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path: root/java/joelib2/example/SMILESExample.class
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0160 6f 65 6c 69 62 32 2f 69 6f 2f 42 61 73 69 63 49 4f 54 79 70 65 3b 4c 6a 6f 65 6c 69 62 32 2f 69 oelib2/io/BasicIOType;Ljoelib2/i
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0260 82 0c 00 84 00 85 01 00 1d 6a 6f 65 6c 69 62 32 2f 65 78 61 6d 70 6c 65 2f 53 4d 49 4c 45 53 45 .........joelib2/example/SMILESE
0280 78 61 6d 70 6c 65 0c 00 3e 00 38 07 00 86 0c 00 87 00 88 07 00 89 0c 00 8a 00 8b 01 00 03 53 44 xample..>.8...................SD
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0320 01 00 26 4d 6f 6c 65 63 75 6c 65 20 63 6f 75 6c 64 20 6e 6f 74 20 62 65 20 67 65 6e 65 72 61 74 ..&Molecule.could.not.be.generat
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0360 64 20 68 79 64 72 6f 67 65 6e 73 3a 01 00 16 6a 61 76 61 2f 6c 61 6e 67 2f 53 74 72 69 6e 67 42 d.hydrogens:...java/lang/StringB
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05a0 04 65 78 69 74 01 00 04 28 49 29 56 01 00 1c 6a 6f 65 6c 69 62 32 2f 69 6f 2f 42 61 73 69 63 49 .exit...(I)V...joelib2/io/BasicI
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0680 13 6a 61 76 61 2f 69 6f 2f 50 72 69 6e 74 53 74 72 65 61 6d 01 00 07 70 72 69 6e 74 6c 6e 01 00 .java/io/PrintStream...println..
06a0 15 28 4c 6a 61 76 61 2f 6c 61 6e 67 2f 53 74 72 69 6e 67 3b 29 56 01 00 1b 6a 6f 65 6c 69 62 32 .(Ljava/lang/String;)V...joelib2
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06e0 6c 65 63 75 6c 65 01 00 42 28 4c 6a 6f 65 6c 69 62 32 2f 6d 6f 6c 65 63 75 6c 65 2f 4d 6f 6c 65 lecule..B(Ljoelib2/molecule/Mole
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07a0 28 4c 6a 61 76 61 2f 69 6f 2f 4f 75 74 70 75 74 53 74 72 65 61 6d 3b 4c 6a 6f 65 6c 69 62 32 2f (Ljava/io/OutputStream;Ljoelib2/
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