本文整理汇总了C++中Molecule::clear方法的典型用法代码示例。如果您正苦于以下问题：C++ Molecule::clear方法的具体用法？C++ Molecule::clear怎么用？C++ Molecule::clear使用的例子？那么, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类Molecule的用法示例。
在下文中一共展示了Molecule::clear方法的4个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的C++代码示例。
示例1: readInputOrientationGeometries
bool GaussianOutputFile::readInputOrientationGeometries(vector<Molecule>& molecules)
{
Atom atom;
Molecule mol;
string line;
bool ok;
ok = false;
int i;
i = 0;
while(isStringInFile("Input orientation"))
{
// if(isStringInFile("Input orientation"))
// {
/*
* Jumping four lines that contains the orientation header
*
*/
for(size_t i = 0; i < 4; i++)
line = readLine();
/*
* Reading the atoms
*
*/
line = readLine();
while(line.find("-------") == string::npos)
{
atom.clear();
atom.setName(line.substr(13,16));
atom.setX(atof(line.substr(33,46).c_str()));
atom.setY(atof(line.substr(47,59).c_str()));
atom.setZ(atof(line.substr(60,70).c_str()));
mol.addAtom(atom);
line = readLine();
}
molecules.push_back(mol);
mol.clear();
ok = true;
// }
}
if(ok)
return true;
else
return false;
}示例2: expand
bool AbbreviationExpander::expand (const char *label, int input_order, int output_order, Molecule &m)
{
TokenChain tokens;
if (!tokensizeAbbreviation(label, tokens))
return false;
if (expand_direction == LEFT)
std::reverse(tokens.begin(), tokens.end());
m.clear();
AttPoint begin_att_point(-1, input_order);
AttPoint end_att_point = begin_att_point;
if (!expandParsedTokens(tokens, m, end_att_point))
return false;
if (end_att_point.order != output_order)
return false;
output_index = end_att_point.index;
return true;
}示例3: loadMolecule
void CmfLoader::loadMolecule (Molecule &mol)
{
int code;
mol.clear();
QS_DEF(Array<int>, cycle_numbers);
QS_DEF(Array<int>, atom_stack);
_atoms.clear();
_bonds.clear();
_pseudo_labels.clear();
_attachments.clear();
cycle_numbers.clear();
atom_stack.clear();
bool first_atom = true;
if (!_getNextCode(code))
return;
bool has_ext_part = false;
/* Main loop */
do
{
_BondDesc *bond = 0;
if (code > CMF_ALPHABET_SIZE)
throw Error("unexpected code");
if (code == CMF_TERMINATOR)
break;
if (code == CMF_EXT)
{
has_ext_part = true;
// Ext part has to be read till CMF_TERMINATOR
break;
}
if (!first_atom)
{
int number;
while (_readCycleNumber(code, number))
{
while (cycle_numbers.size() <= number)
cycle_numbers.push(-1);
if (cycle_numbers[number] >= 0)
throw Error("cycle #%d already in use", number);
cycle_numbers[number] = atom_stack.top();
if (!_getNextCode(code))
break;
}
}
if (code == CMF_SEPARATOR)
{
atom_stack.pop();
first_atom = true;
if (!_getNextCode(code))
break;
continue;
}
if (code == CMF_OPEN_BRACKET)
{
atom_stack.push(atom_stack.top());
if (!_getNextCode(code))
break;
continue;
}
if (code == CMF_CLOSE_BRACKET)
{
atom_stack.pop();
if (!_getNextCode(code))
break;
continue;
}
if (!first_atom)
{
bond = &_bonds.push();
bond->beg = atom_stack.top();
}
if (bond != 0)
{
_readBond(code, *bond);
//.........这里部分代码省略.........
示例4: parseInchiOutput
void IndigoInchi::parseInchiOutput (const inchi_OutputStruct &inchi_output, Molecule &mol)
{
mol.clear();
Array<int> atom_indices;
atom_indices.clear();
// Add atoms
for (AT_NUM i = 0; i < inchi_output.num_atoms; i ++)
{
const inchi_Atom &inchi_atom = inchi_output.atom[i];
int idx = mol.addAtom(Element::fromString(inchi_atom.elname));
atom_indices.push(idx);
}
// Add bonds
for (AT_NUM i = 0; i < inchi_output.num_atoms; i ++)
{
const inchi_Atom &inchi_atom = inchi_output.atom[i];
for (AT_NUM bi = 0; bi < inchi_atom.num_bonds; bi++)
{
AT_NUM nei = inchi_atom.neighbor[bi];
if (i > nei)
// Add bond only once
continue;
int bond_order = inchi_atom.bond_type[bi];
if (bond_order == INCHI_BOND_TYPE_NONE)
throw Molecule::Error("Indigo-InChI: NONE-typed bonds are not supported");
if (bond_order >= INCHI_BOND_TYPE_ALTERN)
throw Molecule::Error("Indigo-InChI: ALTERN-typed bonds are not supported");
int bond = mol.addBond(atom_indices[i], atom_indices[nei], bond_order);
}
}
// Add Hydrogen isotope atoms at the end to preserver
// the same atom ordering
for (AT_NUM i = 0; i < inchi_output.num_atoms; i ++)
{
const inchi_Atom &inchi_atom = inchi_output.atom[i];
int root_atom = atom_indices[i];
for (int iso = 1; iso <= NUM_H_ISOTOPES; iso++)
{
int count = inchi_atom.num_iso_H[iso];
while (count-- > 0)
{
int h = mol.addAtom(ELEM_H);
mol.setAtomIsotope(h, iso);
mol.addBond(root_atom, h, BOND_SINGLE);
}
}
}
// Set atom charges, radicals and etc.
for (int i = 0; i < inchi_output.num_atoms; i++)
{
const inchi_Atom &inchi_atom = inchi_output.atom[i];
int idx = atom_indices[i];
mol.setAtomCharge(idx, inchi_atom.charge);
if (inchi_atom.isotopic_mass)
mol.setAtomIsotope(idx, inchi_atom.isotopic_mass);
if (inchi_atom.radical)
mol.setAtomRadical(idx, inchi_atom.radical);
mol.setImplicitH(idx, inchi_atom.num_iso_H[0]);
}
neutralizeV5Nitrogen(mol);
// Process stereoconfiguration
for (int i = 0; i < inchi_output.num_stereo0D; i++)
{
inchi_Stereo0D &stereo0D = inchi_output.stereo0D[i];
if (stereo0D.type == INCHI_StereoType_DoubleBond)
{
if (stereo0D.parity != INCHI_PARITY_ODD && stereo0D.parity != INCHI_PARITY_EVEN)
continue;
int bond = mol.findEdgeIndex(stereo0D.neighbor[1], stereo0D.neighbor[2]);
bool valid = mol.cis_trans.registerBondAndSubstituents(bond);
if (!valid)
throw IndigoError("Indigo-InChI: Unsupported cis-trans configuration for "
"bond %d (atoms %d-%d-%d-%d)", bond, stereo0D.neighbor[0], stereo0D.neighbor[1],
stereo0D.neighbor[2], stereo0D.neighbor[3]);
int vb, ve;
const Edge &edge = mol.getEdge(bond);
if (edge.beg == stereo0D.neighbor[1])
{
vb = stereo0D.neighbor[0];
ve = stereo0D.neighbor[3];
}
else if (edge.beg == stereo0D.neighbor[2])
{
vb = stereo0D.neighbor[3];
ve = stereo0D.neighbor[0];
}
else
//.........这里部分代码省略.........