2 * This file is part of the GROMACS molecular simulation package.
4 * Copyright (c) 2009,2010,2011,2012,2013 by the GROMACS development team.
5 * Copyright (c) 2014,2015,2016,2017,2018 by the GROMACS development team.
6 * Copyright (c) 2019,2020, by the GROMACS development team, led by
7 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
8 * and including many others, as listed in the AUTHORS file in the
9 * top-level source directory and at http://www.gromacs.org.
11 * GROMACS is free software; you can redistribute it and/or
12 * modify it under the terms of the GNU Lesser General Public License
13 * as published by the Free Software Foundation; either version 2.1
14 * of the License, or (at your option) any later version.
16 * GROMACS is distributed in the hope that it will be useful,
17 * but WITHOUT ANY WARRANTY; without even the implied warranty of
18 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
19 * Lesser General Public License for more details.
21 * You should have received a copy of the GNU Lesser General Public
22 * License along with GROMACS; if not, see
23 * http://www.gnu.org/licenses, or write to the Free Software Foundation,
24 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
26 * If you want to redistribute modifications to GROMACS, please
27 * consider that scientific software is very special. Version
28 * control is crucial - bugs must be traceable. We will be happy to
29 * consider code for inclusion in the official distribution, but
30 * derived work must not be called official GROMACS. Details are found
31 * in the README & COPYING files - if they are missing, get the
32 * official version at http://www.gromacs.org.
34 * To help us fund GROMACS development, we humbly ask that you cite
35 * the research papers on the package. Check out http://www.gromacs.org.
39 * Implements classes in selection.h.
41 * \author Teemu Murtola <teemu.murtola@gmail.com>
42 * \ingroup module_selection
46 #include "selection.h"
50 #include "gromacs/selection/nbsearch.h"
51 #include "gromacs/topology/mtop_lookup.h"
52 #include "gromacs/topology/topology.h"
53 #include "gromacs/utility/exceptions.h"
54 #include "gromacs/utility/gmxassert.h"
55 #include "gromacs/utility/stringutil.h"
56 #include "gromacs/utility/textwriter.h"
68 /********************************************************************
72 SelectionData::SelectionData(SelectionTreeElement* elem, const char* selstr) :
74 selectionText_(selstr),
76 coveredFractionType_(CFRAC_NONE),
77 coveredFraction_(1.0),
78 averageCoveredFraction_(1.0),
80 bDynamicCoveredFraction_(false)
82 if (elem->child->type == SEL_CONST)
84 // TODO: This is not exception-safe if any called function throws.
85 gmx_ana_pos_copy(&rawPositions_, elem->child->v.u.p, true);
89 SelectionTreeElementPointer child = elem->child;
90 child->flags &= ~SEL_ALLOCVAL;
91 _gmx_selvalue_setstore(&child->v, &rawPositions_);
92 /* We should also skip any modifiers to determine the dynamic
94 while (child->type == SEL_MODIFIER)
101 if (child->type == SEL_SUBEXPRREF)
103 child = child->child;
104 /* Because most subexpression elements are created
105 * during compilation, we need to check for them
108 if (child->type == SEL_SUBEXPR)
110 child = child->child;
116 /* For variable references, we should skip the
117 * SEL_SUBEXPRREF and SEL_SUBEXPR elements. */
118 if (child->type == SEL_SUBEXPRREF)
120 child = child->child->child;
122 bDynamic_ = ((child->child->flags & SEL_DYNAMIC) != 0);
125 initCoveredFraction(CFRAC_NONE);
129 SelectionData::~SelectionData() {}
132 bool SelectionData::initCoveredFraction(e_coverfrac_t type)
134 coveredFractionType_ = type;
135 if (type == CFRAC_NONE)
137 bDynamicCoveredFraction_ = false;
139 else if (!_gmx_selelem_can_estimate_cover(rootElement()))
141 coveredFractionType_ = CFRAC_NONE;
142 bDynamicCoveredFraction_ = false;
146 bDynamicCoveredFraction_ = true;
148 coveredFraction_ = bDynamicCoveredFraction_ ? 0.0 : 1.0;
149 averageCoveredFraction_ = coveredFraction_;
150 return type == CFRAC_NONE || coveredFractionType_ != CFRAC_NONE;
157 * Helper function to compute total masses and charges for positions.
159 * \param[in] top Topology to take atom masses from.
160 * \param[in] pos Positions to compute masses and charges for.
161 * \param[out] masses Output masses.
162 * \param[out] charges Output charges.
164 * Does not throw if enough space has been reserved for the output vectors.
166 void computeMassesAndCharges(const gmx_mtop_t* top,
167 const gmx_ana_pos_t& pos,
168 std::vector<real>* masses,
169 std::vector<real>* charges)
171 GMX_ASSERT(top != nullptr, "Should not have been called with NULL topology");
175 for (int b = 0; b < pos.count(); ++b)
179 for (int i = pos.m.mapb.index[b]; i < pos.m.mapb.index[b + 1]; ++i)
181 const int index = pos.m.mapb.a[i];
182 const t_atom& atom = mtopGetAtomParameters(top, index, &molb);
186 masses->push_back(mass);
187 charges->push_back(charge);
193 bool SelectionData::hasSortedAtomIndices() const
196 gmx_ana_index_set(&g, rawPositions_.m.mapb.nra, rawPositions_.m.mapb.a, -1);
197 return gmx_ana_index_check_sorted(&g);
200 void SelectionData::refreshName()
202 rootElement_.fillNameIfMissing(selectionText_.c_str());
203 name_ = rootElement_.name();
206 void SelectionData::initializeMassesAndCharges(const gmx_mtop_t* top)
208 GMX_ASSERT(posMass_.empty() && posCharge_.empty(), "Should not be called more than once");
209 posMass_.reserve(posCount());
210 posCharge_.reserve(posCount());
213 posMass_.resize(posCount(), 1.0);
214 posCharge_.resize(posCount(), 0.0);
218 computeMassesAndCharges(top, rawPositions_, &posMass_, &posCharge_);
223 void SelectionData::refreshMassesAndCharges(const gmx_mtop_t* top)
225 if (top != nullptr && isDynamic() && !hasFlag(efSelection_DynamicMask))
227 computeMassesAndCharges(top, rawPositions_, &posMass_, &posCharge_);
232 void SelectionData::updateCoveredFractionForFrame()
234 if (isCoveredFractionDynamic())
236 real cfrac = _gmx_selelem_estimate_coverfrac(rootElement());
237 coveredFraction_ = cfrac;
238 averageCoveredFraction_ += cfrac;
243 void SelectionData::computeAverageCoveredFraction(int nframes)
245 if (isCoveredFractionDynamic() && nframes > 0)
247 averageCoveredFraction_ /= nframes;
252 void SelectionData::restoreOriginalPositions(const gmx_mtop_t* top)
256 gmx_ana_pos_t& p = rawPositions_;
257 gmx_ana_indexmap_update(&p.m, rootElement().v.u.g, hasFlag(gmx::efSelection_DynamicMask));
258 refreshMassesAndCharges(top);
262 } // namespace internal
264 /********************************************************************
268 Selection::operator AnalysisNeighborhoodPositions() const
270 AnalysisNeighborhoodPositions pos(data().rawPositions_.x, data().rawPositions_.count());
273 pos.exclusionIds(atomIndices());
279 void Selection::setOriginalId(int i, int id)
281 data().rawPositions_.m.mapid[i] = id;
282 data().rawPositions_.m.orgid[i] = id;
286 int Selection::initOriginalIdsToGroup(const gmx_mtop_t* top, e_index_t type)
290 return gmx_ana_indexmap_init_orgid_group(&data().rawPositions_.m, top, type);
292 catch (const InconsistentInputError&)
294 GMX_ASSERT(type == INDEX_RES || type == INDEX_MOL,
295 "Expected that only grouping by residue/molecule would fail");
296 std::string message = formatString(
297 "Cannot group selection '%s' into %s, because some "
298 "positions have atoms from more than one such group.",
300 type == INDEX_MOL ? "molecules" : "residues");
301 GMX_THROW(InconsistentInputError(message));
306 void Selection::printInfo(FILE* fp) const
309 "\"%s\" (%d position%s, %d atom%s%s)",
312 posCount() == 1 ? "" : "s",
314 atomCount() == 1 ? "" : "s",
315 isDynamic() ? ", dynamic" : "");
320 void Selection::printDebugInfo(FILE* fp, int nmaxind) const
322 const gmx_ana_pos_t& p = data().rawPositions_;
326 fprintf(fp, " Group ");
328 gmx_ana_index_set(&g, p.m.mapb.nra, p.m.mapb.a, 0);
329 TextWriter writer(fp);
330 gmx_ana_index_dump(&writer, &g, nmaxind);
332 fprintf(fp, " Block (size=%d):", p.m.mapb.nr);
335 fprintf(fp, " (null)");
340 if (nmaxind >= 0 && n > nmaxind)
344 for (int i = 0; i <= n; ++i)
346 fprintf(fp, " %d", p.m.mapb.index[i]);
356 if (nmaxind >= 0 && n > nmaxind)
360 fprintf(fp, " RefId:");
363 fprintf(fp, " (null)");
367 for (int i = 0; i < n; ++i)
369 fprintf(fp, " %d", p.m.refid[i]);
378 fprintf(fp, " MapId:");
381 fprintf(fp, " (null)");
385 for (int i = 0; i < n; ++i)
387 fprintf(fp, " %d", p.m.mapid[i]);
398 /********************************************************************
402 SelectionPosition::operator AnalysisNeighborhoodPositions() const
404 AnalysisNeighborhoodPositions pos(sel_->rawPositions_.x, sel_->rawPositions_.count());
405 if (sel_->hasOnlyAtoms())
407 // TODO: Move atomIndices() such that it can be reused here as well.
408 pos.exclusionIds(constArrayRefFromArray<int>(sel_->rawPositions_.m.mapb.a,
409 sel_->rawPositions_.m.mapb.nra));
411 return pos.selectSingleFromArray(i_);