@@ -58,26 +58,26 @@ To use it, download the TIRAMISU folder. Two example, one of a full merging and
Example: order=k
### How to use :
Once the input created, use "python Main_exe_1.py input". A tmp_species_traduction.tmp file will be created. This file contains all the temporary translation done by the code and also which translation needs to be done manually.
This file is separated by isomer group. Each isomer group start with its composition (example: c1 o1 h1).
The next line contains all translation possible contained in mech1.
Then, each isomer for mech2 is presented, associated with its translation or a possibility of translations.
Each line starting with !CHECK needs to be looked carefully. Choose the right translation and remove the !CHECK or the species will be treated as if there is no translation.
If you want to remove a translation, you can comment the line with "!" or change the species with a None.
Everything after a "!" on a line will be treated as a comment.
species1: This is the species name given by the first translation method.
species2: This is the species name corresponding to the best arrangement found by the second translation method.
species3: This is the species name corresponding to the second-best arrangement found by the second translation method.
An arrangement here refers to the match found between all the species to be translated (in the isomer group) and all the species used for translation (in the isomer group). The best arrangement is the one with the minimum mean normalized mean absolute difference (mean NMAD).
Second list [value1, value2, value3]
value1: This is the direct NMAD between the species_to_translate and species1, given by the first method.
value2: This is the mean NMAD for the best arrangement of the whole isomer group, given by the second method.
value3: This is the mean NMAD for the second-best arrangement of the whole isomer group, given by the second method.
Once you are satisfied with the translation, copy the file and change the ".tmp" to ".inp". Now you can use "python Main_exe_2.py input".
Once the input created, use "python Main_exe_1.py input". A tmp_species_traduction.tmp file will be created. This file contains all the temporary translation done by the code and also which translation needs to be done manually.
This file is separated by isomer group. Each isomer group start with its composition (example: c1 o1 h1).
The next line contains all translation possible contained in mech1.
Then, each isomer for mech2 is presented, associated with its translation or a possibility of translations.
Each line starting with !CHECK needs to be looked carefully. Choose the right translation and remove the !CHECK or the species will be treated as if there is no translation.
If you want to remove a translation, you can comment the line with "!" or change the species with a None.
Everything after a "!" on a line will be treated as a comment.
species1: This is the species name given by the first translation method.
species2: This is the species name corresponding to the best arrangement found by the second translation method.
species3: This is the species name corresponding to the second-best arrangement found by the second translation method.
An arrangement here refers to the match found between all the species to be translated (in the isomer group) and all the species used for translation (in the isomer group). The best arrangement is the one with the minimum mean normalized mean absolute difference (mean NMAD).
Second list [value1, value2, value3]
value1: This is the direct NMAD between the species_to_translate and species1, given by the first method.
value2: This is the mean NMAD for the best arrangement of the whole isomer group, given by the second method.
value3: This is the mean NMAD for the second-best arrangement of the whole isomer group, given by the second method.
Once you are satisfied with the translation, copy the file and change the ".tmp" to ".inp". Now you can use "python Main_exe_2.py input".
### Example :
Two example are available in this project. They contain the two mechanisms and the input for the two tasks possible (extraction_merging.txt and full_merging.txt).
