File Coverage

blib/lib/Chemistry/File/InChI/Parser.pm

Criterion	Covered	Total	%
statement	9	9	100.0
branch			n/a
condition			n/a
subroutine	3	3	100.0
pod			n/a
total	12	12	100.0

####################################################################
#
#    This file was generated using Parse::Yapp version 1.21.
#
#        Don't edit this file, use source file instead.
#
#             ANY CHANGE MADE HERE WILL BE LOST !
#
####################################################################
package Chemistry::File::InChI::Parser;
use vars qw ( @ISA );
use strict;

@ISA= qw ( Parse::Yapp::Driver );
use Parse::Yapp::Driver;

#line 3 "lib/Chemistry/File/InChI/Parser.yp"


use strict;
use warnings;

use Chemistry::Atom;
use Chemistry::Mol;

use List::Util qw( first );

my @LAYER_ORDER = qw( PREFIX FORMULA CONNECTIONS H_ATOMS CHARGE TETRAHEDRAL STEREOCHEMISTRY );



sub new {
        my($class)=shift;
        ref($class)
    and $class=ref($class);

    my($self)=$class->SUPER::new( yyversion => '1.21',
                                  yystates =>
[
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	},
	{#State 2
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			"/" => 5,
			'formula_first' => 7
		},
		GOTOS => {
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			'tetrahedral' => 12,
			'h_atoms' => 3,
			'connections' => 9,
			'layer' => 8,
			'formula' => 11,
			'stereochemistry' => 4
		}
	},
	{#State 3
		ACTIONS => {
			";" => 13
		},
		DEFAULT => -5
	},
	{#State 4
		DEFAULT => -8
	},
	{#State 5
		ACTIONS => {
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			"t" => 16,
			"h" => 15,
			"c" => 18
		}
	},
	{#State 6
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			";" => 21,
			"+" => 19,
			"-" => 20
		},
		DEFAULT => -6
	},
	{#State 7
		DEFAULT => -9
	},
	{#State 8
		DEFAULT => -2
	},
	{#State 9
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			";" => 22
		},
		DEFAULT => -4
	},
	{#State 10
		DEFAULT => 0
	},
	{#State 11
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			'formula_continuation' => 23
		},
		DEFAULT => -3
	},
	{#State 12
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			";" => 24
		},
		DEFAULT => -7
	},
	{#State 13
		ACTIONS => {
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			"7" => 35,
			"(" => 37,
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			"2" => 39,
			"5" => 41,
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			"1" => 32,
			"8" => 33
		},
		DEFAULT => -17,
		GOTOS => {
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			'index' => 43,
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			'hydrogens' => 31,
			'virtual_hydrogens' => 29,
			'vh_count' => 28,
			'twoplus' => 26
		}
	},
	{#State 14
		DEFAULT => -65
	},
	{#State 15
		ACTIONS => {
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			"8" => 33,
			"4" => 25,
			"9" => 27,
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			"(" => 37,
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			"3" => 38,
			"2" => 39
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		DEFAULT => -15,
		GOTOS => {
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		}
	},
	{#State 16
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			"8" => 33,
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		},
		DEFAULT => -19,
		GOTOS => {
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			'count' => 46,
			'tetrahedral_centers' => 47,
			'index' => 48
		}
	},
	{#State 17
		ACTIONS => {
			"2" => 49,
			"1" => 50
		}
	},
	{#State 18
		ACTIONS => {
			"7" => 35,
			"6" => 36,
			"3" => 38,
			"2" => 39,
			"5" => 41,
			"4" => 25,
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			"1" => 32,
			"8" => 33
		},
		DEFAULT => -11,
		GOTOS => {
			'graph' => 51,
			'twoplus' => 26,
			'count' => 53,
			'chain' => 54,
			'index' => 52
		}
	},
	{#State 19
		ACTIONS => {
			"5" => 41,
			"1" => 56,
			"8" => 33,
			"4" => 25,
			"6" => 36,
			"7" => 35,
			"9" => 27,
			"3" => 38,
			"2" => 39
		},
		GOTOS => {
			'twoplus' => 55,
			'natural' => 57
		}
	},
	{#State 20
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			"3" => 38,
			"2" => 39,
			"4" => 25,
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			"6" => 36,
			"8" => 33,
			"5" => 41,
			"1" => 56
		},
		GOTOS => {
			'twoplus' => 55,
			'natural' => 58
		}
	},
	{#State 21
		DEFAULT => -68
	},
	{#State 22
		ACTIONS => {
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			"1" => 32,
			"9" => 27,
			"4" => 25,
			"5" => 41,
			"2" => 39,
			"3" => 38,
			"6" => 36,
			"7" => 35
		},
		DEFAULT => -13,
		GOTOS => {
			'twoplus' => 26,
			'graph' => 59,
			'index' => 52,
			'count' => 53,
			'chain' => 54
		}
	},
	{#State 23
		DEFAULT => -10
	},
	{#State 24
		ACTIONS => {
			"1" => 32,
			"8" => 33,
			"4" => 25,
			"9" => 27,
			"5" => 41,
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			"6" => 36,
			"3" => 38,
			"2" => 39
		},
		DEFAULT => -21,
		GOTOS => {
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			'twoplus' => 26,
			'count' => 46,
			'tetrahedral_centers' => 60,
			'index' => 48
		}
	},
	{#State 25
		DEFAULT => -82
	},
	{#State 26
		DEFAULT => -73
	},
	{#State 27
		DEFAULT => -87
	},
	{#State 28
		ACTIONS => {
			"," => 62
		},
		DEFAULT => -38,
		GOTOS => {
			'mh_counts' => 61
		}
	},
	{#State 29
		DEFAULT => -43
	},
	{#State 30
		ACTIONS => {
			"(" => 37
		},
		DEFAULT => -42,
		GOTOS => {
			'mobile_hydrogens' => 63
		}
	},
	{#State 31
		DEFAULT => -18
	},
	{#State 32
		ACTIONS => {
			"1" => 64,
			"8" => 33,
			"4" => 25,
			"9" => 27,
			"5" => 41,
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			"0" => 67,
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			"3" => 38
		},
		DEFAULT => -69,
		GOTOS => {
			'twoplus' => 65,
			'digit' => 66
		}
	},
	{#State 33
		DEFAULT => -86
	},
	{#State 34
		ACTIONS => {
			"3" => 38,
			"2" => 39,
			"0" => 67,
			"6" => 36,
			"7" => 35,
			"5" => 41,
			"9" => 27,
			"4" => 25,
			"*" => 69,
			"8" => 33,
			"1" => 64
		},
		DEFAULT => -70,
		GOTOS => {
			'digit' => 68,
			'twoplus' => 65
		}
	},
	{#State 35
		DEFAULT => -85
	},
	{#State 36
		DEFAULT => -84
	},
	{#State 37
		ACTIONS => {
			"H" => 70
		}
	},
	{#State 38
		DEFAULT => -81
	},
	{#State 39
		DEFAULT => -80
	},
	{#State 40
		ACTIONS => {
			"," => 71,
			"-" => 73,
			"H" => 72
		}
	},
	{#State 41
		DEFAULT => -83
	},
	{#State 42
		DEFAULT => -45
	},
	{#State 43
		DEFAULT => -51
	},
	{#State 44
		DEFAULT => -16
	},
	{#State 45
		DEFAULT => -63
	},
	{#State 46
		ACTIONS => {
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		},
		DEFAULT => -70,
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		}
	},
	{#State 47
		ACTIONS => {
			"," => 74
		},
		DEFAULT => -20
	},
	{#State 48
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			"-" => 76,
			"+" => 75,
			"?" => 77
		}
	},
	{#State 49
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	},
	{#State 50
		DEFAULT => -23
	},
	{#State 51
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	},
	{#State 52
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			"-" => 80,
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		},
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	{#State 53
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	{#State 54
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			"-" => 83
		},
		DEFAULT => -25,
		GOTOS => {
			'branch' => 81,
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	},
	{#State 55
		DEFAULT => -75
	},
	{#State 56
		DEFAULT => -74
	},
	{#State 57
		ACTIONS => {
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	{#State 58
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		DEFAULT => -67,
		GOTOS => {
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	{#State 59
		DEFAULT => -14
	},
	{#State 60
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			"," => 74
		},
		DEFAULT => -22
	},
	{#State 61
		ACTIONS => {
			"," => 86
		},
		DEFAULT => -39
	},
	{#State 62
		ACTIONS => {
			"9" => 27,
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	{#State 63
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	},
	{#State 64
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	{#State 65
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	{#State 68
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	{#State 70
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			"," => 92,
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	{#State 72
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			"2" => 39,
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			"7" => 35,
			"8" => 33,
			"1" => 93,
			"9" => 27,
			"4" => 25
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		DEFAULT => -49,
		GOTOS => {
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	{#State 73
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			"1" => 32,
			"4" => 25,
			"7" => 35,
			"6" => 36,
			"3" => 38,
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		},
		GOTOS => {
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	{#State 74
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			"6" => 36,
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	{#State 75
		DEFAULT => -60
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	{#State 76
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	{#State 77
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	{#State 78
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	{#State 80
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	{#State 81
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			"1" => 32,
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			"3" => 38,
			"2" => 39,
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			"1" => 32
		},
		GOTOS => {
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			'index' => 105,
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	},
	{#State 84
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			"7" => 35,
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	{#State 85
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	},
	{#State 86
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		},
		GOTOS => {
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			"(" => 37
		},
		DEFAULT => -47,
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			'mobile_hydrogens' => 63
		}
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	{#State 89
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			"," => 62
		},
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		}
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	{#State 90
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			"," => 92
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		}
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	{#State 91
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		}
	},
	{#State 92
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	{#State 94
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			"1" => 64,
			"2" => 39,
			"3" => 38,
			"," => 92,
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			"0" => 67,
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			"-" => 113
		},
		GOTOS => {
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			'comma_separated_indexes' => 114,
			'digit' => 68
		}
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	{#State 95
		DEFAULT => -52
	},
	{#State 96
		ACTIONS => {
			"1" => 64,
			"8" => 33,
			"4" => 25,
			"9" => 27,
			"5" => 41,
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			"0" => 67,
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		},
		DEFAULT => -50,
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			'twoplus' => 65,
			'digit' => 68
		}
	},
	{#State 97
		DEFAULT => -53
	},
	{#State 98
		DEFAULT => -64
	},
	{#State 99
		DEFAULT => -32
	},
	{#State 100
		ACTIONS => {
			"," => 115,
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			"(" => 78,
			")" => 118
		},
		GOTOS => {
			'branches' => 116,
			'branch' => 81
		}
	},
	{#State 101
		DEFAULT => -37
	},
	{#State 102
		DEFAULT => -28
	},
	{#State 103
		DEFAULT => -27
	},
	{#State 104
		ACTIONS => {
			"(" => 78,
			"-" => 83
		},
		DEFAULT => -26,
		GOTOS => {
			'branch' => 81,
			'branches' => 84
		}
	},
	{#State 105
		DEFAULT => -29
	},
	{#State 106
		DEFAULT => -30
	},
	{#State 107
		ACTIONS => {
			"(" => 37
		},
		DEFAULT => -48,
		GOTOS => {
			'mobile_hydrogens' => 63
		}
	},
	{#State 108
		ACTIONS => {
			"," => 86
		},
		DEFAULT => -41
	},
	{#State 109
		ACTIONS => {
			"," => 110,
			")" => 119
		}
	},
	{#State 110
		ACTIONS => {
			"1" => 32,
			"5" => 41,
			"6" => 36,
			"7" => 35,
			"4" => 25,
			"2" => 39,
			"3" => 38,
			"8" => 33,
			"9" => 27
		},
		GOTOS => {
			'count' => 46,
			'index' => 120,
			'twoplus' => 26
		}
	},
	{#State 111
		DEFAULT => -54
	},
	{#State 112
		DEFAULT => -58
	},
	{#State 113
		ACTIONS => {
			"," => 92
		},
		GOTOS => {
			'comma_separated_indexes' => 121
		}
	},
	{#State 114
		ACTIONS => {
			")" => 122,
			"," => 110
		}
	},
	{#State 115
		ACTIONS => {
			"4" => 25,
			"7" => 35,
			"6" => 36,
			"3" => 38,
			"2" => 39,
			"9" => 27,
			"5" => 41,
			"1" => 32,
			"8" => 33
		},
		GOTOS => {
			'count' => 46,
			'index' => 123,
			'twoplus' => 26
		}
	},
	{#State 116
		ACTIONS => {
			"8" => 33,
			"1" => 32,
			"5" => 41,
			"9" => 27,
			"2" => 39,
			"3" => 38,
			"6" => 36,
			"7" => 35,
			"4" => 25,
			"(" => 78
		},
		GOTOS => {
			'twoplus' => 26,
			'index' => 124,
			'branch' => 101,
			'count' => 46
		}
	},
	{#State 117
		ACTIONS => {
			"2" => 39,
			"3" => 38,
			"8" => 33,
			"9" => 27,
			"1" => 32,
			"5" => 41,
			"7" => 35,
			"6" => 36,
			"4" => 25
		},
		GOTOS => {
			'count' => 46,
			'index' => 125,
			'twoplus' => 26
		}
	},
	{#State 118
		DEFAULT => -31
	},
	{#State 119
		DEFAULT => -55
	},
	{#State 120
		DEFAULT => -59
	},
	{#State 121
		ACTIONS => {
			")" => 126,
			"," => 110
		}
	},
	{#State 122
		DEFAULT => -57
	},
	{#State 123
		DEFAULT => -33
	},
	{#State 124
		DEFAULT => -35
	},
	{#State 125
		DEFAULT => -34
	},
	{#State 126
		DEFAULT => -56
	}
],
                                  yyrules  =>
[
	[#Rule 0
		 '$start', 2, undef
	],
	[#Rule 1
		 'string', 1,
sub
#line 24 "lib/Chemistry/File/InChI/Parser.yp"
{ 'PREFIX' }
	],
	[#Rule 2
		 'string', 2,
sub
#line 26 "lib/Chemistry/File/InChI/Parser.yp"
{
                my $layer1_id = first { $LAYER_ORDER[$_] eq $_[1] } 0..$#LAYER_ORDER;
                my $layer2_id = first { $LAYER_ORDER[$_] eq $_[2] } 0..$#LAYER_ORDER;
                die "unknown layer $_[2]\n" unless defined $layer2_id;
                die "duplicated layer $_[1]\n" if $layer1_id == $layer2_id;
                die "incorrect layer order, $_[2] must appear before $_[1]\n" if $layer1_id > $layer2_id;
                $_[2];
            }
	],
	[#Rule 3
		 'layer', 1,
sub
#line 37 "lib/Chemistry/File/InChI/Parser.yp"
{ 'FORMULA' }
	],
	[#Rule 4
		 'layer', 1,
sub
#line 39 "lib/Chemistry/File/InChI/Parser.yp"
{ 'CONNECTIONS' }
	],
	[#Rule 5
		 'layer', 1,
sub
#line 41 "lib/Chemistry/File/InChI/Parser.yp"
{ 'H_ATOMS' }
	],
	[#Rule 6
		 'layer', 1,
sub
#line 43 "lib/Chemistry/File/InChI/Parser.yp"
{ 'CHARGE' }
	],
	[#Rule 7
		 'layer', 1,
sub
#line 45 "lib/Chemistry/File/InChI/Parser.yp"
{ 'TETRAHEDRAL' }
	],
	[#Rule 8
		 'layer', 1,
sub
#line 47 "lib/Chemistry/File/InChI/Parser.yp"
{ 'STEREOCHEMISTRY' }
	],
	[#Rule 9
		 'formula', 1,
sub
#line 51 "lib/Chemistry/File/InChI/Parser.yp"
{ [ $_[1] ] }
	],
	[#Rule 10
		 'formula', 2,
sub
#line 53 "lib/Chemistry/File/InChI/Parser.yp"
{ push @{$_[1]}, $_[2] }
	],
	[#Rule 11
		 'connections', 2,
sub
#line 57 "lib/Chemistry/File/InChI/Parser.yp"
{ $_[0]->{USER}{CURSOR}++ }
	],
	[#Rule 12
		 'connections', 3,
sub
#line 59 "lib/Chemistry/File/InChI/Parser.yp"
{ $_[0]->{USER}{CURSOR}++ }
	],
	[#Rule 13
		 'connections', 2,
sub
#line 61 "lib/Chemistry/File/InChI/Parser.yp"
{ $_[0]->{USER}{CURSOR}++ }
	],
	[#Rule 14
		 'connections', 3,
sub
#line 63 "lib/Chemistry/File/InChI/Parser.yp"
{ $_[0]->{USER}{CURSOR}++ }
	],
	[#Rule 15
		 'h_atoms', 2,
sub
#line 67 "lib/Chemistry/File/InChI/Parser.yp"
{ $_[0]->{USER}{CURSOR}++ }
	],
	[#Rule 16
		 'h_atoms', 3,
sub
#line 69 "lib/Chemistry/File/InChI/Parser.yp"
{ $_[0]->{USER}{CURSOR}++ }
	],
	[#Rule 17
		 'h_atoms', 2,
sub
#line 71 "lib/Chemistry/File/InChI/Parser.yp"
{ $_[0]->{USER}{CURSOR}++ }
	],
	[#Rule 18
		 'h_atoms', 3,
sub
#line 73 "lib/Chemistry/File/InChI/Parser.yp"
{ $_[0]->{USER}{CURSOR}++ }
	],
	[#Rule 19
		 'tetrahedral', 2, undef
	],
	[#Rule 20
		 'tetrahedral', 3, undef
	],
	[#Rule 21
		 'tetrahedral', 2, undef
	],
	[#Rule 22
		 'tetrahedral', 3, undef
	],
	[#Rule 23
		 'stereochemistry', 3,
sub
#line 83 "lib/Chemistry/File/InChI/Parser.yp"
{ $_[0]->{USER}{MOL}->attr( 'inchi/stereochemistry', $_[3] ) }
	],
	[#Rule 24
		 'stereochemistry', 3,
sub
#line 85 "lib/Chemistry/File/InChI/Parser.yp"
{ $_[0]->{USER}{MOL}->attr( 'inchi/stereochemistry', $_[3] ) }
	],
	[#Rule 25
		 'graph', 1, undef
	],
	[#Rule 26
		 'graph', 3, undef
	],
	[#Rule 27
		 'chain', 3,
sub
#line 96 "lib/Chemistry/File/InChI/Parser.yp"
{ $_[0]->_add_bonds( $_[1], $_[3] ); return $_[3] }
	],
	[#Rule 28
		 'chain', 3,
sub
#line 98 "lib/Chemistry/File/InChI/Parser.yp"
{ $_[0]->_add_bonds( $_[1], [ @{$_[2]}, $_[3] ] ); return $_[3] }
	],
	[#Rule 29
		 'chain', 3,
sub
#line 100 "lib/Chemistry/File/InChI/Parser.yp"
{ $_[0]->_add_bonds( $_[1], $_[3] ); return $_[3] }
	],
	[#Rule 30
		 'chain', 3,
sub
#line 102 "lib/Chemistry/File/InChI/Parser.yp"
{ $_[0]->_add_bonds( $_[1], [ @{$_[2]}, $_[3] ] ); return $_[3] }
	],
	[#Rule 31
		 'branch', 3,
sub
#line 105 "lib/Chemistry/File/InChI/Parser.yp"
{ $_[2]->{bonds} }
	],
	[#Rule 32
		 'branch_body', 1,
sub
#line 109 "lib/Chemistry/File/InChI/Parser.yp"
{ { bonds => [ $_[1] ], last => $_[1] } }
	],
	[#Rule 33
		 'branch_body', 3,
sub
#line 111 "lib/Chemistry/File/InChI/Parser.yp"
{
                    push @{$_[1]->{bonds}}, $_[3];
                    $_[1]->{last} = $_[3];
                    return $_[1];
                }
	],
	[#Rule 34
		 'branch_body', 3,
sub
#line 117 "lib/Chemistry/File/InChI/Parser.yp"
{
                    $_[0]->_add_bonds( $_[1]->{last}, $_[3] );
                    $_[1]->{last} = $_[3];
                    return $_[1];
                }
	],
	[#Rule 35
		 'branch_body', 3,
sub
#line 123 "lib/Chemistry/File/InChI/Parser.yp"
{
                    $_[0]->_add_bonds( $_[1]->{last}, [ @{$_[2]}, $_[3] ] );
                    $_[1]->{last} = $_[3];
                    return $_[1];
                }
	],
	[#Rule 36
		 'branches', 1,
sub
#line 131 "lib/Chemistry/File/InChI/Parser.yp"
{ $_[1] }
	],
	[#Rule 37
		 'branches', 2,
sub
#line 133 "lib/Chemistry/File/InChI/Parser.yp"
{ [ @{$_[1]}, @{$_[2]} ] }
	],
	[#Rule 38
		 'hydrogens', 1, undef
	],
	[#Rule 39
		 'hydrogens', 2, undef
	],
	[#Rule 40
		 'hydrogens', 3, undef
	],
	[#Rule 41
		 'hydrogens', 4, undef
	],
	[#Rule 42
		 'hydrogens', 1, undef
	],
	[#Rule 43
		 'vh_count', 1, undef
	],
	[#Rule 44
		 'vh_count', 3, undef
	],
	[#Rule 45
		 'mh_count', 1, undef
	],
	[#Rule 46
		 'mh_count', 2, undef
	],
	[#Rule 47
		 'mh_counts', 2, undef
	],
	[#Rule 48
		 'mh_counts', 3, undef
	],
	[#Rule 49
		 'virtual_hydrogens', 2,
sub
#line 156 "lib/Chemistry/File/InChI/Parser.yp"
{ $_[0]->_add_hydrogens( $_[1] ) }
	],
	[#Rule 50
		 'virtual_hydrogens', 3,
sub
#line 158 "lib/Chemistry/File/InChI/Parser.yp"
{ $_[0]->_add_hydrogens( $_[1], $_[3] ) }
	],
	[#Rule 51
		 'virtual_hydrogen_receivers', 1,
sub
#line 162 "lib/Chemistry/File/InChI/Parser.yp"
{ [ $_[1] ] }
	],
	[#Rule 52
		 'virtual_hydrogen_receivers', 3,
sub
#line 164 "lib/Chemistry/File/InChI/Parser.yp"
{
                                push @{$_[1]}, $_[3];
                                return $_[1];
                            }
	],
	[#Rule 53
		 'virtual_hydrogen_receivers', 3,
sub
#line 169 "lib/Chemistry/File/InChI/Parser.yp"
{
                                push @{$_[1]}, ($_[1]->[-1] + 1)..$_[3];
                                return $_[1]
                            }
	],
	[#Rule 54
		 'mobile_hydrogens', 4, undef
	],
	[#Rule 55
		 'mobile_hydrogens', 5, undef
	],
	[#Rule 56
		 'mobile_hydrogens', 6, undef
	],
	[#Rule 57
		 'mobile_hydrogens', 5, undef
	],
	[#Rule 58
		 'comma_separated_indexes', 2,
sub
#line 182 "lib/Chemistry/File/InChI/Parser.yp"
{ [ $_[2] ] }
	],
	[#Rule 59
		 'comma_separated_indexes', 3,
sub
#line 184 "lib/Chemistry/File/InChI/Parser.yp"
{
                                push @{$_[1]}, $_[3];
                                return $_[1];
                            }
	],
	[#Rule 60
		 'tetrahedral_center', 2,
sub
#line 191 "lib/Chemistry/File/InChI/Parser.yp"
{ $_[0]->_get_atom( $_[1] )->attr( 'inchi/chirality', $_[2] ) }
	],
	[#Rule 61
		 'tetrahedral_center', 2,
sub
#line 193 "lib/Chemistry/File/InChI/Parser.yp"
{ $_[0]->_get_atom( $_[1] )->attr( 'inchi/chirality', $_[2] ) }
	],
	[#Rule 62
		 'tetrahedral_center', 2, undef
	],
	[#Rule 63
		 'tetrahedral_centers', 1, undef
	],
	[#Rule 64
		 'tetrahedral_centers', 3, undef
	],
	[#Rule 65
		 'charge', 2,
sub
#line 202 "lib/Chemistry/File/InChI/Parser.yp"
{ $_[0]->{USER}{MOL}->attr( 'inchi/charges', [] ) }
	],
	[#Rule 66
		 'charge', 3,
sub
#line 204 "lib/Chemistry/File/InChI/Parser.yp"
{ $_[0]->{USER}{MOL}->attr( 'inchi/charges' )->[$_[0]->{USER}{CURSOR}] = int(  $_[3] ) }
	],
	[#Rule 67
		 'charge', 3,
sub
#line 206 "lib/Chemistry/File/InChI/Parser.yp"
{ $_[0]->{USER}{MOL}->attr( 'inchi/charges' )->[$_[0]->{USER}{CURSOR}] = int( -$_[3] ) }
	],
	[#Rule 68
		 'charge', 2,
sub
#line 208 "lib/Chemistry/File/InChI/Parser.yp"
{ $_[0]->{USER}{CURSOR}++ }
	],
	[#Rule 69
		 'index', 1, undef
	],
	[#Rule 70
		 'index', 1, undef
	],
	[#Rule 71
		 'count', 2,
sub
#line 214 "lib/Chemistry/File/InChI/Parser.yp"
{ join '', @_[1..2] }
	],
	[#Rule 72
		 'count', 2,
sub
#line 216 "lib/Chemistry/File/InChI/Parser.yp"
{ join '', @_[1..2] }
	],
	[#Rule 73
		 'count', 1, undef
	],
	[#Rule 74
		 'natural', 1, undef
	],
	[#Rule 75
		 'natural', 1, undef
	],
	[#Rule 76
		 'natural', 2,
sub
#line 223 "lib/Chemistry/File/InChI/Parser.yp"
{ join '', @_[1..2] }
	],
	[#Rule 77
		 'digit', 1, undef
	],
	[#Rule 78
		 'digit', 1, undef
	],
	[#Rule 79
		 'digit', 1, undef
	],
	[#Rule 80
		 'twoplus', 1, undef
	],
	[#Rule 81
		 'twoplus', 1, undef
	],
	[#Rule 82
		 'twoplus', 1, undef
	],
	[#Rule 83
		 'twoplus', 1, undef
	],
	[#Rule 84
		 'twoplus', 1, undef
	],
	[#Rule 85
		 'twoplus', 1, undef
	],
	[#Rule 86
		 'twoplus', 1, undef
	],
	[#Rule 87
		 'twoplus', 1, undef
	]
],
                                  @_);
    bless($self,$class);
}

#line 230 "lib/Chemistry/File/InChI/Parser.yp"


# Footer section

sub parse
{
    my( $self, $string ) = @_;

    $self->YYData->{INPUT} = $string;
    $self->{USER}{MOL}     = Chemistry::Mol->new;
    $self->{USER}{CURSOR}  = 0;
    $self->YYParse( yylex => \&_Lexer, yyerror => \&_Error, yydebug => 0 );

    return $self->{USER}{MOL};
}

sub _Lexer
{
    my( $self ) = @_;

    # If the line is empty and the input is originating from the file,
    # another line is read.
    if( !$self->YYData->{INPUT} && $self->{USER}{FILEIN} ) {
        my $filein = $self->{USER}{FILEIN};
        $self->YYData->{INPUT} = <$filein>;
        $self->{USER}{CHARNO} = 0;
    }

    # Prefix
    if( $self->YYData->{INPUT} =~ s/^(InChI=1S?)// ) {
        return ( 'prefix', $1 );
    }

    # Formula parts
    # TODO: Check Hill order, require counts > 1
    if( $self->YYData->{INPUT} =~ s/^([\/\.])([2-9]|[1-9][0-9]+)?(([A-Z][a-z]?\d*)+)// ) {
        my( $sep, $count, $formula ) = ( $1, $2, $3 );
        $count = 1 unless $count;
        my %atom_map;

        while( $formula =~ /([A-Z][a-z]?)(\d*)/g ) {
            my( $element, $count ) = ( $1, $2 );
            next if $element eq 'H'; # H atoms will be added later
            $count = 1 unless $count;
            for (1..$count) {
                my $atom = Chemistry::Atom->new( symbol => $element );
                $self->{USER}{MOL}->add_atom( $atom );
                $atom_map{scalar( keys %atom_map ) + 1} = $atom;
            }
        }

        if( $sep eq '/') {
            $self->{USER}{ATOM_MAPS} = [ \%atom_map ];
            $self->{USER}{MOL}->attr( 'inchi/counts', [ $count ] );
            return ( 'formula_first', $formula );
        } else {
            push @{$self->{USER}{ATOM_MAPS}}, \%atom_map;
            push @{$self->{USER}{MOL}->attr( 'inchi/counts' )}, $count;
            return ( 'formula_continuation', $formula );
        }
    }

    # Reset cursor on 'h', 'q' or 't'
    if( $self->YYData->{INPUT} =~ s/^([hqt])// ) {
        $self->{USER}{CURSOR} = 0;
        return ( $1, $1 );
    }

    # Remove unsupported layers
    $self->YYData->{INPUT} =~ s/^(\/[pbmsifo][^\/]*)+//;

    # Any other character
    if( $self->YYData->{INPUT} =~ s/^(.)// ) {
        return ( $1, $1 );
    }

    return ( '', '' );
}

sub _Error
{
    my( $self ) = @_;
    die 'ERROR: ', $self->YYData->{INPUT}, "\n";
}

sub _add_bonds
{
    my( $self, $a, $b ) = @_;

    my @bonds = ref $b eq 'ARRAY' ? @$b : $b;
    for (@bonds) {
        $self->{USER}{MOL}->new_bond( atoms => [ $self->_get_atom( $a ),
                                                 $self->_get_atom( $_ ) ] );
    }
}

sub _add_hydrogens
{
    my( $self, $atoms, $count ) = @_;

    my $atom_map = $self->{USER}{ATOM_MAPS}[$self->{USER}{CURSOR}];
    my @atoms = map { $atom_map->{$_} }
                    ref $atoms ? @$atoms : ( $atoms );
    $count = 1 unless $count;
    for my $atom (@atoms) {
        for (1..$count) {
            my $H = Chemistry::Atom->new( symbol => 'H' );
            $self->{USER}{MOL}->add_atom( $H );
            $self->{USER}{MOL}->new_bond( atoms => [ $atom, $H ] );
        }
    }
}

sub _get_atom
{
    my( $self, $atom ) = @_;

    my $atom_map = $self->{USER}{ATOM_MAPS}[$self->{USER}{CURSOR}];

    if( !exists $atom_map->{$atom} ) {
        # If an atom with given index does not exist, this is probably a hydrogen.
        # FIXME: Check if there are unused hydrogen atoms.

        my $H = Chemistry::Atom->new( symbol => 'H' );
        $self->{USER}{MOL}->add_atom( $H );
        $atom_map->{$atom} = $H;
    }

    return $atom_map->{$atom};
}

1;

1;