const char *selectionText() const { return selectionText_.c_str(); }
//! Returns true if the size of the selection (posCount()) is dynamic.
bool isDynamic() const { return bDynamic_; }
+ //! Returns the type of positions in the selection.
+ e_index_t type() const { return rawPositions_.m.type; }
+
//! Number of positions in the selection.
int posCount() const { return rawPositions_.nr; }
//! Returns the root of the evaluation tree for this selection.
//! Returns true if the size of the selection (posCount()) is dynamic.
bool isDynamic() const { return data().isDynamic(); }
//! Returns the type of positions in the selection.
- e_index_t type() const { return data().rawPositions_.m.type; }
+ e_index_t type() const { return data().type(); }
//! Total number of atoms in the selection.
int atomCount() const
*
* Currently always returns the same as Selection::type().
*/
- e_index_t type() const { return sel_->rawPositions_.m.type; }
+ e_index_t type() const { return sel_->type(); }
//! Returns coordinates for this position.
const rvec &x() const
{
#include "parser.h"
#include "poscalc.h"
#include "scanner.h"
+#include "selection.h"
#include "selectioncollection-impl.h"
#include "selelem.h"
#include "selhelp.h"
SelectionCollection::initOptions(Options *options)
{
const char * const debug_levels[]
- = {"no", "basic", "compile", "eval", "full" };
- /*
- static const char * const desc[] = {
- "This program supports selections in addition to traditional",
- "index files. Use [TT]-select help[tt] for additional information,",
- "or type 'help' in the selection prompt.",
- NULL,
- };
- options.setDescription(desc);
- */
+ = { "no", "basic", "compile", "eval", "full" };
+
+ bool bAllowNonAtomOutput = false;
+ SelectionDataList::const_iterator iter;
+ for (iter = impl_->sc_.sel.begin(); iter != impl_->sc_.sel.end(); ++iter)
+ {
+ const internal::SelectionData &sel = **iter;
+ if (!sel.hasFlag(efSelection_OnlyAtoms))
+ {
+ bAllowNonAtomOutput = true;
+ }
+ }
const char *const *postypes = PositionCalculationCollection::typeEnumValues;
options->addOption(StringOption("selrpos")
.enumValueFromNullTerminatedArray(postypes)
.store(&impl_->rpost_).defaultValue(postypes[0])
.description("Selection reference positions"));
- options->addOption(StringOption("seltype")
- .enumValueFromNullTerminatedArray(postypes)
- .store(&impl_->spost_).defaultValue(postypes[0])
- .description("Default selection output positions"));
+ if (bAllowNonAtomOutput)
+ {
+ options->addOption(StringOption("seltype")
+ .enumValueFromNullTerminatedArray(postypes)
+ .store(&impl_->spost_).defaultValue(postypes[0])
+ .description("Default selection output positions"));
+ }
+ else
+ {
+ impl_->spost_ = postypes[0];
+ }
GMX_RELEASE_ASSERT(impl_->debugLevel_ >= 0 && impl_->debugLevel_ <= 4,
"Debug level out of range");
options->addOption(StringOption("seldebug").hidden(impl_->debugLevel_ == 0)
impl_->sc_.pcc.printTree(stderr);
std::fprintf(stderr, "\n");
}
+
+ // TODO: It would be nicer to associate the name of the selection option
+ // (if available) to the error message.
+ SelectionDataList::const_iterator iter;
+ for (iter = impl_->sc_.sel.begin(); iter != impl_->sc_.sel.end(); ++iter)
+ {
+ const internal::SelectionData &sel = **iter;
+ if (sel.hasFlag(efSelection_OnlyAtoms))
+ {
+ if (sel.type() != INDEX_ATOM)
+ {
+ std::string message = formatString(
+ "Selection '%s' does not evaluate to individual atoms. "
+ "This is not allowed in this context.",
+ sel.selectionText());
+ GMX_THROW(InvalidInputError(message));
+ }
+ }
+ }
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2012, by the GROMACS development team, led by
+ * Copyright (c) 2010,2012,2013, by the GROMACS development team, led by
* David van der Spoel, Berk Hess, Erik Lindahl, and including many
* others, as listed in the AUTHORS file in the top-level source
* directory and at http://www.gromacs.org.
efSelection_OnlyAtoms = 1<<1,
//! Whether ::POS_MASKONLY should be used for output position evaluation.
efSelection_DynamicMask = 1<<2,
- efSelection_DynamicOnlyWhole = 1<<3,
//! Whether velocities of output positions should be evaluated.
efSelection_EvaluateVelocities = 1<<5,
//! Whether forces on output positions should be evaluated.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013, by the GROMACS development team, led by
* David van der Spoel, Berk Hess, Erik Lindahl, and including many
* others, as listed in the AUTHORS file in the top-level source
* directory and at http://www.gromacs.org.
option().setSelectionFlag(efSelection_DynamicMask, bEnabled);
}
-void SelectionOptionInfo::setDynamicOnlyWhole(bool bEnabled)
-{
- option().setSelectionFlag(efSelection_DynamicOnlyWhole, bEnabled);
-}
-
/********************************************************************
* SelectionOption
{ selectionFlags_.set(efSelection_EvaluateForces); return me(); }
/*! \brief
* Only accept selections that evaluate to atom positions.
- *
- * TODO: This option is not yet implemented.
*/
MyClass &onlyAtoms()
{ selectionFlags_.set(efSelection_OnlyAtoms); return me(); }
*/
MyClass &dynamicMask()
{ selectionFlags_.set(efSelection_DynamicMask); return me(); }
- /*! \brief
- * Disallow using atom coordinates as the reference positions.
- *
- * TODO: This option is not yet implemented.
- */
- MyClass &dynamicOnlyWhole()
- { selectionFlags_.set(efSelection_DynamicOnlyWhole); return me(); }
private:
// Disable possibility to allow multiple occurrences, since it isn't
* \param[in] bEnabled If true, the option accepts only positions that
* evaluate to atom positions.
*
- * TODO: This is not yet implemented.
- *
* \see SelectionOption::onlyAtoms()
*/
void setOnlyAtoms(bool bEnabled);
* \see SelectionOption::dynamicMask()
*/
void setDynamicMask(bool bEnabled);
- /*! \brief
- * Sets whether atom coordinates are allowed as reference positions.
- *
- * \param[in] bEnabled If true, the option does not accept atom
- * coordinates as reference positions.
- *
- * TODO: This is not yet implemented.
- *
- * \see SelectionOption::dynamicOnlyWhole()
- */
- void setDynamicOnlyWhole(bool bEnabled);
private:
SelectionOptionStorage &option();
*/
#include <gtest/gtest.h>
+#include "gromacs/legacyheaders/smalloc.h"
+#include "gromacs/legacyheaders/tpxio.h"
+
#include "gromacs/options/options.h"
#include "gromacs/options/optionsassigner.h"
#include "gromacs/selection/selection.h"
{
public:
SelectionOptionTestBase();
+ ~SelectionOptionTestBase();
void setManager();
+ void loadTopology(const char *filename);
gmx::SelectionCollection sc_;
gmx::SelectionOptionManager manager_;
gmx::Options options_;
+ t_topology *top_;
};
SelectionOptionTestBase::SelectionOptionTestBase()
- : manager_(&sc_), options_(NULL, NULL)
+ : manager_(&sc_), options_(NULL, NULL), top_(NULL)
{
sc_.setReferencePosType("atom");
sc_.setOutputPosType("atom");
}
+SelectionOptionTestBase::~SelectionOptionTestBase()
+{
+ if (top_ != NULL)
+ {
+ free_t_atoms(&top_->atoms, TRUE);
+ done_top(top_);
+ sfree(top_);
+ }
+}
+
void SelectionOptionTestBase::setManager()
{
setManagerForSelectionOptions(&options_, &manager_);
}
+void SelectionOptionTestBase::loadTopology(const char *filename)
+{
+ char title[STRLEN];
+ int ePBC;
+ matrix box;
+
+ snew(top_, 1);
+ read_tps_conf(gmx::test::TestFileManager::getInputFilePath(filename).c_str(),
+ title, top_, &ePBC, NULL, NULL, box, FALSE);
+
+ ASSERT_NO_THROW_GMX(sc_.setTopology(top_, -1));
+}
+
+
/********************************************************************
* Tests for SelectionOption
*/
}
+TEST_F(SelectionOptionTest, HandlesNonAtomicSelectionWhenAtomsRequired)
+{
+ gmx::Selection sel;
+ using gmx::SelectionOption;
+ ASSERT_NO_THROW_GMX(options_.addOption(
+ SelectionOption("sel").store(&sel).onlyAtoms()));
+ setManager();
+
+ gmx::OptionsAssigner assigner(&options_);
+ EXPECT_NO_THROW_GMX(assigner.start());
+ ASSERT_NO_THROW_GMX(assigner.startOption("sel"));
+ EXPECT_NO_THROW_GMX(assigner.appendValue("res_cog of resname RA RB"));
+ EXPECT_NO_THROW_GMX(assigner.finishOption());
+ EXPECT_NO_THROW_GMX(assigner.finish());
+ EXPECT_NO_THROW_GMX(options_.finish());
+
+ ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
+ EXPECT_THROW_GMX(sc_.compile(), gmx::InvalidInputError);
+}
+
+
TEST_F(SelectionOptionTest, HandlesTooManySelections)
{
gmx::Selection sel;
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff