BondGraph::VertexIntPropertyMap BondGraph::get_vertex_index_map() const {
if (index_key_== IntKey()) {
std::ostringstream oss;
oss << this << " bond graph index";
index_key_= IntKey(oss.str().c_str());
int last=0;
for (Particles::const_iterator it= sc_.begin(); it != sc_.end(); ++it) {
(*it)->add_attribute(index_key_, last);
++last;
}
}
return VertexIntPropertyMap(index_key_);
}
void
BcTest8(void)
{
/*
* Extensive test of all functions. Want to cover most code paths.
* 1. Dynamically adjust number of records by a factor of 100.
* 2. Randomly pick operations.
* 3. Test iteration intermixed with other operations.
*/
enum { MAX_RECS = 100 * ONE_THOUSAND };
Bc t;
u64 key;
u64 keys[MAX_RECS];
u64 numKeys = 0;
u64 numPuts = 0;
u64 numDeletes = 0;
VAR_LUMP(v, MAX_DATA);
init_twister(37);
BcInit(&t, KEY_LEN);
RandLump(v);
for (u64 i = 0; i < 10; i++) {
u64 maxKeys = twister_urand(MAX_RECS);
PRu(maxKeys);
while (numKeys != maxKeys) {
aver(numKeys <= MAX_RECS);
if (numKeys < maxKeys && Prob(75)) {
key = twister_random();
keys[numKeys++] = key;
BcPut(&t, IntKey(key).s, v);
++numPuts;
} else {
if (numKeys) {
u64 j = twister_urand(numKeys);
key = keys[j];
keys[j] = keys[--numKeys];
BcDelete(&t, IntKey(key).s);
++numDeletes;
}
}
}
}
aver(numPuts - numDeletes == numKeys);
PRu(numPuts);
PRu(numDeletes);
PRu(numKeys);
BcReport(__FUNCTION__, BcDoAudit(&t));
}
BondGraph::~BondGraph() {
if (index_key_ != IntKey()) {
for (unsigned int i = 0; i < sc_.size(); ++i) {
sc_[i]->remove_attribute(index_key_);
}
}
}
//------------------------------------------------------------------------------------------------------------------------------------------------------
int Settings::GetInt(char *name)
{
int retValue = mapIntChild[IntKey(name)];
if(!GetIntFromChild(name, &retValue))
{
SetInt(name, retValue);
}
return retValue;
}
void
BcTest6(void)
{
enum { NUM_RECS = 2000, NUM_TRIALS = ONE_MILLION };
Bc t;
VAR_LUMP(v, MAX_DATA);
Key a[NUM_RECS];
u64 n = 0;
u64 puts = 0;
u64 deletes = 0;
printf("%s\n", __FUNCTION__);
init_twister(37);
BcInit(&t, KEY_LEN);
for (u64 j = 0; j < NUM_TRIALS; j++) {
Key key;
bool found;
if (Prob(((NUM_RECS - n) * 100) / NUM_RECS)) {
aver(n < NUM_RECS);
key = IntKey(twister_urand(10000));
BcGet(&t, key.s, &found);
if (!found) {
a[n++] = key;
RandLump(v);
BcPut(&t, key.s, v);
++puts;
}
if (0 || Prob(2)) Audit("Put", &t, a, n, j);
} else {
aver(0 < n);
u64 i = twister_urand(n);
key = a[i];
BcGet(&t, key.s, &found);
if (!found) {
BcDump("not found", &t);
fatal("didn't find %s %llu %llu", key.s, puts, deletes);
}
BcDelete(&t, key.s);
BcGet(&t, key.s, &found);
if (found) {
BcDump("found", &t);
fatal("found %llu", key);
}
a[i] = a[--n];
++deletes;
if (0 || Prob(2)) Audit("Delete", &t, a, n, j);
}
}
BcDoAudit(&t);
printf("\tputs=%llu deletes=%llu\n", puts, deletes);
BcReport(__FUNCTION__, BcDoAudit(&t));
BcDump(__FUNCTION__, &t);
BcFree(&t);
}
// add key of this container as attribute to all particles
// if there might be overlaps - create a different keys for each instance
void ConsecutivePairContainer::init() {
std::ostringstream oss;
oss << "CPC cache " << key_count;
++key_count;
key_ = IntKey(oss.str());
for (unsigned int i = 0; i < ps_.size(); ++i) {
IMP_USAGE_CHECK(!get_model()->get_has_attribute(key_, ps_[i]),
"You must create containers before reading in the "
<< "saved model: "
<< get_model()->get_particle(ps_[i])->get_name());
get_model()->add_attribute(key_, ps_[i], i);
}
}
// TODO - do not use ProteinsAnchorsSamplingSpace.
// you are not going to use the paths here
ProteomicsEMAlignmentAtomic::ProteomicsEMAlignmentAtomic(
const ProteinsAnchorsSamplingSpace &mapping_data,
multifit::SettingsData *asmb_data, const AlignmentParams &align_param)
: Object("ProteomicsEMAlignmentAtomic%1%"),
mapping_data_(mapping_data),
params_(align_param),
order_key_(IntKey("order")),
asmb_data_(asmb_data) {
fast_scoring_ = false;
IMP_LOG_TERSE("start" << std::endl);
// initialize everything
mdl_ = new Model();
IMP_LOG_VERBOSE("get proteomics data\n");
prot_data_ = mapping_data_.get_proteomics_data();
fit_state_key_ = IntKey("fit_state_key");
load_atomic_molecules();
IMP_LOG_VERBOSE("set NULL \n");
pst_ = nullptr;
states_set_ = false;
filters_set_ = false;
ev_thr_ = 0.001; // TODO make a parameter
IMP_LOG_VERBOSE("end initialization\n");
}
void
BzTest1(void)
{
enum { NUM_RECS = 100 };
VAR_LUMP(v, MAX_DATA);
Bz t;
printf("%s\n", __FUNCTION__);
BzInit(&t, KEY_LEN);
for (u64 i = 0; i < NUM_RECS; i++) {
if (1) IntLump(v, i);
else RandLump(v);
BzPut(&t, IntKey(i+1).s, v);
}
BzDump(__FUNCTION__, &t);
}
void
BzTest2(void)
{
enum { NUM_RECS = 100 };
VAR_LUMP(v, MAX_DATA);
Bz t;
printf("%s\n", __FUNCTION__);
init_twister(17);
BzInit(&t, KEY_LEN);
for (u64 i = 0; i < NUM_RECS; i++) {
if (1) IntLump(v, i);
else IntLump(v, twister_urand(1000));
if (0) BzPut(&t, RandKey().s, v);
else BzPut(&t, IntKey(twister_urand(1000)).s, v);
}
BzDump(__FUNCTION__, &t);
}
#include <IMP/core/GridClosePairsFinder.h>
#include <IMP/core/internal/close_pairs_helpers.h>
#include <IMP/core/pair_predicates.h>
#include <IMP/generic.h>
#include <IMP/PairModifier.h>
#include <IMP/utility.h>
#include <algorithm>
#include <IMP/core/RigidClosePairsFinder.h>
#include <IMP/core/rigid_bodies.h>
IMPCORE_BEGIN_INTERNAL_NAMESPACE
IntKey InList::key_= IntKey("in list temp");
IMP_LIST_IMPL(CoreClosePairContainer,
PairFilter,
pair_filter,
PairFilter*,
PairFilters);
CoreClosePairContainer::CoreClosePairContainer(SingletonContainer *c,
double distance,
ClosePairsFinder *cpf,
double slack):
IMP::internal::ListLikePairContainer(c->get_model(),
"ClosePairContainer") {
initialize(c, distance, slack,
void _TrivialDecorator::do_setup_particle(Model *m, ParticleIndex pi) {
m->add_attribute(IntKey("trivial_attribute"), pi, 1);
}
void _TrivialDerivedDecorator::do_setup_particle(Model *m, ParticleIndex pi) {
m->add_attribute(IntKey("trivial_attribute_2"), pi, 2);
if (!_TrivialDecorator::get_is_setup(m, pi)) {
_TrivialDecorator::setup_particle(m, pi);
}
}
//------------------------------------------------------------------------------------------------------------------------------------------------------
bool Settings::Load()
{
nameFile = String("TVData/settings.xml");
mapIntChild[IntKey(TV_SCREEN_WIDTH)] = SET::WINDOW::WIDTH;
mapIntChild[IntKey(TV_SCREEN_HEIGHT)] = SET::WINDOW::HEIGHT;
mapIntChild[IntKey(TV_LANGUAGE)] = 1;
mapIntChild[IntKey(TV_TEXTURE_QUALITY)] = 2;
mapIntChild[IntKey(TV_BRIGHTNESS)] = 50;
mapIntChild[IntKey(TV_VOLUME)] = 50;
mapIntChild[IntKey(TV_MAX_OCCLUDER_TRIANGLES)] = 5000;
mapIntChild[IntKey(TV_TEXTURE_ANISOTROPY)] = 3;
mapIntChild[IntKey(TV_MATERIAL_QUALITY)] = 3;
mapIntChild[IntKey(TV_SHADOW_DRAW)] = 1;
mapIntChild[IntKey(TV_SPECULAR_LIGHTING)] = 1;
mapIntChild[IntKey(TV_SHADOW_MAP_SIZE)] = 4;
mapIntChild[IntKey(TV_PANEL_BOTTOM_BUTTON_WIDTH)] = SET::PANEL::BOTTOM::BUTTON::WIDTH;
mapIntChild[IntKey(TV_PANEL_BOTTOM_BUTTON_HEIGHT)] = SET::PANEL::BOTTOM::BUTTON::HEIGHT;
mapIntChild[IntKey(TV_PANEL_BOTTOM_HEIGHT)] = SET::PANEL::BOTTOM::HEIGHT;
mapIntChild[IntKey(TV_PANEL_MAP_WIDTH)] = SET::PANEL::MAP::WIDTH;
mapIntChild[IntKey(TV_PANEL_BOTTOM_BUTTON_Y)] = 3;
mapFloatChild[FloatKey(TV_PANEL_SPEED)] = SET::PANEL::SPEED;
File inFile(gContext);
if(inFile.Open(nameFile, Urho3D::FILE_READ))
{
file = new XMLFile(gContext);
bool begined = file->BeginLoad(inFile);
if(begined)
{
root = file->GetRoot();
if(root != XMLElement::EMPTY)
{
return true;
}
}
}
if (file == nullptr)
{
file = new XMLFile(gContext);
}
root = file->CreateRoot("settings");
return false;
}
* Copyright 2007-2012 IMP Inventors. All rights reserved.
*
*/
#include <IMP/saxs/FormFactorTable.h>
#include <IMP/atom/Atom.h>
#include <IMP/constants.h>
#include <IMP/algebra/utility.h>
#include <fstream>
#include <algorithm>
#include <cmath>
IMPSAXS_BEGIN_NAMESPACE
IntKey FormFactorTable::form_factor_type_key_ = IntKey("form factor key");
std::map<atom::Element, FormFactorTable::FormFactorAtomType>
FormFactorTable::element_ff_type_map_;
std::map<atom::ResidueType, FormFactorTable::FormFactor>
FormFactorTable::residue_type_form_factor_map_;
Float FormFactorTable::zero_form_factors_[] = {
-0.720147, -0.720228,
// H He
1.591, 2.591, 3.591, 0.50824, 6.16294, 4.94998, 7.591, 6.993,
// Li Be B C N O F Ne
7.9864, 8.9805, 9.984, 10.984, 13.0855, 9.36656, 13.984, 16.591,
// Na Mg Al Si P S Cl Ar
15.984, 14.9965, 20.984, 21.984, 20.9946, 23.984,
