info string added to python wrappers * Some changes to get the swig wrappers building again
56 lines
2.5 KiB
OpenEdge ABL
56 lines
2.5 KiB
OpenEdge ABL
/*
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* $Id$
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*
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* Copyright (c) 2010, Novartis Institutes for BioMedical Research Inc.
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* All rights reserved.
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*
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* Redistribution and use in source and binary forms, with or without
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* modification, are permitted provided that the following conditions are
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* met:
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*
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* * Redistributions of source code must retain the above copyright
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* notice, this list of conditions and the following disclaimer.
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* * Redistributions in binary form must reproduce the above
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* copyright notice, this list of conditions and the following
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* disclaimer in the documentation and/or other materials provided
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* with the distribution.
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* * Neither the name of Novartis Institutes for BioMedical Research Inc.
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* nor the names of its contributors may be used to endorse or promote
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* products derived from this software without specific prior written permission.
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*
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* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
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* "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
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* LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
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* A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
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* OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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* SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
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* LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
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* DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
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* THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
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* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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* OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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*/
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%{
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#include <DataStructs/ExplicitBitVect.h>
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#include <DataStructs/BitOps.h>
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#include <GraphMol/Fingerprints/FingerprintUtil.h>
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#include <GraphMol/Fingerprints/Fingerprints.h>
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#include <GraphMol/Fingerprints/MACCS.h>
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%}
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%template(UIntPair) std::pair<boost::uint32_t,boost::uint32_t>;
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%template(UIntPairVect) std::vector<std::pair<boost::uint32_t,boost::uint32_t> >;
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%template(BitInfoMap) std::map<boost::uint32_t,std::vector<std::pair<boost::uint32_t,boost::uint32_t> > >;
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%newobject RDKit::RDKFingerprintMol;
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%newobject RDKit::LayeredFingerprintMol;
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%newobject RDKit::PatternFingerprintMol;
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%include <GraphMol/Fingerprints/Fingerprints.h>
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%newobject RDKit::MACCSFingerprints::getFingerprintAsBitVect;
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%rename(MACCSFingerprintMol) RDKit::MACCSFingerprints::getFingerprintAsBitVect;
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%include <GraphMol/Fingerprints/MACCS.h>
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%ignore RDKit::RDKitFPUtils::enumerateAllPaths;
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%include <GraphMol/Fingerprints/FingerprintUtil.h>
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