本文整理汇总了C++中OBAtom类的典型用法代码示例。如果您正苦于以下问题：C++ OBAtom类的具体用法？C++ OBAtom怎么用？C++ OBAtom使用的例子？那么, 这里精选的类代码示例或许可以为您提供帮助。
在下文中一共展示了OBAtom类的15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: FillChargeVectors
void OBChargeModel::FillChargeVectors(OBMol &mol)
{
OBAtom *atom;
vector<OBAtom*>::iterator itr;
m_partialCharges.clear();
m_partialCharges.reserve(mol.NumAtoms());
m_formalCharges.clear();
m_formalCharges.reserve(mol.NumAtoms());
for (atom = mol.BeginAtom(itr);atom;atom = mol.NextAtom(itr))
{
m_partialCharges.push_back(atom->GetPartialCharge());
m_formalCharges.push_back((double)(atom->GetFormalCharge()));
}
}示例2: ReadHIN
bool ReadHIN(istream &ifs,OBMol &mol, const char *title)
{
// Right now only read in the first molecule
int i;
int max, bo;
char buffer[BUFF_SIZE];
string str,str1;
double x,y,z;
OBAtom *atom;
vector<string> vs;
ifs.getline(buffer, BUFF_SIZE);
while (strstr(buffer,"mol") == NULL)
ifs.getline(buffer, BUFF_SIZE);
ifs.getline(buffer, BUFF_SIZE);
mol.BeginModify();
while (strstr(buffer,"endmol") == NULL)
{
tokenize(vs,buffer); // Don't really know how long it'll be
if (vs.size() < 11) break;
atom = mol.NewAtom();
atom->SetAtomicNum(etab.GetAtomicNum(vs[3].c_str()));
x = atof((char*)vs[7].c_str());
y = atof((char*)vs[8].c_str());
z = atof((char*)vs[9].c_str());
atom->SetVector(x,y,z);
max = 11 + 2 * atoi((char *)vs[10].c_str());
for (i = 11; i < max; i+=2)
{
switch(((char*)vs[i+1].c_str())[0]) // First char in next token
{
case 's': bo = 1; break;
case 'd': bo = 2; break;
case 't': bo = 3; break;
case 'a': bo = 5; break;
default : bo = 1; break;
}
mol.AddBond(mol.NumAtoms(), atoi((char *)vs[i].c_str()), bo);
}
ifs.getline(buffer, BUFF_SIZE);
}
mol.EndModify();
mol.SetTitle(title);
return(true);
}示例3: testIdsAddAtom
void testIdsAddAtom()
{
OBMol mol;
// add 5 atoms
for (int i = 0; i < 5; ++i)
mol.NewAtom();
OBAtom a;
a.SetAtomicNum(6);
// add a sixth atom
mol.AddAtom(a);
OB_REQUIRE( mol.NumAtoms() == 6 );
OB_REQUIRE( mol.GetAtomById(5) );
OB_REQUIRE( mol.GetAtomById(5)->GetId() == 5 );
}示例4: _parent
OBMolAtomDFSIter::OBMolAtomDFSIter(OBMol &mol, int StartIndex):
_parent(&mol), _ptr(_parent->GetAtom(StartIndex))
{
_notVisited.Resize(_parent->NumAtoms());
_notVisited.Negate(); // all on
_notVisited.SetBitOff(_ptr->GetIdx() - 1);
vector<OBBond*>::iterator i;
OBAtom *a;
for (a = _ptr->BeginNbrAtom(i); a; a = _ptr->NextNbrAtom(i))
{
_stack.push(a);
_notVisited.SetBitOff(a->GetIdx() - 1);
}
}示例5: WriteGromos96
bool WriteGromos96(ostream &ofs,OBMol &mol,double fac)
{
char type_name[10];
char res_name[10],padded_name[10];
char buffer[BUFF_SIZE];
int res_num;
sprintf(buffer,"#GENERATED BY OPEN BABEL %s",BABEL_VERSION);
ofs << buffer << endl;
/* GROMOS wants a TITLE block, so let's write one*/
sprintf(buffer,"TITLE\n%s\nEND",mol.GetTitle());
ofs << buffer << endl;
ofs << "POSITION" << endl;
OBAtom *atom;
OBResidue *res;
vector<OBNodeBase*>::iterator i;
for(atom = mol.BeginAtom(i);atom;atom = mol.NextAtom(i))
{
if (res = atom->GetResidue())
{
strcpy(res_name,(char*)res->GetName().c_str());
strcpy(type_name,(char*)res->GetAtomID(atom).c_str());
res_num = res->GetNum();
}
else
{
strcpy(type_name,etab.GetSymbol(atom->GetAtomicNum()));
strcpy(res_name,"UNK");
sprintf(padded_name,"%2s",type_name);
strcpy(type_name,padded_name);
res_num = 1;
}
sprintf(buffer,"%5d %5s %5s %6d %15.5f %15.5f %15.5f",
res_num,res_name,type_name,atom->GetIdx(),
atom->x()*fac,atom->y()*fac,atom->z()*fac);
ofs << buffer << endl;
if (!(atom->GetIdx()%10))
{
sprintf(buffer,"# %d",atom->GetIdx());
ofs << buffer << endl;
}
}
ofs << "END" << endl;
return(true);
}示例6: ReadMolecule
bool BoxFormat::ReadMolecule(OBBase* pOb, OBConversion* pConv)
{
OBMol* pmol = pOb->CastAndClear<OBMol>();
if(pmol==NULL)
return false;
//Define some references so we can use the old parameter names
istream &ifs = *pConv->GetInStream();
OBMol &mol = *pmol;
const char* title = pConv->GetTitle();
char buffer[BUFF_SIZE];
vector<string> vs;
vector<string>::iterator i;
OBAtom atom;
mol.BeginModify();
while (ifs.getline(buffer,BUFF_SIZE) && !EQn(buffer,"END",3))
{
if (EQn(buffer,"ATOM",4))
{
string sbuf = &buffer[6];
/* X, Y, Z */
string x = sbuf.substr(24,8);
string y = sbuf.substr(32,8);
string z = sbuf.substr(40,8);
vector3 v(atof(x.c_str()),atof(y.c_str()),atof(z.c_str()));
atom.SetVector(v);
if (!mol.AddAtom(atom))
return(false);
}
if (EQn(buffer,"CONECT",6))
{
tokenize(vs,buffer);
if (!vs.empty() && vs.size() > 2)
for (i = vs.begin(),i+=2; i != vs.end(); i++)
mol.AddBond(atoi(vs[1].c_str()),atoi((*i).c_str()),1);
}
}
mol.EndModify();
mol.SetTitle(title);
return(true);
}示例7: WriteCharges
void WriteCharges(ostream &ofs,OBMol &mol)
{
unsigned int i;
OBAtom *atom;
char buffer[BUFF_SIZE];
for(i = 1;i <= mol.NumAtoms(); i++)
{
atom = mol.GetAtom(i);
sprintf(buffer,"%4s%4d % 2.10f",
etab.GetSymbol(atom->GetAtomicNum()),
i,
atom->GetPartialCharge());
ofs << buffer << endl;
}
}示例8: _parent
OBMolAtomDFSIter::OBMolAtomDFSIter(OBMol *mol, int StartIndex):
_parent(mol), _ptr(_parent->GetAtom(StartIndex))
{
_notVisited.Resize(_parent->NumAtoms());
_notVisited.SetRangeOn(0, _parent->NumAtoms() - 1);
if (!_ptr) return;
_notVisited.SetBitOff(_ptr->GetIdx() - 1);
vector<OBBond*>::iterator i;
OBAtom *a;
for (a = _ptr->BeginNbrAtom(i); a; a = _ptr->NextNbrAtom(i))
{
_stack.push(a);
_notVisited.SetBitOff(a->GetIdx() - 1);
}
}示例9: WriteCharges
void ReportFormat::WriteCharges(ostream &ofs,OBMol &mol)
{
unsigned int i;
OBAtom *atom;
char buffer[BUFF_SIZE];
for(i = 1;i <= mol.NumAtoms(); i++)
{
atom = mol.GetAtom(i);
snprintf(buffer, BUFF_SIZE, "%4s%4d % 2.10f",
OBElements::GetSymbol(atom->GetAtomicNum()),
i,
atom->GetPartialCharge());
ofs << buffer << "\n";
}
}示例10: testIdsNewAtom1
// OBMol::NewAtom()
void testIdsNewAtom1()
{
OBMol mol;
for (int i = 0; i < 10; ++i) {
OBAtom *atom = mol.NewAtom();
OB_REQUIRE(atom->GetId() == i);
}
OB_REQUIRE( mol.GetAtomById(0) );
OB_REQUIRE( mol.GetAtomById(4) );
OB_REQUIRE( mol.GetAtomById(9) );
OB_REQUIRE( !mol.GetAtomById(10) );
OB_REQUIRE( mol.GetAtomById(0)->GetId() == 0 );
OB_REQUIRE( mol.GetAtomById(4)->GetId() == 4 );
OB_REQUIRE( mol.GetAtomById(9)->GetId() == 9 );
}示例11: ring
/** \brief Traverse a potentially aromatic cycle starting at @p root.
\return True if the cycle is likely aromatic
\param root The initial, "root" atom in traversing this ring
\param atom The current atom to visit and check
\param prev The bond traversed in moving to this @p atom
\param er The min and max number of pi electrons for this ring
\param depth The maximum number of atoms to visit in a ring (e.g., 6)
This method traverses a potentially aromatic ring, adding up the possible
pi electrons for each atom. At the end (e.g., when @p atom == @p root)
the Huekel 4n+2 rule is checked to see if there is a possible electronic
configuration which corresponds to aromaticity.
**/
bool OBAromaticTyper::TraverseCycle(OBAtom *root, OBAtom *atom, OBBond *prev,
std::pair<int,int> &er,int depth)
{
if (atom == root)
{
int i;
for (i = er.first;i <= er.second;++i)
if (i%4 == 2 && i > 2)
return(true);
return(false);
}
if (!depth || !_vpa[atom->GetIdx()] || _visit[atom->GetIdx()])
return(false);
bool result = false;
depth--;
er.first += _velec[atom->GetIdx()].first;
er.second += _velec[atom->GetIdx()].second;
_visit[atom->GetIdx()] = true;
OBAtom *nbr;
vector<OBBond*>::iterator i;
for (nbr = atom->BeginNbrAtom(i);nbr;nbr = atom->NextNbrAtom(i))
if (*i != prev && (*i)->IsInRing() && _vpa[nbr->GetIdx()])
{
if (TraverseCycle(root,nbr,(OBBond*)(*i),er,depth))
{
result = true;
((OBBond*) *i)->SetAromatic();
}
}
_visit[atom->GetIdx()] = false;
if (result)
atom->SetAromatic();
er.first -= _velec[atom->GetIdx()].first;
er.second -= _velec[atom->GetIdx()].second;
return(result);
}示例12: WriteChiral
void WriteChiral(ostream &ofs,OBMol &mol)
{
OBAtom *atom;
vector<OBNodeBase*>::iterator i;
char buffer[BUFF_SIZE];
for (atom = mol.BeginAtom(i);atom;atom = mol.NextAtom(i))
{
if (atom->IsChiral())
{
sprintf(buffer,"%4s %5d is chiral: %s",
etab.GetSymbol(atom->GetAtomicNum()),
atom->GetIdx(),
(atom->IsClockwise() ? "clockwise" : "counterclockwise"));
ofs << buffer << endl;
}
}
}示例13: testIdsNewAtom2
// OBMol::NewAtom(unsigned long id)
void testIdsNewAtom2()
{
OBMol mol;
for (int i = 0; i < 10; ++i) {
OBAtom *atom = mol.NewAtom(i*2);
OB_REQUIRE(atom->GetId() == i*2);
}
OB_REQUIRE( mol.GetAtomById(0) );
OB_REQUIRE( !mol.GetAtomById(7) );
OB_REQUIRE( mol.GetAtomById(8) );
OB_REQUIRE( !mol.GetAtomById(9) );
OB_REQUIRE( mol.GetAtomById(18) );
OB_REQUIRE( !mol.GetAtomById(19) );
OB_REQUIRE( mol.GetAtomById(0)->GetId() == 0 );
OB_REQUIRE( mol.GetAtomById(8)->GetId() == 8 );
OB_REQUIRE( mol.GetAtomById(18)->GetId() == 18 );
}示例14: PropagatePotentialAromatic
void OBAromaticTyper::PropagatePotentialAromatic(OBAtom *atom)
{
int count = 0;
OBAtom *nbr;
vector<OBBond*>::iterator i;
for (nbr = atom->BeginNbrAtom(i);nbr;nbr = atom->NextNbrAtom(i))
if ((*i)->IsInRing() && _vpa[nbr->GetIdx()])
count++;
if (count < 2)
{
_vpa[atom->GetIdx()] = false;
if (count == 1)
for (nbr = atom->BeginNbrAtom(i);nbr;nbr = atom->NextNbrAtom(i))
if ((*i)->IsInRing() && _vpa[nbr->GetIdx()])
PropagatePotentialAromatic(nbr);
}
}示例15: atomPos
BoundingBox
NXOpenGLRenderingEngine::GetBoundingBox(OBMol *const molPtr)
{
BoundingBox bbox;
OBAtomIterator atomIter;
OBAtom *atomPtr = NULL;
for(atomPtr = molPtr->BeginAtom(atomIter);
atomPtr != NULL;
atomPtr = molPtr->NextAtom(atomIter))
{
Vector atomPos(real(atomPtr->GetX()),
real(atomPtr->GetY()),
real(atomPtr->GetZ()));
bbox += atomPos;
}
return bbox;
}