/usr/include/gromacs/selection/selectioncollection.h is in libgromacs-dev 2016.1-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 | /*
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2010,2011,2012,2013,2014,2015, 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
* control is crucial - bugs must be traceable. We will be happy to
* 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::SelectionCollection.
*
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \inpublicapi
* \ingroup module_selection
*/
#ifndef GMX_SELECTION_SELECTIONCOLLECTION_H
#define GMX_SELECTION_SELECTIONCOLLECTION_H
#include <cstdio>
#include <string>
#include <vector>
#include "gromacs/selection/selection.h" // For gmx::SelectionList
#include "gromacs/utility/classhelpers.h"
struct gmx_ana_indexgrps_t;
struct t_pbc;
struct t_topology;
struct t_trxframe;
namespace gmx
{
class IOptionsContainer;
class SelectionCompiler;
class SelectionEvaluator;
class TextInputStream;
class TextOutputStream;
/*! \brief
* Collection of selections.
*
* This class is the main interface to the core of the selection engine.
* It is used to initialize and manage a collection of selections that share
* the same topology. Selections within one collection can share variables and
* can be optimized together. Selections from two different collections do not
* interact.
*
* The constructor creates an empty selection collection object. To initialize
* the object, either call initOptions(), or both setReferencePosType() and
* setOutputPosType(). See these methods for more details on the
* initialization options.
*
* 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
* set with setTopology() unless requiresTopology() returns false (the topology
* can also be set earlier).
* setIndexGroups() must also be called if external index group references are
* used in the selections; it can be called at any point before compile().
* Once all selections are parsed, they must be compiled all at once using
* compile().
*
* After compilation, dynamic selections have the maximum number of atoms they
* can evaluate to, but positions have undefined values (see \ref Selection and
* SelectionPosition). evaluate() can be used to update the selections for a
* new frame. evaluateFinal() can be called after all the frames have been
* processed to restore the selection values back to the ones they were after
* compile().
*
* At any point, requiresTopology() can be called to see whether the
* information provided so far requires loading the topology.
* Similarly, requiresIndexGroups() tells whether external index groups are
* requires.
* printTree() can be used to print the internal representation of the
* selections (mostly useful for debugging).
*
* Note that for trajectory analysis using TrajectoryAnalysisModule, the
* SelectionCollection object is managed by Gromacs, and \ref Selection objects
* are obtained from SelectionOption.
*
* \inpublicapi
* \ingroup module_selection
*/
class SelectionCollection
{
public:
//! Flag for initOptions() to select how to behave with -seltype option.
enum SelectionTypeOption
{
/*! \brief
* Add the option for the user to select default value for
* setOutputPosType().
*/
IncludeSelectionTypeOption,
/*! \brief
* Do not add the option, selections will always select atoms by
* default.
*/
AlwaysAtomSelections
};
/*! \brief
* Creates an empty selection collection.
*
* \throws std::bad_alloc if out of memory.
*/
SelectionCollection();
~SelectionCollection();
/*! \brief
* Initializes options for setting global properties on the collection.
*
* \param[in,out] options Options object to initialize.
* \param[in] selectionTypeOption
* Whether to add option to influence setOutputPosType().
* \throws std::bad_alloc if out of memory.
*
* Adds options to \p options that can be used to set the default
* position types (see setReferencePosType() and setOutputPosType())
* and debugging flags.
*/
void initOptions(IOptionsContainer *options, SelectionTypeOption selectionTypeOption);
/*! \brief
* Sets the default reference position handling for a selection
* collection.
*
* \param[in] type Default selection reference position type
* (one of the strings acceptable for
* PositionCalculationCollection::typeFromEnum()).
* \throws InternalError if \p type is invalid.
*
* Should be called before calling the parser functions, unless
* initOptions() has been called. In the latter case, can still be
* used to override the default value (before initOptions() is called)
* and/or the value provided through the Options object.
*
* Strong exception safety.
*/
void setReferencePosType(const char *type);
/*! \brief
* Sets the default reference position handling for a selection
* collection.
*
* \param[in] type Default selection output position type
* (one of the strings acceptable for
* PositionCalculationCollection::typeFromEnum()).
* \throws InternalError if \p type is invalid.
*
* Should be called before calling the parser functions, unless
* initOptions() has been called. In the latter case, can still be
* used to override the default value (before initOptions() is called)
* and/or the value provided through the Options object.
*
* Strong exception safety.
*/
void setOutputPosType(const char *type);
/*! \brief
* Sets the debugging level for the selection collection.
*
* \param[in] debugLevel Debug level to set (0 = no debug
* information).
*
* initOptions() creates debugging options that can also be used to set
* the debug level. These are normally hidden, but if this method is
* called before initOptions() with a non-zero \p debugLevel, they are
* made visible.
*
* Mostly useful for debugging tools.
*
* Does not throw.
*/
void setDebugLevel(int debugLevel);
/*! \brief
* Returns true if the collection requires topology information for
* evaluation.
*
* \returns true if any selection in the collection requires topology
* information.
*
* Before the parser functions have been called, the return value is
* based just on the position types set.
* After parser functions have been called, the return value also takes
* into account the selection keywords used.
*
* Does not throw.
*/
bool requiresTopology() const;
/*! \brief
* Returns true if the collection requires external index groups.
*
* \returns true if any selection has an unresolved index group reference.
*
* The return value is `false` after setIndexGroups() has been called.
*
* Does not throw.
*/
bool requiresIndexGroups() const;
/*! \brief
* Sets the topology for the collection.
*
* \param[in] top Topology data.
* \param[in] natoms Number of atoms. If <=0, the number of
* atoms in the topology is used.
*
* Either the topology must be provided, or \p natoms must be > 0.
*
* \p natoms determines the largest atom index that can be selected by
* the selection: even if the topology contains more atoms, they will
* not be selected.
*
* Does not throw currently, but this is subject to change when more
* underlying code is converted to C++.
*/
void setTopology(t_topology *top, int natoms);
/*! \brief
* Sets the external index groups to use for the selections.
*
* \param[in] grps Index groups to use for the selections.
* \throws std::bad_alloc if out of memory.
* \throws InconsistentInputError if a group reference cannot be resolved.
*
* Only the first call to this method can have a non-NULL \p grps.
* At this point, any selections that have already been provided are
* searched for references to external groups, and the references are
* replaced by the contents of the groups. If any referenced group
* cannot be found in \p grps (or if \p grps is NULL and there are any
* references), InconsistentInputError is thrown.
*
* The selection collection keeps a reference to \p grps until this
* method is called with a NULL \p grps.
* If this method is not called before compile(), it is automatically
* called as setIndexGroups(NULL).
*/
void setIndexGroups(gmx_ana_indexgrps_t *grps);
/*! \brief
* Parses selection(s) from standard input.
*
* \param[in] count Number of selections to parse
* (if -1, parse as many as provided by the user).
* \param[in] bInteractive Whether the parser should behave
* interactively.
* \param[in] context Context to print for interactive input.
* \returns Vector of parsed selections.
* \throws std::bad_alloc if out of memory.
* \throws InvalidInputError if there is a parsing error
* (an interactive parser only throws this if too few selections
* are provided and the user forced the end of input).
*
* The returned objects remain valid for the lifetime of
* the selection collection.
* Some information about the selections only becomes available once
* compile() has been called; see \ref Selection.
*
* The string provided to \p context should be such that it can replace
* the three dots in "Specify selections ...:". It can be empty.
*/
SelectionList parseFromStdin(int count, bool bInteractive,
const std::string &context);
/*! \brief
* Parses selection(s) interactively using provided streams.
*
* \param[in] count Number of selections to parse
* (if -1, parse as many as provided by the user).
* \param[in] inputStream Stream to use for input.
* \param[in] outputStream Stream to use for output
* (if NULL, the parser runs non-interactively and does not
* produce any status messages).
* \param[in] context Context to print for interactive input.
* \returns Vector of parsed selections.
* \throws std::bad_alloc if out of memory.
* \throws InvalidInputError if there is a parsing error
* (an interactive parser only throws this if too few selections
* are provided and the user forced the end of input).
*
* Works the same as parseFromStdin(), except that the caller can
* provide streams to use instead of `stdin` and `stderr`.
*
* Mainly usable for unit testing interactive input.
*/
SelectionList parseInteractive(int count,
TextInputStream *inputStream,
TextOutputStream *outputStream,
const std::string &context);
/*! \brief
* Parses selection(s) from a file.
*
* \param[in] filename Name of the file to parse selections from.
* \returns Vector of parsed selections.
* \throws std::bad_alloc if out of memory.
* \throws InvalidInputError if there is a parsing error.
*
* The returned objects remain valid for the lifetime of
* the selection collection.
* Some information about the selections only becomes available once
* compile() has been called; see \ref Selection.
*/
SelectionList parseFromFile(const std::string &filename);
/*! \brief
* Parses selection(s) from a string.
*
* \param[in] str String to parse selections from.
* \returns Vector of parsed selections.
* \throws std::bad_alloc if out of memory.
* \throws InvalidInputError if there is a parsing error.
*
* The returned objects remain valid for the lifetime of
* the selection collection.
* Some information about the selections only becomes available once
* compile() has been called; see \ref Selection.
*/
SelectionList parseFromString(const std::string &str);
/*! \brief
* Prepares the selections for evaluation and performs optimizations.
*
* \throws InconsistentInputError if topology is required but not set.
* \throws InvalidInputError if setIndexGroups() has not been called
* and there are index group references.
* \throws unspecified if compilation fails (TODO: list/reduce these).
*
* Before compilation, selections should have been added to the
* collection using the parseFrom*() functions.
* The compiled selection collection can be passed to evaluate() to
* evaluate the selection for a frame.
* Before the compiled selection is evaluated, the selections indicate
* the maximal set of atoms/positions to which they can be evaluated;
* see \ref Selection.
*
* If an error occurs, the collection is cleared.
*
* The covered fraction information is initialized to ::CFRAC_NONE for
* all selections.
*/
void compile();
/*! \brief
* Evaluates selections in the collection.
*
* \param[in] fr Frame for which the evaluation should be carried out.
* \param[in] pbc PBC data, or NULL if no PBC should be used.
* \throws unspeficied Multiple possible exceptions to indicate
* evaluation failure (TODO: enumerate).
*/
void evaluate(t_trxframe *fr, t_pbc *pbc);
/*! \brief
* Evaluates the largest possible index groups from dynamic selections.
*
* \param[in] nframes Total number of frames.
*
* This method restores the selections to the state they were after
* compile().
*
* \p nframes should equal the number of times evaluate() has been
* called.
*
* Does not throw.
*/
void evaluateFinal(int nframes);
/*! \brief
* Prints a human-readable version of the internal selection element
* tree.
*
* \param[in] fp File handle to receive the output.
* \param[in] bValues If true, the evaluated values of selection
* elements are printed as well.
*
* The output is very techical, and intended for debugging purposes.
*
* Does not throw.
*/
void printTree(FILE *fp, bool bValues) const;
/*! \brief
* Prints the selection strings into an XVGR file as comments.
*
* \param[in] fp Output file.
*
* Does not throw.
*/
void printXvgrInfo(FILE *fp) const;
private:
class Impl;
PrivateImplPointer<Impl> impl_;
/*! \brief
* Needed for the compiler to freely modify the collection.
*/
friend class SelectionCompiler;
/*! \brief
* Needed for the evaluator to freely modify the collection.
*/
friend class SelectionEvaluator;
};
} // namespace gmx
#endif
|