67 void writeResults(vector<
Result*>& res);
98 void setInputParameters(list<
Size>& selected_results);
100 void selectAllResultsForInput();
103 void disableAutomaticResultCreation();
114 static const
String VERSION;
128 static
bool gmf_new_ligand_read_;
130 String gmf_property_name_;
133 Result::Method gmf_result_method_;
134 String gmf_result_description_;
135 String gmf_receptor_conf_UID_;
136 bool gmf_result_creation_disabled_;
142 QXmlStreamReader* xmlIn_;
146 QTemporaryFile* resultfileTmp_;
147 QTemporaryFile* ligandfileTmp_;
148 QTemporaryFile* receptorfileTmp_;
151 QFile* receptorfile_;
152 QXmlStreamWriter* xmlOutReceptor_;
153 QXmlStreamWriter* xmlOutLigand_;
154 QXmlStreamWriter* xmlOutResult_;
162 Chain* current_chain_;
165 vector<
PDBAtom*> current_PDB_atoms_;
172 String current_ligand_id_;
173 String current_receptor_id_;
175 String current_molecule_id_;
176 String current_conformation_id_;
177 String current_molecule_name_;
178 String current_protein_name_;
181 vector<
Atom*> current_atoms_;
182 vector<
int> bonds_from_;
183 vector<
int> bonds_to_;
184 vector<
int> bonds_order_;
189 String current_Result_InputPoseId_;
192 void addLigand(
Ligand* lig);
195 void writeReceptors(QXmlStreamWriter &out);
196 void writeReceptor(
Receptor* recep, QXmlStreamWriter &out);
197 void writeProtein(
Protein* prot, QXmlStreamWriter &out);
198 void writeResidue(
Residue* res, QXmlStreamWriter &out);
199 void writePDBAtom(
PDBAtom* at, QXmlStreamWriter &out);
200 void writePDBAtom(
Atom* at, QXmlStreamWriter &out);
201 void writeConformation(
Conformation* conf, QXmlStreamWriter &out);
202 void writeFlexibility(const
FlexDefinition &fd, QXmlStreamWriter &out);
203 void writeRotamericFlexibleResidue(
Position idx, QXmlStreamWriter &out);
204 void writeFullyFlexibleResidue(
Position idx, QXmlStreamWriter &out);
206 bool readReceptors_();
207 bool readReceptor_();
214 bool readSubResult();
217 void writeResults(QXmlStreamWriter &out);
218 void writeResult(
Result* result, QXmlStreamWriter &out);
219 void writeResultData(const
Result::ResultData &rd, QXmlStreamWriter &out);
221 void writeLigands(QXmlStreamWriter &out);
222 bool writeLigand(
Ligand* lig, QXmlStreamWriter &out);
223 void writeMolecule(
Molecule* mol, QXmlStreamWriter &out);
224 void writeAtom(
Atom* at, QXmlStreamWriter &out);
225 void writeBond(
Bond* b, QXmlStreamWriter &out);
232 bool readCoordinates();
233 bool readFlexibility();
234 bool readFlexibilities();
235 bool readFullFlexResidue();
236 bool readRotamericResidue();
244 void buildMolecule();
245 void buildReceptor();
250 bool retrieveInt(const
String& s,
int &out);
251 bool retrieveFloat(const
String& s,
float &out);
253 bool setCoordinate(const
int& idx , const
String& coord);
254 static
String fromQString(const QString &s);
255 static QString toQString(const
String &s);
256 static
void attributesToHashMap(const QXmlAttributes& attributes,
HashMap<
String,
String>& map);
257 static
void attributesToHashMap(const QXmlStreamAttributes& attributes,
HashMap<
String,
String>& map);
258 static
bool isAminoAcid(
String s);
267 static
String RECEPTORSTAG;
268 static
String RECEPTORTAG;
269 static
String RECEPTOR_A_ID;
271 static
String PROTEIN_A_NAME;
272 static
String CONFORMATIONSTAG;
273 static
String CONFORMATIONTAG;
274 static
String CONFORMATION_A_ID;
275 static
String FLEXIBILITIESTAG;
276 static
String FLEXIBILITYTAG;
278 static
String RESIDUE_A_NAME;
279 static
String RESIDUE_A_IDX;
281 static
String PDBATOM_A_NAME;
285 static
String RESULT_A_METHOD;
286 static
String RESULT_A_METHODSTRING;
287 static
String SUBRESULTTAG;
288 static
String SUBRESULT_A_LIGCONFID;
289 static
String RESULTDATATAG;
290 static
String POSEDATATAG;
291 static
String RESULTDATA_A_ENERGY;
292 static
String RESULTDATA_A_CONFID;
293 static
String RESULTDATA_A_LIGID;
294 static
String RESULTDATA_A_METHOD;
298 static
String LIGAND_A_ID;
299 static
String MOLECULETAG;
300 static
String MOLECULE_A_NAME;
302 static
String ATOM_A_ELEMENT;
306 static
String BOND_A_FROM;
308 static
String BOND_A_ORDER;