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- * This source code is part of
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*/
/*! \internal \file
* \brief
* Implements classes in selection.h.
*
- * \author Teemu Murtola <teemu.murtola@cbr.su.se>
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_selection
*/
+#include "gmxpre.h"
+
#include "selection.h"
-#include "position.h"
+#include "gromacs/selection/nbsearch.h"
+#include "gromacs/selection/position.h"
+#include "gromacs/topology/topology.h"
+
#include "selelem.h"
#include "selvalue.h"
namespace internal
{
+/********************************************************************
+ * SelectionData
+ */
+
SelectionData::SelectionData(SelectionTreeElement *elem,
- const char *selstr)
+ const char *selstr)
: name_(elem->name()), selectionText_(selstr),
rootElement_(*elem), coveredFractionType_(CFRAC_NONE),
coveredFraction_(1.0), averageCoveredFraction_(1.0),
bDynamic_(false), bDynamicCoveredFraction_(false)
{
- gmx_ana_pos_clear(&rawPositions_);
-
if (elem->child->type == SEL_CONST)
{
// TODO: This is not exception-safe if any called function throws.
SelectionData::~SelectionData()
{
- gmx_ana_pos_deinit(&rawPositions_);
}
}
else if (!_gmx_selelem_can_estimate_cover(rootElement()))
{
- coveredFractionType_ = CFRAC_NONE;
+ coveredFractionType_ = CFRAC_NONE;
bDynamicCoveredFraction_ = false;
}
else
{
bDynamicCoveredFraction_ = true;
}
- coveredFraction_ = bDynamicCoveredFraction_ ? 0.0 : 1.0;
+ coveredFraction_ = bDynamicCoveredFraction_ ? 0.0 : 1.0;
averageCoveredFraction_ = coveredFraction_;
return type == CFRAC_NONE || coveredFractionType_ != CFRAC_NONE;
}
+namespace
+{
-void
-SelectionData::initializeMassesAndCharges(const t_topology *top)
+/*! \brief
+ * Helper function to compute total masses and charges for positions.
+ *
+ * \param[in] top Topology to take atom masses from.
+ * \param[in] pos Positions to compute masses and charges for.
+ * \param[out] masses Output masses.
+ * \param[out] charges Output charges.
+ *
+ * Does not throw if enough space has been reserved for the output vectors.
+ */
+void computeMassesAndCharges(const t_topology *top, const gmx_ana_pos_t &pos,
+ std::vector<real> *masses,
+ std::vector<real> *charges)
{
- posInfo_.reserve(posCount());
- for (int b = 0; b < posCount(); ++b)
+ GMX_ASSERT(top != NULL, "Should not have been called with NULL topology");
+ masses->clear();
+ charges->clear();
+ for (int b = 0; b < pos.count(); ++b)
{
- real mass = 1.0;
+ real mass = 0.0;
real charge = 0.0;
- if (top != NULL)
+ for (int i = pos.m.mapb.index[b]; i < pos.m.mapb.index[b+1]; ++i)
{
- mass = 0.0;
- for (int i = rawPositions_.m.mapb.index[b];
- i < rawPositions_.m.mapb.index[b+1];
- ++i)
- {
- int index = rawPositions_.g->index[i];
- mass += top->atoms.atom[index].m;
- charge += top->atoms.atom[index].q;
- }
+ const int index = pos.m.mapb.a[i];
+ mass += top->atoms.atom[index].m;
+ charge += top->atoms.atom[index].q;
}
- posInfo_.push_back(PositionInfo(mass, charge));
+ masses->push_back(mass);
+ charges->push_back(charge);
}
- if (isDynamic() && !hasFlag(efSelection_DynamicMask))
+}
+
+} // namespace
+
+void
+SelectionData::refreshName()
+{
+ rootElement_.fillNameIfMissing(selectionText_.c_str());
+ name_ = rootElement_.name();
+}
+
+void
+SelectionData::initializeMassesAndCharges(const t_topology *top)
+{
+ GMX_ASSERT(posMass_.empty() && posCharge_.empty(),
+ "Should not be called more than once");
+ posMass_.reserve(posCount());
+ posCharge_.reserve(posCount());
+ if (top == NULL)
{
- originalPosInfo_ = posInfo_;
+ posMass_.resize(posCount(), 1.0);
+ posCharge_.resize(posCount(), 0.0);
+ }
+ else
+ {
+ computeMassesAndCharges(top, rawPositions_, &posMass_, &posCharge_);
}
}
void
-SelectionData::refreshMassesAndCharges()
+SelectionData::refreshMassesAndCharges(const t_topology *top)
{
- if (!originalPosInfo_.empty())
+ if (top != NULL && isDynamic() && !hasFlag(efSelection_DynamicMask))
{
- posInfo_.clear();
- for (int i = 0; i < posCount(); ++i)
- {
- int refid = rawPositions_.m.refid[i];
- posInfo_.push_back(originalPosInfo_[refid]);
- }
+ computeMassesAndCharges(top, rawPositions_, &posMass_, &posCharge_);
}
}
if (isCoveredFractionDynamic())
{
real cfrac = _gmx_selelem_estimate_coverfrac(rootElement());
- coveredFraction_ = cfrac;
+ coveredFraction_ = cfrac;
averageCoveredFraction_ += cfrac;
}
}
void
-SelectionData::restoreOriginalPositions()
+SelectionData::restoreOriginalPositions(const t_topology *top)
{
if (isDynamic())
{
gmx_ana_pos_t &p = rawPositions_;
- gmx_ana_index_copy(p.g, rootElement().v.u.g, false);
- p.g->name = NULL;
- gmx_ana_indexmap_update(&p.m, p.g, hasFlag(gmx::efSelection_DynamicMask));
- p.nr = p.m.nr;
- refreshMassesAndCharges();
+ gmx_ana_indexmap_update(&p.m, rootElement().v.u.g,
+ hasFlag(gmx::efSelection_DynamicMask));
+ refreshMassesAndCharges(top);
}
}
-} // namespace internal
+} // namespace internal
+
+/********************************************************************
+ * Selection
+ */
+
+Selection::operator AnalysisNeighborhoodPositions() const
+{
+ AnalysisNeighborhoodPositions pos(data().rawPositions_.x,
+ data().rawPositions_.count());
+ if (hasOnlyAtoms())
+ {
+ pos.exclusionIds(atomIndices());
+ }
+ return pos;
+}
void
fprintf(fp, " ");
printInfo(fp);
- fprintf(fp, " ");
- gmx_ana_index_dump(fp, p.g, -1, nmaxind);
+ fprintf(fp, " Group ");
+ gmx_ana_index_t g;
+ gmx_ana_index_set(&g, p.m.mapb.nra, p.m.mapb.a, 0);
+ gmx_ana_index_dump(fp, &g, nmaxind);
fprintf(fp, " Block (size=%d):", p.m.mapb.nr);
if (!p.m.mapb.index)
{
int n = p.m.mapb.nr;
if (nmaxind >= 0 && n > nmaxind)
+ {
n = nmaxind;
+ }
for (int i = 0; i <= n; ++i)
+ {
fprintf(fp, " %d", p.m.mapb.index[i]);
+ }
if (n < p.m.mapb.nr)
+ {
fprintf(fp, " ...");
+ }
}
fprintf(fp, "\n");
int n = posCount();
if (nmaxind >= 0 && n > nmaxind)
+ {
n = nmaxind;
+ }
fprintf(fp, " RefId:");
if (!p.m.refid)
{
else
{
for (int i = 0; i < n; ++i)
+ {
fprintf(fp, " %d", p.m.refid[i]);
+ }
if (n < posCount())
+ {
fprintf(fp, " ...");
+ }
}
fprintf(fp, "\n");
else
{
for (int i = 0; i < n; ++i)
+ {
fprintf(fp, " %d", p.m.mapid[i]);
+ }
if (n < posCount())
+ {
fprintf(fp, " ...");
+ }
}
fprintf(fp, "\n");
}
+
+/********************************************************************
+ * SelectionPosition
+ */
+
+SelectionPosition::operator AnalysisNeighborhoodPositions() const
+{
+ AnalysisNeighborhoodPositions pos(sel_->rawPositions_.x,
+ sel_->rawPositions_.count());
+ if (sel_->hasOnlyAtoms())
+ {
+ // TODO: Move atomIndices() such that it can be reused here as well.
+ pos.exclusionIds(constArrayRefFromArray<int>(sel_->rawPositions_.m.mapb.a,
+ sel_->rawPositions_.m.mapb.nra));
+ }
+ return pos.selectSingleFromArray(i_);
+}
+
} // namespace gmx
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff