Add missing header

Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>

diff --git a/include/gromacs/trajectoryanalysis/topologyinformation.h b/include/gromacs/trajectoryanalysis/topologyinformation.h
new file mode 100644 (file)
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+++ b/include/gromacs/trajectoryanalysis/topologyinformation.h
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+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2018,2019, 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.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
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+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \file
+ * \brief
+ * Declares gmx::TopologyInformation.
+ *
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
+ * \author Mark Abraham <mark.j.abraham@gmail.com>
+ * \inlibraryapi
+ * \ingroup module_trajectoryanalysis
+ */
+#ifndef GMX_TRAJECTORYANALYSIS_TOPOLOGYINFORMATION_H
+#define GMX_TRAJECTORYANALYSIS_TOPOLOGYINFORMATION_H
+
+#include <memory>
+#include <string>
+#include <vector>
+
+#include "gromacs/math/vectypes.h"
+#include "gromacs/topology/atoms.h"
+#include "gromacs/topology/topology.h"
+#include "gromacs/utility/classhelpers.h"
+
+//! Forward declaration
+typedef struct gmx_rmpbc* gmx_rmpbc_t;
+
+namespace gmx
+{
+
+template<typename T>
+class ArrayRef;
+
+class TopologyInformation;
+class TrajectoryAnalysisRunnerCommon;
+
+/*! \libinternal
+ * \brief Topology information available to a trajectory analysis module.
+ *
+ * This class is used to provide topology information to trajectory
+ * analysis modules and to manage memory for them. Having a single
+ * wrapper object instead of passing each item separately makes
+ * TrajectoryAnalysisModule interface simpler, and also reduces the
+ * need to change existing code if additional information is added.
+ *
+ * It is intended that eventually most clients of this class will be
+ * analysis tools ported to the new analysis framework, but we will
+ * use this infrastructure also from the legacy analysis tools during
+ * the transition period. That will make it easier to put those tools
+ * under tests, and eventually port them.
+ *
+ * Methods in this class do not throw if not explicitly stated.
+ *
+ * The main data content is constant once loaded, but some content is
+ * constructed only when required (e.g. atoms_ and
+ * expandedTopology_). Their data members are mutable, so that the
+ * lazy construction idiom works properly. Some clients wish to modify
+ * the t_atoms, so there is an efficient mechanism for them to get a
+ * copy they can modify without disturbing this class. (The
+ * implementation releases the cached lazily constructed atoms_, but
+ * from the point of view of the caller, that is a copy.) The getters
+ * and copy functions are const for callers, which correctly expresses
+ * that the topology information is not being changed, merely copied
+ * and presented in a different form.
+ *
+ * \ingroup module_trajectoryanalysis
+ */
+class TopologyInformation
+{
+public:
+    //! Returns true if a topology file was loaded.
+    bool hasTopology() const { return hasLoadedMtop_; }
+    //! Returns true if a full topology file was loaded.
+    bool hasFullTopology() const { return bTop_; }
+    /*! \brief Builder function to fill the contents of
+     * TopologyInformation in \c topInfo from \c filename.
+     *
+     * Different tools require, might need, would benefit from, or
+     * do not need topology information. This functions implements
+     * the two-phase construction that is currently needed to
+     * support that.
+     *
+     * Any coordinate or run input file format will work, but the
+     * kind of data available from the getter methods afterwards
+     * will vary. For example, the mtop() available after reading
+     * a plain structure file will have a single molecule block and
+     * molecule type, regardless of contents.
+     *
+     * After reading, this object can return many kinds of primary
+     * and derived data structures to its caller.
+     *
+     * \todo This should throw upon error but currently does
+     * not. */
+    void fillFromInputFile(const std::string& filename);
+    /*! \brief Returns the loaded topology, or nullptr if not loaded. */
+    gmx_mtop_t* mtop() const { return mtop_.get(); }
+    //! Returns the loaded topology fully expanded, or nullptr if no topology is available.
+    const gmx_localtop_t* expandedTopology() const;
+    /*! \brief Returns a read-only handle to the fully expanded
+     * atom data arrays, which might be valid but empty if no
+     * topology is available. */
+    const t_atoms* atoms() const;
+    /*! \brief Copies the fully expanded atom data arrays, which
+     * might be valid but empty if no topology is available. */
+    AtomsDataPtr copyAtoms() const;
+    //! Returns the ePBC field from the topology.
+    int ePBC() const { return ePBC_; }
+    /*! \brief
+     * Gets the configuration positions from the topology file.
+     *
+     * If TrajectoryAnalysisSettings::efUseTopX has not been specified,
+     * this method should not be called.
+     *
+     * \throws  APIError if topology position coordinates are not available
+     */
+    ArrayRef<const RVec> x() const;
+    /*! \brief
+     * Gets the configuration velocities from the topology file.
+     *
+     * If TrajectoryAnalysisSettings::efUseTopV has not been specified,
+     * this method should not be called.
+     *
+     * \throws  APIError if topology velocity coordinates are not available
+     */
+    ArrayRef<const RVec> v() const;
+    /*! \brief
+     * Gets the configuration box from the topology file.
+     *
+     * \param[out] box   Box size from the topology file, must not be nullptr.
+     */
+    void getBox(matrix box) const;
+    /*! \brief Returns a name for the topology.
+     *
+     * If a full topology was read from a a file, returns the name
+     * it contained, otherwise the empty string. */
+    const char* name() const;
+
+    TopologyInformation();
+    ~TopologyInformation();
+
+private:
+    //! The topology structure, or nullptr if no topology loaded.
+    std::unique_ptr<gmx_mtop_t> mtop_;
+    //! Whether a topology has been loaded.
+    bool hasLoadedMtop_;
+    //! The fully expanded topology structure, nullptr if not yet constructed.
+    mutable ExpandedTopologyPtr expandedTopology_;
+    //! The fully expanded atoms data structure, nullptr if not yet constructed.
+    mutable AtomsDataPtr atoms_;
+    //! true if full tpx file was loaded, false otherwise.
+    bool bTop_;
+    //! Position coordinates from the topology (can be nullptr).
+    std::vector<RVec> xtop_;
+    //! Velocity coordinates from the topology (can be nullptr).
+    std::vector<RVec> vtop_;
+    //! The box loaded from the topology file.
+    matrix boxtop_{};
+    //! The ePBC field loaded from the topology file.
+    int ePBC_;
+
+    // TODO This type is probably movable if we need that.
+    GMX_DISALLOW_COPY_AND_ASSIGN(TopologyInformation);
+
+    /*! \brief
+     * Needed to initialize the data.
+     */
+    friend class TrajectoryAnalysisRunnerCommon;
+};
+
+//! Convenience overload useful for implementing legacy tools.
+gmx_rmpbc_t gmx_rmpbc_init(const gmx::TopologyInformation& topInfo);
+
+} // namespace gmx
+
+#endif