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%{
#include <BALL/FORMAT/GAMESSLogFile.h>
#include <iostream>
#include <malloc.h>
using namespace BALL;
using namespace std;
extern int yylex();
extern void yyerror(char const* s);
%}
%union {
char* text;
float value;
int number;
}
%token <text> TK_LINE
%token <text> TK_OPTION
%token <text> TK_EIGEN_LINE
%token <text> TK_ATOM
%token <value> TK_FLOAT
%token <text> TK_BOND
%token <text> TK_OTHER
%token <text> TK_CHARGE
%token <text> TK_POPULATION
%token <text> TK_COEFFICIENTS
%token TK_TITLE
%token TK_COORDS_BOHR
%token TK_COORDS_ANGSTROM
%token TK_END_MOL
%token TK_ZMAT_START
%token TK_ZMAT_END
%token TK_CHARGE_START
%token TK_CHARGE_END
%token TK_POPULATION_START
%token TK_POPULATION_END
%token TK_EIGEN_START
%token TK_EIGEN_END
%token TK_BASIS_OPTIONS_START
%token TK_BASIS_OPTIONS_END
%token TK_BOND_START
%token TK_BOND_END
%%
gamessfile: /* empty */
| gamessfile molecule {}
| gamessfile geometry {}
| gamessfile zmat {}
| gamessfile basis_set {}
| gamessfile bond {}
| gamessfile charges {}
| gamessfile population {}
| gamessfile eigenvectors {}
| gamessfile TK_LINE {
String s($2);
s.toUpper();
if (s.hasSubstring("ALPHA"))
GAMESSLogFile::state.current_parser->current_set = 1;
else
GAMESSLogFile::state.current_parser->current_set = 2;
}
;
//non_blocked:
// non_blocked TK_LINE {printf("1 %s", $2);}
// | TK_LINE {printf("2 %s\n", $1);}
// ;
molecule: molecule_header {};
molecule_header:
TK_TITLE TK_LINE TK_LINE {
GAMESSLogFile::state.current_parser->newMolecule();
GAMESSLogFile::state.current_parser->setMoleculeName($2);
};
geometry: unit coordinates TK_END_MOL {
GAMESSLogFile::state.current_parser->molecule_already_defined = true;
};
unit:
TK_COORDS_BOHR {
GAMESSLogFile::state.current_parser->current_atom = 0;
GAMESSLogFile::state.current_parser->setUnitConversionFactor(0.529177);
}
| TK_COORDS_ANGSTROM {
GAMESSLogFile::state.current_parser->current_atom = 0;
GAMESSLogFile::state.current_parser->setUnitConversionFactor(1.0);
}
;
coordinates: /* empty */
| coordinates TK_ATOM
{
String line($2);
GAMESSLogFile::state.current_parser->insertAtom(line.getField(0).c_str(),
0.,
line.getField(2).toFloat(),
line.getField(3).toFloat(),
line.getField(4).toFloat());
}
;
zmat: TK_ZMAT_START zmat_data TK_ZMAT_END {};
zmat_data: /* empty */
| zmat_data TK_BOND {
String s($2);
GAMESSLogFile::state.current_parser->insertBond(s.getField(2).toInt()-1, s.getField(3).toInt()-1);
}
| zmat_data TK_OTHER {}
;
bond: start_bond bonds TK_BOND_END {};
start_bond: TK_BOND_START {
GAMESSLogFile::state.current_parser->clearBonds();
}
bonds: /* empty */
| bonds TK_LINE {}
| bonds TK_BOND {
String line($2);
std::vector<String> fields;
line.split(fields);
/** TODO: is this a sensible threshold?? **/
if (fields[3].toFloat() > 0.3)
GAMESSLogFile::state.current_parser->insertBond(fields[0].toInt()-1, fields[1].toInt()-1);
free($2);
}
;
basis_set: TK_BASIS_OPTIONS_START basis_options TK_BASIS_OPTIONS_END {};
basis_options: /* empty */
| basis_options TK_OPTION {
/** Some of this stuff should really be done in flex. But if we add those
* rules, flex gets terribly slow... **/
String line($2);
std::vector<String> fields;
line.split(fields, "=");
GAMESSLogFile::state.current_parser->addBasisOption(fields[0], fields[1]);
free($2);
}
;
charges: charges_header charges_data TK_CHARGE_END {};
charges_header: TK_CHARGE_START {
GAMESSLogFile::state.current_parser->current_atom = 0;
};
charges_data: /* empty */
| charges_data TK_CHARGE {
/** Do we always want to overwrite those? **/
String s($2);
GAMESSLogFile::state.current_parser->setCurrentCharge(s.getField(1).toFloat());
GAMESSLogFile::state.current_parser->current_atom++;
}
;
population: TK_POPULATION_START population_data TK_POPULATION_END {};
population_data: /* empty */
| population_data TK_POPULATION {
/** Do we really always want this? This will always set the mulliken charges... **/
String line($2);
GAMESSLogFile::state.current_parser->current_atom = line.getField(0).toInt()-1;
GAMESSLogFile::state.current_parser->setCurrentCharge(line.getField(3).toFloat());
}
;
eigenvectors: TK_EIGEN_START eigendata TK_EIGEN_END {};
eigendata: /* empty */
| eigendata TK_LINE {}
| eigendata TK_COEFFICIENTS {
String s($2);
std::vector<String> fields;
s.split(fields);
GAMESSLogFile::state.current_parser->current_coefficient_line += fields.size();
for (Size i=0; i<fields.size(); i++)
{
GAMESSLogFile::state.current_parser->addCoefficient(fields[i].toFloat());
}
}
;
%%
void yyerror(char* s)
{
/** throw Exception::ParseError(__FILE__, 0,
SmilesParser::state.buffer,
String(s) + String(" (at position ")
+ String(SmilesParser::state.char_count) + String(")"));
*/
printf("Parse Error! %s\n", s);
}
|
