void
TrajectoryAnalysisRunnerCommon::initTopology(SelectionCollection *selections)
{
// Return immediately if the topology has already been loaded.
if (impl_->topInfo_.hasTopology())
{
return;
}
const TrajectoryAnalysisSettings &settings = impl_->settings_;
const bool bRequireTop
= settings.hasFlag(TrajectoryAnalysisSettings::efRequireTop)
|| selections->requiresTopology();
if (bRequireTop && impl_->topfile_.empty())
{
GMX_THROW(InconsistentInputError("No topology provided, but one is required for analysis"));
}
// Load the topology if requested.
if (!impl_->topfile_.empty())
{
char title[STRLEN];
snew(impl_->topInfo_.top_, 1);
impl_->topInfo_.bTop_ = read_tps_conf(impl_->topfile_.c_str(), title,
impl_->topInfo_.top_, &impl_->topInfo_.ePBC_,
&impl_->topInfo_.xtop_, NULL, impl_->topInfo_.boxtop_, TRUE);
if (hasTrajectory()
&& !settings.hasFlag(TrajectoryAnalysisSettings::efUseTopX))
{
sfree(impl_->topInfo_.xtop_);
impl_->topInfo_.xtop_ = NULL;
}
}
// Read the first frame if we don't know the maximum number of atoms
// otherwise.
int natoms = -1;
if (!impl_->topInfo_.hasTopology())
{
initFirstFrame();
natoms = impl_->fr->natoms;
}
selections->setTopology(impl_->topInfo_.topology(), natoms);
/*
if (impl_->bSelDump)
{
gmx_ana_poscalc_coll_print_tree(stderr, impl_->pcc);
fprintf(stderr, "\n");
}
*/
}
virtual int getAtomCount()
{
if (!topInfo_.hasTopology())
{
if (trajectoryGroup_.isValid())
{
GMX_THROW(InconsistentInputError("-fgroup is only supported when -s is also specified"));
}
// Read the first frame if we don't know the maximum number of
// atoms otherwise.
initFirstFrame();
return fr->natoms;
}
return -1;
}
