src/mdParser/MDTreeParser.g

header
{
#include <stack>
#include "io/Globals.hpp"
#include "utils/StringUtils.hpp"
using namespace std;
using namespace oopse;
}
options
  {
  language = "Cpp";
  }
                     
class MDTreeParser extends TreeParser;

options
{
        k = 1;
        importVocab = MD;
}
{
  public:
    Globals* walkTree(ANTLR_USE_NAMESPACE(antlr)RefAST tree)
    {
      currConf = new Globals;
      blockStack.push(currConf);
      mdfile(tree);
      return currConf;
    }
  private:
    Globals* currConf;
    stack<DataHolder*> blockStack;    
}
mdfile  : (statement)* {blockStack.top()->validate(); blockStack.pop();}
        ;

statement : assignment
          | componentblock
          | moleculeblock
          | zconstraintblock
          ;


assignment  : #(ASSIGNEQUAL id:ID constant[#id]) //{blockStack.top()->assign(#ID->getText(),);}
            ;
            
constant [ANTLR_USE_NAMESPACE(antlr)RefAST id]
{
  int ival;
  RealType dval;
}    
            : ival=intConst {blockStack.top()->assign(id->getText(), ival);}
            | dval=floatConst {blockStack.top()->assign(id->getText(), dval);}
            | str1:ID {blockStack.top()->assign(id->getText(), str1->getText());}
            | str2:StringLiteral { std::string s =  str2->getText();
                                   s = s.substr(1, s.length()-2);
                                   blockStack.top()->assign(id->getText(),s);
                                 }
            ;
            

componentblock  : #(COMPONENT  {Component* currComponet = new Component(); blockStack.push(currComponet);}
                      (assignment)* 
                       ENDBLOCK ) {blockStack.top()->validate();blockStack.pop(); currConf->addComponent(currComponet);}
                ;
    
zconstraintblock  : #(ZCONSTRAINT {ZConsStamp* currZConsStamp = new ZConsStamp(); blockStack.push(currZConsStamp);}
                        (assignment)* 
                         ENDBLOCK ) {blockStack.top()->validate();blockStack.pop(); currConf->addZConsStamp(currZConsStamp);}
                  ;
  
moleculeblock : #(MOLECULE {MoleculeStamp* currMoleculeStamp = new MoleculeStamp(); blockStack.push(currMoleculeStamp);}
                    (moleculestatement)* 
                     ENDBLOCK ) {blockStack.top()->validate(); blockStack.pop(); currConf->addMoleculeStamp(currMoleculeStamp);}
              ;

moleculestatement : assignment
                  | atomblock
                  | bondblock
                  | bendblock
                  | torsionblock
                  | inversionblock
                  | rigidbodyblock
                  | cutoffgroupblock
                  | fragmentblock
                  ;

atomblock 
{
  int index;
}
          : #(ATOM index=intConst {AtomStamp* currAtomStamp = new AtomStamp(index); blockStack.push(currAtomStamp);} 
                  (atomstatement)* 
                  ENDBLOCK ) {
                                blockStack.top()->validate();
                                blockStack.pop(); 
                                MoleculeStamp* currMoleculeStamp = static_cast<MoleculeStamp*>(blockStack.top());
                                currMoleculeStamp->addAtomStamp(currAtomStamp); 
                             }
          ;

atomstatement 
{
vector<RealType> dvec;
AtomStamp* currAtomStamp =  static_cast<AtomStamp*>(blockStack.top());

}
              : assignment
              | #(POSITION dvec=doubleNumberTuple) {currAtomStamp->setPosition(dvec);}
              | #(ORIENTATION dvec=doubleNumberTuple) {currAtomStamp->setOrientation(dvec);}
              ;

                      
bondblock : #(BOND {BondStamp* currBondStamp = new BondStamp(); blockStack.push(currBondStamp);}
                (bondstatement)* 
                 ENDBLOCK )  {
                                blockStack.pop(); 
                                MoleculeStamp* currMoleculeStamp = static_cast<MoleculeStamp*>(blockStack.top());
                                currMoleculeStamp->addBondStamp(currBondStamp); 
                             }
          ;

bondstatement 
{
  vector<int> ivec;
  BondStamp* currBondStamp = static_cast<BondStamp*>(blockStack.top());
}
              : assignment
              | #(MEMBERS ivec=inttuple) {currBondStamp->setMembers(ivec);}
              ;

bendblock : #(BEND {BendStamp* currBendStamp = new BendStamp(); blockStack.push(currBendStamp);}
                  (bendstatement)* 
                   ENDBLOCK)  {
                                blockStack.top()->validate();
                                blockStack.pop(); 
                                MoleculeStamp* currMoleculeStamp = static_cast<MoleculeStamp*>(blockStack.top());
                                currMoleculeStamp->addBendStamp(currBendStamp); 
                             }
          ;

bendstatement 
{
  vector<int> ivec;
  BendStamp* currBendStamp = static_cast<BendStamp*>(blockStack.top());
}
              : assignment
              | #(MEMBERS ivec=inttuple) {currBendStamp->setMembers(ivec);}
              ;

torsionblock  : #(TORSION {TorsionStamp* currTorsionStamp = new TorsionStamp(); blockStack.push(currTorsionStamp);}
                   (torsionstatement)*
                    ENDBLOCK )  {
                                  blockStack.top()->validate();
                                  blockStack.pop(); 
                                  MoleculeStamp* currMoleculeStamp = static_cast<MoleculeStamp*>(blockStack.top());
                                  currMoleculeStamp->addTorsionStamp(currTorsionStamp); 
                                }
          ;

torsionstatement
{
  vector<int> ivec;
  TorsionStamp* currTorsionStamp = static_cast<TorsionStamp*>(blockStack.top());
}  
              : assignment
              | #(MEMBERS ivec=inttuple) {currTorsionStamp->setMembers(ivec);}
              ;

inversionblock  : #(INVERSION {InversionStamp* currInversionStamp = new InversionStamp(); blockStack.push(currInversionStamp);}
                   (inversionstatement)*
                    ENDBLOCK )  {
                                  blockStack.top()->validate();
                                  blockStack.pop(); 
                                  MoleculeStamp* currMoleculeStamp = static_cast<MoleculeStamp*>(blockStack.top());
                                  currMoleculeStamp->addInversionStamp(currInversionStamp); 
                                }
          ;

inversionstatement
{
  int icent;
  InversionStamp* currInversionStamp = static_cast<InversionStamp*>(blockStack.top());
}  
              : assignment
              | #(CENTER icent=intConst) {currInversionStamp->setCenter(icent);}
              ;

rigidbodyblock
{
int index;
}
              : #(RIGIDBODY index=intConst {RigidBodyStamp* currRigidBodyStamp = new RigidBodyStamp(index); blockStack.push(currRigidBodyStamp);}
                        (rigidbodystatement)* 
                        ENDBLOCK )  {
                                      blockStack.top()->validate();
                                      blockStack.pop(); 
                                      MoleculeStamp* currMoleculeStamp = static_cast<MoleculeStamp*>(blockStack.top());
                                      currMoleculeStamp->addRigidBodyStamp(currRigidBodyStamp); 
                                    }
                ;

rigidbodystatement  
{
  vector<int> ivec;
  RigidBodyStamp* currRigidBodyStamp = static_cast<RigidBodyStamp*>(blockStack.top());
}
              : assignment
              | #(MEMBERS ivec=inttuple) {currRigidBodyStamp->setMembers(ivec);}
              ;

cutoffgroupblock  : #(CUTOFFGROUP  {CutoffGroupStamp* currCutoffGroupStamp = new CutoffGroupStamp(); blockStack.push(currCutoffGroupStamp);}
                          (cutoffgroupstatement)* 
                           ENDBLOCK ) {
                                        blockStack.top()->validate();
                                        blockStack.pop(); 
                                        MoleculeStamp* currMoleculeStamp = static_cast<MoleculeStamp*>(blockStack.top());
                                        currMoleculeStamp->addCutoffGroupStamp(currCutoffGroupStamp); 
                                      }
                  ;

cutoffgroupstatement
{
  vector<int> ivec;
  CutoffGroupStamp* currCutoffGroupStamp = static_cast<CutoffGroupStamp*>(blockStack.top());
}  
              : assignment
              | #(MEMBERS ivec=inttuple) {currCutoffGroupStamp->setMembers(ivec);}             
              ;

fragmentblock {int ival;}
               : #(FRAGMENT ival=intConst {FragmentStamp* currFragmentStamp = new FragmentStamp(ival); blockStack.push(currFragmentStamp);}
                      (fragmentstatement)* 
                      ENDBLOCK) {
                                  blockStack.top()->validate();
                                  blockStack.pop(); 
                                  MoleculeStamp* currMoleculeStamp = static_cast<MoleculeStamp*>(blockStack.top());
                                  currMoleculeStamp->addFragmentStamp(currFragmentStamp); 
                                }
              ;

fragmentstatement : assignment
              ;


doubleNumberTuple   returns [vector<RealType> dvec]
{
  RealType dval;
}
              : (dval=doubleNumber {dvec.push_back(dval);})+  
              ;
                          
inttuple  returns [vector<int> ivec]
{
  int ival;
}
              : (ival=intConst {ivec.push_back(ival);})+ 
              ;

protected
intConst returns [int ival]
        : i1:NUM_INT {ival = lexi_cast<int>(i1->getText());} 
        | i2:NUM_LONG {ival = lexi_cast<int>(i2->getText());}
        ;

protected
doubleNumber  returns [RealType dval]
              : 
                ic:intConst {dval = lexi_cast<RealType>(ic->getText());}
                | fc:floatConst {dval = lexi_cast<RealType>(fc->getText());} 
                               
              ;
              
protected
floatConst returns [RealType dval]
        : d1:NUM_FLOAT {dval = lexi_cast<RealType>(d1->getText());}  
        | d2:NUM_DOUBLE {dval = lexi_cast<RealType>(d2->getText());} 
        ;
        
Revision:	1277
Committed:	Mon Jul 14 12:35:58 2008 UTC (16 years, 9 months ago) by gezelter
Original Path:	*trunk/src/mdParser/MDTreeParser.g*
File size:	10447 byte(s)
Log Message:	Changes for implementing Amber force field: Added Inversions and worked on BaseAtomTypes so that they'd function with the fortran side.
#	Content
1	header
2	{
3	#include <stack>
4	#include "io/Globals.hpp"
5	#include "utils/StringUtils.hpp"
6	using namespace std;
7	using namespace oopse;
8	}
9	options
10	{
11	language = "Cpp";
12	}
13
14	class MDTreeParser extends TreeParser;
15
16	options
17	{
18	k = 1;
19	importVocab = MD;
20	}
21	{
22	public:
23	Globals* walkTree(ANTLR_USE_NAMESPACE(antlr)RefAST tree)
24	{
25	currConf = new Globals;
26	blockStack.push(currConf);
27	mdfile(tree);
28	return currConf;
29	}
30	private:
31	Globals* currConf;
32	stack<DataHolder*> blockStack;
33	}
34	mdfile : (statement)* {blockStack.top()->validate(); blockStack.pop();}
35	;
36
37	statement : assignment
38	\| componentblock
39	\| moleculeblock
40	\| zconstraintblock
41	;
42
43
44	assignment : #(ASSIGNEQUAL id:ID constant[#id]) //{blockStack.top()->assign(#ID->getText(),);}
45	;
46
47	constant [ANTLR_USE_NAMESPACE(antlr)RefAST id]
48	{
49	int ival;
50	RealType dval;
51	}
52	: ival=intConst {blockStack.top()->assign(id->getText(), ival);}
53	\| dval=floatConst {blockStack.top()->assign(id->getText(), dval);}
54	\| str1:ID {blockStack.top()->assign(id->getText(), str1->getText());}
55	\| str2:StringLiteral { std::string s = str2->getText();
56	s = s.substr(1, s.length()-2);
57	blockStack.top()->assign(id->getText(),s);
58	}
59	;
60
61
62	componentblock : #(COMPONENT {Component* currComponet = new Component(); blockStack.push(currComponet);}
63	(assignment)*
64	ENDBLOCK ) {blockStack.top()->validate();blockStack.pop(); currConf->addComponent(currComponet);}
65	;
66
67	zconstraintblock : #(ZCONSTRAINT {ZConsStamp* currZConsStamp = new ZConsStamp(); blockStack.push(currZConsStamp);}
68	(assignment)*
69	ENDBLOCK ) {blockStack.top()->validate();blockStack.pop(); currConf->addZConsStamp(currZConsStamp);}
70	;
71
72	moleculeblock : #(MOLECULE {MoleculeStamp* currMoleculeStamp = new MoleculeStamp(); blockStack.push(currMoleculeStamp);}
73	(moleculestatement)*
74	ENDBLOCK ) {blockStack.top()->validate(); blockStack.pop(); currConf->addMoleculeStamp(currMoleculeStamp);}
75	;
76
77	moleculestatement : assignment
78	\| atomblock
79	\| bondblock
80	\| bendblock
81	\| torsionblock
82	\| inversionblock
83	\| rigidbodyblock
84	\| cutoffgroupblock
85	\| fragmentblock
86	;
87
88	atomblock
89	{
90	int index;
91	}
92	: #(ATOM index=intConst {AtomStamp* currAtomStamp = new AtomStamp(index); blockStack.push(currAtomStamp);}
93	(atomstatement)*
94	ENDBLOCK ) {
95	blockStack.top()->validate();
96	blockStack.pop();
97	MoleculeStamp* currMoleculeStamp = static_cast<MoleculeStamp*>(blockStack.top());
98	currMoleculeStamp->addAtomStamp(currAtomStamp);
99	}
100	;
101
102	atomstatement
103	{
104	vector<RealType> dvec;
105	AtomStamp* currAtomStamp = static_cast<AtomStamp*>(blockStack.top());
106
107	}
108	: assignment
109	\| #(POSITION dvec=doubleNumberTuple) {currAtomStamp->setPosition(dvec);}
110	\| #(ORIENTATION dvec=doubleNumberTuple) {currAtomStamp->setOrientation(dvec);}
111	;
112
113
114	bondblock : #(BOND {BondStamp* currBondStamp = new BondStamp(); blockStack.push(currBondStamp);}
115	(bondstatement)*
116	ENDBLOCK ) {
117	blockStack.pop();
118	MoleculeStamp* currMoleculeStamp = static_cast<MoleculeStamp*>(blockStack.top());
119	currMoleculeStamp->addBondStamp(currBondStamp);
120	}
121	;
122
123	bondstatement
124	{
125	vector<int> ivec;
126	BondStamp* currBondStamp = static_cast<BondStamp*>(blockStack.top());
127	}
128	: assignment
129	\| #(MEMBERS ivec=inttuple) {currBondStamp->setMembers(ivec);}
130	;
131
132	bendblock : #(BEND {BendStamp* currBendStamp = new BendStamp(); blockStack.push(currBendStamp);}
133	(bendstatement)*
134	ENDBLOCK) {
135	blockStack.top()->validate();
136	blockStack.pop();
137	MoleculeStamp* currMoleculeStamp = static_cast<MoleculeStamp*>(blockStack.top());
138	currMoleculeStamp->addBendStamp(currBendStamp);
139	}
140	;
141
142	bendstatement
143	{
144	vector<int> ivec;
145	BendStamp* currBendStamp = static_cast<BendStamp*>(blockStack.top());
146	}
147	: assignment
148	\| #(MEMBERS ivec=inttuple) {currBendStamp->setMembers(ivec);}
149	;
150
151	torsionblock : #(TORSION {TorsionStamp* currTorsionStamp = new TorsionStamp(); blockStack.push(currTorsionStamp);}
152	(torsionstatement)*
153	ENDBLOCK ) {
154	blockStack.top()->validate();
155	blockStack.pop();
156	MoleculeStamp* currMoleculeStamp = static_cast<MoleculeStamp*>(blockStack.top());
157	currMoleculeStamp->addTorsionStamp(currTorsionStamp);
158	}
159	;
160
161	torsionstatement
162	{
163	vector<int> ivec;
164	TorsionStamp* currTorsionStamp = static_cast<TorsionStamp*>(blockStack.top());
165	}
166	: assignment
167	\| #(MEMBERS ivec=inttuple) {currTorsionStamp->setMembers(ivec);}
168	;
169
170	inversionblock : #(INVERSION {InversionStamp* currInversionStamp = new InversionStamp(); blockStack.push(currInversionStamp);}
171	(inversionstatement)*
172	ENDBLOCK ) {
173	blockStack.top()->validate();
174	blockStack.pop();
175	MoleculeStamp* currMoleculeStamp = static_cast<MoleculeStamp*>(blockStack.top());
176	currMoleculeStamp->addInversionStamp(currInversionStamp);
177	}
178	;
179
180	inversionstatement
181	{
182	int icent;
183	InversionStamp* currInversionStamp = static_cast<InversionStamp*>(blockStack.top());
184	}
185	: assignment
186	\| #(CENTER icent=intConst) {currInversionStamp->setCenter(icent);}
187	;
188
189	rigidbodyblock
190	{
191	int index;
192	}
193	: #(RIGIDBODY index=intConst {RigidBodyStamp* currRigidBodyStamp = new RigidBodyStamp(index); blockStack.push(currRigidBodyStamp);}
194	(rigidbodystatement)*
195	ENDBLOCK ) {
196	blockStack.top()->validate();
197	blockStack.pop();
198	MoleculeStamp* currMoleculeStamp = static_cast<MoleculeStamp*>(blockStack.top());
199	currMoleculeStamp->addRigidBodyStamp(currRigidBodyStamp);
200	}
201	;
202
203	rigidbodystatement
204	{
205	vector<int> ivec;
206	RigidBodyStamp* currRigidBodyStamp = static_cast<RigidBodyStamp*>(blockStack.top());
207	}
208	: assignment
209	\| #(MEMBERS ivec=inttuple) {currRigidBodyStamp->setMembers(ivec);}
210	;
211
212	cutoffgroupblock : #(CUTOFFGROUP {CutoffGroupStamp* currCutoffGroupStamp = new CutoffGroupStamp(); blockStack.push(currCutoffGroupStamp);}
213	(cutoffgroupstatement)*
214	ENDBLOCK ) {
215	blockStack.top()->validate();
216	blockStack.pop();
217	MoleculeStamp* currMoleculeStamp = static_cast<MoleculeStamp*>(blockStack.top());
218	currMoleculeStamp->addCutoffGroupStamp(currCutoffGroupStamp);
219	}
220	;
221
222	cutoffgroupstatement
223	{
224	vector<int> ivec;
225	CutoffGroupStamp* currCutoffGroupStamp = static_cast<CutoffGroupStamp*>(blockStack.top());
226	}
227	: assignment
228	\| #(MEMBERS ivec=inttuple) {currCutoffGroupStamp->setMembers(ivec);}
229	;
230
231	fragmentblock {int ival;}
232	: #(FRAGMENT ival=intConst {FragmentStamp* currFragmentStamp = new FragmentStamp(ival); blockStack.push(currFragmentStamp);}
233	(fragmentstatement)*
234	ENDBLOCK) {
235	blockStack.top()->validate();
236	blockStack.pop();
237	MoleculeStamp* currMoleculeStamp = static_cast<MoleculeStamp*>(blockStack.top());
238	currMoleculeStamp->addFragmentStamp(currFragmentStamp);
239	}
240	;
241
242	fragmentstatement : assignment
243	;
244
245
246
247	doubleNumberTuple returns [vector<RealType> dvec]
248	{
249	RealType dval;
250	}
251	: (dval=doubleNumber {dvec.push_back(dval);})+
252	;
253
254	inttuple returns [vector<int> ivec]
255	{
256	int ival;
257	}
258	: (ival=intConst {ivec.push_back(ival);})+
259	;
260
261	protected
262	intConst returns [int ival]
263	: i1:NUM_INT {ival = lexi_cast<int>(i1->getText());}
264	\| i2:NUM_LONG {ival = lexi_cast<int>(i2->getText());}
265	;
266
267	protected
268	doubleNumber returns [RealType dval]
269	:
270	ic:intConst {dval = lexi_cast<RealType>(ic->getText());}
271	\| fc:floatConst {dval = lexi_cast<RealType>(fc->getText());}
272
273	;
274
275	protected
276	floatConst returns [RealType dval]
277	: d1:NUM_FLOAT {dval = lexi_cast<RealType>(d1->getText());}
278	\| d2:NUM_DOUBLE {dval = lexi_cast<RealType>(d2->getText());}
279	;
280