bool hasFlag(SelectionFlag flag) const { return flags_.test(flag); }
//! Sets the flags for this selection.
void setFlags(SelectionFlags flags) { flags_ = flags; }
+ //! Returns the current flags.
+ SelectionFlags flags() const { return flags_; }
//! \copydoc Selection::initCoveredFraction()
bool initCoveredFraction(e_coverfrac_t type);
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2010-2018, The GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <cstdio>
#include <memory>
+#include <optional>
#include <string>
#include <vector>
#include "gromacs/options/ioptionscontainer.h"
#include "gromacs/selection/selection.h"
#include "gromacs/selection/selhelp.h"
-#include "gromacs/topology/mtop_util.h"
#include "gromacs/topology/topology.h"
#include "gromacs/trajectory/trajectoryframe.h"
#include "gromacs/utility/exceptions.h"
SelectionCollection::SelectionCollection() : impl_(new Impl) {}
-SelectionCollection::~SelectionCollection() {}
+SelectionCollection::~SelectionCollection() = default;
+SelectionCollection::SelectionCollection(const SelectionCollection& rhs) :
+ impl_(std::make_unique<Impl>())
+{
+ setReferencePosType(rhs.impl_->rpost_.empty() ? PositionCalculationCollection::typeEnumValues[0]
+ : rhs.impl_->rpost_.c_str());
+ setOutputPosType(rhs.impl_->spost_.empty() ? PositionCalculationCollection::typeEnumValues[0]
+ : rhs.impl_->spost_.c_str());
+ setDebugLevel(static_cast<int>(rhs.impl_->debugLevel_));
+
+ for (size_t i = 0; i < rhs.impl_->sc_.sel.size(); i++)
+ {
+ const auto& selectionOption = rhs.impl_->sc_.sel[i];
+ parseFromString(selectionOption->selectionText());
+ impl_->sc_.sel[i]->setFlags(selectionOption->flags());
+ }
+
+ // Topology has been initialized in rhs if top is non-null or natoms is set.
+ // Note this needs to be set after selections are parsed to register topology requirements properly.
+ if (rhs.impl_->sc_.top != nullptr || rhs.impl_->sc_.gall.isize > 0)
+ {
+ setTopology(rhs.impl_->sc_.top, rhs.impl_->sc_.gall.isize);
+ gmx_ana_index_copy(&impl_->sc_.gall, &rhs.impl_->sc_.gall, /*balloc=*/false);
+ }
+
+ if (rhs.impl_->grps_ != nullptr)
+ {
+ setIndexGroups(rhs.impl_->grps_);
+ }
+
+ // Only compile the selection if rhs is compiled.
+ if (rhs.impl_->sc_.mempool != nullptr)
+ {
+ compile();
+ }
+}
+
+SelectionCollection& SelectionCollection::operator=(SelectionCollection rhs)
+{
+ rhs.swap(*this);
+ return *this;
+}
+
+void SelectionCollection::swap(SelectionCollection& rhs)
+{
+ using std::swap;
+ swap(impl_, rhs.impl_);
+}
void SelectionCollection::initOptions(IOptionsContainer* options, SelectionTypeOption selectionTypeOption)
{
}
-void SelectionCollection::setTopology(gmx_mtop_t* top, int natoms)
+void SelectionCollection::setTopology(const gmx_mtop_t* top, int natoms)
{
GMX_RELEASE_ASSERT(natoms > 0 || top != nullptr,
"The number of atoms must be given if there is no topology");
evaluator.evaluateFinal(this, nframes);
}
+std::optional<Selection> SelectionCollection::selection(std::string_view selName) const
+{
+ const auto& selections = impl_->sc_.sel;
+ if (const auto foundIter = std::find_if(
+ selections.cbegin(),
+ selections.cend(),
+ [selName](const auto& selection) { return selection->name() == selName; });
+ foundIter != selections.end())
+ {
+ return Selection(foundIter->get());
+ }
+ return std::nullopt;
+}
+
void SelectionCollection::printTree(FILE* fp, bool bValues) const
{
std::fprintf(out, "#\n");
}
+void swap(SelectionCollection& lhs, SelectionCollection& rhs)
+{
+ lhs.swap(rhs);
+}
+
} // namespace gmx
#include <cstdio>
#include <memory>
+#include <optional>
#include <string>
#include <vector>
{
class IOptionsContainer;
-class SelectionCompiler;
class SelectionEvaluator;
class TextInputStream;
class TextOutputStream;
* setOutputPosType(). See these methods for more details on the
* initialization options.
*
+ * SelectionCollections can be copied. Copies retain the same pointers to external indices (if set)
+ * and the topology (if set), and are compiled if the copied collection is compiled. Selection
+ * objects created from a given SelectionCollection are tied only to the original collection, so
+ * a copy of a SelectionCollection will not update pre-existing Selections on evaluate() calls.
+ *
* After setting the default values, one or more selections can be parsed with
* one or more calls to parseInteractive(), parseFromStdin(), parseFromFile(), and/or
* parseFromString(). After all selections are parsed, the topology must be
SelectionCollection();
~SelectionCollection();
+ SelectionCollection(const SelectionCollection& rhs);
+ SelectionCollection& operator=(SelectionCollection rhs);
+ void swap(SelectionCollection& rhs);
+
/*! \brief
* Initializes options for setting global properties on the collection.
*
* Does not throw currently, but this is subject to change when more
* underlying code is converted to C++.
*/
- void setTopology(gmx_mtop_t* top, int natoms);
+ void setTopology(const gmx_mtop_t* top, int natoms);
/*! \brief
* Sets the external index groups to use for the selections.
*
* Does not throw.
*/
void evaluateFinal(int nframes);
-
+ /*! \brief
+ * Retrieves a Selection handle for the selection with the given name
+ *
+ * @param selName name of the selection to return
+ * @return The selection with the given name, or nullopt if no such selection exists.
+ */
+ [[nodiscard]] std::optional<Selection> selection(std::string_view selName) const;
/*! \brief
* Prints a human-readable version of the internal selection element
* tree.
friend class SelectionEvaluator;
};
+void swap(SelectionCollection& lhs, SelectionCollection& rhs);
+
} // namespace gmx
#endif
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <ParsedSelections Name="Parsed">
+ <ParsedSelection Name="Selection1">
+ <String Name="Input">group "GrpA"</String>
+ <String Name="Name">GrpA</String>
+ <String Name="Text">group "GrpA"</String>
+ <Bool Name="Dynamic">false</Bool>
+ </ParsedSelection>
+ <ParsedSelection Name="Selection2">
+ <String Name="Input">GrpB</String>
+ <String Name="Name">GrpB</String>
+ <String Name="Text">GrpB</String>
+ <Bool Name="Dynamic">false</Bool>
+ </ParsedSelection>
+ <ParsedSelection Name="Selection3">
+ <String Name="Input">1</String>
+ <String Name="Name">GrpB</String>
+ <String Name="Text">1</String>
+ <Bool Name="Dynamic">false</Bool>
+ </ParsedSelection>
+ <ParsedSelection Name="Selection4">
+ <String Name="Input">group "GrpB" and resname RB</String>
+ <String Name="Name">group "GrpB" and resname RB</String>
+ <String Name="Text">group "GrpB" and resname RB</String>
+ <Bool Name="Dynamic">false</Bool>
+ </ParsedSelection>
+ <ParsedSelection Name="Selection5">
+ <String Name="Input">group "GrpA" permute 5 3 2 1 4</String>
+ <String Name="Name">group "GrpA" permute 5 3 2 1 4</String>
+ <String Name="Text">group "GrpA" permute 5 3 2 1 4</String>
+ <Bool Name="Dynamic">false</Bool>
+ </ParsedSelection>
+ <ParsedSelection Name="Selection6">
+ <String Name="Input">group "GrpA" plus group "GrpB"</String>
+ <String Name="Name">group "GrpA" plus group "GrpB"</String>
+ <String Name="Text">group "GrpA" plus group "GrpB"</String>
+ <Bool Name="Dynamic">false</Bool>
+ </ParsedSelection>
+ <ParsedSelection Name="Selection7">
+ <String Name="Input">res_cog of group "GrpA"</String>
+ <String Name="Name">res_cog of group "GrpA"</String>
+ <String Name="Text">res_cog of group "GrpA"</String>
+ <Bool Name="Dynamic">false</Bool>
+ </ParsedSelection>
+ </ParsedSelections>
+ <CompiledSelections Name="Compiled">
+ <Selection Name="Selection1">
+ <String Name="Name">GrpA</String>
+ <Sequence Name="Atoms">
+ <Int Name="Length">5</Int>
+ <Int>0</Int>
+ <Int>1</Int>
+ <Int>2</Int>
+ <Int>3</Int>
+ <Int>4</Int>
+ </Sequence>
+ </Selection>
+ <Selection Name="Selection2">
+ <String Name="Name">GrpB</String>
+ <Sequence Name="Atoms">
+ <Int Name="Length">5</Int>
+ <Int>3</Int>
+ <Int>4</Int>
+ <Int>5</Int>
+ <Int>6</Int>
+ <Int>7</Int>
+ </Sequence>
+ </Selection>
+ <Selection Name="Selection3">
+ <String Name="Name">GrpB</String>
+ <Sequence Name="Atoms">
+ <Int Name="Length">5</Int>
+ <Int>3</Int>
+ <Int>4</Int>
+ <Int>5</Int>
+ <Int>6</Int>
+ <Int>7</Int>
+ </Sequence>
+ </Selection>
+ <Selection Name="Selection4">
+ <String Name="Name">group "GrpB" and resname RB</String>
+ <Sequence Name="Atoms">
+ <Int Name="Length">3</Int>
+ <Int>3</Int>
+ <Int>4</Int>
+ <Int>5</Int>
+ </Sequence>
+ </Selection>
+ <Selection Name="Selection5">
+ <String Name="Name">group "GrpA" permute 5 3 2 1 4</String>
+ <Sequence Name="Atoms">
+ <Int Name="Length">5</Int>
+ <Int>3</Int>
+ <Int>2</Int>
+ <Int>1</Int>
+ <Int>4</Int>
+ <Int>0</Int>
+ </Sequence>
+ </Selection>
+ <Selection Name="Selection6">
+ <String Name="Name">group "GrpA" plus group "GrpB"</String>
+ <Sequence Name="Atoms">
+ <Int Name="Length">10</Int>
+ <Int>0</Int>
+ <Int>1</Int>
+ <Int>2</Int>
+ <Int>3</Int>
+ <Int>4</Int>
+ <Int>3</Int>
+ <Int>4</Int>
+ <Int>5</Int>
+ <Int>6</Int>
+ <Int>7</Int>
+ </Sequence>
+ </Selection>
+ <Selection Name="Selection7">
+ <String Name="Name">res_cog of group "GrpA"</String>
+ <Sequence Name="Atoms">
+ <Int Name="Length">5</Int>
+ <Int>0</Int>
+ <Int>1</Int>
+ <Int>2</Int>
+ <Int>3</Int>
+ <Int>4</Int>
+ </Sequence>
+ </Selection>
+ </CompiledSelections>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <ParsedSelections Name="Parsed">
+ <ParsedSelection Name="Selection1">
+ <String Name="Input">x > 2</String>
+ <String Name="Text">x > 2</String>
+ <Bool Name="Dynamic">true</Bool>
+ </ParsedSelection>
+ <ParsedSelection Name="Selection2">
+ <String Name="Input">2 < x</String>
+ <String Name="Text">2 < x</String>
+ <Bool Name="Dynamic">true</Bool>
+ </ParsedSelection>
+ <ParsedSelection Name="Selection3">
+ <String Name="Input">y > resnr</String>
+ <String Name="Text">y > resnr</String>
+ <Bool Name="Dynamic">true</Bool>
+ </ParsedSelection>
+ <ParsedSelection Name="Selection4">
+ <String Name="Input">resnr < 2.5</String>
+ <String Name="Text">resnr < 2.5</String>
+ <Bool Name="Dynamic">false</Bool>
+ </ParsedSelection>
+ <ParsedSelection Name="Selection5">
+ <String Name="Input">2.5 > resnr</String>
+ <String Name="Text">2.5 > resnr</String>
+ <Bool Name="Dynamic">false</Bool>
+ </ParsedSelection>
+ </ParsedSelections>
+ <CompiledSelections Name="Compiled">
+ <Selection Name="Selection1">
+ <Sequence Name="Atoms">
+ <Int Name="Length">15</Int>
+ <Int>0</Int>
+ <Int>1</Int>
+ <Int>2</Int>
+ <Int>3</Int>
+ <Int>4</Int>
+ <Int>5</Int>
+ <Int>6</Int>
+ <Int>7</Int>
+ <Int>8</Int>
+ <Int>9</Int>
+ <Int>10</Int>
+ <Int>11</Int>
+ <Int>12</Int>
+ <Int>13</Int>
+ <Int>14</Int>
+ </Sequence>
+ </Selection>
+ <Selection Name="Selection2">
+ <Sequence Name="Atoms">
+ <Int Name="Length">15</Int>
+ <Int>0</Int>
+ <Int>1</Int>
+ <Int>2</Int>
+ <Int>3</Int>
+ <Int>4</Int>
+ <Int>5</Int>
+ <Int>6</Int>
+ <Int>7</Int>
+ <Int>8</Int>
+ <Int>9</Int>
+ <Int>10</Int>
+ <Int>11</Int>
+ <Int>12</Int>
+ <Int>13</Int>
+ <Int>14</Int>
+ </Sequence>
+ </Selection>
+ <Selection Name="Selection3">
+ <Sequence Name="Atoms">
+ <Int Name="Length">15</Int>
+ <Int>0</Int>
+ <Int>1</Int>
+ <Int>2</Int>
+ <Int>3</Int>
+ <Int>4</Int>
+ <Int>5</Int>
+ <Int>6</Int>
+ <Int>7</Int>
+ <Int>8</Int>
+ <Int>9</Int>
+ <Int>10</Int>
+ <Int>11</Int>
+ <Int>12</Int>
+ <Int>13</Int>
+ <Int>14</Int>
+ </Sequence>
+ </Selection>
+ <Selection Name="Selection4">
+ <Sequence Name="Atoms">
+ <Int Name="Length">6</Int>
+ <Int>0</Int>
+ <Int>1</Int>
+ <Int>2</Int>
+ <Int>3</Int>
+ <Int>4</Int>
+ <Int>5</Int>
+ </Sequence>
+ </Selection>
+ <Selection Name="Selection5">
+ <Sequence Name="Atoms">
+ <Int Name="Length">6</Int>
+ <Int>0</Int>
+ <Int>1</Int>
+ <Int>2</Int>
+ <Int>3</Int>
+ <Int>4</Int>
+ <Int>5</Int>
+ </Sequence>
+ </Selection>
+ </CompiledSelections>
+ <EvaluatedSelections Name="Frame1">
+ <Selection Name="Selection1">
+ <Sequence Name="Atoms">
+ <Int Name="Length">7</Int>
+ <Int>8</Int>
+ <Int>9</Int>
+ <Int>10</Int>
+ <Int>11</Int>
+ <Int>12</Int>
+ <Int>13</Int>
+ <Int>14</Int>
+ </Sequence>
+ <Sequence Name="Positions">
+ <Int Name="Length">7</Int>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">3</Real>
+ <Real Name="Y">1</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">3</Real>
+ <Real Name="Y">2</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">3</Real>
+ <Real Name="Y">3</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">3</Real>
+ <Real Name="Y">4</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">4</Real>
+ <Real Name="Y">1</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">4</Real>
+ <Real Name="Y">2</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">4</Real>
+ <Real Name="Y">3</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ </Sequence>
+ </Selection>
+ <Selection Name="Selection2">
+ <Sequence Name="Atoms">
+ <Int Name="Length">7</Int>
+ <Int>8</Int>
+ <Int>9</Int>
+ <Int>10</Int>
+ <Int>11</Int>
+ <Int>12</Int>
+ <Int>13</Int>
+ <Int>14</Int>
+ </Sequence>
+ <Sequence Name="Positions">
+ <Int Name="Length">7</Int>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">3</Real>
+ <Real Name="Y">1</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">3</Real>
+ <Real Name="Y">2</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">3</Real>
+ <Real Name="Y">3</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">3</Real>
+ <Real Name="Y">4</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">4</Real>
+ <Real Name="Y">1</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">4</Real>
+ <Real Name="Y">2</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">4</Real>
+ <Real Name="Y">3</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ </Sequence>
+ </Selection>
+ <Selection Name="Selection3">
+ <Sequence Name="Atoms">
+ <Int Name="Length">4</Int>
+ <Int>1</Int>
+ <Int>2</Int>
+ <Int>3</Int>
+ <Int>7</Int>
+ </Sequence>
+ <Sequence Name="Positions">
+ <Int Name="Length">4</Int>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">1</Real>
+ <Real Name="Y">2</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">1</Real>
+ <Real Name="Y">3</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">1</Real>
+ <Real Name="Y">4</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">2</Real>
+ <Real Name="Y">4</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ </Sequence>
+ </Selection>
+ <Selection Name="Selection4">
+ <Sequence Name="Atoms">
+ <Int Name="Length">6</Int>
+ <Int>0</Int>
+ <Int>1</Int>
+ <Int>2</Int>
+ <Int>3</Int>
+ <Int>4</Int>
+ <Int>5</Int>
+ </Sequence>
+ <Sequence Name="Positions">
+ <Int Name="Length">6</Int>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">1</Real>
+ <Real Name="Y">1</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">1</Real>
+ <Real Name="Y">2</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">1</Real>
+ <Real Name="Y">3</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">1</Real>
+ <Real Name="Y">4</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">2</Real>
+ <Real Name="Y">1</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">2</Real>
+ <Real Name="Y">2</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ </Sequence>
+ </Selection>
+ <Selection Name="Selection5">
+ <Sequence Name="Atoms">
+ <Int Name="Length">6</Int>
+ <Int>0</Int>
+ <Int>1</Int>
+ <Int>2</Int>
+ <Int>3</Int>
+ <Int>4</Int>
+ <Int>5</Int>
+ </Sequence>
+ <Sequence Name="Positions">
+ <Int Name="Length">6</Int>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">1</Real>
+ <Real Name="Y">1</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">1</Real>
+ <Real Name="Y">2</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">1</Real>
+ <Real Name="Y">3</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">1</Real>
+ <Real Name="Y">4</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">2</Real>
+ <Real Name="Y">1</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">2</Real>
+ <Real Name="Y">2</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ </Sequence>
+ </Selection>
+ </EvaluatedSelections>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <ParsedSelections Name="Parsed">
+ <ParsedSelection Name="Selection1">
+ <String Name="Input">x > 2</String>
+ <String Name="Text">x > 2</String>
+ <Bool Name="Dynamic">true</Bool>
+ </ParsedSelection>
+ <ParsedSelection Name="Selection2">
+ <String Name="Input">2 < x</String>
+ <String Name="Text">2 < x</String>
+ <Bool Name="Dynamic">true</Bool>
+ </ParsedSelection>
+ <ParsedSelection Name="Selection3">
+ <String Name="Input">y > resnr</String>
+ <String Name="Text">y > resnr</String>
+ <Bool Name="Dynamic">true</Bool>
+ </ParsedSelection>
+ <ParsedSelection Name="Selection4">
+ <String Name="Input">resnr < 2.5</String>
+ <String Name="Text">resnr < 2.5</String>
+ <Bool Name="Dynamic">false</Bool>
+ </ParsedSelection>
+ <ParsedSelection Name="Selection5">
+ <String Name="Input">2.5 > resnr</String>
+ <String Name="Text">2.5 > resnr</String>
+ <Bool Name="Dynamic">false</Bool>
+ </ParsedSelection>
+ </ParsedSelections>
+ <CompiledSelections Name="Compiled">
+ <Selection Name="Selection1">
+ <Sequence Name="Atoms">
+ <Int Name="Length">15</Int>
+ <Int>0</Int>
+ <Int>1</Int>
+ <Int>2</Int>
+ <Int>3</Int>
+ <Int>4</Int>
+ <Int>5</Int>
+ <Int>6</Int>
+ <Int>7</Int>
+ <Int>8</Int>
+ <Int>9</Int>
+ <Int>10</Int>
+ <Int>11</Int>
+ <Int>12</Int>
+ <Int>13</Int>
+ <Int>14</Int>
+ </Sequence>
+ </Selection>
+ <Selection Name="Selection2">
+ <Sequence Name="Atoms">
+ <Int Name="Length">15</Int>
+ <Int>0</Int>
+ <Int>1</Int>
+ <Int>2</Int>
+ <Int>3</Int>
+ <Int>4</Int>
+ <Int>5</Int>
+ <Int>6</Int>
+ <Int>7</Int>
+ <Int>8</Int>
+ <Int>9</Int>
+ <Int>10</Int>
+ <Int>11</Int>
+ <Int>12</Int>
+ <Int>13</Int>
+ <Int>14</Int>
+ </Sequence>
+ </Selection>
+ <Selection Name="Selection3">
+ <Sequence Name="Atoms">
+ <Int Name="Length">15</Int>
+ <Int>0</Int>
+ <Int>1</Int>
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+ <Int>10</Int>
+ <Int>11</Int>
+ <Int>12</Int>
+ <Int>13</Int>
+ <Int>14</Int>
+ </Sequence>
+ </Selection>
+ <Selection Name="Selection4">
+ <Sequence Name="Atoms">
+ <Int Name="Length">6</Int>
+ <Int>0</Int>
+ <Int>1</Int>
+ <Int>2</Int>
+ <Int>3</Int>
+ <Int>4</Int>
+ <Int>5</Int>
+ </Sequence>
+ </Selection>
+ <Selection Name="Selection5">
+ <Sequence Name="Atoms">
+ <Int Name="Length">6</Int>
+ <Int>0</Int>
+ <Int>1</Int>
+ <Int>2</Int>
+ <Int>3</Int>
+ <Int>4</Int>
+ <Int>5</Int>
+ </Sequence>
+ </Selection>
+ </CompiledSelections>
+ <EvaluatedSelections Name="Frame1">
+ <Selection Name="Selection1">
+ <Sequence Name="Atoms">
+ <Int Name="Length">7</Int>
+ <Int>8</Int>
+ <Int>9</Int>
+ <Int>10</Int>
+ <Int>11</Int>
+ <Int>12</Int>
+ <Int>13</Int>
+ <Int>14</Int>
+ </Sequence>
+ <Sequence Name="Positions">
+ <Int Name="Length">7</Int>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">3</Real>
+ <Real Name="Y">1</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">3</Real>
+ <Real Name="Y">2</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">3</Real>
+ <Real Name="Y">3</Real>
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+ <Position>
+ <Vector Name="Coordinates">
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+ <Real Name="Y">2</Real>
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+ </Vector>
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+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">4</Real>
+ <Real Name="Y">3</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ </Sequence>
+ </Selection>
+ <Selection Name="Selection2">
+ <Sequence Name="Atoms">
+ <Int Name="Length">7</Int>
+ <Int>8</Int>
+ <Int>9</Int>
+ <Int>10</Int>
+ <Int>11</Int>
+ <Int>12</Int>
+ <Int>13</Int>
+ <Int>14</Int>
+ </Sequence>
+ <Sequence Name="Positions">
+ <Int Name="Length">7</Int>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">3</Real>
+ <Real Name="Y">1</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">3</Real>
+ <Real Name="Y">2</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">3</Real>
+ <Real Name="Y">3</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">3</Real>
+ <Real Name="Y">4</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">4</Real>
+ <Real Name="Y">1</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
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+ <Real Name="Y">2</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">4</Real>
+ <Real Name="Y">3</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ </Sequence>
+ </Selection>
+ <Selection Name="Selection3">
+ <Sequence Name="Atoms">
+ <Int Name="Length">4</Int>
+ <Int>1</Int>
+ <Int>2</Int>
+ <Int>3</Int>
+ <Int>7</Int>
+ </Sequence>
+ <Sequence Name="Positions">
+ <Int Name="Length">4</Int>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">1</Real>
+ <Real Name="Y">2</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">1</Real>
+ <Real Name="Y">3</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">1</Real>
+ <Real Name="Y">4</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">2</Real>
+ <Real Name="Y">4</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ </Sequence>
+ </Selection>
+ <Selection Name="Selection4">
+ <Sequence Name="Atoms">
+ <Int Name="Length">6</Int>
+ <Int>0</Int>
+ <Int>1</Int>
+ <Int>2</Int>
+ <Int>3</Int>
+ <Int>4</Int>
+ <Int>5</Int>
+ </Sequence>
+ <Sequence Name="Positions">
+ <Int Name="Length">6</Int>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">1</Real>
+ <Real Name="Y">1</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">1</Real>
+ <Real Name="Y">2</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">1</Real>
+ <Real Name="Y">3</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">1</Real>
+ <Real Name="Y">4</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">2</Real>
+ <Real Name="Y">1</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">2</Real>
+ <Real Name="Y">2</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ </Sequence>
+ </Selection>
+ <Selection Name="Selection5">
+ <Sequence Name="Atoms">
+ <Int Name="Length">6</Int>
+ <Int>0</Int>
+ <Int>1</Int>
+ <Int>2</Int>
+ <Int>3</Int>
+ <Int>4</Int>
+ <Int>5</Int>
+ </Sequence>
+ <Sequence Name="Positions">
+ <Int Name="Length">6</Int>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">1</Real>
+ <Real Name="Y">1</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">1</Real>
+ <Real Name="Y">2</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">1</Real>
+ <Real Name="Y">3</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">1</Real>
+ <Real Name="Y">4</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">2</Real>
+ <Real Name="Y">1</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">2</Real>
+ <Real Name="Y">2</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ </Sequence>
+ </Selection>
+ </EvaluatedSelections>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <ParsedSelections Name="Parsed">
+ <ParsedSelection Name="Selection1">
+ <String Name="Input">x > 2</String>
+ <String Name="Text">x > 2</String>
+ <Bool Name="Dynamic">true</Bool>
+ </ParsedSelection>
+ <ParsedSelection Name="Selection2">
+ <String Name="Input">2 < x</String>
+ <String Name="Text">2 < x</String>
+ <Bool Name="Dynamic">true</Bool>
+ </ParsedSelection>
+ <ParsedSelection Name="Selection3">
+ <String Name="Input">y > resnr</String>
+ <String Name="Text">y > resnr</String>
+ <Bool Name="Dynamic">true</Bool>
+ </ParsedSelection>
+ <ParsedSelection Name="Selection4">
+ <String Name="Input">resnr < 2.5</String>
+ <String Name="Text">resnr < 2.5</String>
+ <Bool Name="Dynamic">false</Bool>
+ </ParsedSelection>
+ <ParsedSelection Name="Selection5">
+ <String Name="Input">2.5 > resnr</String>
+ <String Name="Text">2.5 > resnr</String>
+ <Bool Name="Dynamic">false</Bool>
+ </ParsedSelection>
+ </ParsedSelections>
+ <CompiledSelections Name="Compiled">
+ <Selection Name="Selection1">
+ <Sequence Name="Atoms">
+ <Int Name="Length">15</Int>
+ <Int>0</Int>
+ <Int>1</Int>
+ <Int>2</Int>
+ <Int>3</Int>
+ <Int>4</Int>
+ <Int>5</Int>
+ <Int>6</Int>
+ <Int>7</Int>
+ <Int>8</Int>
+ <Int>9</Int>
+ <Int>10</Int>
+ <Int>11</Int>
+ <Int>12</Int>
+ <Int>13</Int>
+ <Int>14</Int>
+ </Sequence>
+ </Selection>
+ <Selection Name="Selection2">
+ <Sequence Name="Atoms">
+ <Int Name="Length">15</Int>
+ <Int>0</Int>
+ <Int>1</Int>
+ <Int>2</Int>
+ <Int>3</Int>
+ <Int>4</Int>
+ <Int>5</Int>
+ <Int>6</Int>
+ <Int>7</Int>
+ <Int>8</Int>
+ <Int>9</Int>
+ <Int>10</Int>
+ <Int>11</Int>
+ <Int>12</Int>
+ <Int>13</Int>
+ <Int>14</Int>
+ </Sequence>
+ </Selection>
+ <Selection Name="Selection3">
+ <Sequence Name="Atoms">
+ <Int Name="Length">15</Int>
+ <Int>0</Int>
+ <Int>1</Int>
+ <Int>2</Int>
+ <Int>3</Int>
+ <Int>4</Int>
+ <Int>5</Int>
+ <Int>6</Int>
+ <Int>7</Int>
+ <Int>8</Int>
+ <Int>9</Int>
+ <Int>10</Int>
+ <Int>11</Int>
+ <Int>12</Int>
+ <Int>13</Int>
+ <Int>14</Int>
+ </Sequence>
+ </Selection>
+ <Selection Name="Selection4">
+ <Sequence Name="Atoms">
+ <Int Name="Length">6</Int>
+ <Int>0</Int>
+ <Int>1</Int>
+ <Int>2</Int>
+ <Int>3</Int>
+ <Int>4</Int>
+ <Int>5</Int>
+ </Sequence>
+ </Selection>
+ <Selection Name="Selection5">
+ <Sequence Name="Atoms">
+ <Int Name="Length">6</Int>
+ <Int>0</Int>
+ <Int>1</Int>
+ <Int>2</Int>
+ <Int>3</Int>
+ <Int>4</Int>
+ <Int>5</Int>
+ </Sequence>
+ </Selection>
+ </CompiledSelections>
+ <EvaluatedSelections Name="Frame1">
+ <Selection Name="Selection1">
+ <Sequence Name="Atoms">
+ <Int Name="Length">7</Int>
+ <Int>8</Int>
+ <Int>9</Int>
+ <Int>10</Int>
+ <Int>11</Int>
+ <Int>12</Int>
+ <Int>13</Int>
+ <Int>14</Int>
+ </Sequence>
+ <Sequence Name="Positions">
+ <Int Name="Length">7</Int>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">3</Real>
+ <Real Name="Y">1</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">3</Real>
+ <Real Name="Y">2</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">3</Real>
+ <Real Name="Y">3</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">3</Real>
+ <Real Name="Y">4</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">4</Real>
+ <Real Name="Y">1</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">4</Real>
+ <Real Name="Y">2</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">4</Real>
+ <Real Name="Y">3</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ </Sequence>
+ </Selection>
+ <Selection Name="Selection2">
+ <Sequence Name="Atoms">
+ <Int Name="Length">7</Int>
+ <Int>8</Int>
+ <Int>9</Int>
+ <Int>10</Int>
+ <Int>11</Int>
+ <Int>12</Int>
+ <Int>13</Int>
+ <Int>14</Int>
+ </Sequence>
+ <Sequence Name="Positions">
+ <Int Name="Length">7</Int>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">3</Real>
+ <Real Name="Y">1</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">3</Real>
+ <Real Name="Y">2</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">3</Real>
+ <Real Name="Y">3</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">3</Real>
+ <Real Name="Y">4</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">4</Real>
+ <Real Name="Y">1</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">4</Real>
+ <Real Name="Y">2</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">4</Real>
+ <Real Name="Y">3</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ </Sequence>
+ </Selection>
+ <Selection Name="Selection3">
+ <Sequence Name="Atoms">
+ <Int Name="Length">4</Int>
+ <Int>1</Int>
+ <Int>2</Int>
+ <Int>3</Int>
+ <Int>7</Int>
+ </Sequence>
+ <Sequence Name="Positions">
+ <Int Name="Length">4</Int>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">1</Real>
+ <Real Name="Y">2</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">1</Real>
+ <Real Name="Y">3</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">1</Real>
+ <Real Name="Y">4</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">2</Real>
+ <Real Name="Y">4</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ </Sequence>
+ </Selection>
+ <Selection Name="Selection4">
+ <Sequence Name="Atoms">
+ <Int Name="Length">6</Int>
+ <Int>0</Int>
+ <Int>1</Int>
+ <Int>2</Int>
+ <Int>3</Int>
+ <Int>4</Int>
+ <Int>5</Int>
+ </Sequence>
+ <Sequence Name="Positions">
+ <Int Name="Length">6</Int>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">1</Real>
+ <Real Name="Y">1</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">1</Real>
+ <Real Name="Y">2</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">1</Real>
+ <Real Name="Y">3</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">1</Real>
+ <Real Name="Y">4</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">2</Real>
+ <Real Name="Y">1</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">2</Real>
+ <Real Name="Y">2</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ </Sequence>
+ </Selection>
+ <Selection Name="Selection5">
+ <Sequence Name="Atoms">
+ <Int Name="Length">6</Int>
+ <Int>0</Int>
+ <Int>1</Int>
+ <Int>2</Int>
+ <Int>3</Int>
+ <Int>4</Int>
+ <Int>5</Int>
+ </Sequence>
+ <Sequence Name="Positions">
+ <Int Name="Length">6</Int>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">1</Real>
+ <Real Name="Y">1</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">1</Real>
+ <Real Name="Y">2</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">1</Real>
+ <Real Name="Y">3</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">1</Real>
+ <Real Name="Y">4</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">2</Real>
+ <Real Name="Y">1</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">2</Real>
+ <Real Name="Y">2</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ </Sequence>
+ </Selection>
+ </EvaluatedSelections>
+</ReferenceData>
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2010-2018, The GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
sc_.setIndexGroups(grps_);
}
-
/********************************************************************
* Test fixture for interactive SelectionCollection tests
*/
void runTest(int natoms, const gmx::ArrayRef<const char* const>& selections);
void runTest(const char* filename, const gmx::ArrayRef<const char* const>& selections);
+ void checkCompiled();
+
private:
static void checkSelection(gmx::test::TestReferenceChecker* checker,
const gmx::Selection& sel,
TestFlags flags);
- void checkCompiled();
gmx::test::TestReferenceData data_;
gmx::test::TestReferenceChecker checker_;
// TODO: Tests for more evaluation errors
+
+/********************************************************************
+ * Tests for retrieving selections.
+ */
+TEST_F(SelectionCollectionTest, RetrieveValidSelection)
+{
+ ASSERT_NO_THROW_GMX(sel_ = sc_.parseFromString("atomnr 1 to 10; none"));
+ const std::optional<gmx::Selection> retrievedSel = sc_.selection(sel_[0].name());
+ ASSERT_TRUE(retrievedSel.has_value());
+ EXPECT_STREQ(sel_[0].name(), retrievedSel->name());
+}
+
+TEST_F(SelectionCollectionTest, RetrieveInvalidSelection)
+{
+ ASSERT_FALSE(sc_.selection("some invalid key").has_value());
+}
+
+/********************************************************************
+ * Tests for assignment/copying.
+ */
+TEST_F(SelectionCollectionTest, CanCopyEmptyCollection)
+{
+ EXPECT_NO_THROW_GMX(gmx::SelectionCollection sc2(sc_));
+}
+
+TEST_F(SelectionCollectionTest, CopiedSelectionListsAreHandledSeparately)
+{
+ ASSERT_NO_THROW_GMX(sel_ = sc_.parseFromString("atomnr 1 to 10; none"));
+ EXPECT_FALSE(sc_.requiredTopologyProperties().hasAny());
+ ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
+ ASSERT_EQ(2U, sel_.size());
+ gmx::SelectionCollection sc2(sc_);
+ ASSERT_NO_THROW_GMX(sel_[1].setEvaluateVelocities(true));
+ ASSERT_NO_THROW_GMX(sel_[1].setEvaluateForces(true));
+ ASSERT_NO_THROW_GMX(sc2.compile());
+ // These would only be populated if sc_.compile() was called
+ EXPECT_FALSE(sel_[1].hasVelocities());
+ EXPECT_FALSE(sel_[1].hasForces());
+}
+
+
/********************************************************************
* Tests for interactive selection input
*/
runTest("simple.gro", selections);
}
+/*******************************************************************
+ * Tests for copy validation.
+ *
+ * These tests ensure that copies of a SelectionCollection behave as the original while being
+ * independently evaluated.
+ */
+TEST_F(SelectionCollectionDataTest, CopiedSelectionWorksPreCompilation)
+{
+ static const char* const selections[] = {
+ "x > 2", "2 < x", "y > resnr", "resnr < 2.5", "2.5 > resnr"
+ };
+ setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
+ ASSERT_NO_FATAL_FAILURE(runParser(selections));
+ ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
+ std::vector<std::string> selNames;
+ for (const auto& sel : sel_)
+ {
+ selNames.emplace_back(sel.name());
+ }
+ // Swap copied selection with original and update selections, to reuse the testing machinery.
+ gmx::SelectionCollection sc2(sc_);
+ sc_ = sc2;
+ std::vector<gmx::Selection> sel2;
+ for (const std::string_view selName : selNames)
+ {
+ std::optional<gmx::Selection> maybeSel = sc_.selection(selName);
+ ASSERT_TRUE(maybeSel.has_value());
+ sel2.push_back(*maybeSel);
+ }
+ sel_ = std::move(sel2);
+
+ ASSERT_NO_FATAL_FAILURE(runCompiler());
+ ASSERT_NO_FATAL_FAILURE(runEvaluate());
+ ASSERT_NO_FATAL_FAILURE(runEvaluateFinal());
+}
+
+TEST_F(SelectionCollectionDataTest, CopiedSelectionWorksPostCompilation)
+{
+ static const char* const selections[] = {
+ "x > 2", "2 < x", "y > resnr", "resnr < 2.5", "2.5 > resnr"
+ };
+ setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
+ ASSERT_NO_FATAL_FAILURE(runParser(selections));
+ ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
+
+ ASSERT_NO_FATAL_FAILURE(runCompiler());
+ // Note the copy is made post-compilation.
+ std::vector<std::string> selNames;
+ for (const auto& sel : sel_)
+ {
+ selNames.emplace_back(sel.name());
+ }
+ gmx::SelectionCollection sc2(sc_);
+ sc_ = sc2;
+ std::vector<gmx::Selection> sel2;
+ for (const std::string_view selName : selNames)
+ {
+ std::optional<gmx::Selection> maybeSel = sc_.selection(selName);
+ ASSERT_TRUE(maybeSel.has_value());
+ sel2.push_back(*maybeSel);
+ }
+ sel_ = std::move(sel2);
+
+ ASSERT_NO_FATAL_FAILURE(runEvaluate());
+ ASSERT_NO_FATAL_FAILURE(runEvaluateFinal());
+}
+
+TEST_F(SelectionCollectionDataTest, CopiedSelectionsAreIndependent)
+{
+ static const char* const selections[] = {
+ "x > 2", "2 < x", "y > resnr", "resnr < 2.5", "2.5 > resnr"
+ };
+ setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
+ ASSERT_NO_FATAL_FAILURE(runParser(selections));
+ ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
+
+ ASSERT_NO_FATAL_FAILURE(runCompiler());
+ // Check that copy evaluation does not conflict with original.
+ gmx::SelectionCollection sc2(sc_);
+ ASSERT_NO_THROW_GMX(sc2.evaluate(topManager_.frame(), nullptr));
+
+ ASSERT_NO_FATAL_FAILURE(runEvaluate());
+ ASSERT_NO_FATAL_FAILURE(runEvaluateFinal());
+}
+
+TEST_F(SelectionCollectionDataTest, CopiedSelectionWithIndexPostCompilation)
+{
+ static const char* const selections[] = { "group \"GrpA\"",
+ "GrpB",
+ "1",
+ "group \"GrpB\" and resname RB",
+ "group \"GrpA\" permute 5 3 2 1 4",
+ "group \"GrpA\" plus group \"GrpB\"",
+ "res_cog of group \"GrpA\"" };
+ setFlags(TestFlags() | efTestSelectionNames);
+ ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
+ ASSERT_NO_FATAL_FAILURE(runParser(selections));
+ ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
+ ASSERT_NO_FATAL_FAILURE(runCompiler());
+ std::vector<std::string> selNames;
+ for (const auto& sel : sel_)
+ {
+ selNames.emplace_back(sel.name());
+ }
+ gmx::SelectionCollection sc2(sc_);
+ sc_ = sc2;
+ std::vector<gmx::Selection> sel2;
+ for (const std::string_view selName : selNames)
+ {
+ std::optional<gmx::Selection> maybeSel = sc_.selection(selName);
+ ASSERT_TRUE(maybeSel.has_value());
+ sel2.push_back(*maybeSel);
+ }
+ sel_ = std::move(sel2);
+ checkCompiled();
+}
} // namespace
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff