bool MopacAux::read(std::istream &in, Core::Molecule &molecule) { // Read the log file line by line, most sections are terminated by an empty // line, so they should be retained. while (!in.eof()) processLine(in); SlaterSet *basis = new SlaterSet; for (unsigned int i = 0; i < m_atomPos.size(); ++i) { Atom a = molecule.addAtom(static_cast<unsigned char>(m_atomNums[i])); a.setPosition3d(m_atomPos[i]); } // Do simple bond perception. molecule.perceiveBondsSimple(); molecule.setBasisSet(basis); basis->setMolecule(&molecule); load(basis); return true; }
bool MoldenFile::read(std::istream &in, Core::Molecule &molecule) { // Read the log file line by line, most sections are terminated by an empty // line, so they should be retained. while (!in.eof()) processLine(in); GaussianSet *basis = new GaussianSet; int nAtom = 0; for (unsigned int i = 0; i < m_aPos.size(); i += 3) { Atom a = molecule.addAtom(static_cast<unsigned char>(m_aNums[nAtom++])); a.setPosition3d(Vector3(m_aPos[i ], m_aPos[i + 1], m_aPos[i + 2])); } // Do simple bond perception. molecule.perceiveBondsSimple(); molecule.setBasisSet(basis); basis->setMolecule(&molecule); load(basis); return true; }
bool PdbFormat::read(std::istream& in, Core::Molecule& mol) { string buffer; std::vector<int> terList; Residue* r; size_t currentResidueId = 0; bool ok(false); int coordSet = 0; Array<Vector3> positions; while (getline(in, buffer)) { // Read Each line one by one if (startsWith(buffer, "ENDMDL")) { if (coordSet == 0) { mol.setCoordinate3d(mol.atomPositions3d(), coordSet++); positions.reserve(mol.atomCount()); } else { mol.setCoordinate3d(positions, coordSet++); positions.clear(); } } else if (startsWith(buffer, "ATOM") || startsWith(buffer, "HETATM")) { // First we initialize the residue instance size_t residueId = lexicalCast<size_t>(buffer.substr(22, 4), ok); if (!ok) { appendError("Failed to parse residue sequence number: " + buffer.substr(22, 4)); return false; } if (residueId != currentResidueId) { currentResidueId = residueId; string residueName = lexicalCast<string>(buffer.substr(17, 3), ok); if (!ok) { appendError("Failed to parse residue name: " + buffer.substr(17, 3)); return false; } char chainId = lexicalCast<char>(buffer.substr(21, 1), ok); if (!ok) { appendError("Failed to parse chain identifier: " + buffer.substr(21, 1)); return false; } r = &mol.addResidue(residueName, currentResidueId, chainId); } string atomName = lexicalCast<string>(buffer.substr(12, 4), ok); if (!ok) { appendError("Failed to parse atom name: " + buffer.substr(12, 4)); return false; } Vector3 pos; // Coordinates pos.x() = lexicalCast<Real>(buffer.substr(30, 8), ok); if (!ok) { appendError("Failed to parse x coordinate: " + buffer.substr(30, 8)); return false; } pos.y() = lexicalCast<Real>(buffer.substr(38, 8), ok); if (!ok) { appendError("Failed to parse y coordinate: " + buffer.substr(38, 8)); return false; } pos.z() = lexicalCast<Real>(buffer.substr(46, 8), ok); if (!ok) { appendError("Failed to parse z coordinate: " + buffer.substr(46, 8)); return false; } string element; // Element symbol, right justififed element = buffer.substr(76, 2); element = trimmed(element); if (element == "SE") // For Sulphur element = 'S'; unsigned char atomicNum = Elements::atomicNumberFromSymbol(element); if (atomicNum == 255) appendError("Invalid element"); if (coordSet == 0) { Atom newAtom = mol.addAtom(atomicNum); newAtom.setPosition3d(pos); if (r) { r->addResidueAtom(atomName, newAtom); } } else { positions.push_back(pos); } } else if (startsWith(buffer, "TER")) { // This is very important, each TER // record also counts in the serial. // Need to account for that when comparing with CONECT terList.push_back(lexicalCast<int>(buffer.substr(6, 5), ok)); if (!ok) { appendError("Failed to parse TER serial"); return false; } } else if (startsWith(buffer, "CONECT")) { int a = lexicalCast<int>(buffer.substr(6, 5), ok); if (!ok) { appendError("Failed to parse coordinate a " + buffer.substr(6, 5)); return false; } --a; size_t terCount; for (terCount = 0; terCount < terList.size() && a > terList[terCount]; ++terCount) ; // semicolon is intentional a = a - terCount; int bCoords[] = { 11, 16, 21, 26 }; for (int i = 0; i < 4; i++) { if (trimmed(buffer.substr(bCoords[i], 5)) == "") break; else { int b = lexicalCast<int>(buffer.substr(bCoords[i], 5), ok) - 1; if (!ok) { appendError("Failed to parse coordinate b" + std::to_string(i) + " " + buffer.substr(bCoords[i], 5)); return false; } for (terCount = 0; terCount < terList.size() && b > terList[terCount]; ++terCount) ; // semicolon is intentional b = b - terCount; if (a < b) { mol.Avogadro::Core::Molecule::addBond(a, b, 1); } } } } } // End while loop mol.perceiveBondsSimple(); mol.perceiveBondsFromResidueData(); return true; } // End read