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- put SnapshotVect in the RDKit namespace

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This commit is contained in:
Paolo Tosco
2016-05-11 23:41:31 +01:00
parent 471fd9a3c3
commit 779ec747ac
6 changed files with 8 additions and 8 deletions
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2
Code/ForceField/ForceField.cpp
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@@ -185,7 +185,7 @@ int ForceField::minimize(unsigned int maxIts, double forceTol,
return minimize(0, NULL, maxIts, forceTol, energyTol);
}
int ForceField::minimize(unsigned int snapshotFreq, SnapshotVect *snapshotVect,
int ForceField::minimize(unsigned int snapshotFreq, RDKit::SnapshotVect *snapshotVect,
unsigned int maxIts, double forceTol, double energyTol) {
PRECONDITION(df_init, "not initialized");
PRECONDITION(static_cast<unsigned int>(d_numPoints) == d_positions.size(),

2
Code/ForceField/ForceField.h
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@@ -129,7 +129,7 @@ class ForceField {
- 0: indicates success
- 1: the minimization did not converge in \c maxIts iterations.
*/
int minimize(unsigned int snapshotFreq, SnapshotVect *snapshotVect,
int minimize(unsigned int snapshotFreq, RDKit::SnapshotVect *snapshotVect,
unsigned int maxIts = 200, double forceTol = 1e-4,
double energyTol = 1e-6);

4
Code/ForceField/Wrap/ForceField.cpp
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@@ -132,11 +132,11 @@ PyObject *ForceFieldGetExtraPointLoc(PyForceField *self, unsigned int idx) {
python::tuple PyForceField::minimizeTrajectory(unsigned int snapshotFreq, int maxIts, double forceTol, double energyTol) {
PRECONDITION(this->field, "no force field");
SnapshotVect snapshotVect;
RDKit::SnapshotVect snapshotVect;
int resInt = this->field->minimize(snapshotFreq, &snapshotVect,
maxIts, forceTol, energyTol);
python::list l;
for (SnapshotVect::const_iterator it = snapshotVect.begin(); it != snapshotVect.end(); ++it)
for (RDKit::SnapshotVect::const_iterator it = snapshotVect.begin(); it != snapshotVect.end(); ++it)
l.append(new RDKit::Snapshot(*it));
return python::make_tuple(resInt, l);

2
Code/GraphMol/Trajectory/Snapshot.h
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@@ -16,8 +16,8 @@
namespace RDKit {
class Snapshot;
class Trajectory;
typedef std::vector<Snapshot> SnapshotVect;
}
typedef std::vector<RDKit::Snapshot> SnapshotVect;
namespace RDKit {

4
Code/GraphMol/Trajectory/Trajectory.h
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@@ -23,9 +23,9 @@ class Trajectory {
\param dimension represents the dimensionality of this Trajectory's coordinate tuples;
this is normally 2 (2D coordinates) or 3 (3D coordinates)
\param numPoints is the number of coordinate tuples associated to each Snapshot
\param snapshotVect (optional, defaults to NULL) is a pointer to a snapshotVect
\param snapshotVect (optional, defaults to NULL) is a pointer to a SnapshotVect
used to initialize the Trajectory; if not NULL, the Trajectory takes ownership
of the snapshotVect
of the SnapshotVect
*/
Trajectory(unsigned int dimension, unsigned int numPoints, SnapshotVect *snapshotVect = NULL);
/*! \brief Copy constructor

2
Code/Numerics/Optimizer/BFGSOpt.h
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@@ -184,7 +184,7 @@ template <typename EnergyFunctor, typename GradientFunctor>
int minimize(unsigned int dim, double *pos, double gradTol,
unsigned int &numIters, double &funcVal, EnergyFunctor func,
GradientFunctor gradFunc, unsigned int snapshotFreq,
SnapshotVect *snapshotVect, double funcTol = TOLX,
RDKit::SnapshotVect *snapshotVect, double funcTol = TOLX,
unsigned int maxIts = MAXITS) {
RDUNUSED_PARAM(funcTol);
PRECONDITION(pos, "bad input array");