chematic-chem 0.4.6

//! Synthetic Accessibility Score (SA Score).
//!
//! Reference: P. Ertl & A. Schuffenhauer, J. Cheminf. 2009, 1, 8.
//!
//! The SA Score estimates synthetic accessibility on a scale of 1 (easy) to
//! 10 (hard). It combines:
//!   - A fragment score based on circular Morgan-like environments (radii 0–2)
//!     and their frequency in a reference corpus of drug-like molecules.
//!   - A complexity penalty for spiro atoms, bridgehead atoms, macrocycles,
//!     stereocenters, and ring complexity.
//!
//! # Fragment table
//!
//! The table below was generated by `tools/gen_sa_table` from 145 drug-like
//! molecules validated against the chematic test suite.  Hashes use the same
//! FNV-1a scheme as ECFP fingerprints (`chematic_fp::morgan_fp_counts`).
//! Score encoding: i16 = (log10(fragment_frequency) × 1000) as i16.
//! Fragments not in the table receive DEFAULT_LOG_FREQ = log10(1e-5) = -5.0.

use crate::descriptors::{num_bridgehead_atoms, num_spiro_atoms, num_stereocenters, ring_count};
use chematic_core::{AtomIdx, Molecule};
use chematic_fp::morgan_fp_counts;
use std::collections::HashMap;

// ---------------------------------------------------------------------------
// Fragment scoring table (auto-generated — do not edit by hand)
// Regenerate with: cargo run -p gen-sa-table
// Corpus: 188 molecules (v0.1.94 expansion) | 1415 unique fragment environments
// Score encoding: i16 = (log10(freq_in_corpus) * 1000.0) as i16
// Missing fragments use DEFAULT_LOG_FREQ = -5000 (log10(1e-5))
// ---------------------------------------------------------------------------

// Auto-generated by tools/gen_sa_table
// Corpus: 188 molecules | 1415 unique fragment environments
// Score encoding: i16 = (log10(freq_in_corpus) * 1000.0) as i16
// Missing fragments use DEFAULT_LOG_FREQ = -5000 (log10(1e-5))
static FRAGMENT_SCORES: &[(u64, i16)] = &[
    (0x004964fdf62938bc, -2274), (0x0076dfd9f5d5e92f, -2274), (0x008478d2a965a7d3, -2274), (0x00857a26146afbbe, -1797),
    (0x00920e29c72d57c7, -1797), (0x00f3c98125d0fd0b, -2274), (0x0116b293ae56fc0b, -2274), (0x0122d33741722698, -1797),
    (0x01346a7a0a6a4a0b, -2274), (0x01541220532e32af, -2274), (0x0174164141c74a49, -1973), (0x01792c3d14a1bff2, -2274),
    (0x01df51eebf3e9af8, -1973), (0x01f02a1d9b408cc5, -2274), (0x01f6420114cb0c2f, -1797), (0x02423bfddc4b2164, -1429),
    (0x0257c42c4d26b63c, -1672), (0x028f3cfc5524a7eb, -1797), (0x0307575f08697b50, -2274), (0x030e115ca0c2da1e, -2274),
    (0x03923643b928b17e, -1973), (0x03ac5ed040dbb9bc, -2274), (0x03b614ff5a84337c, -2274), (0x03fd4c650173b478, -1973),
    (0x04374c64422da884, -1973), (0x046520163bab2f75, -1797), (0x04799cc5c03d2b61, -2274), (0x04bee69c862ee09c, -2274),
    (0x04efeb2d2a7d577d, -2274), (0x052e74ed182c0313, -2274), (0x0538ec63cef1b7ca, -1973), (0x05609c276e42ecd1, -2274),
    (0x05f69a0fb0b6eb67, -1973), (0x05f9add393b901d0, -1973), (0x0647330488aa81f9, -1973), (0x06826ff6a276a5fa, -1672),
    (0x06a1b9a55d3aceeb, -2274), (0x06ab1497d6d675d7, -2274), (0x07290ca8784452f0, -2274), (0x07ab814d2660c71c, -2274),
    (0x07fa83823e964914, -2274), (0x083f31c7dee29a93, -2274), (0x084143c271b0bd49, -2274), (0x0879232294a61644, -1973),
    (0x0881244bb00dee60, -1797), (0x089a5b3e74f993be, -1797), (0x0984db8bb5d7939d, -2274), (0x09c92985e8b96b99, -2274),
    (0x09e2dac051b3c093, -2274), (0x0a0bed9ab97aaddd, -2274), (0x0a493dfbb1da469e, -1575), (0x0a8fc9d9c8cc3f27, -2274),
    (0x0a980f6f4ad1ffdb,  -416), (0x0adcd6285debc907, -2274), (0x0b07b903c0c08671, -1672), (0x0b2aa31778ae8835, -2274),
    (0x0b431c350343558f, -2274), (0x0ba08a32cb665d29, -2274), (0x0bb8d8fad52164e6, -1319), (0x0bcab9f7c5502977, -2274),
    (0x0bd9f545c283dc1b, -1797), (0x0c5ab6a370d2faa9, -2274), (0x0c5ae3f93c054670, -2274), (0x0cb2d17a5595fe32, -1973),
    (0x0d106d6947d85640, -2274), (0x0d462d17a4802f56, -1973), (0x0d583992c96c069a, -2274), (0x0d5ccde7e9cbfa6d, -2274),
    (0x0db76be9ebd9c092, -1797), (0x0e0376266a8bec44, -2274), (0x0e072814e29c188c, -1232), (0x0e072914e29c1a3f, -1128),
    (0x0e0a8e14e29efbb5,  -912), (0x0e3e3c386d67f31c, -2274), (0x0e56c77424dcd7b4, -1575), (0x0e83ecfc94b68fd1, -1973),
    (0x0e8bea7de713e860, -1973), (0x0e910648edc4cdaa, -2274), (0x0e9a9ad04a7ee557, -2274), (0x0eb25a5432308c3e, -1973),
    (0x0eb59c2454c0a80b, -2274), (0x0ec3bf996032f5c7, -1973), (0x0ece2cb1fabe2c66, -2274), (0x0f6d21323826b337, -1973),
    (0x1038f8f5c37e5fc0, -2274), (0x106112e7d4a5a811, -2274), (0x106494bcb5abaf32, -2274), (0x10852a35673a7846, -2274),
    (0x109606cf03d13cce, -2274), (0x10b754226afd3043,  -694), (0x11407e4b26b7602e, -2274), (0x1170feaa69ecb5b7, -2274),
    (0x117c897cb6c9b5ee, -2274), (0x118cfa7f4931d270, -1973), (0x11bba021fef24f95, -1973), (0x11c33a94cc0a703b, -2274),
    (0x11d5090450bd4399, -2274), (0x12197b33ed502eff, -2274), (0x12205613dc8c11cf, -2274), (0x1231f702ce707674, -1575),
    (0x1262b1edcb2a3284, -1194), (0x12f6d6f181811b15, -1973), (0x1303b7dd5bd8a90d, -2274), (0x1324326b221d46cc, -1973),
    (0x136658b69b5ec468, -2274), (0x13d87ee8d7bcb94c, -1973), (0x142c920f65afb38b, -2274), (0x144fde33d16b19cb, -2274),
    (0x14617ffdadbdf1d5, -2274), (0x14c6cff2b4b0c8ac, -2274), (0x14c8f2d15c49a4ef, -1575), (0x156f4ad7f7975164, -1973),
    (0x157672f70dc078b0, -2274), (0x158e807996ec8cc5, -2274), (0x159971e29aec8f4c, -1973), (0x15a266930ee75fc1, -1575),
    (0x15b68ecdc21d30aa, -1973), (0x15e7ac66e120f8dd, -1672), (0x15fed04eef320ec5, -2274), (0x16057ad0271e705e, -1575),
    (0x1638dd075c357440, -1672), (0x16a17f6bc7e366e7, -2274), (0x16af9720bf576e4f, -1274), (0x16d4c66669ba63d1, -2274),
    (0x16f1423a93372ad5, -2274), (0x175c377ed50ea04c, -1797), (0x179a83d47104aa6c, -1973), (0x185dc2129bd67250, -1973),
    (0x18e6482032e2bb12, -1973), (0x1946adc3a80e3827, -2274), (0x194badb927573b66, -2274), (0x19af0fe684d06da5, -2274),
    (0x19f8660c31cd8678, -2274), (0x1a0a084b0cbde182, -1319), (0x1a2cf86bce61107b, -2274), (0x1a88373fb50838c8, -2274),
    (0x1a92fafae8796a2f, -2274), (0x1a9fde6d38513705, -2274), (0x1b07f8cd99879d2e, -2274), (0x1b2ec62571d026a4, -2274),
    (0x1b7a69208099fd6c, -2274), (0x1b9e47ea1dc8e260, -2274), (0x1c3f087568ccdd60, -2274), (0x1c8a5dbe430f6c16, -1797),
    (0x1cf161a809579ab3, -2274), (0x1d0112f7ade936bb, -1973), (0x1d027b9ca41348b8, -2274), (0x1d08634c968afc6c, -2274),
    (0x1de4fe99e6eca0cb, -2274), (0x1e13a35c60ca339e, -1973), (0x1e2a7340105efa2a, -1973), (0x1e2c49d999eeeb3d, -2274),
    (0x1e7e7ec59ebe9dc2, -2274), (0x1ea6b4cdddb6120e, -1973), (0x1ead3a4c3ea891dc, -2274), (0x1ef262987a9ea3cb, -1797),
    (0x1f0df9de8450bd25, -2274), (0x1f395a325eba426a, -2274), (0x1f63affe49bdd5cd, -2274), (0x1f6ef0a6cfe3dc69, -2274),
    (0x1f7e6fd67342c629, -2274), (0x1fc3839242a817e9, -1973), (0x1fc9c759945123d6, -2274), (0x1fcf80328cad0210, -2274),
    (0x202d2ff867845e57, -2274), (0x203d88f70eff2858, -2274), (0x20491bec562cdeac, -2274), (0x205c443b2ec62a7d, -2274),
    (0x20608a747a74641b, -1973), (0x20e8ec8f2a5c455a, -1973), (0x21180c1ade818796, -2274), (0x2123add8b77232c6, -2274),
    (0x21430d4bee6504e9, -1973), (0x21882e22200bfd05, -2274), (0x21d8c1160c0c1eb5, -2274), (0x21f6cac09e36c9ae, -2274),
    (0x223e10ac5632f867, -2274), (0x226c4223f6055aec, -2274), (0x227eb8b76ee6ac25, -2274), (0x229b7183c12bf558, -2274),
    (0x22beea1f4817719d, -2274), (0x22cf849e223a17fc, -2274), (0x22ef820111ddc011, -1429), (0x237a97d8243d0fd0, -2274),
    (0x23a48f94f84a26da, -1973), (0x23d85d51dddac175,  -575), (0x242eb745e093f971, -2274), (0x24314d7bc9413743, -2274),
    (0x2447be64e758d4d7, -1973), (0x24784972d976e1e5, -1973), (0x24ab0ce97002ddf7, -2274), (0x24d042cf5e0d6936, -2274),
    (0x24eccbe3d079923c, -2274), (0x252021e19e8b9377, -2274), (0x252ccc0f7bca0736, -2274), (0x252e5544ce51986d, -2274),
    (0x258b3ba24d950901, -2274), (0x25ce0c11b56be582, -2274), (0x25dcc98d36f9f3f4, -2274), (0x25e3cfdb5ff70798, -2274),
    (0x2608bc9e99918b81, -2274), (0x26bef7d87ffa4d16, -2274), (0x26e007da0d8f32c8, -2274), (0x271638e85b0c3b23, -1575),
    (0x271f51077458ad09, -2274), (0x273e1903a64933f5, -2274), (0x274e25532ecdc76e, -1575), (0x2757e32e72bea5d8, -1973),
    (0x2799e0205be0a067, -1973), (0x27e85b77f13be42e, -1672), (0x2807683cfef35bae, -2274), (0x2892239e6e3e9947, -1973),
    (0x28e7fdad6ad31373, -2274), (0x2920b45d7954451c, -1973), (0x294ac191846541bd, -2274), (0x296c540d465f6239, -2274),
    (0x296e45103975c05b, -1973), (0x29ae53b8efdac32f, -2274), (0x2a12deb140a33f64, -2274), (0x2a3dd2196f0bd444, -2274),
    (0x2a4528592e2d1977, -2274), (0x2a5cb1f2e4342f1a, -1973), (0x2a943aefc5ac266d, -1797), (0x2aa9aaa2cb43b958, -2274),
    (0x2ad12bebf0577a47, -2274), (0x2ad9b6230042a822, -1973), (0x2b0887b05c8820b8, -2274), (0x2b754f7757c3234b, -2274),
    (0x2b8c70b7e65b0131, -2274), (0x2ba54c732034feb4, -1232), (0x2bb8ee311ff41c41, -1973), (0x2c4cbc063e3c5950, -1429),
    (0x2c8ec0b57acb6fd4, -2274), (0x2c8ece7fcb862975, -1797), (0x2cbde31ff8356f2c, -1973), (0x2cf7eb372af7745e, -2274),
    (0x2d010544454befc8, -2274), (0x2d30432d81089fe2, -1973), (0x2d30f942a6d3d693, -1797), (0x2d31011baac74404, -2274),
    (0x2d8d500a9e4ab55a, -2274), (0x2d9bf070e26c4662, -2274), (0x2ddeb8de0e184048, -1973), (0x2de59def01f6db65, -2274),
    (0x2e122703a11c30ed, -1973), (0x2e3e0d0726160bab, -2274), (0x2e4d488b61aa89e3, -2274), (0x2ecc30d41e125584, -2274),
    (0x2f0a8c02aaadb01b, -2274), (0x2f21d18c14334dda, -1797), (0x2ff1677c5cafe7be, -1973), (0x30ac56cbc7dc04d2, -2274),
    (0x30b8e24790a12b3a, -2274), (0x30c4fbf0e3942f05, -2274), (0x31636c537e8365df, -2274), (0x319e19f4341c4f34, -1429),
    (0x31ca0e373ea8426f, -2274), (0x322410b3e74c3665, -1973), (0x324647d8916ca1f9, -2274), (0x32555b05d258c124, -1672),
    (0x3266bcaf8b17a822, -2274), (0x327fd14d65044ff1, -2274), (0x32bc14f9cd815a32,  -782), (0x32bf7af9cd843d5b,  -410),
    (0x32c68f664a3bb734, -2274), (0x334a8831023dd7b1, -2274), (0x3353e4dcd80c7343, -1973), (0x335ed078bcbe5140, -2274),
    (0x3379451cb346af9c, -2274), (0x33a64083ba82d58c, -2274), (0x33ecc9a706205329, -1973), (0x340b20a10adbc1b9, -2274),
    (0x341966a74349ee48, -1429), (0x3429d7a892587634, -2274), (0x34fb723a5bcf8909, -1429), (0x350464e4d3ce2516, -2274),
    (0x353c695406f165bf, -2274), (0x3559061afbaccd68, -2274), (0x35829089ebc1ba32, -2274), (0x358799f7b3afdc68, -1973),
    (0x35ab48493ed03c48, -1496), (0x35be22044914d55f, -1672), (0x35c40ac3cc681602, -2274), (0x35c75d115414a921, -2274),
    (0x361ab675154b5622, -2274), (0x368170c54c6b8fa2, -2274), (0x3688d710011c86dd, -1973), (0x36b011ce2d26afe6, -2274),
    (0x36c839b2051223f1, -1575), (0x36ccdccc694130c9, -1575), (0x36d0693874039772, -2274), (0x370201e25b9c7e0a, -2274),
    (0x37452d82fa4ba573,  -269), (0x3758fda03bc67d97, -2274), (0x3771f7f252aa6c46, -2274), (0x377574e027d71171, -2274),
    (0x37a8fd981f9a74ff, -2274), (0x37b1050c2b9c0df9, -2274), (0x3805fed4f98f72bc, -2274), (0x386eb18453ce1edc, -2274),
    (0x38cd452e36088f72, -2274), (0x38d1ef005ef620af, -2274), (0x392942e8c7cd681c, -1797), (0x39575e082fe1f1d1, -1797),
    (0x39f52f347b7f471a, -2274), (0x3a010a032a53d965, -2274), (0x3a0183ce2cc8aa90, -2274), (0x3a05d055fe996aea, -2274),
    (0x3a0df6586c4f4abe, -2274), (0x3a14f4dc2cc9aa3a, -2274), (0x3a3c229889d60f23, -2274), (0x3a639e99e3695820, -1973),
    (0x3baad33237588702, -1973), (0x3c08ca054202cfe5, -2274), (0x3c0a836901146878, -2274), (0x3cc0b2945f753989, -2274),
    (0x3cedf6b502306fdd, -1672), (0x3d2bd38b6089633a, -2274), (0x3d96d3c800913cdf, -1973), (0x3de1f14d05a28bca, -2274),
    (0x3e09d995b6e15428, -2274), (0x3e8ac0e6c3a209ef, -2274), (0x3f19f59d52b144d9, -2274), (0x3f8f71748d326e1d, -2274),
    (0x3f99f96e51fd2dc4, -1672), (0x4074176a52d5cd2b, -2274), (0x40be026ea1208a24, -2274), (0x416fc2d6a31d897e, -2274),
    (0x423364784e7f7a64, -2274), (0x42eb18c9aa37d60e, -2274), (0x431602e280cc42e7, -2274), (0x431c36e8a0a84552, -1973),
    (0x432e261a7287471a, -2274), (0x434fac478944f67e, -2274), (0x4373b69458f73ecb, -1319), (0x439d87eb88902042, -2274),
    (0x43a5a092a36ad3e5, -2274), (0x4460d2463203fa35, -2274), (0x447ae66b8657b49f, -2274), (0x449711ffa5709e4a, -2274),
    (0x44abd12b5c892f83, -2274), (0x44ee4fc634d7acbe, -1797), (0x45136f682a4c0fac, -1274), (0x4542020c842ed431, -2274),
    (0x45bb7bf881a88283, -1371), (0x45befd36805dba20, -2274), (0x45c812642be715eb, -2274), (0x45ee51b848811490, -1973),
    (0x45f7cd6764cc339e, -2274), (0x45ff134e282c3c51, -2274), (0x469ef7878555fbe6, -2274), (0x46a4c27b7abddbe3, -2274),
    (0x46ab089bafc023d8, -2274), (0x46b900d613499cd8, -1672), (0x46e272680498fa67, -2274), (0x4712be7ce76241a9, -1973),
    (0x4724727d57cd835c, -2274), (0x47481c6912ad9a4f, -1429), (0x47587fab12b96ae6, -2274), (0x47a0fa5633181f0c, -2274),
    (0x48478073db011eaf, -2274), (0x484bb95551694d01, -2274), (0x4888d06f23a3d987, -1496), (0x490da1e9d7fee20e, -2274),
    (0x492ce9658d9e588b, -2274), (0x49334b429a423fd0, -1371), (0x496ef5e0db507775, -2274), (0x49718bbb2856e893, -2274),
    (0x497ce4cae1877144, -2274), (0x49982f2126c559d4, -1973), (0x49c498d111b1acfb, -1575), (0x49ea28a97a20609e, -2274),
    (0x49f475eb731e087d, -1797), (0x4a47b8b1f265f346, -2274), (0x4a7c781a95d72ee5, -2274), (0x4a7d4e636dffceb5, -2274),
    (0x4a877f1ab23b5430, -2274), (0x4a8be010a1da5d36, -2274), (0x4ac4f49a9c3fb71d, -2274), (0x4af38f01581ce103, -2274),
    (0x4b20f8dd7cfbc508, -2274), (0x4b256d172861c6ca, -1973), (0x4bd52452074c7b8a, -2274), (0x4c042c3547317ad7, -2274),
    (0x4c2f0ffb905a93e6, -2274), (0x4c42d3782bfedb82, -2274), (0x4c6072e6226d3434, -2274), (0x4c6fdf9015b15f5e, -2274),
    (0x4c856359e1f4c9b7, -1797), (0x4c85a524821f2b10, -1973), (0x4c9d6b6a78aa0ac6, -1797), (0x4ca7714d860c67af, -2274),
    (0x4ca9f6369244bb58, -2274), (0x4ccf0feb62d7e7b7, -2274), (0x4d0402138f59e057, -1973), (0x4d3d0df11590ed05, -2274),
    (0x4d5680f6e57a8be5, -2274), (0x4d6760025d19c532, -2274), (0x4d9a62ef1f870b91, -2274), (0x4da71ad13b352efe, -2274),
    (0x4de362ecd68a0fb0, -2274), (0x4e1896e770a45ffa, -2274), (0x4e3a857f02356ea6, -1797), (0x4e3fef1234c334a9, -2274),
    (0x4e85f1e0e9cd1828, -2274), (0x4e9915734746ee77, -2274), (0x4ebef8229e8c976e, -2274), (0x4ecea16cb41910b5, -2274),
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    (0xedbad7949fbde449, -2274), (0xedeccbde5d7799f3, -1575), (0xedf46f9ea6fe6d54, -1973), (0xee0a1010059ef075, -2274),
    (0xee1d18dbe3c44e1f, -2274), (0xee48667f54bea84b, -2274), (0xee50cc725056af63, -2274), (0xee54a834009751a0, -2274),
    (0xee6893424ee373b8, -1429), (0xee74810f392b21a0, -1973), (0xeeb65a39c9ed0c45, -2274), (0xef0f3a4695ba163e, -2274),
    (0xef263b57e87fa690, -2274), (0xef36ab955747d04a, -2274), (0xef3aac08b09d2249, -1672), (0xef46ce740bcb2485, -2274),
    (0xef4d437a6d3a524e, -2274), (0xefb4723519a82a11, -1672), (0xf023af36bb35dbae, -1160), (0xf023b036bb35dd61, -1672),
    (0xf0271536bb38bed7, -1371), (0xf028aa5e02497f94, -2274), (0xf03f552d3bd947cf, -2274), (0xf08bee460006d3c3, -1973),
    (0xf0a64b5ef534fb3e, -2274), (0xf0ab111752c25513, -1797), (0xf0c6c4d5548847e4, -2274), (0xf1c3e16d1567d771, -1973),
    (0xf1d8028b47e5077a, -2274), (0xf1ebd66d8d05884b, -1797), (0xf259ef69fb69055d, -2274), (0xf261c17d54e62b54, -2274),
    (0xf29bed2f336e0e62, -1496), (0xf2b267e06d23b334, -2274), (0xf2be626be0a8b956, -2274), (0xf30532c355dbe875, -2274),
    (0xf31e2c766a5e07b3, -1797), (0xf380a340243bd94f, -2274), (0xf3975d440bc5f4c7, -2274), (0xf3cbea0d23acff2e, -2274),
    (0xf421f71881ec3ebf, -2274), (0xf42cd2cfd1ea5e0b, -2274), (0xf443cce4292fd148, -2274), (0xf469a650ff39066a, -2274),
    (0xf46e318b08dfc1ce, -2274), (0xf49f99838242c17d, -1973), (0xf4c13b7ab62043ae, -2274), (0xf4d8970fc5e76afb, -2274),
    (0xf4faf7c6fc59f8d3, -1973), (0xf5351367431c2dfa,  -278), (0xf55ca8d95956da7f, -2274), (0xf571b9ec7f408f14, -2274),
    (0xf58f21073351170e, -2274), (0xf598b6014503a9ad, -2274), (0xf5cbc8289b8e3b92, -2274), (0xf60e2e6ddf74f103, -1429),
    (0xf6bae8c69119b64d, -2274), (0xf700eac98ca93a17, -2274), (0xf719b1fb03ea9707, -1797), (0xf730d59531bd325a, -2274),
    (0xf73680a01e19424a, -2274), (0xf75983109756681e, -2274), (0xf761a7b3b81c6ae6, -1429), (0xf7720f5e3edb7a1a, -1797),
    (0xf7acde0c3ee83218, -2274), (0xf7fd4aee5c95982a,  -826), (0xf80c18ba79d3249c, -1973), (0xf84fbf7dd4dd616b, -2274),
    (0xf895fa94621a19b2, -2274), (0xf8b5fdb86c5c724a,  -371), (0xf8dcf3f1984cd6b4, -2274), (0xf8def55e446b6d49, -1232),
    (0xf8fdeb49f66761ab, -2274), (0xf96f96602bfc60bf, -2274), (0xf9746470d0aaea09, -1575), (0xf9a084f8c51ab19a, -2274),
    (0xf9dc240a576cf703, -1973), (0xfa1e836f6645134a, -2274), (0xfa3272dab6783338, -2274), (0xfa5ac66e0de0efbb, -2274),
    (0xfa72d21f91f6726a, -2274), (0xfaa1cc9e41e6dedb, -1797), (0xfaab156a2ea98378, -2274), (0xfaac3148f0973fd0, -2274),
    (0xfacec7cbbb840262, -2274), (0xfadfb5545e2d0e01, -1496), (0xfaef20c7ccaa5c8e, -2274), (0xfaf6be64f9238a2a, -1973),
    (0xfb19960664481d36, -2274), (0xfb1b31d98c5d6650, -2274), (0xfb33e9cc4397a662, -2274), (0xfb5c1b735603cc40, -1973),
    (0xfb686e4d6675a140, -1319), (0xfb9e60a825cb0404, -2274), (0xfbaa27a0955e4ee9, -2274), (0xfbb834dd2a162ba4, -1797),
    (0xfbf5a5f8fc152312, -2274), (0xfc19ede177184d7e, -2274), (0xfc258f05bb50ec30, -2274), (0xfc382071b5ac689b, -2274),
    (0xfcbed3fb98880984, -1973), (0xfcd62fdf2d29ccae, -2274), (0xfd1bc33167637957, -2274), (0xfd4b3cd1601caf52, -1128),
    (0xfd6f7bc3d9adb20d, -1973), (0xfda56976c632fa2d, -1973), (0xfdacc6b2e03f4267, -1973), (0xfdd373bf87555078, -2274),
    (0xfdfb50692e48fb44, -2274), (0xfe1b60ab53800382, -1797), (0xfe875568bc4611c7, -1973), (0xfeb557f1070a6a57, -1797),
    (0xfee63fc5280c4b76, -2274), (0xff1550139397a305, -2274), (0xff23115b6e867650, -2274), (0xff66871f6556f2e9, -2274),
    (0xff76f0274ea81c2d, -2274), (0xff7b9ba5052ffe35, -1672), (0xff898f9fe471ed19, -2274),
];

const DEFAULT_LOG_FREQ: f64 = -5.0;

#[inline]
fn lookup_score(hash: u64) -> f64 {
    let idx = FRAGMENT_SCORES.partition_point(|&(h, _)| h < hash);
    if idx < FRAGMENT_SCORES.len() && FRAGMENT_SCORES[idx].0 == hash {
        FRAGMENT_SCORES[idx].1 as f64 / 1000.0
    } else {
        DEFAULT_LOG_FREQ
    }
}

// ---------------------------------------------------------------------------
// Complexity corrections
// ---------------------------------------------------------------------------

fn complexity_penalty(mol: &Molecule) -> f64 {
    let n = mol.atom_count() as f64;
    if n == 0.0 {
        return 0.0;
    }

    let spiro = num_spiro_atoms(mol) as f64;
    let bridge = num_bridgehead_atoms(mol) as f64;
    let rings = ring_count(mol) as f64;
    let stereo = num_stereocenters(mol) as f64;

    let macro_count = count_macrorings(mol) as f64;

    let bond_n = mol.bond_count() as f64;
    let ring_bond_frac = if bond_n > 0.0 {
        ring_bond_count(mol) as f64 / bond_n
    } else {
        0.0
    };

    let penalty = spiro * 0.25
        + bridge * 0.35
        + macro_count * 0.30
        + stereo * 0.10
        + (rings - 1.0).max(0.0) * 0.05
        + ring_bond_frac * 0.50;

    let size_penalty = (n / 10.0 - 1.0).max(0.0) * 0.05;

    penalty + size_penalty
}

fn count_macrorings(mol: &Molecule) -> usize {
    let n = mol.atom_count();
    let rings = ring_count(mol);
    if rings == 0 {
        return 0;
    }
    let avg_ring_size = n as f64 / rings as f64;
    if avg_ring_size > 8.0 { 1 } else { 0 }
}

fn ring_bond_count(mol: &Molecule) -> usize {
    let n = mol.atom_count();
    let mut in_ring = vec![false; mol.bond_count()];
    let mut visited = vec![false; n];
    let mut bond_idx_map: HashMap<(usize, usize), usize> = HashMap::new();
    for (bidx, bond) in mol.bonds() {
        let i = bond.atom1.0 as usize;
        let j = bond.atom2.0 as usize;
        bond_idx_map.insert((i.min(j), i.max(j)), bidx.0 as usize);
    }

    let adj: Vec<Vec<usize>> = (0..n)
        .map(|i| {
            mol.neighbors(AtomIdx(i as u32))
                .map(|(nb, _)| nb.0 as usize)
                .collect()
        })
        .collect();

    let mut stack: Vec<(usize, usize, usize)> = Vec::new();
    for root in 0..n {
        if visited[root] {
            continue;
        }
        stack.push((root, usize::MAX, 0));
        while let Some((cur, par, d)) = stack.pop() {
            if visited[cur] {
                continue;
            }
            visited[cur] = true;
            let _ = d;
            for &nb in &adj[cur] {
                if nb == par {
                    continue;
                }
                if visited[nb] {
                    let key = (cur.min(nb), cur.max(nb));
                    if let Some(&bi) = bond_idx_map.get(&key) {
                        in_ring[bi] = true;
                    }
                } else {
                    stack.push((nb, cur, 0));
                }
            }
        }
    }
    in_ring.iter().filter(|&&r| r).count()
}

// ---------------------------------------------------------------------------
// Public API
// ---------------------------------------------------------------------------

/// Compute the Synthetic Accessibility Score for `mol`.
///
/// Returns a value in \[1, 10\]: 1 = trivially easy, 10 = very hard to synthesize.
///
/// Fragment environments use the same FNV-1a hash scheme as ECFP fingerprints
/// (`chematic_fp::morgan_fp_counts`), so the fragment table is directly
/// compatible with ECFP4 lookups.
pub fn sa_score(mol: &Molecule) -> f64 {
    let n = mol.atom_count();
    if n == 0 {
        return 10.0;
    }

    // Collect all circular environments at radii 0–2 with their occurrence counts.
    let counts = morgan_fp_counts(mol, 2);
    let total_frags: u32 = counts.values().sum();
    if total_frags == 0 {
        return 10.0;
    }

    // Fragment score = mean of log10(frequency) over all environment instances.
    // Environments not in the table use DEFAULT_LOG_FREQ (very rare).
    let total_score: f64 = counts
        .iter()
        .map(|(&hash, &count)| lookup_score(hash) * count as f64)
        .sum();
    let fscore = total_score / total_frags as f64;

    let cscore = complexity_penalty(mol);

    // Raw score: higher fscore (common fragments) → easier; higher cscore → harder.
    let raw = fscore * 2.0 - cscore * 4.5;

    // Map raw ∈ (−∞, 0] → sa ∈ [1, 10].
    let sa = 1.0 + (-raw).max(0.0);
    sa.clamp(1.0, 10.0)
}

#[cfg(test)]
mod tests {
    use super::*;
    use chematic_smiles::parse;

    fn mol(s: &str) -> Molecule {
        parse(s).unwrap()
    }

    #[test]
    fn sa_score_in_range_1_to_10() {
        for s in &["C", "CC(=O)O", "c1ccccc1", "CC(=O)Oc1ccccc1C(=O)O"] {
            let score = sa_score(&mol(s));
            assert!(
                (1.0..=10.0).contains(&score),
                "SA score for {s} = {score:.2} is out of [1, 10]"
            );
        }
    }

    #[test]
    fn simple_molecule_lower_than_complex() {
        let simple = sa_score(&mol("CC"));
        let complex = sa_score(&mol("C1CC2(CC1)CCCC2")); // spiro bicyclic
        assert!(
            simple <= complex,
            "simple {simple:.2} should be ≤ complex {complex:.2}"
        );
    }

    #[test]
    fn methane_is_easy() {
        let score = sa_score(&mol("C"));
        assert!(
            score < 6.0,
            "methane SA score should be < 6, got {score:.2}"
        );
    }

    #[test]
    fn taxol_harder_than_aspirin() {
        let aspirin = sa_score(&mol("CC(=O)Oc1ccccc1C(=O)O"));
        let taxol = sa_score(&mol(
            "CC1=C2C(C(=O)C3(C(CC4C(C3C(C(=C2OC1=O)C)(C)C)OC(=O)C5=CC=CC=C5)OC(=O)C4)O)(C)C",
        ));
        assert!(
            aspirin < taxol,
            "aspirin ({aspirin:.2}) should be easier than taxol ({taxol:.2})"
        );
    }
}