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%%{
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
# NOTES:
#
# 1. Will need to 'include utilities "utilities.rl";' before including this file
#
# 2. Make declarations for the following variables visible in scope
# int intVal, intVal2;
# int x, y, z;
# std::string stringVal, stringVal2;
# int atomId, atomicNum;
# char *lineStart;
#
# 3. Define the following functions
# void newAtom(int atomId, int x, int y, int z, std::string const& atomStyle);
# void newBond(std::string const& bondType, int targetAtomId);
# void newBondDirection(int atomId1, int atomId2);
# void newAtomInfo(std::string const& key, std::string const& value);
# void syntaxError(std::string const& errorMessage);
machine atom;
atom_id =
whole_number
% { atomId = intVal; /*cerr << "atomId = " << atomId << endl;*/ }
;
atomic_num =
'(' nonNEWLINEspace* whole_number nonNEWLINEspace* ')'
% { atomicNum = intVal; /*cerr << "atomId = " << atomId << endl;*/}
;
xcoord = nonNEWLINEspace* integer nonNEWLINEspace* %{x = intVal; };
ycoord = nonNEWLINEspace* integer nonNEWLINEspace* %{y = intVal; };
zcoord = nonNEWLINEspace* integer nonNEWLINEspace* %{z = intVal; };
atom_coords =
'(' xcoord ',' ycoord ',' zcoord ')'
#% { cerr << "atom_coords = (" << x << ',' << y << ',' << z << ')' << endl; }
;
atom_style =
char_string_with_space
% { atomStyle = stringVal;
/*cerr << "atom_style = " << stringVal << endl;*/
}
;
atom_decl_line =
'atom'
nonNEWLINEspace+
atom_id
nonNEWLINEspace+
atomic_num
nonNEWLINEspace+
atom_coords
(nonNEWLINEspace+ atom_style)?
nonNEWLINEspace*
EOL
@ { newAtom(atomId, atomicNum, x, y, z, atomStyle); }
;
action newBondAction {
newBond(stringVal, intVal);
}
bond_line =
'bond'
[123acg] @ { stringVal = *p; }
(nonNEWLINEspace+
whole_number
% newBondAction
)+
nonNEWLINEspace*
EOL
;
action newBondDirectionAction {
newBondDirection(intVal, intVal2);
}
bond_direction_line =
'bond_direction'
nonNEWLINEspace+
whole_number
nonNEWLINEspace+
whole_number2
nonNEWLINEspace*
EOL
@ newBondDirectionAction
;
action newInfoAtomAction {
// stripTrailingWhiteSpaces(stringVal);
// stripTrailingWhiteSpaces(stringVal2);
newAtomInfo(stringVal, stringVal2);
}
info_atom_line =
'info'
nonNEWLINEspace+
'atom'
nonNEWLINEspace+
char_string_with_space
nonNEWLINEspace*
'='
nonNEWLINEspace*
char_string_with_space2
nonNEWLINEspace*
EOL
@ newInfoAtomAction
;
atom_attrib_line =
(bond_line | bond_direction_line | info_atom_line);
}%%
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