*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2016,2018, 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 "gromacs/math/vectypes.h"
-#ifdef __cplusplus
-extern "C" {
-#endif
-
struct t_atoms;
struct t_idef;
struct t_trxframe;
* similar file.
*/
-#ifdef __cplusplus
-}
-#endif
-
#endif
init_atom(at);
}
+void done_and_delete_atoms(t_atoms *atoms)
+{
+ done_atom(atoms);
+ delete atoms;
+}
+
void done_atomtypes(t_atomtypes *atype)
{
atype->nr = 0;
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/real.h"
+#include "gromacs/utility/unique_cptr.h"
struct t_symtab;
void init_atom(t_atoms *at);
void init_atomtypes(t_atomtypes *at);
void done_atom(t_atoms *at);
+void done_and_delete_atoms(t_atoms *atoms);
void done_atomtypes(t_atomtypes *at);
void init_t_atoms(t_atoms *atoms, int natoms, gmx_bool bPdbinfo);
*/
void atomsSetMassesBasedOnNames(t_atoms *atoms, gmx_bool printMissingMasses);
+//! Deleter for t_atoms, needed until it has a proper destructor.
+using AtomsDataPtr = gmx::unique_cptr<t_atoms, done_and_delete_atoms>;
+
+
#endif
}
}
+void done_localtop(gmx_localtop_t *top)
+{
+ if (top == nullptr)
+ {
+ return;
+ }
+ sfree(top->idef.cmap_grid.cmapdata);
+ sfree(top->idef.functype);
+ sfree(top->idef.iparams);
+ done_block(&top->cgs);
+ done_blocka(&top->excls);
+ for (int f = 0; f < F_NRE; f++)
+ {
+ sfree(top->idef.il[f].iatoms);
+ }
+ sfree(top->idef.iparams_posres);
+ sfree(top->idef.iparams_fbposres);
+ done_atomtypes(&top->atomtypes);
+}
+
+void done_and_sfree_localtop(gmx_localtop_t *top)
+{
+ done_localtop(top);
+ sfree(top);
+}
+
bool gmx_mtop_has_masses(const gmx_mtop_t *mtop)
{
if (mtop == nullptr)
#include "gromacs/topology/block.h"
#include "gromacs/topology/idef.h"
#include "gromacs/topology/symtab.h"
+#include "gromacs/utility/unique_cptr.h"
enum
{
// Frees both t_topology and gmx_mtop_t when the former has been created from
// the latter.
void done_top_mtop(t_topology *top, gmx_mtop_t *mtop);
+void done_localtop(gmx_localtop_t *top);
+void done_and_sfree_localtop(gmx_localtop_t *top);
bool gmx_mtop_has_masses(const gmx_mtop_t *mtop);
bool gmx_mtop_has_charges(const gmx_mtop_t *mtop);
void cmp_groups(FILE *fp, const gmx_groups_t *g0, const gmx_groups_t *g1,
int natoms0, int natoms1);
+//! Deleter for gmx_localtop_t, needed until it has a proper destructor.
+using ExpandedTopologyPtr = gmx::unique_cptr<gmx_localtop_t, done_and_sfree_localtop>;
+
#endif
/*! \brief
* Requests topology coordinates.
*
- * If this flag is specified, the coordinates loaded from the
+ * If this flag is specified, the position coordinates loaded from the
* topology can be accessed, otherwise they are not loaded.
*
* \see TopologyInformation
*/
efUseTopX = 1<<1,
+ /*! \brief
+ * Requests topology coordinates.
+ *
+ * If this flag is specified, the velocity coordinates loaded from the
+ * topology can be accessed, otherwise they are not loaded.
+ *
+ * \see TopologyInformation
+ */
+ efUseTopV = 1<<2,
/*! \brief
* Disallows the user from changing PBC handling.
*
#include "gromacs/selection/selection.h"
#include "gromacs/selection/selectionoption.h"
#include "gromacs/topology/atomprop.h"
+#include "gromacs/topology/mtop_util.h"
#include "gromacs/topology/topology.h"
#include "gromacs/trajectory/trajectoryframe.h"
#include "gromacs/trajectoryanalysis/analysissettings.h"
cutoff_ = 0;
int nnovdw = 0;
gmx_atomprop_t aps = gmx_atomprop_init();
- t_atoms *atoms = &(top.topology()->atoms);
+ auto atoms = top.copyAtoms();
// Compute total mass
mtot_ = 0;
}
// Extracts number of molecules
- nmol_ = top.topology()->mols.nr;
+ nmol_ = gmx_mtop_num_molecules(*top.mtop());
// Loop over atoms in the selection using an iterator
const int maxnovdw = 10;
AnalysisDataAverageModulePointer normAve_;
//! Neighborhood search with `refSel_` as the reference positions.
AnalysisNeighborhood nb_;
+ //! Topology exclusions used by neighborhood searching.
+ const gmx_localtop_t *localTop_;
// User input options.
double binwidth_;
: surface_(SurfaceType_None),
pairCounts_(new AnalysisDataSimpleHistogramModule()),
normAve_(new AnalysisDataAverageModule()),
+ localTop_(nullptr),
binwidth_(0.002), cutoff_(0.0), rmax_(0.0),
normalization_(Normalization_Rdf), bNormalizationSet_(false), bXY_(false),
bExclusions_(false),
GMX_THROW(InconsistentInputError("-excl only works with selections that consist of atoms"));
}
}
- const t_topology *topology = top.topology();
- if (topology->excls.nr == 0)
+ localTop_ = top.expandedTopology();
+ if (localTop_->excls.nr == 0)
{
GMX_THROW(InconsistentInputError("-excl is set, but the file provided to -s does not define exclusions"));
}
- nb_.setTopologyExclusions(&topology->excls);
+ nb_.setTopologyExclusions(&localTop_->excls);
}
}
double dgsDefault_;
bool bIncludeSolute_;
- t_topology *top_;
+ //! Global topology corresponding to the input.
+ gmx_mtop_t *mtop_;
+ //! Per-atom data corresponding to the input.
+ AtomsDataPtr atoms_;
//! Combined VdW and probe radii for each atom in the calculation group.
std::vector<real> radii_;
/*! \brief
};
Sasa::Sasa()
- : solsize_(0.14), ndots_(24), dgsDefault_(0), bIncludeSolute_(true), top_(nullptr)
+ : solsize_(0.14), ndots_(24), dgsDefault_(0), bIncludeSolute_(true),
+ mtop_(nullptr), atoms_(nullptr)
{
//minarea_ = 0.5;
registerAnalysisDataset(&area_, "area");
Sasa::initAnalysis(const TrajectoryAnalysisSettings &settings,
const TopologyInformation &top)
{
- const t_atoms &atoms = top.topology()->atoms;
- top_ = top.topology();
+ mtop_ = top.mtop();
+ atoms_ = top.copyAtoms();
//bITP = opt2bSet("-i", nfile, fnm);
const bool bResAt =
}
else
{
- if (strcmp(*(atoms.atomtype[0]), "?") == 0)
+ if (strcmp(*(atoms_->atomtype[0]), "?") == 0)
{
GMX_THROW(InconsistentInputError("Your input tpr file is too old (does not contain atom types). Cannot not compute Delta G of solvation"));
}
for (int i = 0; i < surfaceSel_.posCount(); i++)
{
const int ii = atomIndices[i];
- const int resind = atoms.atom[ii].resind;
+ const int resind = atoms_->atom[ii].resind;
real radius;
if (!gmx_atomprop_query(aps, epropVDW,
- *(atoms.resinfo[resind].name),
- *(atoms.atomname[ii]), &radius))
+ *(atoms_->resinfo[resind].name),
+ *(atoms_->atomname[ii]), &radius))
{
ndefault++;
}
{
real dgsFactor;
if (!gmx_atomprop_query(aps, epropDGsol,
- *(atoms.resinfo[resind].name),
- *(atoms.atomtype[ii]), &dgsFactor))
+ *(atoms_->resinfo[resind].name),
+ *(atoms_->atomtype[ii]), &dgsFactor))
{
dgsFactor = dgsDefault_;
}
GMX_ASSERT(residueGroup == nextRow,
"Inconsistent (non-uniformly increasing) residue grouping");
const int atomIndex = surfaceSel_.position(i).atomIndices()[0];
- const int residueIndex = atoms.atom[atomIndex].resind;
- avem->setXAxisValue(nextRow, atoms.resinfo[residueIndex].nr);
+ const int residueIndex = atoms_->atom[atomIndex].resind;
+ avem->setXAxisValue(nextRow, atoms_->resinfo[residueIndex].nr);
++nextRow;
}
}
if (bConnolly)
{
- if (fr.natoms != top_->atoms.nr)
+ if (fr.natoms != mtop_->natoms)
{
GMX_THROW(InconsistentInputError("Connolly plot (-q) is only supported for trajectories that contain all the atoms"));
}
// one else uses the topology after initialization, it may just work
// even with future parallelization.
connolly_plot(fnConnolly_.c_str(),
- nsurfacedots, surfacedots, fr.x, &top_->atoms,
- &top_->symtab, fr.ePBC, fr.box, bIncludeSolute_);
+ nsurfacedots, surfacedots, fr.x, atoms_.get(),
+ &mtop_->symtab, fr.ePBC, fr.box, bIncludeSolute_);
}
ah.startFrame(frnr, fr.time);
ResidueNumbering resNumberType_;
PdbAtomsSelection pdbAtoms_;
+ //! The input topology.
const TopologyInformation *top_;
std::vector<int> totsize_;
AnalysisData sdata_;
AnalysisDataHandle idh = pdata->dataHandle(idata_);
AnalysisDataHandle mdh = pdata->dataHandle(mdata_);
const SelectionList &sel = pdata->parallelSelections(sel_);
- t_topology *top = top_->topology();
sdh.startFrame(frnr, fr.time);
for (size_t g = 0; g < sel.size(); ++g)
const SelectionPosition &p = sel[g].position(i);
if (sel[g].type() == INDEX_RES && !bResInd_)
{
- idh.setPoint(1, top->atoms.resinfo[p.mappedId()].nr);
+ idh.setPoint(1, top_->atoms()->resinfo[p.mappedId()].nr);
}
else
{
{
GMX_RELEASE_ASSERT(top_->hasTopology(),
"Topology should have been loaded or an error given earlier");
- t_atoms atoms;
- atoms = top_->topology()->atoms;
- // Replace the pbdbinfo so that we can change it, without
- // changing the content of top_, and never leak memory.
- sfree_guard pdbinfoGuard;
+ auto atoms = top_->copyAtoms();
+ if (!atoms->havePdbInfo)
{
- t_pdbinfo *pdbinfo;
- snew(pdbinfo, atoms.nr);
- pdbinfoGuard.reset(pdbinfo);
- if (atoms.havePdbInfo)
- {
- std::memcpy(pdbinfo, atoms.pdbinfo, atoms.nr*sizeof(*pdbinfo));
- }
- else
- {
- atoms.havePdbInfo = TRUE;
- }
- atoms.pdbinfo = pdbinfo;
+ snew(atoms->pdbinfo, atoms->nr);
+ atoms->havePdbInfo = TRUE;
}
- for (int i = 0; i < atoms.nr; ++i)
+ for (int i = 0; i < atoms->nr; ++i)
{
- atoms.pdbinfo[i].occup = 0.0;
+ atoms->pdbinfo[i].occup = 0.0;
}
for (size_t g = 0; g < sel_.size(); ++g)
{
ArrayRef<const int>::const_iterator ai;
for (ai = atomIndices.begin(); ai != atomIndices.end(); ++ai)
{
- atoms.pdbinfo[*ai].occup += occupancyModule_->average(g, i);
+ atoms->pdbinfo[*ai].occup += occupancyModule_->average(g, i);
}
}
}
- t_trxframe fr;
+ std::vector<RVec> x = copyOf(top_->x());
+ t_trxframe fr;
clear_trxframe(&fr, TRUE);
fr.bAtoms = TRUE;
- fr.atoms = &atoms;
+ fr.atoms = atoms.get();
fr.bX = TRUE;
fr.bBox = TRUE;
- top_->getTopologyConf(&fr.x, fr.box);
+ fr.x = as_rvec_array(x.data());
+ top_->getBox(fr.box);
switch (pdbAtoms_)
{
case PdbAtomsSelection_Selected:
{
std::vector<int> indices;
- for (int i = 0; i < atoms.nr; ++i)
+ for (int i = 0; i < atoms->nr; ++i)
{
- if (atoms.pdbinfo[i].occup > 0.0)
+ if (atoms->pdbinfo[i].occup > 0.0)
{
indices.push_back(i);
}
if (hasTrajectory()
&& !settings_.hasFlag(TrajectoryAnalysisSettings::efUseTopX))
{
- sfree(topInfo_.xtop_);
- topInfo_.xtop_ = nullptr;
+ topInfo_.xtop_.clear();
+ }
+ if (hasTrajectory()
+ && !settings_.hasFlag(TrajectoryAnalysisSettings::efUseTopV))
+ {
+ topInfo_.vtop_.clear();
}
}
}
if (topInfo_.hasTopology())
{
- const int topologyAtomCount = topInfo_.topology()->atoms.nr;
+ const int topologyAtomCount = topInfo_.mtop()->natoms;
if (fr->natoms > topologyAtomCount)
{
const std::string message
else
{
// Prepare a frame from topology information.
- // TODO: Initialize more of the fields.
- if (frflags & (TRX_NEED_V))
- {
- GMX_THROW(NotImplementedError("Velocity reading from a topology not implemented"));
- }
if (frflags & (TRX_NEED_F))
{
GMX_THROW(InvalidInputError("Forces cannot be read from a topology"));
}
- fr->natoms = topInfo_.topology()->atoms.nr;
+ fr->natoms = topInfo_.mtop()->natoms;
fr->bX = TRUE;
snew(fr->x, fr->natoms);
- memcpy(fr->x, topInfo_.xtop_,
+ memcpy(fr->x, topInfo_.xtop_.data(),
sizeof(*fr->x) * fr->natoms);
+ if (frflags & (TRX_NEED_V))
+ {
+ if (topInfo_.vtop_.empty())
+ {
+ GMX_THROW(InvalidInputError("Velocities were required, but could not be read from the topology file"));
+ }
+ fr->bV = TRUE;
+ snew(fr->v, fr->natoms);
+ memcpy(fr->v, topInfo_.vtop_.data(),
+ sizeof(*fr->v) * fr->natoms);
+ }
fr->bBox = TRUE;
copy_mat(topInfo_.boxtop_, fr->box);
}
set_trxframe_ePBC(fr, topInfo_.ePBC());
if (topInfo_.hasTopology() && settings_.hasRmPBC())
{
- gpbc_ = gmx_rmpbc_init(&topInfo_.topology()->idef, topInfo_.ePBC(),
- fr->natoms);
+ gpbc_ = gmx_rmpbc_init(topInfo_);
}
}
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2010,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
+# Copyright (c) 2010,2012,2013,2014,2015,2016,2017,2018, 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.
sasa.cpp
select.cpp
surfacearea.cpp
+ topologyinformation.cpp
trajectory.cpp
unionfind.cpp
$<TARGET_OBJECTS:analysisdata-test-shared>)
First 10 residues from 1AKI
- 155
+ 156
1LYS N 1 3.536 2.234 -1.198
1LYS H1 2 3.612 2.288 -1.236
1LYS H2 3 3.470 2.214 -1.270
6CYS HB1 97 3.770 1.034 -0.158
6CYS HB2 98 3.834 1.072 -0.013
6CYS SG 99 3.654 0.920 0.014
- 6CYS C 100 3.775 1.305 -0.078
- 6CYS O 101 3.815 1.361 0.026
- 7GLU N 102 3.786 1.348 -0.202
- 7GLU H 103 3.740 1.300 -0.276
- 7GLU CA 104 3.868 1.469 -0.231
- 7GLU HA 105 3.960 1.455 -0.193
- 7GLU CB 106 3.878 1.485 -0.382
- 7GLU HB1 107 3.923 1.402 -0.417
- 7GLU HB2 108 3.785 1.489 -0.417
- 7GLU CG 109 3.954 1.605 -0.438
- 7GLU HG1 110 3.913 1.687 -0.399
- 7GLU HG2 111 4.049 1.598 -0.407
- 7GLU CD 112 3.958 1.624 -0.587
- 7GLU OE1 113 3.867 1.564 -0.649
- 7GLU OE2 114 4.042 1.695 -0.638
- 7GLU C 115 3.805 1.593 -0.166
- 7GLU O 116 3.874 1.673 -0.101
- 8LEU N 117 3.674 1.605 -0.182
- 8LEU H 118 3.626 1.535 -0.235
- 8LEU CA 119 3.596 1.716 -0.125
- 8LEU HA 120 3.640 1.801 -0.156
- 8LEU CB 121 3.453 1.717 -0.181
- 8LEU HB1 122 3.457 1.722 -0.281
- 8LEU HB2 123 3.406 1.633 -0.153
- 8LEU CG 124 3.372 1.835 -0.131
- 8LEU HG 125 3.378 1.842 -0.031
- 8LEU CD1 126 3.430 1.966 -0.184
- 8LEU HD11 127 3.376 2.043 -0.150
- 8LEU HD12 128 3.524 1.975 -0.153
- 8LEU HD13 129 3.427 1.965 -0.284
- 8LEU CD2 130 3.225 1.814 -0.160
- 8LEU HD21 131 3.172 1.893 -0.126
- 8LEU HD22 132 3.211 1.805 -0.258
- 8LEU HD23 133 3.193 1.731 -0.114
- 8LEU C 134 3.605 1.713 0.027
- 8LEU O 135 3.616 1.817 0.092
- 9ALA N 136 3.575 1.598 0.083
- 9ALA H 137 3.546 1.522 0.024
- 9ALA CA 138 3.584 1.576 0.228
- 9ALA HA 139 3.508 1.626 0.269
- 9ALA CB 140 3.566 1.429 0.262
- 9ALA HB1 141 3.572 1.416 0.361
- 9ALA HB2 142 3.476 1.398 0.230
- 9ALA HB3 143 3.637 1.375 0.218
- 9ALA C 144 3.714 1.631 0.284
- 9ALA O 145 3.715 1.698 0.390
- 10ALA N 146 3.827 1.598 0.220
- 10ALA H 147 3.820 1.539 0.140
- 10ALA CA 148 3.961 1.643 0.262
- 10ALA HA 149 3.969 1.619 0.358
- 10ALA CB 150 4.071 1.571 0.184
- 10ALA HB1 151 4.160 1.603 0.215
- 10ALA HB2 152 4.064 1.472 0.201
- 10ALA HB3 153 4.060 1.589 0.086
- 10ALA C 154 3.974 1.794 0.246
- 10ALA O 155 4.019 1.850 0.347
+ 6CYS HG 100 3.707 0.836 0.012
+ 6CYS C 101 3.775 1.305 -0.078
+ 6CYS O 102 3.815 1.361 0.026
+ 7GLU N 103 3.786 1.348 -0.202
+ 7GLU H 104 3.740 1.300 -0.276
+ 7GLU CA 105 3.868 1.469 -0.231
+ 7GLU HA 106 3.960 1.455 -0.193
+ 7GLU CB 107 3.878 1.485 -0.382
+ 7GLU HB1 108 3.923 1.402 -0.417
+ 7GLU HB2 109 3.785 1.489 -0.417
+ 7GLU CG 110 3.954 1.605 -0.438
+ 7GLU HG1 111 3.913 1.687 -0.399
+ 7GLU HG2 112 4.049 1.598 -0.407
+ 7GLU CD 113 3.958 1.624 -0.587
+ 7GLU OE1 114 3.867 1.564 -0.649
+ 7GLU OE2 115 4.042 1.695 -0.638
+ 7GLU C 116 3.805 1.593 -0.166
+ 7GLU O 117 3.874 1.673 -0.101
+ 8LEU N 118 3.674 1.605 -0.182
+ 8LEU H 119 3.626 1.535 -0.235
+ 8LEU CA 120 3.596 1.716 -0.125
+ 8LEU HA 121 3.640 1.801 -0.156
+ 8LEU CB 122 3.453 1.717 -0.181
+ 8LEU HB1 123 3.457 1.722 -0.281
+ 8LEU HB2 124 3.406 1.633 -0.153
+ 8LEU CG 125 3.372 1.835 -0.131
+ 8LEU HG 126 3.378 1.842 -0.031
+ 8LEU CD1 127 3.430 1.966 -0.184
+ 8LEU HD11 128 3.376 2.043 -0.150
+ 8LEU HD12 129 3.524 1.975 -0.153
+ 8LEU HD13 130 3.427 1.965 -0.284
+ 8LEU CD2 131 3.225 1.814 -0.160
+ 8LEU HD21 132 3.172 1.893 -0.126
+ 8LEU HD22 133 3.211 1.805 -0.258
+ 8LEU HD23 134 3.193 1.731 -0.114
+ 8LEU C 135 3.605 1.713 0.027
+ 8LEU O 136 3.616 1.817 0.092
+ 9ALA N 137 3.575 1.598 0.083
+ 9ALA H 138 3.546 1.522 0.024
+ 9ALA CA 139 3.584 1.576 0.228
+ 9ALA HA 140 3.508 1.626 0.269
+ 9ALA CB 141 3.566 1.429 0.262
+ 9ALA HB1 142 3.572 1.416 0.361
+ 9ALA HB2 143 3.476 1.398 0.230
+ 9ALA HB3 144 3.637 1.375 0.218
+ 9ALA C 145 3.714 1.631 0.284
+ 9ALA O 146 3.715 1.698 0.390
+ 10ALA N 147 3.827 1.598 0.220
+ 10ALA H 148 3.820 1.539 0.140
+ 10ALA CA 149 3.961 1.643 0.262
+ 10ALA HA 150 3.969 1.619 0.358
+ 10ALA CB 151 4.071 1.571 0.184
+ 10ALA HB1 152 4.160 1.603 0.215
+ 10ALA HB2 153 4.064 1.472 0.201
+ 10ALA HB3 154 4.060 1.589 0.086
+ 10ALA C 155 3.974 1.794 0.246
+ 10ALA O 156 4.019 1.850 0.347
5.90620 6.84510 3.05170
--- /dev/null
+TITLE First 10 residues from 1AKI
+REMARK THIS IS A SIMULATION BOX
+CRYST1 59.062 68.451 30.517 90.00 90.00 90.00 P 1 1
+MODEL 1
+ATOM 1 N LYS B 1 35.360 22.340 -11.980 1.00 0.00 N
+ATOM 2 H1 LYS B 1 36.120 22.880 -12.360 1.00 0.00 H
+ATOM 3 H2 LYS B 1 34.700 22.140 -12.700 1.00 0.00 H
+ATOM 4 H3 LYS B 1 34.920 22.860 -11.250 1.00 0.00 H
+ATOM 5 CA LYS B 1 35.890 21.070 -11.430 1.00 0.00 C
+ATOM 6 HA LYS B 1 36.330 20.550 -12.160 1.00 0.00 H
+ATOM 7 CB LYS B 1 36.870 21.440 -10.310 1.00 0.00 C
+ATOM 8 HB1 LYS B 1 37.630 21.950 -10.700 1.00 0.00 H
+ATOM 9 HB2 LYS B 1 36.390 22.010 -9.640 1.00 0.00 H
+ATOM 10 CG LYS B 1 37.450 20.250 -9.560 1.00 0.00 C
+ATOM 11 HG1 LYS B 1 36.760 19.890 -8.940 1.00 0.00 H
+ATOM 12 HG2 LYS B 1 37.700 19.540 -10.230 1.00 0.00 H
+ATOM 13 CD LYS B 1 38.690 20.650 -8.770 1.00 0.00 C
+ATOM 14 HD1 LYS B 1 39.450 20.830 -9.400 1.00 0.00 H
+ATOM 15 HD2 LYS B 1 38.490 21.470 -8.240 1.00 0.00 H
+ATOM 16 CE LYS B 1 39.060 19.510 -7.840 1.00 0.00 C
+ATOM 17 HE1 LYS B 1 38.410 19.460 -7.080 1.00 0.00 H
+ATOM 18 HE2 LYS B 1 39.060 18.640 -8.330 1.00 0.00 H
+ATOM 19 NZ LYS B 1 40.420 19.770 -7.300 1.00 0.00 N
+ATOM 20 HZ1 LYS B 1 40.690 19.030 -6.680 1.00 0.00 H
+ATOM 21 HZ2 LYS B 1 41.080 19.820 -8.060 1.00 0.00 H
+ATOM 22 HZ3 LYS B 1 40.420 20.640 -6.800 1.00 0.00 H
+ATOM 23 C LYS B 1 34.740 20.260 -10.840 1.00 0.00 C
+ATOM 24 O LYS B 1 33.950 20.810 -10.080 1.00 0.00 O
+ATOM 25 N VAL B 2 34.740 18.960 -11.040 1.00 0.00 N
+ATOM 26 H VAL B 2 35.360 18.600 -11.740 1.00 0.00 H
+ATOM 27 CA VAL B 2 33.900 18.000 -10.330 1.00 0.00 C
+ATOM 28 HA VAL B 2 33.170 18.520 -9.900 1.00 0.00 H
+ATOM 29 CB VAL B 2 33.140 17.030 -11.230 1.00 0.00 C
+ATOM 30 HB VAL B 2 33.860 16.520 -11.700 1.00 0.00 H
+ATOM 31 CG1 VAL B 2 32.250 16.080 -10.430 1.00 0.00 C
+ATOM 32 1HG1 VAL B 2 31.770 15.470 -11.060 1.00 0.00 H
+ATOM 33 2HG1 VAL B 2 32.820 15.550 -9.810 1.00 0.00 H
+ATOM 34 3HG1 VAL B 2 31.580 16.610 -9.910 1.00 0.00 H
+ATOM 35 CG2 VAL B 2 32.290 17.710 -12.290 1.00 0.00 C
+ATOM 36 1HG2 VAL B 2 31.830 17.020 -12.840 1.00 0.00 H
+ATOM 37 2HG2 VAL B 2 31.620 18.300 -11.850 1.00 0.00 H
+ATOM 38 3HG2 VAL B 2 32.880 18.270 -12.880 1.00 0.00 H
+ATOM 39 C VAL B 2 34.800 17.310 -9.290 1.00 0.00 C
+ATOM 40 O VAL B 2 35.760 16.610 -9.660 1.00 0.00 O
+ATOM 41 N PHE B 3 34.490 17.550 -8.040 1.00 0.00 N
+ATOM 42 H PHE B 3 33.750 18.190 -7.840 1.00 0.00 H
+ATOM 43 CA PHE B 3 35.190 16.900 -6.920 1.00 0.00 C
+ATOM 44 HA PHE B 3 36.150 16.970 -7.170 1.00 0.00 H
+ATOM 45 CB PHE B 3 34.970 17.630 -5.590 1.00 0.00 C
+ATOM 46 HB1 PHE B 3 34.050 18.020 -5.580 1.00 0.00 H
+ATOM 47 HB2 PHE B 3 35.060 16.980 -4.840 1.00 0.00 H
+ATOM 48 CG PHE B 3 35.940 18.740 -5.380 1.00 0.00 C
+ATOM 49 CD1 PHE B 3 35.670 20.050 -5.800 1.00 0.00 C
+ATOM 50 HD1 PHE B 3 34.810 20.250 -6.270 1.00 0.00 H
+ATOM 51 CD2 PHE B 3 37.000 18.560 -4.470 1.00 0.00 C
+ATOM 52 HD2 PHE B 3 37.130 17.660 -4.050 1.00 0.00 H
+ATOM 53 CE1 PHE B 3 36.580 21.080 -5.570 1.00 0.00 C
+ATOM 54 HE1 PHE B 3 36.480 21.950 -6.040 1.00 0.00 H
+ATOM 55 CE2 PHE B 3 37.870 19.590 -4.160 1.00 0.00 C
+ATOM 56 HE2 PHE B 3 38.660 19.420 -3.570 1.00 0.00 H
+ATOM 57 CZ PHE B 3 37.640 20.870 -4.670 1.00 0.00 C
+ATOM 58 HZ PHE B 3 38.220 21.640 -4.390 1.00 0.00 H
+ATOM 59 C PHE B 3 34.740 15.440 -6.770 1.00 0.00 C
+ATOM 60 O PHE B 3 33.520 15.160 -6.860 1.00 0.00 O
+ATOM 61 N GLY B 4 35.720 14.640 -6.330 1.00 0.00 N
+ATOM 62 H GLY B 4 36.670 14.950 -6.320 1.00 0.00 H
+ATOM 63 CA GLY B 4 35.370 13.280 -5.870 1.00 0.00 C
+ATOM 64 HA1 GLY B 4 34.620 12.920 -6.430 1.00 0.00 H
+ATOM 65 HA2 GLY B 4 36.160 12.680 -5.940 1.00 0.00 H
+ATOM 66 C GLY B 4 34.920 13.420 -4.420 1.00 0.00 C
+ATOM 67 O GLY B 4 35.300 14.400 -3.780 1.00 0.00 O
+ATOM 68 N ARG B 5 34.050 12.540 -3.970 1.00 0.00 N
+ATOM 69 H ARG B 5 33.710 11.840 -4.600 1.00 0.00 H
+ATOM 70 CA ARG B 5 33.560 12.540 -2.590 1.00 0.00 C
+ATOM 71 HA ARG B 5 32.980 13.340 -2.520 1.00 0.00 H
+ATOM 72 CB ARG B 5 32.760 11.260 -2.330 1.00 0.00 C
+ATOM 73 HB1 ARG B 5 32.000 11.220 -2.970 1.00 0.00 H
+ATOM 74 HB2 ARG B 5 33.360 10.470 -2.470 1.00 0.00 H
+ATOM 75 CG ARG B 5 32.210 11.200 -0.920 1.00 0.00 C
+ATOM 76 HG1 ARG B 5 32.970 11.170 -0.270 1.00 0.00 H
+ATOM 77 HG2 ARG B 5 31.650 12.010 -0.750 1.00 0.00 H
+ATOM 78 CD ARG B 5 31.380 10.000 -0.720 1.00 0.00 C
+ATOM 79 HD1 ARG B 5 31.040 9.990 0.220 1.00 0.00 H
+ATOM 80 HD2 ARG B 5 30.600 10.050 -1.350 1.00 0.00 H
+ATOM 81 NE ARG B 5 32.060 8.750 -0.960 1.00 0.00 N
+ATOM 82 HE ARG B 5 32.020 8.400 -1.890 1.00 0.00 H
+ATOM 83 CZ ARG B 5 32.730 8.010 -0.100 1.00 0.00 C
+ATOM 84 NH1 ARG B 5 32.840 8.330 1.190 1.00 0.00 N
+ATOM 85 1HH1 ARG B 5 32.390 9.160 1.530 1.00 0.00 H
+ATOM 86 2HH1 ARG B 5 33.360 7.750 1.810 1.00 0.00 H
+ATOM 87 NH2 ARG B 5 33.250 6.840 -0.530 1.00 0.00 N
+ATOM 88 1HH2 ARG B 5 33.110 6.550 -1.470 1.00 0.00 H
+ATOM 89 2HH2 ARG B 5 33.760 6.260 0.100 1.00 0.00 H
+ATOM 90 C ARG B 5 34.670 12.730 -1.560 1.00 0.00 C
+ATOM 91 O ARG B 5 34.670 13.650 -0.700 1.00 0.00 O
+ATOM 92 N CYS B 6 35.670 11.850 -1.610 1.00 0.00 N
+ATOM 93 H CYS B 6 35.670 11.160 -2.330 1.00 0.00 H
+ATOM 94 CA CYS B 6 36.780 11.870 -0.650 1.00 0.00 C
+ATOM 95 HA CYS B 6 36.310 12.020 0.220 1.00 0.00 H
+ATOM 96 CB CYS B 6 37.490 10.530 -0.620 1.00 0.00 C
+ATOM 97 HB1 CYS B 6 37.700 10.340 -1.580 1.00 0.00 H
+ATOM 98 HB2 CYS B 6 38.340 10.720 -0.130 1.00 0.00 H
+ATOM 99 SG CYS B 6 36.540 9.200 0.140 1.00 0.00 S
+ATOM 100 HG CYS B 6 37.075 8.355 0.120 1.00 0.00 H
+ATOM 101 C CYS B 6 37.750 13.050 -0.780 1.00 0.00 C
+ATOM 102 O CYS B 6 38.150 13.610 0.260 1.00 0.00 O
+ATOM 103 N GLU B 7 37.860 13.480 -2.020 1.00 0.00 N
+ATOM 104 H GLU B 7 37.400 13.000 -2.760 1.00 0.00 H
+ATOM 105 CA GLU B 7 38.680 14.690 -2.310 1.00 0.00 C
+ATOM 106 HA GLU B 7 39.600 14.550 -1.930 1.00 0.00 H
+ATOM 107 CB GLU B 7 38.780 14.850 -3.820 1.00 0.00 C
+ATOM 108 HB1 GLU B 7 39.230 14.020 -4.170 1.00 0.00 H
+ATOM 109 HB2 GLU B 7 37.850 14.890 -4.170 1.00 0.00 H
+ATOM 110 CG GLU B 7 39.540 16.050 -4.380 1.00 0.00 C
+ATOM 111 HG1 GLU B 7 39.130 16.870 -3.990 1.00 0.00 H
+ATOM 112 HG2 GLU B 7 40.490 15.980 -4.070 1.00 0.00 H
+ATOM 113 CD GLU B 7 39.580 16.240 -5.870 1.00 0.00 C
+ATOM 114 OE1 GLU B 7 38.670 15.640 -6.490 1.00 0.00 O
+ATOM 115 OE2 GLU B 7 40.420 16.950 -6.380 1.00 0.00 O
+ATOM 116 C GLU B 7 38.050 15.930 -1.660 1.00 0.00 C
+ATOM 117 O GLU B 7 38.740 16.730 -1.010 1.00 0.00 O
+ATOM 118 N LEU B 8 36.740 16.050 -1.820 1.00 0.00 N
+ATOM 119 H LEU B 8 36.260 15.350 -2.350 1.00 0.00 H
+ATOM 120 CA LEU B 8 35.960 17.160 -1.250 1.00 0.00 C
+ATOM 121 HA LEU B 8 36.400 18.010 -1.560 1.00 0.00 H
+ATOM 122 CB LEU B 8 34.530 17.170 -1.810 1.00 0.00 C
+ATOM 123 HB1 LEU B 8 34.570 17.220 -2.810 1.00 0.00 H
+ATOM 124 HB2 LEU B 8 34.060 16.330 -1.530 1.00 0.00 H
+ATOM 125 CG LEU B 8 33.720 18.350 -1.310 1.00 0.00 C
+ATOM 126 HG LEU B 8 33.780 18.420 -0.310 1.00 0.00 H
+ATOM 127 CD1 LEU B 8 34.300 19.660 -1.840 1.00 0.00 C
+ATOM 128 1HD1 LEU B 8 33.760 20.430 -1.500 1.00 0.00 H
+ATOM 129 2HD1 LEU B 8 35.240 19.750 -1.530 1.00 0.00 H
+ATOM 130 3HD1 LEU B 8 34.270 19.650 -2.840 1.00 0.00 H
+ATOM 131 CD2 LEU B 8 32.250 18.140 -1.600 1.00 0.00 C
+ATOM 132 1HD2 LEU B 8 31.720 18.930 -1.260 1.00 0.00 H
+ATOM 133 2HD2 LEU B 8 32.110 18.050 -2.580 1.00 0.00 H
+ATOM 134 3HD2 LEU B 8 31.930 17.310 -1.140 1.00 0.00 H
+ATOM 135 C LEU B 8 36.050 17.130 0.270 1.00 0.00 C
+ATOM 136 O LEU B 8 36.160 18.170 0.920 1.00 0.00 O
+ATOM 137 N ALA B 9 35.750 15.980 0.830 1.00 0.00 N
+ATOM 138 H ALA B 9 35.460 15.220 0.240 1.00 0.00 H
+ATOM 139 CA ALA B 9 35.840 15.760 2.280 1.00 0.00 C
+ATOM 140 HA ALA B 9 35.080 16.260 2.690 1.00 0.00 H
+ATOM 141 CB ALA B 9 35.660 14.290 2.620 1.00 0.00 C
+ATOM 142 HB1 ALA B 9 35.720 14.160 3.610 1.00 0.00 H
+ATOM 143 HB2 ALA B 9 34.760 13.980 2.300 1.00 0.00 H
+ATOM 144 HB3 ALA B 9 36.370 13.750 2.180 1.00 0.00 H
+ATOM 145 C ALA B 9 37.140 16.310 2.840 1.00 0.00 C
+ATOM 146 O ALA B 9 37.150 16.980 3.900 1.00 0.00 O
+ATOM 147 N ALA B 10 38.270 15.980 2.200 1.00 0.00 N
+ATOM 148 H ALA B 10 38.200 15.390 1.400 1.00 0.00 H
+ATOM 149 CA ALA B 10 39.610 16.430 2.620 1.00 0.00 C
+ATOM 150 HA ALA B 10 39.690 16.190 3.580 1.00 0.00 H
+ATOM 151 CB ALA B 10 40.710 15.710 1.840 1.00 0.00 C
+ATOM 152 HB1 ALA B 10 41.600 16.030 2.150 1.00 0.00 H
+ATOM 153 HB2 ALA B 10 40.640 14.720 2.010 1.00 0.00 H
+ATOM 154 HB3 ALA B 10 40.600 15.890 0.860 1.00 0.00 H
+ATOM 155 C ALA B 10 39.740 17.940 2.460 1.00 0.00 C
+ATOM 156 O ALA B 10 40.190 18.500 3.470 1.00 0.00 O
+TER
+ENDMDL
--- /dev/null
+; Include forcefield parameters
+#include "oplsaa.ff/forcefield.itp"
+
+[ moleculetype ]
+; Name nrexcl
+Protein_chain_B 3
+
+[ atoms ]
+; nr type resnr residue atom cgnr charge mass typeB chargeB massB
+; residue 1 LYS rtp LYSH q +2.0
+ 1 opls_287 1 LYS N 1 -0.3 14.0027 ; qtot -0.3
+ 2 opls_290 1 LYS H1 1 0.33 1.008 ; qtot 0.03
+ 3 opls_290 1 LYS H2 1 0.33 1.008 ; qtot 0.36
+ 4 opls_290 1 LYS H3 1 0.33 1.008 ; qtot 0.69
+ 5 opls_293B 1 LYS CA 1 0.25 12.011 ; qtot 0.94
+ 6 opls_140 1 LYS HA 1 0.06 1.008 ; qtot 1
+ 7 opls_136 1 LYS CB 2 -0.12 12.011 ; qtot 0.88
+ 8 opls_140 1 LYS HB1 2 0.06 1.008 ; qtot 0.94
+ 9 opls_140 1 LYS HB2 2 0.06 1.008 ; qtot 1
+ 10 opls_136 1 LYS CG 3 -0.12 12.011 ; qtot 0.88
+ 11 opls_140 1 LYS HG1 3 0.06 1.008 ; qtot 0.94
+ 12 opls_140 1 LYS HG2 3 0.06 1.008 ; qtot 1
+ 13 opls_136 1 LYS CD 4 -0.12 12.011 ; qtot 0.88
+ 14 opls_140 1 LYS HD1 4 0.06 1.008 ; qtot 0.94
+ 15 opls_140 1 LYS HD2 4 0.06 1.008 ; qtot 1
+ 16 opls_292 1 LYS CE 5 0.19 12.011 ; qtot 1.19
+ 17 opls_140 1 LYS HE1 5 0.06 1.008 ; qtot 1.25
+ 18 opls_140 1 LYS HE2 5 0.06 1.008 ; qtot 1.31
+ 19 opls_287 1 LYS NZ 6 -0.3 14.0067 ; qtot 1.01
+ 20 opls_290 1 LYS HZ1 6 0.33 1.008 ; qtot 1.34
+ 21 opls_290 1 LYS HZ2 6 0.33 1.008 ; qtot 1.67
+ 22 opls_290 1 LYS HZ3 6 0.33 1.008 ; qtot 2
+ 23 opls_235 1 LYS C 7 0.5 12.011 ; qtot 2.5
+ 24 opls_236 1 LYS O 7 -0.5 15.9994 ; qtot 2
+; residue 2 VAL rtp VAL q 0.0
+ 25 opls_238 2 VAL N 8 -0.5 14.0067 ; qtot 1.5
+ 26 opls_241 2 VAL H 8 0.3 1.008 ; qtot 1.8
+ 27 opls_224B 2 VAL CA 8 0.14 12.011 ; qtot 1.94
+ 28 opls_140 2 VAL HA 8 0.06 1.008 ; qtot 2
+ 29 opls_137 2 VAL CB 9 -0.06 12.011 ; qtot 1.94
+ 30 opls_140 2 VAL HB 9 0.06 1.008 ; qtot 2
+ 31 opls_135 2 VAL CG1 10 -0.18 12.011 ; qtot 1.82
+ 32 opls_140 2 VAL HG11 10 0.06 1.008 ; qtot 1.88
+ 33 opls_140 2 VAL HG12 10 0.06 1.008 ; qtot 1.94
+ 34 opls_140 2 VAL HG13 10 0.06 1.008 ; qtot 2
+ 35 opls_135 2 VAL CG2 11 -0.18 12.011 ; qtot 1.82
+ 36 opls_140 2 VAL HG21 11 0.06 1.008 ; qtot 1.88
+ 37 opls_140 2 VAL HG22 11 0.06 1.008 ; qtot 1.94
+ 38 opls_140 2 VAL HG23 11 0.06 1.008 ; qtot 2
+ 39 opls_235 2 VAL C 12 0.5 12.011 ; qtot 2.5
+ 40 opls_236 2 VAL O 12 -0.5 15.9994 ; qtot 2
+; residue 3 PHE rtp PHE q 0.0
+ 41 opls_238 3 PHE N 13 -0.5 14.0067 ; qtot 1.5
+ 42 opls_241 3 PHE H 13 0.3 1.008 ; qtot 1.8
+ 43 opls_224B 3 PHE CA 13 0.14 12.011 ; qtot 1.94
+ 44 opls_140 3 PHE HA 13 0.06 1.008 ; qtot 2
+ 45 opls_149 3 PHE CB 14 -0.005 12.011 ; qtot 1.995
+ 46 opls_140 3 PHE HB1 14 0.06 1.008 ; qtot 2.055
+ 47 opls_140 3 PHE HB2 14 0.06 1.008 ; qtot 2.115
+ 48 opls_145 3 PHE CG 14 -0.115 12.011 ; qtot 2
+ 49 opls_145 3 PHE CD1 15 -0.115 12.011 ; qtot 1.885
+ 50 opls_146 3 PHE HD1 15 0.115 1.008 ; qtot 2
+ 51 opls_145 3 PHE CD2 16 -0.115 12.011 ; qtot 1.885
+ 52 opls_146 3 PHE HD2 16 0.115 1.008 ; qtot 2
+ 53 opls_145 3 PHE CE1 17 -0.115 12.011 ; qtot 1.885
+ 54 opls_146 3 PHE HE1 17 0.115 1.008 ; qtot 2
+ 55 opls_145 3 PHE CE2 18 -0.115 12.011 ; qtot 1.885
+ 56 opls_146 3 PHE HE2 18 0.115 1.008 ; qtot 2
+ 57 opls_145 3 PHE CZ 19 -0.115 12.011 ; qtot 1.885
+ 58 opls_146 3 PHE HZ 19 0.115 1.008 ; qtot 2
+ 59 opls_235 3 PHE C 20 0.5 12.011 ; qtot 2.5
+ 60 opls_236 3 PHE O 20 -0.5 15.9994 ; qtot 2
+; residue 4 GLY rtp GLY q 0.0
+ 61 opls_238 4 GLY N 21 -0.5 14.0067 ; qtot 1.5
+ 62 opls_241 4 GLY H 21 0.3 1.008 ; qtot 1.8
+ 63 opls_223B 4 GLY CA 21 0.08 12.011 ; qtot 1.88
+ 64 opls_140 4 GLY HA1 21 0.06 1.008 ; qtot 1.94
+ 65 opls_140 4 GLY HA2 21 0.06 1.008 ; qtot 2
+ 66 opls_235 4 GLY C 22 0.5 12.011 ; qtot 2.5
+ 67 opls_236 4 GLY O 22 -0.5 15.9994 ; qtot 2
+; residue 5 ARG rtp ARG q +1.0
+ 68 opls_238 5 ARG N 23 -0.5 14.0067 ; qtot 1.5
+ 69 opls_241 5 ARG H 23 0.3 1.008 ; qtot 1.8
+ 70 opls_224B 5 ARG CA 23 0.14 12.011 ; qtot 1.94
+ 71 opls_140 5 ARG HA 23 0.06 1.008 ; qtot 2
+ 72 opls_136 5 ARG CB 24 -0.12 12.011 ; qtot 1.88
+ 73 opls_140 5 ARG HB1 24 0.06 1.008 ; qtot 1.94
+ 74 opls_140 5 ARG HB2 24 0.06 1.008 ; qtot 2
+ 75 opls_308 5 ARG CG 25 -0.05 12.011 ; qtot 1.95
+ 76 opls_140 5 ARG HG1 25 0.06 1.008 ; qtot 2.01
+ 77 opls_140 5 ARG HG2 25 0.06 1.008 ; qtot 2.07
+ 78 opls_307 5 ARG CD 26 0.19 12.011 ; qtot 2.26
+ 79 opls_140 5 ARG HD1 26 0.06 1.008 ; qtot 2.32
+ 80 opls_140 5 ARG HD2 26 0.06 1.008 ; qtot 2.38
+ 81 opls_303 5 ARG NE 27 -0.7 14.0067 ; qtot 1.68
+ 82 opls_304 5 ARG HE 27 0.44 1.008 ; qtot 2.12
+ 83 opls_302 5 ARG CZ 27 0.64 12.011 ; qtot 2.76
+ 84 opls_300 5 ARG NH1 28 -0.8 14.0067 ; qtot 1.96
+ 85 opls_301 5 ARG HH11 28 0.46 1.008 ; qtot 2.42
+ 86 opls_301 5 ARG HH12 28 0.46 1.008 ; qtot 2.88
+ 87 opls_300 5 ARG NH2 29 -0.8 14.0067 ; qtot 2.08
+ 88 opls_301 5 ARG HH21 29 0.46 1.008 ; qtot 2.54
+ 89 opls_301 5 ARG HH22 29 0.46 1.008 ; qtot 3
+ 90 opls_235 5 ARG C 30 0.5 12.011 ; qtot 3.5
+ 91 opls_236 5 ARG O 30 -0.5 15.9994 ; qtot 3
+; residue 6 CYS rtp CYSH q 0.0
+ 92 opls_238 6 CYS N 31 -0.5 14.0067 ; qtot 2.5
+ 93 opls_241 6 CYS H 31 0.3 1.008 ; qtot 2.8
+ 94 opls_224B 6 CYS CA 31 0.14 12.011 ; qtot 2.94
+ 95 opls_140 6 CYS HA 31 0.06 1.008 ; qtot 3
+ 96 opls_206 6 CYS CB 32 0.06 12.011 ; qtot 3.06
+ 97 opls_140 6 CYS HB1 32 0.06 1.008 ; qtot 3.12
+ 98 opls_140 6 CYS HB2 32 0.06 1.008 ; qtot 3.18
+ 99 opls_200 6 CYS SG 33 -0.335 32.06 ; qtot 2.845
+ 100 opls_204 6 CYS HG 33 0.155 1.008 ; qtot 3
+ 101 opls_235 6 CYS C 34 0.5 12.011 ; qtot 3.5
+ 102 opls_236 6 CYS O 34 -0.5 15.9994 ; qtot 3
+; residue 7 GLU rtp GLU q -1.0
+ 103 opls_238 7 GLU N 35 -0.5 14.0067 ; qtot 2.5
+ 104 opls_241 7 GLU H 35 0.3 1.008 ; qtot 2.8
+ 105 opls_224B 7 GLU CA 35 0.14 12.011 ; qtot 2.94
+ 106 opls_140 7 GLU HA 35 0.06 1.008 ; qtot 3
+ 107 opls_136 7 GLU CB 36 -0.12 12.011 ; qtot 2.88
+ 108 opls_140 7 GLU HB1 36 0.06 1.008 ; qtot 2.94
+ 109 opls_140 7 GLU HB2 36 0.06 1.008 ; qtot 3
+ 110 opls_274 7 GLU CG 37 -0.22 12.011 ; qtot 2.78
+ 111 opls_140 7 GLU HG1 37 0.06 1.008 ; qtot 2.84
+ 112 opls_140 7 GLU HG2 37 0.06 1.008 ; qtot 2.9
+ 113 opls_271 7 GLU CD 38 0.7 12.011 ; qtot 3.6
+ 114 opls_272 7 GLU OE1 38 -0.8 15.9994 ; qtot 2.8
+ 115 opls_272 7 GLU OE2 38 -0.8 15.9994 ; qtot 2
+ 116 opls_235 7 GLU C 39 0.5 12.011 ; qtot 2.5
+ 117 opls_236 7 GLU O 39 -0.5 15.9994 ; qtot 2
+; residue 8 LEU rtp LEU q 0.0
+ 118 opls_238 8 LEU N 40 -0.5 14.0067 ; qtot 1.5
+ 119 opls_241 8 LEU H 40 0.3 1.008 ; qtot 1.8
+ 120 opls_224B 8 LEU CA 40 0.14 12.011 ; qtot 1.94
+ 121 opls_140 8 LEU HA 40 0.06 1.008 ; qtot 2
+ 122 opls_136 8 LEU CB 41 -0.12 12.011 ; qtot 1.88
+ 123 opls_140 8 LEU HB1 41 0.06 1.008 ; qtot 1.94
+ 124 opls_140 8 LEU HB2 41 0.06 1.008 ; qtot 2
+ 125 opls_137 8 LEU CG 42 -0.06 12.011 ; qtot 1.94
+ 126 opls_140 8 LEU HG 42 0.06 1.008 ; qtot 2
+ 127 opls_135 8 LEU CD1 43 -0.18 12.011 ; qtot 1.82
+ 128 opls_140 8 LEU HD11 43 0.06 1.008 ; qtot 1.88
+ 129 opls_140 8 LEU HD12 43 0.06 1.008 ; qtot 1.94
+ 130 opls_140 8 LEU HD13 43 0.06 1.008 ; qtot 2
+ 131 opls_135 8 LEU CD2 44 -0.18 12.011 ; qtot 1.82
+ 132 opls_140 8 LEU HD21 44 0.06 1.008 ; qtot 1.88
+ 133 opls_140 8 LEU HD22 44 0.06 1.008 ; qtot 1.94
+ 134 opls_140 8 LEU HD23 44 0.06 1.008 ; qtot 2
+ 135 opls_235 8 LEU C 45 0.5 12.011 ; qtot 2.5
+ 136 opls_236 8 LEU O 45 -0.5 15.9994 ; qtot 2
+; residue 9 ALA rtp ALA q 0.0
+ 137 opls_238 9 ALA N 46 -0.5 14.0067 ; qtot 1.5
+ 138 opls_241 9 ALA H 46 0.3 1.008 ; qtot 1.8
+ 139 opls_224B 9 ALA CA 46 0.14 12.011 ; qtot 1.94
+ 140 opls_140 9 ALA HA 46 0.06 1.008 ; qtot 2
+ 141 opls_135 9 ALA CB 47 -0.18 12.011 ; qtot 1.82
+ 142 opls_140 9 ALA HB1 47 0.06 1.008 ; qtot 1.88
+ 143 opls_140 9 ALA HB2 47 0.06 1.008 ; qtot 1.94
+ 144 opls_140 9 ALA HB3 47 0.06 1.008 ; qtot 2
+ 145 opls_235 9 ALA C 48 0.5 12.011 ; qtot 2.5
+ 146 opls_236 9 ALA O 48 -0.5 15.9994 ; qtot 2
+; residue 10 ALA rtp ALA q 0.0
+ 147 opls_238 10 ALA N 49 -0.5 14.0067 ; qtot 1.5
+ 148 opls_241 10 ALA H 49 0.3 1.008 ; qtot 1.8
+ 149 opls_224B 10 ALA CA 49 0.14 12.011 ; qtot 1.94
+ 150 opls_140 10 ALA HA 49 0.06 1.008 ; qtot 2
+ 151 opls_135 10 ALA CB 50 -0.18 12.011 ; qtot 1.82
+ 152 opls_140 10 ALA HB1 50 0.06 1.008 ; qtot 1.88
+ 153 opls_140 10 ALA HB2 50 0.06 1.008 ; qtot 1.94
+ 154 opls_140 10 ALA HB3 50 0.06 1.008 ; qtot 2
+ 155 opls_235 10 ALA C 51 0.5 12.011 ; qtot 2.5
+ 156 opls_236 10 ALA O 51 -0.5 15.9994 ; qtot 2
+
+[ bonds ]
+; ai aj funct c0 c1 c2 c3
+ 1 2 1
+ 1 3 1
+ 1 4 1
+ 1 5 1
+ 5 6 1
+ 5 7 1
+ 5 23 1
+ 7 8 1
+ 7 9 1
+ 7 10 1
+ 10 11 1
+ 10 12 1
+ 10 13 1
+ 13 14 1
+ 13 15 1
+ 13 16 1
+ 16 17 1
+ 16 18 1
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+[ dihedrals ]
+; ai aj ak al funct c0 c1 c2 c3
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+
+[ system ]
+; Name
+First 10 residues from 1AKI
+
+[ molecules ]
+; Compound #mols
+Protein_chain_B 1
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ATOM 97 HB1 CYS 6 37.700 10.340 -1.580 1.00 0.00
ATOM 98 HB2 CYS 6 38.340 10.720 -0.130 1.00 0.00
ATOM 99 SG CYS 6 36.540 9.200 0.140 1.00 0.00
-ATOM 100 C CYS 6 37.750 13.050 -0.780 1.00 0.00
-ATOM 101 O CYS 6 38.150 13.610 0.260 1.00 0.00
-ATOM 102 N GLU 7 37.860 13.480 -2.020 1.00 0.00
-ATOM 103 H GLU 7 37.400 13.000 -2.760 1.00 0.00
-ATOM 104 CA GLU 7 38.680 14.690 -2.310 1.00 0.00
-ATOM 105 HA GLU 7 39.600 14.550 -1.930 1.00 0.00
-ATOM 106 CB GLU 7 38.780 14.850 -3.820 1.00 0.00
-ATOM 107 HB1 GLU 7 39.230 14.020 -4.170 1.00 0.00
-ATOM 108 HB2 GLU 7 37.850 14.890 -4.170 1.00 0.00
-ATOM 109 CG GLU 7 39.540 16.050 -4.380 1.00 0.00
-ATOM 110 HG1 GLU 7 39.130 16.870 -3.990 1.00 0.00
-ATOM 111 HG2 GLU 7 40.490 15.980 -4.070 1.00 0.00
-ATOM 112 CD GLU 7 39.580 16.240 -5.870 1.00 0.00
-ATOM 113 OE1 GLU 7 38.670 15.640 -6.490 1.00 0.00
-ATOM 114 OE2 GLU 7 40.420 16.950 -6.380 1.00 0.00
-ATOM 115 C GLU 7 38.050 15.930 -1.660 1.00 0.00
-ATOM 116 O GLU 7 38.740 16.730 -1.010 1.00 0.00
-ATOM 117 N LEU 8 36.740 16.050 -1.820 1.00 0.00
-ATOM 118 H LEU 8 36.260 15.350 -2.350 1.00 0.00
-ATOM 119 CA LEU 8 35.960 17.160 -1.250 1.00 0.00
-ATOM 120 HA LEU 8 36.400 18.010 -1.560 1.00 0.00
-ATOM 121 CB LEU 8 34.530 17.170 -1.810 1.00 0.00
-ATOM 122 HB1 LEU 8 34.570 17.220 -2.810 1.00 0.00
-ATOM 123 HB2 LEU 8 34.060 16.330 -1.530 1.00 0.00
-ATOM 124 CG LEU 8 33.720 18.350 -1.310 1.00 0.00
-ATOM 125 HG LEU 8 33.780 18.420 -0.310 1.00 0.00
-ATOM 126 CD1 LEU 8 34.300 19.660 -1.840 1.00 0.00
-ATOM 127 1HD1 LEU 8 33.760 20.430 -1.500 1.00 0.00
-ATOM 128 2HD1 LEU 8 35.240 19.750 -1.530 1.00 0.00
-ATOM 129 3HD1 LEU 8 34.270 19.650 -2.840 1.00 0.00
-ATOM 130 CD2 LEU 8 32.250 18.140 -1.600 1.00 0.00
-ATOM 131 1HD2 LEU 8 31.720 18.930 -1.260 1.00 0.00
-ATOM 132 2HD2 LEU 8 32.110 18.050 -2.580 1.00 0.00
-ATOM 133 3HD2 LEU 8 31.930 17.310 -1.140 1.00 0.00
-ATOM 134 C LEU 8 36.050 17.130 0.270 1.00 0.00
-ATOM 135 O LEU 8 36.160 18.170 0.920 1.00 0.00
-ATOM 136 N ALA 9 35.750 15.980 0.830 1.00 0.00
-ATOM 137 H ALA 9 35.460 15.220 0.240 1.00 0.00
-ATOM 138 CA ALA 9 35.840 15.760 2.280 1.00 0.00
-ATOM 139 HA ALA 9 35.080 16.260 2.690 1.00 0.00
-ATOM 140 CB ALA 9 35.660 14.290 2.620 1.00 0.00
-ATOM 141 HB1 ALA 9 35.720 14.160 3.610 1.00 0.00
-ATOM 142 HB2 ALA 9 34.760 13.980 2.300 1.00 0.00
-ATOM 143 HB3 ALA 9 36.370 13.750 2.180 1.00 0.00
-ATOM 144 C ALA 9 37.140 16.310 2.840 1.00 0.00
-ATOM 145 O ALA 9 37.150 16.980 3.900 1.00 0.00
-ATOM 146 N ALA 10 38.270 15.980 2.200 1.00 0.00
-ATOM 147 H ALA 10 38.200 15.390 1.400 1.00 0.00
-ATOM 148 CA ALA 10 39.610 16.430 2.620 1.00 0.00
-ATOM 149 HA ALA 10 39.690 16.190 3.580 1.00 0.00
-ATOM 150 CB ALA 10 40.710 15.710 1.840 1.00 0.00
-ATOM 151 HB1 ALA 10 41.600 16.030 2.150 1.00 0.00
-ATOM 152 HB2 ALA 10 40.640 14.720 2.010 1.00 0.00
-ATOM 153 HB3 ALA 10 40.600 15.890 0.860 1.00 0.00
-ATOM 154 C ALA 10 39.740 17.940 2.460 1.00 0.00
-ATOM 155 O ALA 10 40.190 18.500 3.470 1.00 0.00
-ATOM 156 DOT DOT 11 33.016 20.637 -12.533 1.00 0.00
-ATOM 157 DOT DOT 11 33.225 20.789 -10.661 1.00 0.00
-ATOM 158 DOT DOT 11 32.462 22.340 -11.427 1.00 0.00
-ATOM 159 DOT DOT 11 33.569 22.340 -9.636 1.00 0.00
-ATOM 160 DOT DOT 11 32.721 22.340 -13.299 1.00 0.00
-ATOM 161 DOT DOT 11 33.016 24.043 -12.533 1.00 0.00
-ATOM 162 DOT DOT 11 33.225 23.891 -10.661 1.00 0.00
-ATOM 163 DOT DOT 11 34.545 19.831 -13.299 1.00 0.00
-ATOM 164 DOT DOT 11 34.465 19.584 -11.427 1.00 0.00
-ATOM 165 DOT DOT 11 34.807 20.637 -9.636 1.00 0.00
-ATOM 166 DOT DOT 11 33.911 21.287 -14.324 1.00 0.00
-ATOM 167 DOT DOT 11 33.911 23.393 -14.324 1.00 0.00
-ATOM 168 DOT DOT 11 34.545 24.849 -13.299 1.00 0.00
-ATOM 169 DOT DOT 11 34.465 25.096 -11.427 1.00 0.00
-ATOM 170 DOT DOT 11 34.807 24.043 -9.636 1.00 0.00
-ATOM 171 DOT DOT 11 35.913 20.637 -14.324 1.00 0.00
-ATOM 172 DOT DOT 11 36.255 19.584 -12.533 1.00 0.00
-ATOM 173 DOT DOT 11 36.175 19.831 -10.661 1.00 0.00
-ATOM 174 DOT DOT 11 36.809 21.287 -9.636 1.00 0.00
-ATOM 175 DOT DOT 11 35.360 22.340 -14.930 1.00 0.00
-ATOM 176 DOT DOT 11 36.809 23.393 -9.636 1.00 0.00
-ATOM 177 DOT DOT 11 35.360 22.340 -9.030 1.00 0.00
-ATOM 178 DOT DOT 11 35.913 24.043 -14.324 1.00 0.00
-ATOM 179 DOT DOT 11 36.255 25.096 -12.533 1.00 0.00
-ATOM 180 DOT DOT 11 36.175 24.849 -10.661 1.00 0.00
-ATOM 181 DOT DOT 11 37.495 20.789 -13.299 1.00 0.00
-ATOM 182 DOT DOT 11 37.704 20.637 -11.427 1.00 0.00
-ATOM 183 DOT DOT 11 37.151 22.340 -14.324 1.00 0.00
-ATOM 184 DOT DOT 11 38.258 22.340 -12.533 1.00 0.00
-ATOM 185 DOT DOT 11 37.999 22.340 -10.661 1.00 0.00
-ATOM 186 DOT DOT 11 37.495 23.891 -13.299 1.00 0.00
-ATOM 187 DOT DOT 11 37.704 24.043 -11.427 1.00 0.00
+ATOM 100 HG CYS 6 37.070 8.360 0.120 1.00 0.00
+ATOM 101 C CYS 6 37.750 13.050 -0.780 1.00 0.00
+ATOM 102 O CYS 6 38.150 13.610 0.260 1.00 0.00
+ATOM 103 N GLU 7 37.860 13.480 -2.020 1.00 0.00
+ATOM 104 H GLU 7 37.400 13.000 -2.760 1.00 0.00
+ATOM 105 CA GLU 7 38.680 14.690 -2.310 1.00 0.00
+ATOM 106 HA GLU 7 39.600 14.550 -1.930 1.00 0.00
+ATOM 107 CB GLU 7 38.780 14.850 -3.820 1.00 0.00
+ATOM 108 HB1 GLU 7 39.230 14.020 -4.170 1.00 0.00
+ATOM 109 HB2 GLU 7 37.850 14.890 -4.170 1.00 0.00
+ATOM 110 CG GLU 7 39.540 16.050 -4.380 1.00 0.00
+ATOM 111 HG1 GLU 7 39.130 16.870 -3.990 1.00 0.00
+ATOM 112 HG2 GLU 7 40.490 15.980 -4.070 1.00 0.00
+ATOM 113 CD GLU 7 39.580 16.240 -5.870 1.00 0.00
+ATOM 114 OE1 GLU 7 38.670 15.640 -6.490 1.00 0.00
+ATOM 115 OE2 GLU 7 40.420 16.950 -6.380 1.00 0.00
+ATOM 116 C GLU 7 38.050 15.930 -1.660 1.00 0.00
+ATOM 117 O GLU 7 38.740 16.730 -1.010 1.00 0.00
+ATOM 118 N LEU 8 36.740 16.050 -1.820 1.00 0.00
+ATOM 119 H LEU 8 36.260 15.350 -2.350 1.00 0.00
+ATOM 120 CA LEU 8 35.960 17.160 -1.250 1.00 0.00
+ATOM 121 HA LEU 8 36.400 18.010 -1.560 1.00 0.00
+ATOM 122 CB LEU 8 34.530 17.170 -1.810 1.00 0.00
+ATOM 123 HB1 LEU 8 34.570 17.220 -2.810 1.00 0.00
+ATOM 124 HB2 LEU 8 34.060 16.330 -1.530 1.00 0.00
+ATOM 125 CG LEU 8 33.720 18.350 -1.310 1.00 0.00
+ATOM 126 HG LEU 8 33.780 18.420 -0.310 1.00 0.00
+ATOM 127 CD1 LEU 8 34.300 19.660 -1.840 1.00 0.00
+ATOM 128 1HD1 LEU 8 33.760 20.430 -1.500 1.00 0.00
+ATOM 129 2HD1 LEU 8 35.240 19.750 -1.530 1.00 0.00
+ATOM 130 3HD1 LEU 8 34.270 19.650 -2.840 1.00 0.00
+ATOM 131 CD2 LEU 8 32.250 18.140 -1.600 1.00 0.00
+ATOM 132 1HD2 LEU 8 31.720 18.930 -1.260 1.00 0.00
+ATOM 133 2HD2 LEU 8 32.110 18.050 -2.580 1.00 0.00
+ATOM 134 3HD2 LEU 8 31.930 17.310 -1.140 1.00 0.00
+ATOM 135 C LEU 8 36.050 17.130 0.270 1.00 0.00
+ATOM 136 O LEU 8 36.160 18.170 0.920 1.00 0.00
+ATOM 137 N ALA 9 35.750 15.980 0.830 1.00 0.00
+ATOM 138 H ALA 9 35.460 15.220 0.240 1.00 0.00
+ATOM 139 CA ALA 9 35.840 15.760 2.280 1.00 0.00
+ATOM 140 HA ALA 9 35.080 16.260 2.690 1.00 0.00
+ATOM 141 CB ALA 9 35.660 14.290 2.620 1.00 0.00
+ATOM 142 HB1 ALA 9 35.720 14.160 3.610 1.00 0.00
+ATOM 143 HB2 ALA 9 34.760 13.980 2.300 1.00 0.00
+ATOM 144 HB3 ALA 9 36.370 13.750 2.180 1.00 0.00
+ATOM 145 C ALA 9 37.140 16.310 2.840 1.00 0.00
+ATOM 146 O ALA 9 37.150 16.980 3.900 1.00 0.00
+ATOM 147 N ALA 10 38.270 15.980 2.200 1.00 0.00
+ATOM 148 H ALA 10 38.200 15.390 1.400 1.00 0.00
+ATOM 149 CA ALA 10 39.610 16.430 2.620 1.00 0.00
+ATOM 150 HA ALA 10 39.690 16.190 3.580 1.00 0.00
+ATOM 151 CB ALA 10 40.710 15.710 1.840 1.00 0.00
+ATOM 152 HB1 ALA 10 41.600 16.030 2.150 1.00 0.00
+ATOM 153 HB2 ALA 10 40.640 14.720 2.010 1.00 0.00
+ATOM 154 HB3 ALA 10 40.600 15.890 0.860 1.00 0.00
+ATOM 155 C ALA 10 39.740 17.940 2.460 1.00 0.00
+ATOM 156 O ALA 10 40.190 18.500 3.470 1.00 0.00
+ATOM 157 DOT DOT 11 33.016 20.637 -12.533 1.00 0.00
+ATOM 158 DOT DOT 11 33.225 20.789 -10.661 1.00 0.00
+ATOM 159 DOT DOT 11 32.462 22.340 -11.427 1.00 0.00
+ATOM 160 DOT DOT 11 33.569 22.340 -9.636 1.00 0.00
+ATOM 161 DOT DOT 11 32.721 22.340 -13.299 1.00 0.00
+ATOM 162 DOT DOT 11 33.016 24.043 -12.533 1.00 0.00
+ATOM 163 DOT DOT 11 33.225 23.891 -10.661 1.00 0.00
+ATOM 164 DOT DOT 11 34.545 19.831 -13.299 1.00 0.00
+ATOM 165 DOT DOT 11 34.465 19.584 -11.427 1.00 0.00
+ATOM 166 DOT DOT 11 34.807 20.637 -9.636 1.00 0.00
+ATOM 167 DOT DOT 11 33.911 21.287 -14.324 1.00 0.00
+ATOM 168 DOT DOT 11 33.911 23.393 -14.324 1.00 0.00
+ATOM 169 DOT DOT 11 34.545 24.849 -13.299 1.00 0.00
+ATOM 170 DOT DOT 11 34.465 25.096 -11.427 1.00 0.00
+ATOM 171 DOT DOT 11 34.807 24.043 -9.636 1.00 0.00
+ATOM 172 DOT DOT 11 35.913 20.637 -14.324 1.00 0.00
+ATOM 173 DOT DOT 11 36.255 19.584 -12.533 1.00 0.00
+ATOM 174 DOT DOT 11 36.175 19.831 -10.661 1.00 0.00
+ATOM 175 DOT DOT 11 36.809 21.287 -9.636 1.00 0.00
+ATOM 176 DOT DOT 11 35.360 22.340 -14.930 1.00 0.00
+ATOM 177 DOT DOT 11 36.809 23.393 -9.636 1.00 0.00
+ATOM 178 DOT DOT 11 35.360 22.340 -9.030 1.00 0.00
+ATOM 179 DOT DOT 11 35.913 24.043 -14.324 1.00 0.00
+ATOM 180 DOT DOT 11 36.255 25.096 -12.533 1.00 0.00
+ATOM 181 DOT DOT 11 36.175 24.849 -10.661 1.00 0.00
+ATOM 182 DOT DOT 11 37.495 20.789 -13.299 1.00 0.00
+ATOM 183 DOT DOT 11 37.704 20.637 -11.427 1.00 0.00
+ATOM 184 DOT DOT 11 37.151 22.340 -14.324 1.00 0.00
+ATOM 185 DOT DOT 11 38.258 22.340 -12.533 1.00 0.00
+ATOM 186 DOT DOT 11 37.999 22.340 -10.661 1.00 0.00
+ATOM 187 DOT DOT 11 37.495 23.891 -13.299 1.00 0.00
+ATOM 188 DOT DOT 11 37.704 24.043 -11.427 1.00 0.00
TER
ENDMDL
]]></String>
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2018, 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.
+ */
+/*! \internal \file
+ * \brief
+ * Tests for TopologyInformation
+ *
+ * \author Mark Abraham <mark.j.abraham@gmail.com>
+ * \ingroup module_trajectoryanalysis
+ */
+#include "gmxpre.h"
+
+#include "gromacs/trajectoryanalysis/topologyinformation.h"
+
+#include <gtest/gtest.h>
+
+#include "gromacs/gmxpreprocess/grompp.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/topology/topology.h"
+#include "gromacs/utility/arrayref.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/textwriter.h"
+
+#include "testutils/cmdlinetest.h"
+#include "testutils/testfilemanager.h"
+
+#include "moduletest.h"
+
+namespace gmx
+{
+namespace test
+{
+namespace
+{
+
+TEST(TopologyInformation, CantWorkWithoutReadingAFile)
+{
+ TopologyInformation topInfo;
+ EXPECT_FALSE(topInfo.hasTopology());
+ EXPECT_FALSE(topInfo.hasFullTopology());
+ ASSERT_TRUE(topInfo.mtop());
+ EXPECT_EQ(0, topInfo.mtop()->natoms);
+ EXPECT_FALSE(topInfo.expandedTopology());
+ auto atoms1 = topInfo.copyAtoms();
+ EXPECT_TRUE(atoms1);
+ auto atoms2 = topInfo.copyAtoms();
+ ASSERT_TRUE(atoms2);
+ EXPECT_NE(atoms1.get(), atoms2.get());
+ EXPECT_EQ(0, atoms1->nr);
+ EXPECT_EQ(-1, topInfo.ePBC());
+ EXPECT_THROW(topInfo.x().size(), gmx::APIError);
+ EXPECT_THROW(topInfo.v().size(), gmx::APIError);
+ matrix box {{
+ -2
+ }};
+ topInfo.getBox(box);
+ EXPECT_EQ(0, box[XX][XX]);
+ EXPECT_EQ(0, box[XX][YY]);
+ EXPECT_EQ(0, box[XX][ZZ]);
+ EXPECT_EQ(0, box[YY][XX]);
+ EXPECT_EQ(0, box[YY][YY]);
+ EXPECT_EQ(0, box[YY][ZZ]);
+ EXPECT_EQ(0, box[ZZ][XX]);
+ EXPECT_EQ(0, box[ZZ][YY]);
+ EXPECT_EQ(0, box[ZZ][ZZ]);
+ EXPECT_FALSE(topInfo.name());
+}
+
+//! Common test code to reduce duplication
+void runCommonTests(const TopologyInformation &topInfo, const int numAtoms)
+{
+ EXPECT_TRUE(topInfo.hasTopology());
+ ASSERT_TRUE(topInfo.mtop());
+ EXPECT_EQ(numAtoms, topInfo.mtop()->natoms);
+ // TODO Dump mtop to refdata when that is possible
+ ASSERT_TRUE(topInfo.expandedTopology());
+ auto atoms1 = topInfo.copyAtoms();
+ EXPECT_TRUE(atoms1);
+ auto atoms2 = topInfo.copyAtoms();
+ EXPECT_TRUE(atoms2);
+ // Must be different pointer to a deep copy.
+ EXPECT_NE(atoms1.get(), atoms2.get());
+ auto atoms = topInfo.atoms();
+ // Must be a pointer to a different instance.
+ EXPECT_NE(atoms1.get(), atoms);
+ EXPECT_NE(atoms2.get(), atoms);
+ EXPECT_EQ(numAtoms, topInfo.x().size());
+ EXPECT_EQ(numAtoms, topInfo.v().size());
+ matrix box {{
+ -2
+ }};
+ topInfo.getBox(box);
+ EXPECT_FLOAT_EQ(5.9062, box[XX][XX]);
+ EXPECT_FLOAT_EQ(0, box[XX][YY]);
+ EXPECT_FLOAT_EQ(0, box[XX][ZZ]);
+ EXPECT_FLOAT_EQ(0, box[YY][XX]);
+ EXPECT_FLOAT_EQ(6.8451, box[YY][YY]);
+ EXPECT_FLOAT_EQ(0, box[YY][ZZ]);
+ EXPECT_FLOAT_EQ(0, box[ZZ][XX]);
+ EXPECT_FLOAT_EQ(0, box[ZZ][YY]);
+ EXPECT_FLOAT_EQ(3.0517, box[ZZ][ZZ]);
+ EXPECT_STREQ("First 10 residues from 1AKI", topInfo.name());
+}
+
+TEST(TopologyInformation, WorksWithGroFile)
+{
+ const int numAtoms = 156;
+ TopologyInformation topInfo;
+ topInfo.fillFromInputFile(TestFileManager::getInputFilePath("lysozyme.gro"));
+ EXPECT_FALSE(topInfo.hasFullTopology());
+ runCommonTests(topInfo, numAtoms);
+ EXPECT_EQ(-1, topInfo.ePBC());
+
+ // Check the per-atom data
+ auto atoms = topInfo.copyAtoms();
+ ASSERT_EQ(numAtoms, atoms->nr);
+ EXPECT_TRUE(atoms->haveMass);
+ // TODO atommass.dat assumes united atom CA, which is probably not expected behaviour
+ EXPECT_FLOAT_EQ(13.019, atoms->atom[26].m);
+ EXPECT_FALSE(atoms->haveCharge);
+ EXPECT_FALSE(atoms->haveType);
+ EXPECT_EQ(0, atoms->atom[26].type);
+ EXPECT_EQ(0, atoms->atom[26].atomnumber);
+ EXPECT_EQ(1, atoms->atom[26].resind);
+ // gro files don't have the information that pdb files might
+ EXPECT_FALSE(atoms->havePdbInfo);
+ EXPECT_FALSE(atoms->pdbinfo);
+ EXPECT_EQ(10, atoms->nres);
+ ASSERT_TRUE(atoms->resinfo);
+ ASSERT_TRUE(atoms->resinfo[4].name);
+ EXPECT_STREQ("ARG", *atoms->resinfo[4].name);
+ EXPECT_EQ(5, atoms->resinfo[4].nr);
+ EXPECT_EQ(0, atoms->resinfo[4].chainnum);
+ EXPECT_EQ(' ', atoms->resinfo[4].chainid);
+}
+
+TEST(TopologyInformation, WorksWithPdbFile)
+{
+ const int numAtoms = 156;
+ TopologyInformation topInfo;
+ topInfo.fillFromInputFile(TestFileManager::getInputFilePath("lysozyme.pdb"));
+ EXPECT_FALSE(topInfo.hasFullTopology());
+ runCommonTests(topInfo, numAtoms);
+ // TODO why does this differ from .gro?
+ EXPECT_EQ(0, topInfo.ePBC());
+
+ // Check the per-atom data
+ auto atoms = topInfo.copyAtoms();
+ ASSERT_EQ(numAtoms, atoms->nr);
+ EXPECT_TRUE(atoms->haveMass);
+ // TODO atommass.dat assumes united atom CA, which is probably not expected behaviour
+ EXPECT_FLOAT_EQ(13.019, atoms->atom[26].m);
+ EXPECT_FALSE(atoms->haveCharge);
+ EXPECT_FALSE(atoms->haveType);
+ EXPECT_EQ(0, atoms->atom[26].type);
+ EXPECT_EQ(0, atoms->atom[26].atomnumber);
+ EXPECT_EQ(1, atoms->atom[26].resind);
+ // pdb files can carry more information than gro
+ EXPECT_TRUE(atoms->havePdbInfo);
+ ASSERT_TRUE(atoms->pdbinfo);
+ EXPECT_EQ(10, atoms->nres);
+ ASSERT_TRUE(atoms->resinfo);
+ ASSERT_TRUE(atoms->resinfo[4].name);
+ EXPECT_STREQ("ARG", *atoms->resinfo[4].name);
+ EXPECT_EQ(5, atoms->resinfo[4].nr);
+ EXPECT_EQ(0, atoms->resinfo[4].chainnum);
+ EXPECT_EQ('B', atoms->resinfo[4].chainid);
+}
+
+TEST(TopologyInformation, WorksWithTprFromPdbFile)
+{
+ TestFileManager fileManager;
+
+ // Make the tpr file to use
+ std::string name = "lysozyme";
+ const std::string mdpInputFileName = fileManager.getTemporaryFilePath(name + ".mdp");
+ // Ensure the seeds have a value so that the resulting .tpr dump
+ // is reproducible.
+ TextWriter::writeFileFromString(mdpInputFileName, "");
+ std::string tprName = fileManager.getTemporaryFilePath(name + ".tpr");
+ {
+ CommandLine caller;
+ caller.append("grompp");
+ caller.addOption("-f", mdpInputFileName);
+ caller.addOption("-p", TestFileManager::getInputFilePath(name));
+ caller.addOption("-c", TestFileManager::getInputFilePath(name + ".pdb"));
+ caller.addOption("-o", tprName);
+ ASSERT_EQ(0, gmx_grompp(caller.argc(), caller.argv()));
+ }
+
+ const int numAtoms = 156;
+ TopologyInformation topInfo;
+ topInfo.fillFromInputFile(tprName);
+ EXPECT_TRUE(topInfo.hasFullTopology());
+ runCommonTests(topInfo, numAtoms);
+ // TODO why does this differ from .gro?
+ EXPECT_EQ(0, topInfo.ePBC());
+
+ // Check the per-atom data
+ auto atoms = topInfo.copyAtoms();
+ ASSERT_EQ(numAtoms, atoms->nr);
+ EXPECT_TRUE(atoms->haveMass);
+ EXPECT_FLOAT_EQ(12.011, atoms->atom[26].m);
+ EXPECT_TRUE(atoms->haveCharge);
+ EXPECT_TRUE(atoms->haveType);
+ EXPECT_EQ(2, atoms->atom[26].type);
+ EXPECT_EQ(6, atoms->atom[26].atomnumber);
+ EXPECT_EQ(1, atoms->atom[26].resind);
+ // tpr files also don't carry pdb information
+ EXPECT_FALSE(atoms->havePdbInfo);
+ EXPECT_FALSE(atoms->pdbinfo);
+ EXPECT_EQ(10, atoms->nres);
+ ASSERT_TRUE(atoms->resinfo);
+ ASSERT_TRUE(atoms->resinfo[4].name);
+ EXPECT_STREQ("ARG", *atoms->resinfo[4].name);
+ EXPECT_EQ(5, atoms->resinfo[4].nr);
+ EXPECT_EQ(0, atoms->resinfo[4].chainnum);
+ // In particular, chain ID does not get recorded in the .tpr file
+ EXPECT_EQ(0, atoms->resinfo[4].chainid);
+}
+
+} // namespace
+} // namespace test
+} // namespace gmx
#include "gromacs/compat/make_unique.h"
#include "gromacs/fileio/confio.h"
#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/rmpbc.h"
#include "gromacs/topology/mtop_util.h"
#include "gromacs/topology/topology.h"
#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/unique_cptr.h"
namespace gmx
{
TopologyInformation::TopologyInformation()
- : mtop_(nullptr), top_(nullptr), bTop_(false), xtop_(nullptr), boxtop_(), ePBC_(-1)
+ : mtop_(compat::make_unique<gmx_mtop_t>()),
+ hasLoadedMtop_(false),
+ expandedTopology_(nullptr),
+ atoms_ (nullptr),
+ bTop_(false), ePBC_(-1)
{
}
TopologyInformation::~TopologyInformation()
{
- done_top_mtop(top_, mtop_.get());
- sfree(top_);
- sfree(xtop_);
-}
-
-
-t_topology *TopologyInformation::topology() const
-{
- if (top_ == nullptr && mtop_ != nullptr)
- {
- snew(top_, 1);
- *top_ = gmx_mtop_t_to_t_topology(mtop_.get(), false);
- }
- return top_;
}
void TopologyInformation::fillFromInputFile(const std::string &filename)
{
mtop_ = gmx::compat::make_unique<gmx_mtop_t>();
+ // TODO When filename is not a .tpr, then using readConfAndAtoms
+ // would be efficient for not doing multiple conversions for
+ // makeAtomsData. However we'd also need to be able to copy the
+ // t_atoms that we'd keep, which we currently can't do.
+ // TODO Once there are fewer callers of the file-reading
+ // functionality, make them read directly into std::vector.
+ rvec *x, *v;
readConfAndTopology(filename.c_str(), &bTop_, mtop_.get(),
- &ePBC_, &xtop_, nullptr,
+ &ePBC_, &x, &v,
boxtop_);
+ xtop_.assign(x, x + mtop_->natoms);
+ vtop_.assign(v, v + mtop_->natoms);
+ sfree(x);
+ sfree(v);
+ hasLoadedMtop_ = true;
// TODO: Only load this here if the tool actually needs it; selections
// take care of themselves.
for (gmx_moltype_t &moltype : mtop_->moltype)
}
}
-void
-TopologyInformation::getTopologyConf(rvec **x, matrix box) const
+const gmx_localtop_t *TopologyInformation::expandedTopology() const
{
- if (box)
+ // Do lazy initialization
+ if (expandedTopology_ == nullptr && hasTopology())
{
- copy_mat(const_cast<rvec *>(boxtop_), box);
+ expandedTopology_.reset(gmx_mtop_generate_local_top(mtop_.get(), false));
}
- if (x)
+
+ return expandedTopology_.get();
+}
+
+namespace
+{
+
+//! Helps implement lazy initialization.
+AtomsDataPtr makeAtoms(const TopologyInformation &top_)
+{
+ AtomsDataPtr atoms(new t_atoms);
+ if (top_.hasTopology())
{
- if (!xtop_)
- {
- *x = nullptr;
- GMX_THROW(APIError("Topology coordinates requested without setting efUseTopX"));
- }
- *x = xtop_;
+ *atoms = gmx_mtop_global_atoms(top_.mtop());
+ }
+ else
+ {
+ init_atom(atoms.get());
+ }
+ return atoms;
+}
+
+} // namespace
+
+const t_atoms *TopologyInformation::atoms() const
+{
+ // Do lazy initialization
+ if (atoms_ == nullptr)
+ {
+ atoms_ = makeAtoms(*this);
+ }
+
+ return atoms_.get();
+}
+
+AtomsDataPtr TopologyInformation::copyAtoms() const
+{
+ // Note that we do not return atoms_, so that regardless of
+ // whether the user has already used it, or will use it in the
+ // future, any transformation operations on the data structure
+ // returned here cannot have unintended effects.
+ return makeAtoms(*this);
+}
+
+ArrayRef<const RVec>
+TopologyInformation::x() const
+{
+ if (xtop_.empty())
+ {
+ GMX_THROW(APIError("Topology coordinates requested without setting efUseTopX"));
}
+ return xtop_;
+}
+
+ArrayRef<const RVec>
+TopologyInformation::v() const
+{
+ if (vtop_.empty())
+ {
+ GMX_THROW(APIError("Topology coordinates requested without setting efUseTopV"));
+ }
+ return vtop_;
+}
+
+void
+TopologyInformation::getBox(matrix box) const
+{
+ GMX_RELEASE_ASSERT(box != nullptr, "Must have valid box to fill");
+ copy_mat(const_cast<rvec *>(boxtop_), box);
+}
+
+const char *
+TopologyInformation::name() const
+{
+ if (hasTopology() && mtop_->name)
+ {
+ return *mtop_->name;
+ }
+ return nullptr;
+}
+
+gmx_rmpbc_t gmx_rmpbc_init(const gmx::TopologyInformation &topInfo)
+{
+ GMX_RELEASE_ASSERT(topInfo.hasTopology(), "Cannot remove PBC without a topology");
+
+ return gmx_rmpbc_init(&topInfo.expandedTopology()->idef, topInfo.ePBC(), topInfo.mtop()->natoms);
}
} // namespace gmx
#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"
-struct gmx_mtop_t;
-struct t_topology;
+//! Forward declaration
+typedef struct gmx_rmpbc *gmx_rmpbc_t;
namespace gmx
{
+template<typename T> class ArrayRef;
+
class TopologyInformation;
class TrajectoryAnalysisRunnerCommon;
/*! \libinternal
- * \brief Topology information passed to a trajectory analysis module.
+ * \brief Topology information available to a trajectory analysis module.
*
- * This class is used to pass 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.
+ * 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
*
* 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 mtop_ != nullptr; }
+ 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
* 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. */
+ * 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);
- //! Returns the loaded topology, or NULL if not loaded.
- const gmx_mtop_t *mtop() const { return mtop_.get(); }
- //! Returns the loaded topology, or NULL if not loaded.
- t_topology *topology() const;
+ /*! \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 from the topology.
- *
- * \param[out] x Topology coordinate pointer to initialize.
- * (can be NULL, in which case it is not used).
- * \param[out] box Box size from the topology file
- * (can be NULL, in which case it is not used).
- * \throws APIError if topology coordinates are not available and
- * \p x is not NULL.
+ * Gets the configuration positions from the topology file.
*
* If TrajectoryAnalysisSettings::efUseTopX has not been specified,
- * \p x should be NULL.
+ * this method should not be called.
*
- * The pointer returned in \p *x should not be freed.
+ * \throws APIError if topology position coordinates are not available
*/
- void getTopologyConf(rvec **x, matrix box) const;
+ 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;
- private:
TopologyInformation();
~TopologyInformation();
+ private:
+ //! The topology structure, or nullptr if no topology loaded.
std::unique_ptr<gmx_mtop_t> mtop_;
- //! The topology structure, or NULL if no topology loaded.
- // TODO: Replace fully with mtop.
- mutable t_topology *top_;
+ //! 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_;
- //! Coordinates from the topology (can be NULL).
- rvec *xtop_;
+ 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_;
+ matrix boxtop_ {};
//! The ePBC field loaded from the topology file.
- int ePBC_;
+ int ePBC_;
+ // TODO This type is probably movable if we need that.
GMX_DISALLOW_COPY_AND_ASSIGN(TopologyInformation);
/*! \brief
friend class TrajectoryAnalysisRunnerCommon;
};
+//! Convenience overload useful for implementing legacy tools.
+gmx_rmpbc_t gmx_rmpbc_init(const gmx::TopologyInformation &topInfo);
+
} // namespace gmx
#endif
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2010,2011,2012,2013,2014,2015,2017, by the GROMACS development team, led by
+# Copyright (c) 2010,2011,2012,2013,2014,2015,2017,2018, 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.
real.h
smalloc.h
stringutil.h
+ unique_cptr.h
)
if (BUILD_TESTING)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014,2015,2016,2017,2018, 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.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-/*! \libinternal \file
+/*! \file
* \brief
* Declares gmx::unique_cptr and gmx::sfree_guard.
*
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff