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9f551aedbe
* First import of GaussianShape. * Tidying. * Custom features. * Optimise. * Optimise. * Return 3 scores rather than 2 including combo score. * Rename useFeatures to useColors. * Python wrappers. * Python tests. * Take out big test. * Add new start mode, as PubChem does it. * Doh! * Fix MolTransforms eigenvalue return. * Two cycle optimisation, mostly working. * Take out bestSoFar score from SCA. * Take out DTYPE. * Tidy out redundant variables. * Optimisation in 2 parts. * More fiddling in pursuit of speed. * Update Python wrapper. * Tweak. * Atom subsets and different radii. * Fix test. * Revert pubchem_shape's test.cpp. * Serialize ShapeInput. * Trigger build * Remove pointers to std::arrays in ShapeInput. * ShapeInput virtual d'tor. * Precondition - ShapeInput needs a molecule with at least 1 conformer. * Rename ShapeInput::d_centroid to ShapeInput::d_canonTrans. * Fix normalization bugs. * Select start mode using moments of inertia rather than eigenvalues of canonical transformation. * Include color features in moments of inertia. * Smidge faster. * Tversky similarity. * Tidy tests. * Tests working on Linux. * Revert force of right handed axes in MolTransforms::computePrincipalAxesAndMomentsFromGyrationMatrix replacing with a comment in the code. * Response to review. * Sneaky allCarbon bug. * add multithreaded test * Response to review. * Doh! Don't recalculate normalization after every transformation. * Re-instate d_normalizationOK. * Re-name functions for fetching canonical transformations. * Separate alpha from coords. * MultiConf works with single conf extraction. * Extract all conformations. Max and best similarities. * Renames d_currConformer to d_activeShape. * Update shapeToMol. * Update shapeToMol. * Changes from synthon shape searching. * Fix normalization of multiple confs. * Update Python wrappers. * Fix shape merge. * Improve bestSimilarity. * Fix python wrapper. * Pull in changes from SynthonShapeSearch: make pruneShapes public. function to negate Alpha values. * clang-tidy suggestions. * clang-tidy suggestions. * Bug in quaternion gradients - we now have only 3 coordinates. * Tidy tests. * Mac result slightly different. * Multi conformer molecule alignment. * Optionally return raw overlap volumes in score functions. * Python wrappers for raw overlap volumes. * Update Python wrapper ShapeInputOptions. * Tidy for PR. * Extra include file. * Extra library * Tidy forward declarations. * Don't prune if threshold < 0.0. * Windows exporty thing. * Check SMILES on merge of ShapeInputs. * PRECONDITION of SMILES on merge of ShapeInputs. * Response to review - rename some functions. * change how overlapVols is passed add a test for it * API suggestions * Response to review. * Remove debugging writes. * Fix Python wrappers. --------- Co-authored-by: David Cosgrove <david@cozchemix.co.uk> Co-authored-by: greg landrum <greg.landrum@gmail.com>
92 lines
2.8 KiB
Plaintext
92 lines
2.8 KiB
Plaintext
2244
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RDKit 3D
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13 13 0 0 0 0 0 0 0 0999 V2000
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-17.2334 -5.4951 2.3053 O 0 0 0 0 0 0 0 0 0 0 0 0
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-14.0938 -3.8235 0.2824 O 0 0 0 0 0 0 0 0 0 0 0 0
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-15.9621 -3.2015 1.3992 O 0 0 0 0 0 0 0 0 0 0 0 0
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-17.3818 -6.7019 0.3049 O 0 0 0 0 0 0 0 0 0 0 0 0
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-15.9632 -5.9632 2.4646 C 0 0 0 0 0 0 0 0 0 0 0 0
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-14.8724 -5.2643 1.9474 C 0 0 0 0 0 0 0 0 0 0 0 0
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-15.7617 -7.1573 3.1570 C 0 0 0 0 0 0 0 0 0 0 0 0
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-13.5802 -5.7595 2.1226 C 0 0 0 0 0 0 0 0 0 0 0 0
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-14.4695 -7.6525 3.3323 C 0 0 0 0 0 0 0 0 0 0 0 0
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-13.3789 -6.9536 2.8151 C 0 0 0 0 0 0 0 0 0 0 0 0
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-15.0605 -4.0152 1.2226 C 0 0 0 0 0 0 0 0 0 0 0 0
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-17.8696 -5.9525 1.1405 C 0 0 0 0 0 0 0 0 0 0 0 0
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-19.2553 -5.3841 1.0571 C 0 0 0 0 0 0 0 0 0 0 0 0
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1 5 1 0
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1 12 1 0
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2 11 1 0
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3 11 2 0
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4 12 2 0
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5 6 2 0
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5 7 1 0
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6 8 1 0
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6 11 1 0
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7 9 2 0
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8 10 2 0
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9 10 1 0
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12 13 1 0
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M END
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> <PUBCHEM_PHARMACOPHORE_FEATURES>
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5
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1 2 acceptor
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1 3 acceptor
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1 4 acceptor
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3 2 3 11 anion
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6 5 6 7 8 9 10 rings
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$$$$
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166295140
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RDKit 3D
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16 17 0 0 1 0 0 0 0 0999 V2000
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-2.8293 0.2150 1.4768 F 0 0 0 0 0 0 0 0 0 0 0 0
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-4.0626 0.7806 -0.2297 F 0 0 0 0 0 0 0 0 0 0 0 0
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0.1990 -2.7308 -0.6547 O 0 0 0 0 0 0 0 0 0 0 0 0
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2.1655 0.9098 0.9439 O 0 0 0 0 0 0 0 0 0 0 0 0
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0.2386 -1.4812 1.2511 O 0 0 0 0 0 0 0 0 0 0 0 0
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-0.5537 0.6911 -0.1687 N 0 0 0 0 0 0 0 0 0 0 0 0
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3.9396 -0.0288 -0.0987 N 0 0 0 0 0 0 0 0 0 0 0 0
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-0.8484 -0.6331 -0.7303 C 0 0 2 0 0 0 0 0 0 0 0 0
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-2.3589 -0.8260 -0.5838 C 0 0 0 0 0 0 0 0 0 0 0 0
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-2.8195 0.4211 0.1395 C 0 0 0 0 0 0 0 0 0 0 0 0
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-1.7941 1.4679 -0.2225 C 0 0 0 0 0 0 0 0 0 0 0 0
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0.5493 1.3657 -0.8388 C 0 0 0 0 0 0 0 0 0 0 0 0
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-0.0875 -1.6304 0.0829 C 0 0 0 0 0 0 0 0 0 0 0 0
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1.8856 0.8393 -0.3872 C 0 0 0 0 0 0 0 0 0 0 0 0
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2.9644 0.2690 -1.0161 C 0 0 0 0 0 0 0 0 0 0 0 0
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3.4121 0.3708 1.0364 C 0 0 0 0 0 0 0 0 0 0 0 0
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1 10 1 0
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2 10 1 0
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3 13 1 0
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4 14 1 0
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4 16 1 0
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5 13 2 0
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6 8 1 0
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6 11 1 0
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6 12 1 0
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7 15 1 0
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7 16 2 0
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8 9 1 0
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8 13 1 1
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9 10 1 0
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10 11 1 0
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12 14 1 0
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14 15 2 0
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M END
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> <PUBCHEM_PHARMACOPHORE_FEATURES>
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6
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1 3 acceptor
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1 5 acceptor
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1 6 cation
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3 3 5 13 anion
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5 4 7 14 15 16 rings
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5 6 8 9 10 11 rings
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$$$$
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