// $Id$ // // Copyright (c) 2010, Novartis Institutes for BioMedical Research Inc. // All rights reserved. // // Redistribution and use in source and binary forms, with or without // modification, are permitted provided that the following conditions are // met: // // * Redistributions of source code must retain the above copyright // notice, this list of conditions and the following disclaimer. // * Redistributions in binary form must reproduce the above // copyright notice, this list of conditions and the following // disclaimer in the documentation and/or other materials provided // with the distribution. // * Neither the name of Novartis Institutes for BioMedical Research Inc. // nor the names of its contributors may be used to endorse or promote // products derived from this software without specific prior written // permission. // // THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS // "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT // LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR // A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT // OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, // SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT // LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, // DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY // THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT // (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE // OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. // #include #include namespace RDDepict { void compute2DCoordsForReaction(RDKit::ChemicalReaction &rxn, double spacing, bool updateProps, bool canonOrient, unsigned int nFlipsPerSample, unsigned int nSamples, int sampleSeed, bool permuteDeg4Nodes) { double xOffset = 0.0; for (auto &reactant : rxn.getReactants()) { if (updateProps) { reactant->updatePropertyCache(false); RDKit::MolOps::setConjugation(*reactant); RDKit::MolOps::setHybridization(*reactant); } compute2DCoords(*reactant, nullptr, canonOrient, true, nFlipsPerSample, nSamples, sampleSeed, permuteDeg4Nodes); double minX = 1e8, maxX = -1e8; for (auto &pt : reactant->getConformer().getPositions()) { minX = std::min(pt.x, minX); maxX = std::max(pt.x, maxX); } xOffset += (maxX - minX) / 2; for (auto &pt : reactant->getConformer().getPositions()) { pt.x += xOffset; maxX = std::max(pt.x, maxX); } xOffset = maxX + spacing; } for (auto &product : rxn.getProducts()) { if (updateProps) { product->updatePropertyCache(false); RDKit::MolOps::setConjugation(*product); RDKit::MolOps::setHybridization(*product); } compute2DCoords(*product, nullptr, canonOrient, true, nFlipsPerSample, nSamples, sampleSeed, permuteDeg4Nodes); double minX = 100., maxX = -100.; for (auto &pt : product->getConformer().getPositions()) { minX = std::min(pt.x, minX); maxX = std::max(pt.x, maxX); } xOffset += (maxX - minX) / 2; for (auto &pt : product->getConformer().getPositions()) { pt.x += xOffset; maxX = std::max(pt.x, maxX); } xOffset = maxX + spacing; } } } // namespace RDDepict