mirror of
https://github.com/rdkit/rdkit.git
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229 lines
6.7 KiB
C++
229 lines
6.7 KiB
C++
//
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// Copyright (C) 2020 Greg Landrum and T5 Informatics GmbH
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//
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// @@ All Rights Reserved @@
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// This file is part of the RDKit.
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// The contents are covered by the terms of the BSD license
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// which is included in the file license.txt, found at the root
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// of the RDKit source tree.
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//
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#include "Abbreviations.h"
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#include <GraphMol/RDKitBase.h>
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#include <GraphMol/SmilesParse/SmilesParse.h>
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#include <GraphMol/RDKitQueries.h>
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#include <boost/tokenizer.hpp>
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using tokenizer = boost::tokenizer<boost::char_separator<char>>;
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namespace RDKit {
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namespace Abbreviations {
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namespace common_properties {
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const std::string numDummies = "_numDummies";
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const std::string origAtomMapping = "_origAtomMapping";
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const std::string origBondMapping = "_origBondMapping";
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} // namespace common_properties
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namespace Utils {
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namespace data {
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/*
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Translations of superatom labels to SMILES.
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First atom of SMILES string should be the one connected to the rest of
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the molecule.
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ADAPTED FROM: https://github.com/openbabel/superatoms/blob/master/superatom.txt
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Originally from http://cactus.nci.nih.gov/osra/
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The left-aligned form is the one recognized in MDL alias lines;
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the right-aligned form may be used in 2D depiction.
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label smiles display_label display_label_w
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*/
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const std::string defaultAbbreviations =
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R"ABBREVS(CO2Et C(=O)OCC CO<sub>2</sub>Et EtO<sub>2</sub>C
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COOEt C(=O)OCC CO<sub>2</sub>Et EtO<sub>2</sub>C
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OiBu OCC(C)C OiBu iBuO
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nDec CCCCCCCCCC nDec
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nNon CCCCCCCCC nNon
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nOct CCCCCCCC nOct
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nHept CCCCCCC nHept
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nHex CCCCCC nHex
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nPent CCCCC nPent
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iPent C(C)CCC iPent
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tBu C(C)(C)C tBu
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iBu C(C)CC iBu
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nBu CCCC nBu
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iPr C(C)C iPr
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nPr CCC nPr
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Et CC Et
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NCF3 NC(F)(F)F NCF<sub>3</sub> F<sub>3</sub>CN
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CF3 C(F)(F)F CF<sub>3</sub> F<sub>3</sub>C
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CCl3 C(Cl)(Cl)Cl CCl<sub>3</sub> Cl<sub>3</sub>C
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CN C#N CN NC
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NC [N+]#[C-] NC CN
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N(OH)CH3 N([OH])C N(OH)CH<sub>3</sub> CH<sub>3</sub>(OH)N
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NO2 [N+](=O)[O-] NO<sub>2</sub> O<sub>2</sub>N
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NO N=O NO ON
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SO3H S(=O)(=O)[OH] SO<sub>3</sub>H HO<sub>3</sub>S
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CO2H C(=O)[OH] CO<sub>2</sub>H HO<sub>2</sub>C
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COOH C(=O)[OH] COOH HOOC
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OEt OCC OEt EtO
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OAc OC(=O)C OAc AcO
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NHAc NC(=O)C NHAc AcNH
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Ac C(=O)C Ac
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CHO C=O CHO OHC
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NMe NC NMe MeN
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SMe SC SMe MeS
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OMe OC OMe MeO
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CO2- C(=O)[O-] COO<sup>-</sup> <sup>-</sup>OOC
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COO- C(=O)[O-] COO<sup>-</sup> <sup>-</sup>OOC)ABBREVS";
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/*
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Translations of linker superatom labels to SMILES.
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First atom of SMILES string should be a dummy connected to the rest of
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the molecule. The other linker dummy/dummies show the other attachments
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*/
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const std::string defaultLinkers =
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R"ABBREVS(PEG6 *OCCOCCOCCOCCOCCOCC* PEG6
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PEG5 *OCCOCCOCCOCCOCC* PEG5
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PEG4 *OCCOCCOCCOCC* PEG4
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PEG3 *OCCOCCOCC* PEG3
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Dec *CCCCCCCCCC*
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Non *CCCCCCCCC*
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Oct *CCCCCCCC*
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Hept *CCCCCCC*)ABBREVS";
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// other possible abbreviations that might be useful:
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/*
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PEG6 *OCCOCCOCCOCCOCC* PEG6
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PEG5 *OCCOCCOCCOCCOCC* PEG5
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PEG4 *OCCOCCOCCOCC* PEG4
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PEG3 *OCCOCCOCC* PEG3
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Dec *CCCCCCCCCC*
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Non *CCCCCCCCC*
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Oct *CCCCCCCC*
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Hept *CCCCCCC*
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Hex *CCCCCC*
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Pent *CCCCC*
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Cy *C1CCC(*)CC1 Cy
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ala *N[C@@H](C)C(=O)* ala
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arg *N[C@@H](CCCNC(N)=[NH])C(=O)* arg
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asn *N[C@@H](CC(N)=O)C(=O)* asn
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asp *N[C@@H](CC(O)=O)C(=O)* asp
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cys *N[C@@H](CS)C(=O)* cys
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gln *N[C@@H](CCC(N)=O)C(=O)* gln
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glu *N[C@@H](CCC(O)=O)C(=O)* glu
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gly *NCC(=O)* gly
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his *N[C@@H](Cc1c[nH]cn1)C(=O)* his
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ile *N[C@@H](C(C)CC)C(=O)* ile
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leu *N[C@@H](CC(C)C)C(=O)* leu
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lys *N[C@@H](CCCCN)C(=O)* lys
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met *N[C@@H](CCSC)C(=O)* met
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phe *N[C@@H](Cc1ccccc1)C(=O)* phe
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pro *N1[C@@H](CCC1)C(=O)* pro
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ser *N[C@@H](CO)C(=O)* ser
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thr *N[C@@H](C(O)C)C(=O)* thr
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trp *N[C@@H](Cc1c[nH]c2ccccc21)C(=O)* trp
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tyr *N[C@@H](Cc1ccc(O)cc1)C(=O)* tyr
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val *N[C@@H](C(C)C)C(=O)* val
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*/
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} // namespace data
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namespace detail {
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ROMol *createAbbreviationMol(const std::string &txt, bool removeExtraDummies,
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bool allowConnectionToDummies) {
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std::string smarts;
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if (txt[0] != '*') {
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smarts = "*" + txt;
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} else {
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smarts = txt;
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}
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RWMol *q = SmartsToMol(smarts);
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if (!q) {
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return q;
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}
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if (q->getNumAtoms() < 2) {
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BOOST_LOG(rdErrorLog) << "abbreviation with <2 atoms ignored" << std::endl;
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delete q;
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return nullptr;
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}
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MolOps::AdjustQueryParameters ps;
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ps.adjustDegree = true;
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ps.adjustDegreeFlags = MolOps::AdjustQueryWhichFlags::ADJUST_IGNOREDUMMIES;
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ps.adjustRingCount = true;
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ps.adjustRingCountFlags = MolOps::AdjustQueryWhichFlags::ADJUST_IGNOREDUMMIES;
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MolOps::adjustQueryProperties(*q, &ps);
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if (!allowConnectionToDummies) {
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auto qry = makeAtomNumQuery(0);
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qry->setNegation(true);
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q->getAtomWithIdx(0)->expandQuery(qry);
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}
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unsigned int nDummies = std::count_if(smarts.begin(), smarts.end(),
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[](char c) { return c == '*'; });
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if (removeExtraDummies) {
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q->beginBatchEdit();
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for (const auto at : q->atoms()) {
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if (!at->getIdx()) {
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// skip the first atom
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continue;
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}
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if (at->hasQuery() && at->getQuery()->getDescription() == "AtomNull") {
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q->removeAtom(at->getIdx());
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--nDummies;
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}
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}
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q->commitBatchEdit();
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}
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q->setProp(common_properties::numDummies, nDummies);
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return q;
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}
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} // namespace detail
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std::vector<AbbreviationDefinition> parseAbbreviations(
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const std::string &text, bool removeExtraDummies,
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bool allowConnectionToDummies) {
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std::vector<AbbreviationDefinition> res;
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boost::char_separator<char> lineSep("\n");
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tokenizer lines(text, lineSep);
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boost::char_separator<char> fieldSep(" \t");
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for (const auto &line : lines) {
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AbbreviationDefinition defn;
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tokenizer fields(line, fieldSep);
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tokenizer::iterator field = fields.begin();
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defn.label = *field;
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++field;
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defn.smarts = *field;
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++field;
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if (field != fields.end()) {
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defn.displayLabel = *field;
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++field;
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if (field != fields.end()) {
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defn.displayLabelW = *field;
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}
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}
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defn.mol.reset(detail::createAbbreviationMol(
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defn.smarts, removeExtraDummies, allowConnectionToDummies));
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if (defn.mol) {
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res.push_back(defn);
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}
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}
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return res;
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}
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std::vector<AbbreviationDefinition> getDefaultAbbreviations() {
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static auto defs = parseAbbreviations(data::defaultAbbreviations);
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return defs;
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}
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std::vector<AbbreviationDefinition> getDefaultLinkers() {
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static auto defs = parseAbbreviations(data::defaultLinkers, true, true);
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return defs;
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}
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} // namespace Utils
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} // namespace Abbreviations
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} // namespace RDKit
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