mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-04 21:54:27 +08:00
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>
12 lines
5.9 KiB
Plaintext
12 lines
5.9 KiB
Plaintext
CN/C(=C\[N+](=O)[O-])NCCSCc1ccc(CN(C)C)o1 |(-5.75638,1.64389,0.339481;-5.29962,0.375706,0.88353;-4.80142,-0.679132,0.0704169;-5.57222,-1.69807,-0.281357;-6.9327,-1.8123,0.120372;-7.81675,-1.00769,-0.233715;-7.24154,-2.88261,0.943388;-3.45634,-0.711221,-0.415137;-2.39705,-1.26208,0.406128;-1.10115,-1.14534,-0.399887;-0.818204,0.610732,-0.754202;0.728638,0.79049,-1.71784;1.84691,0.385321,-0.84412;2.29848,-0.937124,-0.784727;3.33995,-0.967307,0.117124;3.47748,0.349381,0.570429;4.51293,0.716493,1.56801;5.77053,1.1047,0.959975;5.61644,2.25078,0.091636;6.32536,-0.0256005,0.224903;2.58283,1.10456,-0.0195067)|
|
|
CN/C(=C\[N+](=O)[O-])NCCSCc1ccc(CN(C)C)o1 |(4.51284,1.33313,1.92564;4.20597,0.0825839,1.26359;4.40781,-0.136005,-0.12875;5.47643,0.281129,-0.783021;6.5463,0.994651,-0.175899;6.87972,2.13417,-0.605961;7.26531,0.496946,0.89138;3.42665,-0.837789,-0.885599;2.2844,-0.187578,-1.49902;1.37904,0.283177,-0.367628;0.884921,-1.18597,0.57728;-0.148781,-2.22382,-0.491889;-1.40445,-1.4809,-0.764455;-1.69942,-0.597892,-1.78355;-3.00423,-0.190622,-1.57561;-3.44127,-0.841117,-0.445475;-4.76559,-0.762903,0.215971;-4.8438,0.270869,1.20702;-4.58844,1.54655,0.586489;-6.15485,0.235814,1.80606;-2.46731,-1.60819,0.0239325)|
|
|
CN/C(=C\[N+](=O)[O-])NCCSCc1ccc(CN(C)C)o1 |(5.74542,-2.50628,0.674713;5.54601,-1.08718,0.465206;4.34229,-0.526556,-0.0371992;4.41214,0.331472,-1.04291;5.70223,0.667491,-1.59251;6.16961,1.7683,-1.17081;6.35936,-0.124866,-2.4808;3.05197,-0.861361,0.51642;2.25408,0.2543,0.966464;0.92643,-0.113942,1.53823;0.122211,1.46059,2.02576;-0.217723,2.39156,0.482409;-1.25818,1.5762,-0.240872;-1.0572,0.567077,-1.16029;-2.34272,0.157568,-1.50991;-3.22049,0.926832,-0.797014;-4.70742,0.912544,-0.784737;-5.26475,0.0294569,0.207516;-6.72363,0.159602,0.0653491;-4.95826,-1.36274,0.000804639;-2.53615,1.77862,-0.0355077)|
|
|
CN/C(=C\[N+](=O)[O-])NCCSCc1ccc(CN(C)C)o1 |(6.54305,-0.909422,0.625898;5.79299,-0.448044,-0.497913;4.56789,0.272778,-0.24673;4.54369,1.5885,-0.121558;5.78371,2.29471,-0.242738;6.06745,3.27599,0.485597;6.72763,1.92262,-1.17346;3.39811,-0.543506,-0.145087;2.33798,-0.528492,-1.13089;1.29607,-1.54317,-0.664981;0.671558,-1.07204,0.959097;-0.271399,0.463124,0.891462;-1.5098,0.184306,0.0896425;-1.69127,0.311447,-1.27291;-3.0075,-0.064632,-1.5337;-3.55023,-0.399187,-0.311977;-4.92515,-0.872382,0.0147464;-5.76169,0.274447,0.311718;-7.08556,-0.216636,0.63203;-5.19882,1.09171,1.35868;-2.63357,-0.239186,0.624061)|
|
|
CN/C(=C\[N+](=O)[O-])NCCSCc1ccc(CN(C)C)o1 |(6.82876,0.0744723,-0.0859065;5.5418,-0.515567,0.206674;4.49281,0.339321,0.690171;4.54824,0.896363,1.8835;5.67963,0.636371,2.70157;6.00568,-0.545152,2.98036;6.43414,1.69833,3.19909;3.40105,0.535631,-0.21547;2.38885,-0.479244,-0.445064;1.41646,0.0958672,-1.47756;0.67902,1.60017,-0.820159;-0.370923,1.1148,0.594409;-1.48403,0.304418,0.0353544;-1.51226,-1.05375,-0.12346;-2.72978,-1.36856,-0.674528;-3.39981,-0.157349,-0.828012;-4.76718,-0.0608357,-1.39908;-5.72342,-0.159378,-0.345975;-5.66029,0.844452,0.661487;-7.04209,-0.556759,-0.72793;-2.61715,0.814468,-0.390408)|
|
|
CN/C(=C\[N+](=O)[O-])NCCSCc1ccc(CN(C)C)o1 |(5.79708,-1.3169,0.129351;5.60097,0.0902381,0.384918;5.06872,1.00488,-0.561195;5.65973,2.18362,-0.656847;6.77689,2.39881,0.214227;7.6581,1.51897,0.30947;6.87766,3.57274,0.94428;3.96151,0.735912,-1.39388;2.6309,0.609107,-0.841933;2.46076,-0.606132,0.00601144;0.761367,-0.642772,0.636231;-0.373712,-0.894168,-0.764989;-1.75807,-0.931712,-0.218857;-2.34884,-2.10079,0.228566;-3.62121,-1.791,0.668466;-3.7565,-0.422233,0.467626;-4.91771,0.45116,0.760659;-5.81205,0.549851,-0.344116;-6.36906,-0.756763,-0.627795;-6.88915,1.46946,-0.0314991;-2.63173,0.0186918,-0.0538856)|
|
|
CN/C(=C\[N+](=O)[O-])NCCSCc1ccc(CN(C)C)o1 |(6.45571,-0.234524,1.40588;5.10302,0.222237,1.05949;4.24146,-0.640116,0.291936;4.48663,-0.786632,-1.00009;5.59921,-0.0822584,-1.58487;6.48707,-0.711357,-2.23303;5.72065,1.29095,-1.451;3.16985,-1.28945,0.963102;2.02393,-1.8224,0.210888;1.30759,-0.585161,-0.327492;0.802714,0.420145,1.07151;-0.051951,1.93474,0.565937;-1.35779,1.61859,-0.0663397;-1.63803,1.36901,-1.39512;-2.99796,1.13556,-1.43818;-3.49986,1.24694,-0.158583;-4.89005,1.09146,0.335502;-5.14776,-0.293716,0.686027;-5.00291,-1.17411,-0.445312;-6.46152,-0.462733,1.26963;-2.47721,1.53484,0.611095)|
|
|
CN/C(=C\[N+](=O)[O-])NCCSCc1ccc(CN(C)C)o1 |(-5.13876,2.14859,-0.926944;-4.70605,0.801038,-1.22147;-4.28486,-0.0284512,-0.149175;-4.91077,-1.19646,-0.00799895;-5.95924,-1.60685,-0.888934;-5.90898,-2.66305,-1.55247;-7.04721,-0.742153,-0.956174;-3.23858,0.34065,0.754838;-1.96373,0.856627,0.317836;-1.13473,1.10377,1.58481;-1.00314,-0.52844,2.39876;-0.0163036,-1.59329,1.3211;1.37446,-1.05826,1.28283;2.33362,-1.49465,2.20356;3.47155,-0.793657,1.86218;3.16111,0.015246,0.778694;4.1336,0.943889,0.0973721;4.74116,0.229556,-0.967234;5.72992,0.908513,-1.7298;4.90116,-1.17253,-0.800592;1.90597,-0.176361,0.471236)|
|
|
CN/C(=C\[N+](=O)[O-])NCCSCc1ccc(CN(C)C)o1 |(-6.15067,-0.546919,-1.70149;-5.50653,0.134178,-0.588546;-4.28228,-0.367703,-0.0288948;-4.25726,-1.02344,1.10507;-5.48868,-1.23308,1.78495;-5.55489,-1.49545,3.00343;-6.68608,-1.15302,1.11035;-3.10343,-0.0951529,-0.804491;-2.94068,1.25241,-1.2853;-1.63874,1.40897,-1.97806;-0.231909,1.17666,-0.903468;-0.0522882,-0.464912,-0.214144;1.27799,-0.513995,0.523292;1.51434,-0.211783,1.83712;2.8769,-0.412909,2.01854;3.38105,-0.824744,0.801954;4.76355,-1.17807,0.418005;5.5174,-0.0610087,-0.058567;5.65997,1.01229,0.896743;6.83932,-0.537069,-0.424422;2.37584,-0.867898,-0.0605732)|
|
|
CN/C(=C\[N+](=O)[O-])NCCSCc1ccc(CN(C)C)o1 |(-5.92487,-1.32841,-0.0091739;-5.35979,0.0191155,-0.00931145;-3.98455,0.186799,0.351258;-3.6065,1.10461,1.20867;-4.62374,1.93945,1.7759;-5.7576,2.00654,1.28744;-4.36155,2.70576,2.90398;-3.06275,-0.713844,-0.289638;-2.97888,-0.660361,-1.70961;-1.9068,-1.58599,-2.20196;-0.289943,-1.11464,-1.65293;0.00466957,-1.19041,0.0941783;1.45989,-0.916719,0.426239;2.41322,-1.93765,0.492299;3.5977,-1.31267,0.813084;3.31997,0.0448138,0.927475;4.33142,1.09321,1.26657;4.87703,1.55407,0.0276043;5.51859,0.559194,-0.767917;5.52328,2.82356,0.071238;2.03302,0.213064,0.685665)|
|
|
|