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root/OpenMD/trunk/src/selection/SelectionEvaluator.cpp
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Comparing trunk/src/selection/SelectionEvaluator.cpp (file contents):
Revision 278 by tim, Tue Feb 1 22:49:23 2005 UTC vs.
Revision 283 by tim, Thu Feb 3 23:14:05 2005 UTC

# Line 39 | Line 39
39   * such damages.
40   */
41  
42 + #include <stack>
43   #include "selection/SelectionEvaluator.hpp"
44 + #include "primitives/Atom.hpp"
45 + #include "primitives/DirectionalAtom.hpp"
46 + #include "primitives/RigidBody.hpp"
47 + #include "primitives/Molecule.hpp"
48 +
49   namespace oopse {
50  
51  
52 + SelectionEvaluator::SelectionEvaluator(SimInfo* si, const std::string& script) : info(si), finder(info){
53 + }            
54 +
55   bool SelectionEvaluator::loadScript(const std::string& filename, const std::string& script) {
56      this->filename = filename;
57      this->script = script;
# Line 61 | Line 70 | void SelectionEvaluator::clearState() {
70  
71   void SelectionEvaluator::clearState() {
72      for (int i = scriptLevelMax; --i >= 0; )
73 <        stack[i] = null;
73 >        stack[i].clear();
74      scriptLevel = 0;
75      error = false;
76 <    errorMessage = null;
76 >    errorMessage = "";
77   }
78  
79   bool SelectionEvaluator::loadScriptString(const std::string& script) {
80      clearState();
81 <    return loadScript(null, script);
81 >    return loadScript("", script);
82   }
83  
84   bool SelectionEvaluator::loadScriptFile(const std::string& filename) {
# Line 77 | Line 86 | bool SelectionEvaluator::loadScriptFile(const std::str
86      return loadScriptFileInternal(filename);
87   }
88  
89 + bool SelectionEvaluator::loadScriptFileInternal(const  std::string & filename) {
90 +    return true; /**@todo */
91 + }
92  
93   void SelectionEvaluator::instructionDispatchLoop(){
94  
95 <    while ( pc < aatoken.length) {
95 >    while ( pc < aatoken.size()) {
96          statement = aatoken[pc++];
97 <        statementLength = statement.length;
97 >        statementLength = statement.size();
98          Token token = statement[0];
99          switch (token.tok) {
100 <            case Token.define:
100 >            case Token::define:
101                  define();
102              break;
103 <            case Token.select:
103 >            case Token::select:
104                  select();
105              break;
106              default:
# Line 98 | Line 110 | void SelectionEvaluator::instructionDispatchLoop(){
110      }
111   }
112  
113 <  void SelectionEvaluator::predefine(String script) {
102 <    if (compiler.compile("#predefine", script)) {
103 <      Token [][] aatoken = compiler.getAatokenCompiled();
104 <      if (aatoken.length != 1) {
105 <        viewer.scriptStatus("predefinition does not have exactly 1 command:"
106 <                            + script);
107 <        return;
108 <      }
109 <      Token[] statement = aatoken[0];
110 <      if (statement.length > 2) {
111 <        int tok = statement[1].tok;
112 <        if (tok == Token.identifier ||
113 <            (tok & Token.predefinedset) == Token.predefinedset) {
114 <          String variable = (String)statement[1].value;
115 <          variables.put(variable, statement);
116 <        } else {
117 <          viewer.scriptStatus("invalid variable name:" + script);
118 <        }
119 <      } else {
120 <        viewer.scriptStatus("bad predefinition length:" + script);
121 <      }
122 <    } else {
123 <      viewer.scriptStatus("predefined set compile error:" + script +
124 <                          "\ncompile error:" + compiler.getErrorMessage());
125 <    }
126 <  }
127 <
128 <
129 <
130 <  BitSet SelectionEvaluator::expression(Token[] code, int pcStart) throws ScriptException {
131 <    int numberOfAtoms = viewer.getAtomCount();
113 >  BitSet SelectionEvaluator::expression(const std::vector<Token>& code, int pcStart) {
114      BitSet bs;
115 <    BitSet[] stack = new BitSet[10];
116 <    int sp = 0;
135 <
115 >    std::stack<BitSet> stack;
116 >    
117      for (int pc = pcStart; ; ++pc) {
118        Token instruction = code[pc];
119 <      if (logMessages)
139 <        viewer.scriptStatus("instruction=" + instruction);
119 >
120        switch (instruction.tok) {
121 <      case Token.expressionBegin:
121 >      case Token::expressionBegin:
122          break;
123 <      case Token.expressionEnd:
144 <        break expression_loop;
145 <      case Token.all:
146 <        bs = stack[sp++] = new BitSet(numberOfAtoms);
147 <        for (int i = numberOfAtoms; --i >= 0; )
148 <          bs.set(i);
123 >      case Token::expressionEnd:
124          break;
125 <      case Token.none:
126 <        stack[sp++] = new BitSet();
125 >      case Token::all:
126 >        bs = BitSet(nStuntDouble);
127 >        bs.setAll();
128 >        stack.push(bs);            
129          break;
130 <      case Token.opOr:
131 <        bs = stack[--sp];
132 <        stack[sp-1].or(bs);
130 >      case Token::none:
131 >        bs = BitSet(nStuntDouble);
132 >        stack.push(bs);            
133          break;
134 <      case Token.opAnd:
135 <        bs = stack[--sp];
136 <        stack[sp-1].and(bs);
134 >      case Token::opOr:
135 >        bs = stack.top();
136 >        stack.pop();
137 >        stack.top() |= bs;
138          break;
139 <      case Token.opNot:
140 <        bs = stack[sp - 1];
141 <        notSet(bs);
139 >      case Token::opAnd:
140 >        bs = stack.top();
141 >        stack.pop();
142 >        stack.top() &= bs;
143          break;
144 <      case Token.within:
145 <        bs = stack[sp - 1];
167 <        stack[sp - 1] = new BitSet();
168 <        withinInstruction(instruction, bs, stack[sp - 1]);
144 >      case Token::opNot:
145 >        stack.top().flip();
146          break;
147 <      case Token.selected:
148 <        stack[sp++] = copyBitSet(viewer.getSelectionSet());
147 >      case Token::within:
148 >
149 >        withinInstruction(instruction, stack.top());
150          break;
151 <      case Token.y:
152 <      case Token.amino:
153 <      case Token.backbone:
154 <      case Token.solvent:
155 <      case Token.identifier:
178 <      case Token.sidechain:
179 <      case Token.surface:
180 <        stack[sp++] = lookupIdentifierValue((String)instruction.value);
151 >      //case Token::selected:
152 >      //  stack.push(getSelectionSet());
153 >      //  break;
154 >      case Token::name:
155 >        stack.push(nameInstruction(boost::any_cast<std::string>(instruction.value)));
156          break;
182 –      case Token.opLT:
183 –      case Token.opLE:
184 –      case Token.opGE:
185 –      case Token.opGT:
186 –      case Token.opEQ:
187 –      case Token.opNE:
188 –        bs = stack[sp++] = new BitSet();
189 –        comparatorInstruction(instruction, bs);
157          break;
158 +      case Token::identifier:
159 +        stack.push(lookupValue(boost::any_cast<std::string>(instruction.value)));
160 +        break;
161 +      case Token::opLT:
162 +      case Token::opLE:
163 +      case Token::opGE:
164 +      case Token::opGT:
165 +      case Token::opEQ:
166 +      case Token::opNE:
167 +        stack.push(comparatorInstruction(instruction));
168 +        break;
169        default:
170          unrecognizedExpression();
171        }
172      }
173 <    if (sp != 1)
173 >    if (stack.size() != 1)
174        evalError("atom expression compiler error - stack over/underflow");
175 <    return stack[0];
175 >          
176 >    return stack.top();
177    }
178  
179  
180  
181 <  void SelectionEvaluator::comparatorInstruction(Token instruction, BitSet bs) {
181 > BitSet SelectionEvaluator::comparatorInstruction(const Token& instruction) {
182      int comparator = instruction.tok;
183      int property = instruction.intValue;
184 <    float propertyValue = 0; // just for temperature
185 <    int comparisonValue = ((Integer)instruction.value).intValue();
186 <    int numberOfAtoms = viewer.getAtomCount();
187 <    Frame frame = viewer.getFrame();
188 <    for (int i = 0; i < numberOfAtoms; ++i) {
189 <      Atom atom = frame.getAtomAt(i);
190 <      switch (property) {
191 <      case Token.atomno:
192 <        propertyValue = atom.getAtomNumber();
193 <        break;
194 <      case Token.elemno:
195 <        propertyValue = atom.getElementNumber();
196 <        break;
197 <      case Token.temperature:
198 <        propertyValue = atom.getBfactor100();
199 <        if (propertyValue < 0)
200 <          continue;
201 <        propertyValue /= 100;
202 <        break;
203 <      case Token._atomID:
204 <        propertyValue = atom.getSpecialAtomID();
226 <        if (propertyValue < 0)
227 <          continue;
228 <        break;
229 <      case Token._structure:
230 <        propertyValue = getProteinStructureType(atom);
231 <        if (propertyValue == -1)
232 <          continue;
233 <        break;
234 <      case Token.radius:
235 <        propertyValue = atom.getRasMolRadius();
236 <        break;
237 <      case Token._bondedcount:
238 <        propertyValue = atom.getCovalentBondCount();
239 <        break;
240 <      case Token.model:
241 <        propertyValue = atom.getModelTagNumber();
242 <        break;
243 <      default:
244 <        unrecognizedAtomProperty(property);
245 <      }
246 <      boolean match = false;
247 <      switch (comparator) {
248 <      case Token.opLT:
249 <        match = propertyValue < comparisonValue;
250 <        break;
251 <      case Token.opLE:
252 <        match = propertyValue <= comparisonValue;
253 <        break;
254 <      case Token.opGE:
255 <        match = propertyValue >= comparisonValue;
256 <        break;
257 <      case Token.opGT:
258 <        match = propertyValue > comparisonValue;
259 <        break;
260 <      case Token.opEQ:
261 <        match = propertyValue == comparisonValue;
262 <        break;
263 <      case Token.opNE:
264 <        match = propertyValue != comparisonValue;
265 <        break;
266 <      }
267 <      if (match)
268 <        bs.set(i);
184 >    float comparisonValue = boost::any_cast<float>(instruction.value);
185 >    float propertyValue;
186 >    BitSet bs(nStuntDouble);
187 >    
188 >    SimInfo::MoleculeIterator mi;
189 >    Molecule* mol;
190 >    Molecule::AtomIterator ai;
191 >    Atom* atom;
192 >    Molecule::RigidBodyIterator rbIter;
193 >    RigidBody* rb;
194 >    
195 >    for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
196 >
197 >        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
198 >            compareProperty(atom, bs, property, comparator, comparisonValue);
199 >        }
200 >        
201 >        //change the positions of atoms which belong to the rigidbodies
202 >        for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
203 >            compareProperty(rb, bs, property, comparator, comparisonValue);
204 >        }        
205      }
270 –  }
206  
207 < void SelectionEvaluator::withinInstruction(Token instruction, BitSet bs, BitSet bsResult)
207 >    return bs;
208 > }
209  
210 <    Object withinSpec = instruction.value;
211 <    if (withinSpec instanceof Float) {
212 <        withinDistance(((Float)withinSpec).floatValue(), bs, bsResult);
210 > void SelectionEvaluator::compareProperty(StuntDouble* sd, BitSet& bs, int property, int comparator, float comparisonValue) {
211 >        double propertyValue;
212 >        switch (property) {
213 >        case Token::mass:
214 >            propertyValue = sd->getMass();
215 >            break;
216 >        case Token::charge:
217 >            return;
218 >            //break;
219 >        case Token::dipole:
220 >            return;
221 >            //break;
222 >        default:
223 >            unrecognizedAtomProperty(property);
224 >        }
225 >        
226 >        bool match = false;
227 >        switch (comparator) {
228 >            case Token::opLT:
229 >                match = propertyValue < comparisonValue;
230 >                break;
231 >            case Token::opLE:
232 >                match = propertyValue <= comparisonValue;
233 >                break;
234 >            case Token::opGE:
235 >                match = propertyValue >= comparisonValue;
236 >                break;
237 >            case Token::opGT:
238 >                match = propertyValue > comparisonValue;
239 >                break;
240 >            case Token::opEQ:
241 >                match = propertyValue == comparisonValue;
242 >                break;
243 >            case Token::opNE:
244 >                match = propertyValue != comparisonValue;
245 >                break;
246 >        }
247 >        if (match)
248 >            bs.setBitOn(sd->getGlobalIndex());
249 >
250 > }
251 >
252 > void SelectionEvaluator::withinInstruction(const Token& instruction, BitSet& bs){
253 >
254 >    boost::any withinSpec = instruction.value;
255 >    if (withinSpec.type() == typeid(float)){
256 >        //
257          return;
258      }
259 <    evalError("Unrecognized within parameter:" + withinSpec);
259 >    
260 >    evalError("Unrecognized within parameter");
261   }
262  
263 <  void SelectionEvaluator::withinDistance(float distance, BitSet bs, BitSet bsResult) {
264 <    Frame frame = viewer.getFrame();
265 <    for (int i = frame.getAtomCount(); --i >= 0; ) {
266 <      if (bs.get(i)) {
267 <        Atom atom = frame.getAtomAt(i);
268 <        AtomIterator iterWithin =
269 <          frame.getWithinIterator(atom, distance);
270 <        while (iterWithin.hasNext())
271 <          bsResult.set(iterWithin.next().getAtomIndex());
272 <      }
263 > void SelectionEvaluator::define() {
264 >    assert(statement.size() >= 3);
265 >
266 >    std::string variable = boost::any_cast<std::string>(statement[1].value);
267 >
268 >    variables.insert(std::make_pair(variable, expression(statement, 2)));
269 > }
270 >
271 >
272 > /** @todo */
273 > void SelectionEvaluator::predefine(const std::string& script) {
274 >
275 >    if (compiler.compile("#predefine", script)) {
276 >        std::vector<std::vector<Token> > aatoken = compiler.getAatokenCompiled();
277 >        if (aatoken.size() != 1) {
278 >            evalError("predefinition does not have exactly 1 command:"
279 >                + script);
280 >            return;
281 >        }
282 >        std::vector<Token> statement = aatoken[0];
283 >        if (statement.size() > 2) {
284 >            int tok = statement[1].tok;
285 >            if (tok == Token::identifier || (tok & Token::predefinedset) == Token::predefinedset) {
286 >                std::string variable = boost::any_cast<std::string>(statement[1].value);
287 >                variables.insert(std::make_pair(variable, statement));
288 >
289 >            } else {
290 >                evalError("invalid variable name:" + script);
291 >            }
292 >        }else {
293 >            evalError("bad predefinition length:" + script);
294 >        }
295 >
296 >        
297 >    } else {
298 >        evalError("predefined set compile error:" + script +
299 >          "\ncompile error:" + compiler.getErrorMessage());
300      }
293 –  }
301  
295 –  void SelectionEvaluator::define() throws ScriptException {
296 –    String variable = (String)statement[1].value;
297 –    variables.put(variable, (expression(statement, 2)));
298 –  }
302   }
303  
304 <  void SelectionEvaluator::predefine(Token[] statement) {
305 <    String variable = (String)statement[1].value;
306 <    variables.put(variable, statement);
304 <  }
304 > void SelectionEvaluator::select(){
305 >    //viewer.setSelectionSet(expression(statement, 1));
306 > }
307  
308 <  void SelectionEvaluator::select(){
309 <    // NOTE this is called by restrict()
310 <    if (statementLength == 1) {
311 <      viewer.selectAll();
312 <      if (!viewer.getRasmolHydrogenSetting())
313 <        viewer.excludeSelectionSet(getHydrogenSet());
314 <      if (!viewer.getRasmolHeteroSetting())
315 <        viewer.excludeSelectionSet(getHeteroSet());
308 > BitSet SelectionEvaluator::lookupValue(const std::string& variable){
309 >
310 >    std::map<std::string, boost::any>::iterator i = variables.find(variable);
311 >
312 >    if (i != variables.end()) {
313 >        if (i->second.type() == typeid(BitSet)) {
314 >            return boost::any_cast<BitSet>(i->second);
315 >        } else if (i->second.type() ==  typeid(std::vector<Token>)){
316 >            BitSet bs = expression(boost::any_cast<std::vector<Token> >(i->second), 2);
317 >            i->second =  bs; /**@todo fixme */
318 >            return bs;
319 >        }
320      } else {
321 <      viewer.setSelectionSet(expression(statement, 1));
321 >        unrecognizedIdentifier(variable);
322      }
323 <    viewer.scriptStatus("" + viewer.getSelectionCount() + " atoms selected");
324 <  }
325 <  
326 <  }
323 > }
324 >
325 > BitSet SelectionEvaluator::nameInstruction(const std::string& name){
326 >    BitSet bs(nStuntDouble);
327 >    
328 >    bool hasError = finder.match(name, bs);
329 >    
330 >    return bs;    
331 > }    
332 >
333 >
334 > }

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