RetroSearch Browse

Home - News ( United States | United Kingdom | Italy | Germany ) - Football scores

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/atom__set_8cpp_source.html below:

NCBI C++ ToolKit: src/app/cn3d/atom_set.cpp Source File

66 unsigned int

nAtoms = coords.GetNumber_of_points();

67 TRACEMSG

(

"model has "

<< nAtoms <<

" atomic coords"

);

69 bool

haveTemp = coords.IsSetTemperature_factors(),

70

haveOccup = coords.IsSetOccupancies(),

71

haveAlt = coords.IsSetAlternate_conf_ids();

74 if

(coords.GetAtoms().GetMolecule_ids().size()!=nAtoms ||

75

coords.GetAtoms().GetResidue_ids().size()!=nAtoms ||

76

coords.GetAtoms().GetAtom_ids().size()!=nAtoms ||

77

coords.GetSites().GetX().size()!=nAtoms ||

78

coords.GetSites().GetY().size()!=nAtoms ||

79

coords.GetSites().GetZ().size()!=nAtoms ||

81

((coords.GetTemperature_factors().IsIsotropic() &&

82

coords.GetTemperature_factors().GetIsotropic().GetB().size()!=nAtoms) ||

83

(coords.GetTemperature_factors().IsAnisotropic() &&

84

(coords.GetTemperature_factors().GetAnisotropic().GetB_11().size()!=nAtoms ||

85

coords.GetTemperature_factors().GetAnisotropic().GetB_12().size()!=nAtoms ||

86

coords.GetTemperature_factors().GetAnisotropic().GetB_13().size()!=nAtoms ||

87

coords.GetTemperature_factors().GetAnisotropic().GetB_22().size()!=nAtoms ||

88

coords.GetTemperature_factors().GetAnisotropic().GetB_23().size()!=nAtoms ||

89

coords.GetTemperature_factors().GetAnisotropic().GetB_33().size()!=nAtoms)))) ||

90

(haveOccup && coords.GetOccupancies().GetO().size()!=nAtoms) ||

91

(haveAlt && coords.GetAlternate_conf_ids().Get().size()!=nAtoms))

92 ERRORMSG

(

"AtomSet: confused by list length mismatch"

);

95

CAtom_pntrs::TMolecule_ids::const_iterator

96

i_mID = coords.GetAtoms().GetMolecule_ids().begin();

97

CAtom_pntrs::TResidue_ids::const_iterator

98

i_rID = coords.GetAtoms().GetResidue_ids().begin();

99

CAtom_pntrs::TAtom_ids::const_iterator

100

i_aID = coords.GetAtoms().GetAtom_ids().begin();

103 double

siteScale =

static_cast<double>

(coords.GetSites().GetScale_factor());

104

CModel_space_points::TX::const_iterator i_X = coords.GetSites().GetX().begin();

105

CModel_space_points::TY::const_iterator i_Y = coords.GetSites().GetY().begin();

106

CModel_space_points::TZ::const_iterator i_Z = coords.GetSites().GetZ().begin();

109

CAtomic_occupancies::TO::const_iterator i_occup;

110 double

occupScale = 0.0;

112

occupScale =

static_cast<double>

(coords.GetOccupancies().GetScale_factor());

113

i_occup = coords.GetOccupancies().GetO().begin();

117

CAlternate_conformation_ids::Tdata::const_iterator i_alt;

118 if

(haveAlt) i_alt = coords.GetAlternate_conf_ids().Get().begin();

121 double

tempScale = 0.0;

122

CIsotropic_temperature_factors::TB::const_iterator i_tempI;

123

CAnisotropic_temperature_factors::TB_11::const_iterator i_tempA11;

124

CAnisotropic_temperature_factors::TB_12::const_iterator i_tempA12;

125

CAnisotropic_temperature_factors::TB_13::const_iterator i_tempA13;

126

CAnisotropic_temperature_factors::TB_22::const_iterator i_tempA22;

127

CAnisotropic_temperature_factors::TB_23::const_iterator i_tempA23;

128

CAnisotropic_temperature_factors::TB_33::const_iterator i_tempA33;

130 if

(coords.GetTemperature_factors().IsIsotropic()) {

131

tempScale =

static_cast<double> 132

(coords.GetTemperature_factors().GetIsotropic().GetScale_factor());

133

i_tempI = coords.GetTemperature_factors().GetIsotropic().GetB().begin();

135

tempScale =

static_cast<double> 136

(coords.GetTemperature_factors().GetAnisotropic().GetScale_factor());

137

i_tempA11 = coords.GetTemperature_factors().GetAnisotropic().GetB_11().begin();

138

i_tempA12 = coords.GetTemperature_factors().GetAnisotropic().GetB_12().begin();

139

i_tempA13 = coords.GetTemperature_factors().GetAnisotropic().GetB_13().begin();

140

i_tempA22 = coords.GetTemperature_factors().GetAnisotropic().GetB_22().begin();

141

i_tempA23 = coords.GetTemperature_factors().GetAnisotropic().GetB_23().begin();

142

i_tempA33 = coords.GetTemperature_factors().GetAnisotropic().GetB_33().begin();

147 if

(!GetParentOfType(&constObject))

return

;

151 for

(

unsigned int i

=0;

<nAtoms; ++

) {

154

atom->

site

= (

static_cast<double>

(*(i_X++)))/siteScale;

155

atom->

site

= (

static_cast<double>

(*(i_Y++)))/siteScale;

156

atom->

site

= (

static_cast<double>

(*(i_Z++)))/siteScale;

158

atom->

occupancy

= (

static_cast<double>

(*(i_occup++)))/occupScale;

162 if

(coords.GetTemperature_factors().IsIsotropic()) {

164

(

static_cast<double>

(*(i_tempI++)))/tempScale;

167

(

static_cast<double>

(*(i_tempA11++))) +

168

(

static_cast<double>

(*(i_tempA12++))) +

169

(

static_cast<double>

(*(i_tempA13++))) +

170

(

static_cast<double>

(*(i_tempA22++))) +

171

(

static_cast<double>

(*(i_tempA23++))) +

172

(

static_cast<double>

(*(i_tempA33++)))) / (tempScale * 6.0);

188 if

(atomMap.find(

key

) != atomMap.end()) {

189

AtomAltList::const_iterator i_atom, e=atomMap[

key

].end();

190 for

(i_atom=atomMap[

key

].begin(); i_atom!=e; ++i_atom) {

191 if

((*i_atom)->altConfID == atom->

altConfID

)

192 ERRORMSG

(

"confused by multiple atoms of same pntr+altConfID"

);

195

atomMap[

key

].push_back(atom);

198 ", y "

<< atom->

site

199 ", z "

<< atom->

site

201 ", altConfId '"

<< atom->

altConfID

"'"

206 if

(haveAlt && coords.IsSetConf_ensembles()) {

207

CAtomic_coordinates::TConf_ensembles::const_iterator i_ensemble,

208

e_ensemble = coords.GetConf_ensembles().end();

209 for

(i_ensemble=coords.GetConf_ensembles().begin(); i_ensemble!=e_ensemble; ++i_ensemble) {

211 string

*ensembleStr =

new string

();

212

CConformation_ensemble::TAlt_conf_ids::const_iterator i_altIDs,

215

i_altIDs!=e_altIDs; ++i_altIDs) {

216

(*ensembleStr) += i_altIDs->Get()[0];

218

ensembles.push_back(ensembleStr);

219 TRACEMSG

(

"alt conf ensemble '"

<< (*ensembleStr) <<

"'"

);

226

EnsembleList::iterator

, e=

ensembles

.end();

228 delete const_cast<string

>

(*i);

239

EnsembleList::const_iterator e, ee=

ensembles

.end();

240 for

(e=

ensembles

.begin(); e!=ee; ++e) {

241 if

(*e == ensemble)

break

;

244 ERRORMSG

(

"AtomSet::SetActiveEnsemble received invalid ensemble"

);

253 bool

getAny,

bool

suppressWarning)

const 256 if

(atomConfs ==

atomMap

.end()) {

257 if

(!suppressWarning)

258 WARNINGMSG

(

"can't find atom(s) from pointer ("

<< ap.

mID

',' 259

<< ap.

rID

','

<< ap.

aID

')'

);

262

AtomAltList::const_iterator atom = atomConfs->second.begin();

268

AtomAltList::const_iterator e = atomConfs->second.end();

269 for

(; atom!=e; ++atom) {

275 if

(getAny)

return

atomConfs->second.front();

282

averageTemperature(NO_TEMPERATURE),

283

occupancy(NO_OCCUPANCY),

284

altConfID(NO_ALTCONFID)

User-defined methods of the data storage class.

double averageTemperature

static const double NO_TEMPERATURE

static const double NO_OCCUPANCY

static const char NO_ALTCONFID

AtomCoord(StructureBase *parent)

const AtomCoord * GetAtom(const AtomPntr &atom, bool getAny=false, bool suppressWarning=false) const

const std::string * activeEnsemble

AtomPntrKey MakeKey(const AtomPntr &ap) const

std::pair< int, std::pair< int, int > > AtomPntrKey

bool SetActiveEnsemble(const std::string *ensemble)

CConformation_ensemble â.

static const double NO_TEMPERATURE

static string MakeKey(CScoreValue const &)

Include a standard set of the NCBI C++ Toolkit most basic headers.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_SCOPE(ns)

Define a new scope.

const TAlt_conf_ids & GetAlt_conf_ids(void) const

Get the Alt_conf_ids member data.

const TYPE & Get(const CNamedParameterList *param)

const struct ncbi::grid::netcache::search::fields::KEY key

RetroSearch is an open source project built by @garambo | Open a GitHub Issue

Search and Browse the WWW like it's 1997 | Search results from DuckDuckGo

HTML: 3.2 | Encoding: UTF-8 | Version: 0.7.4