random small fixes

@@ -6,4 +6,4 @@ GGACAUACAAUCGCGUGGAUAUGGCACGCAAGUUUCUGCCGGGCACCGUAAAUGUCCGACUAUGUCCa
 (((((((...(((((((.[[..[[)))))))........((((((]]...]]))))))..))))))).
 >__'SOLUTION_STRUCTURE_OF_THE_P2B-P3_PSEUDOKNOT_FROM_HUMAN_TELOMERASE_RNA_'_(PDB_00857)
 GGGCUGUUUUUCUCGCUGACUUUCAGCCCCAAACAAAAAAGUCAGCA
-[[[[[[........(((((((((]]]]]]........))))))))).
\ No newline at end of file
+[[[[[[........(((((((((]]]]]]........))))))))).

->>__'CRYSTAL_STRUCTURE_ANALYSIS_OF_A_TRNA-NEOMYCIN_COMPLEX_'_(PDB_00095)
-GCGGAUUUAGCUCAGUUGGGAGAGCGCCAGACUGAAGACUGGAGGUCCUGUGUUCGAUCCACAGAAUUCGCACCA
-(((((((..((((........))))(((((........)))))....(((((.......))))))))))))....
->>__'YEAST_INITIATOR_TRNA_'_(PDB_00229)
-AGCGCCGUGGCGCAGUGGAAGCGCGCAGGGCUCAUAACCCUGAUGUCCUCGGAUCGAAACCGAGCGGCGCUACCA
-(((((((..((((.......))))(((((((.....)))))))....(((((.......))))))))))))....
->>__'THE_CRYSTAL_STRUCTURE_OF_PHENYLALANYL-TRNA_SYNTHETASE_FROM_THERMUS_THERMOPHILUS_COMPLEXED_WITH_COGNATE_TRNAPHE_'_(PDB_00362)
-GCCGAGGUAGCUCAGUUGGUAGAGCAUGCGACUGAAAAUCGCAGUGUCCGCGGUUCGAUUCCGCGCCUCGGCACCA
-(((((((..((((........))))((((((.......))))))....(((((.......))))))))))))....
->>__'CRYSTAL_STRUCTURE_OF_GLUTAMINYL-TRNA_SYNTHETASE_COMPLEXED_WITH_A_TRNA-GLN_MUTANT_AND_AN_ACTIVE-SITE_INHIBITOR_'_(PDB_00373)
-GGGGUAUCGCCAAGCGGUAAGGCACCGGAUUCUGAUUCCGGCAGCGAGGUUCGAAUCCUCGUACCCCAGCCA
-((((((..((((.......))))((((((((...))))))))..(((((.......))))))))))).....
->>__'GLUTAMINYL-TRNA_SYNTHETASE_COMPLEXED_WITH_A_TRNA_MUTANT_AND_AN_ACTIVE_SITE_INHIBITOR_'_(PDB_00374)
-GGGGUAUCGCCAAGCGGUAAGGCACCGGAUUCUGAUUCCGGCAAGCGAGGUUCGAAUCCUCGUACCCCAGCCA
-((((((..((((.......))))((((((((...))))))))...(((((.......))))))))))).....
->>__'CRYSTAL_STRUCTURE_OF_A_TIGHT-BINDING_GLUTAMINE_TRNA_BOUND_TO_GLUTAMINE_AMINOACYL_TRNA_SYNTHETASE_'_(PDB_00376)
-GGGGUAUCGCCAAGCGGUAAGGCACCGGAUUCUGAUUCCGGAGGUCGAGGUUCGAAUCCUCGUACCCCAGCCA
-((((((..(((.........)))((((((((...))))))))...(((((.......))))))))))).....
->>__'INSIGHTS_INTO_EDITING_FROM_AN_ILE-TRNA_SYNTHETASE_STRUCTURE_WITH_TRNA(ILE)_AND_MUPIROCIN_'_(PDB_00402)
-GGGCUUGUAGCUCAGGUGGUUAGAGCGCACCCCUGAUAAGGGUGAGGUCGGUGGUUCAAGUCCACUCAGGCCCAC
-(((((((..((((.........))))(((((((.....)))))))....(((((.......))))))))))))..
->>__'STRUCTURAL_BASIS_OF_ANTICODON_LOOP_RECOGNITION_BY_GLUTAMINYL-TRNA_SYNTHETASE_'_(PDB_00425)
-GGGGUAUCGCCAAGCGGUAAGGCACCGGAUUCUGAUUCCGGCAUUCCGAGGUUCGAAUCCUCGUACCCCAGCCA
-((((((..(((.........)))((((((((...))))))))....(((((.......))))))))))).....
->>__'STRUCTURAL_BASIS_FOR_TRANSFER_RNA_AMINOACEYLATION_BY_ESCHERICHIA_COLI_GLUTAMINYL-TRNA_SYNTHETASE_'_(PDB_00426)
-GGGGUAUCGCCAAGCGGUAAGGCACCGGAUUCUGAUUCCGGCAUUCCGAGGUUCGAAUCCUCGUACCCCAGCCA
-((((((..(((.........))).(((((((...))))))).....(((((.......))))))))))).....
->>__'CRYSTAL_STRUCTURE_OF_ARCHAEAL_TYROSYL-TRNA_SYNTHETASE_COMPLEXED_WITH_TRNA(TYR)_AND_L-TYROSINE_'_(PDB_00474)
-CCGGCGGUAGUUCAGCCUGGUAGAACGGCGGACUGUAGAUCCGCAUGUCGCUGGUUCAAAUCCGGCCCGCCGGA
-(((((((..((((.........))))(((((((.....)))))))....(((((.......)))))))))))).
->>__'CRYSTAL_STRUCTURE_OF_L-GLUTAMINE_AND_AMPCPP_BOUND_TO_GLUTAMINE_AMINOACYL_TRNA_SYNTHETASE_'_(PDB_00620)
-GGGGUAUCGCCAAGCGGUAAGGCACCGGAUUCUGAUUCCGGCAUUCCGAGGUUCGAAUCCUCGUACCCCAGCCA
-((((((..((((.......))))(((((((.....)))))))....(((((.......))))))))))).....
->>__'CRYSTAL_STRUCTURE_OF_L-GLUTAMATE_AND_AMPCPP_BOUND_TO_GLUTAMINE_AMINOACYL_TRNA_SYNTHETASE_'_(PDB_00621)
-GGGGUAUCGCCAAGCGGUAAGGCACCGGAUUCUGAUUCCGGCAUUCCGAGGUUCGAAUCCUCGUACCCCAGCCA
-((((((..((((.......)))).(((((((...))))))).....(((((.......))))))))))).....
->>__'CRYSTAL_STRUCTURE_OF_THE_TRNA_DOMAIN_OF_TRANSFER-MESSENGER_RNA_IN_COMPLEX_WITH_SMPB_'_(PDB_00637)
-GAUUCGACGGGGACUUCGGUCCUCGGACGCGGGUUCGAUUCCCGCUCGACGGGGACUUCGGUCCUCGGA
-......((((((((....))))))))..(((((.......)))))...((((((((....)))))))).
->>__'GLUTAMINYL-TRNA_SYNTHETASE_MUTANT_D235N_COMPLEXED_WITH_GLUTAMINE_TRANSFER_RNA_'_(PDB_00669)
-GGGGUAUCGCCAAGCGGUAAGGCACCGGAUUCUGAUUCCGGCAUUCCGAGGUUCGAAUCCUCGUACCCCAGCCA
-((((((..(((.........)))((((((((...))))))))....(((((.......))))))))))).....
->>__'GLUTAMINYL-TRNA_SYNTHETASE_MUTANT_D235G_COMPLEXED_WITH_GLUTAMINE_TRANSFER_RNA_'_(PDB_00670)
-GGGGUAUCGCCAAGCGGUAAGGCACCGGAUUCUGAUUCCGGCAUUCCGAGGUUCGAAUCCUCGUACCCCAGCCA
-((((((..(((.........)))(((((((.....)))))))....(((((.......))))))))))).....
->>__'GLUTAMINYL-TRNA_SYNTHETASE_MUTANT_I129T_COMPLEXED_WITH_GLUTAMINE_TRANSFER_RNA_'_(PDB_00671)
-GGGGUAUCGCCAAGCGGUAAGGCACCGGAUUCUGAUUCCGGCAUUCCGAGGUUCGAAUCCUCGUACCCCAGCCA
-((((((..(((.........)))((((((.......))))))....(((((.......))))))))))).....
->>__'GLUTAMINYL-TRNA_SYNTHETASE_COMPLEXED_WITH_TRNA_AND_AN_AMINO_ACID_ANALOG_'_(PDB_00672)
-GGGGUAUCGCCAAGCGGUAAGGCACCGGAUUCUGAUUCCGGCAUUCCGAGGUUCGAAUCCUCGUACCCCAGCCA
-((((((..((((.......))))((((((((...))))))))....(((((.......))))))))))).....
->>__'INSIGHTS_INTO_EDITING_FROM_AN_ILE-TRNA_SYNTHETASE_STRUCTURE_WITH_TRNA(ILE)_AND_MUPIROCIN_'_(PDB_00673)
-GGGCUUGUAGCUCAGGUGGUUAGAGCGCACCCCUGAUAAGGGUGAGGUCGGUGGUUCAAGUCCACUCAGGCCCAC
-(((((((..((((.........))))(((((((.....)))))))....(((((.......))))))))))))..
->>__'INSIGHTS_INTO_EDITING_FROM_AN_ILE-TRNA_SYNTHETASE_STRUCTURE_WITH_TRNA(ILE)_AND_MUPIROCIN_'_(PDB_00674)
-GGGCUUGUAGCUCAGGUGGUUAGAGCGCACCCCUGAUAAGGGUGAGGUCGGUGGUUCAAGUCCACUCAGGCCCAC
-(((((((..((((.........))))(((((((.....)))))))....(((((.......))))))))))))..
->>__'CRYSTAL_STRUCTURE_OF_CYSTEINYL-TRNA_SYNTHETASE_BINARY_COMPLEX_WITH_TRNACYS_'_(PDB_00742)
-GGCGCGUUAACAAAGCGGUUAUGUAGCGGAUUGCAAAUCCGUCUAGUCCGGUUCGACUCCGGAACGCGCCUCCA
-(((((((..(((.........))).((((((.....))))))....(((((.......))))))))))))....
->>__'CRYSTAL_STRUCTURE_OF_TRNA_NUCLEOTIDYLTRANSFERASE_COMPLEXED_WITH_A_PRIMER_TRNA_AND_AN_INCOMING_ATP_ANALOG_'_(PDB_00767)
-GGCCAGGGGCGGUUCGAUUCCGCCCCUGGCCGGCCAGGGGCGGUUCGAUUCCGCCCCUGGCCACCAA
-(((((((.(((.........))).)))))))(((((((.(((.........))).))))))).....
->>__'GLUTAMINYL-TRNA_SYNTHETASE_COMPLEXED_TO_GLUTAMINE_AND_2\'DEOXY_A76_GLUTAMINE_TRNA_'_(PDB_00901)
-GGGGUAUCGCCAAGCGGUAAGGCACCGGAUUCUGAUUCCGGCAUUCCGAGGUUCGAAUCCUCGUACCCCAGCCA
-((((((..((((.......)))).(((((((...))))))).....(((((.......))))))))))).....
->>__'IF2,_IF1,_AND_TRNA_FITTED_TO_CRYO-EM_DATA_OF_E._COLI_70S_INITIATION_COMPLEX_'_(PDB_00903)
-GCGGAUUUAGCUCAGUUGGGAGAGCGCCAGACUGAAGAUCUGGAGGUCCUGUGUUCGAUCCACAGAAUUCGCACCA
-(((((((..((((........))))((((((.......))))))....(((((.......))))))))))))....
->>__'STRUCTURE_OF_HUMAN_TRYPTOPHANYL-TRNA_SYNTHETASE_IN_COMPLEX_WITH_TRNA(TRP)_'_(PDB_00926)
-GACCUCGUGGCGCAAUGGUAGCGCGUCUGACUCCAGAUCAGAAGGUUGCGUGUUCGAAUCACGUCGGGGUCA
-((.((((..(((((.....)))))...((((.....)))).......(((((.......))))))))).)).
->>__'CRYSTAL_STRUCTURE_OF_STAPHYLOCOCCUS_AUREUS_TRNA_ADENOSINE_DEAMINASE,_TADA,_IN_COMPLEX_WITH_RNA_'_(PDB_00943)
-UUGACUACGGAUCAAUUGACUACGGAUCAAGACUACGGUUUGACUACGGAUCAA
-(((((.....)))))(((((.....))))).........(((((.....)))))
->>__'COCRYSTAL_STRUCTURE_OF_AN_RNA_SULFURATION_ENZYME_MNMA_AND_TRNA-GLU_IN_THE_PRE-REACTION_STATE_'_(PDB_00999)
-GUCCCCUUCGUCUAGAGGCCCAGGACACCGCCCUUUCACGGCGGUAACAGGGGUUCGAAUCCCCUAGGGG
-..((.....(((((.......)))))(((((((.....)))))))....((((.......))))...)).
->>__'STRUCTURE_OF_HUMAN_TRYPTOPHANYL-TRNA_SYNTHETASE_IN_COMPLEX_WITH_TRNA(TRP)_'_(PDB_01002)
-GACCUCGUGGCGCAAUGGUAGCGCGUCUGACUCCAGAUCAGAAGGUUGCGUGUUCGAAUCACGUCGGGGUCACCA
-(((((((....(((.....)))...((((((.....)))))).....(((((.......))))))))))))....
->>__'CRYSTAL_STRUCTURE_OF_ARCHAEOGLOBUS_FULGIDUS_O-PHOSPHOSERYL-_TRNA_SYNTHETASE_COMPLEXED_WITH_TRNACYS_AND_O-PHOSPHOSERINE_'_(PDB_01009)
-GCCAGGGUGGCAGAGGGGCUUUGCGGCGGACUGCAGAUCCGCUUUACCCCGGUUCGAAUCCGGGCCCUGGC
-((((((([[(((]].......)))..((((.......))))......(((((.......))))))))))))
->>__'CRYSTAL_STRUCTURE_OF_ARCHAEOGLOBUS_FULGIDUS_O-PHOSPHOSERYL-_TRNA_SYNTHETASE_COMPLEXED_WITH_TRNACYS_'_(PDB_01010)
-GCCAGGGUGGCAGAGGGGCUUUGCGGCGGACUGCAGAUCCGCUUUACCCCGGUUCGAAUCCGGGCCCUGGC
-..((((([[(((]].......)))..(((((.....)))))......(((((.......))))))))))..
->>__'CRYSTAL_STRUCTURE_OF_ARCHAEOGLOBUS_FULGIDUS_O-PHOSPHOSERYL-_TRNA_SYNTHETASE_E418N/E420N_MUTANT_COMPLEXED_WITH_TRNAOPAL_AND_O-PHOSPHOSERINE_("OPAL_COMPLEX")_'_(PDB_01011)
-GCCAGGGUGGCAGAGGGGCUUUGCGGCGGACUUCAGAUCCGCUUUACCCCGGUUCGAAUCCGGGCCCUGGC
-(((((((..(((.........))).(((((.......))))).....(((((.......))))))))))))
->>__'CRYSTAL_STRUCTURE_OF_ARCHAEOGLOBUS_FULGIDUS_O-PHOSPHOSERYL-_TRNA_SYNTHETASE_E418N/E420N_MUTANT_COMPLEXED_WITH_TRNAAMBER_AND_O-PHOSPHOSERINE_("AMBER_COMPLEX")_'_(PDB_01012)
-GCCAGGGUGGCAGAGGGGCUUUGCGGCGGACUCUAGAUCCGCUUUACCCCGGUUCGAAUCCGGGCCCUGGC
-(((((((..(((.........))).(((((.......))))).....(((((.......))))))))))))
->>__'CRYSTAL_STRUCTURE_OF_RNASE_Z/TRNA(THR)_COMPLEX_'_(PDB_01053)
-GCUUCCAUAGCUCAGCAGGUAGAGCGUCAGCGGUUCGAGCCCGCUUGGAAGCU
-(((((((..((((........))))...(((((.......)))))))))))).
->>__'PHENYLALANYL-TRNA_SYNTHETASE_FROM_THERMUS_THERMOPHILUS_COMPLEXED_WITH_TRNA_AND_A_PHENYLALANYL-ADENYLATE_ANALOG_'_(PDB_01134)
-GCCGAGGUAGCUCAGUUGGUAGAGCAUGCGACUGAAAAUCGCAGUGUCCGCGGUUCGAUUCCGCGCCUCGGCACCA
-(((((((....((........))...((((((.....)))))).....((((.........)))))))))))....
->>__'GLUTAMINYL-TRNA_SYNTHETASE_MUTANT_C229R_WITH_BOUND_ANALOG_5\'-O-[N-(L-GLUTAMINYL)-SULFAMOYL]ADENOSINE_'_(PDB_01258)
-GGGGUAUCGCCAAGCGGUAAGGCACCGGAUUCUGAUUCCGGCAUUCCGAGGUUCGAAUCCUCGUACCCCAGCCA
-((((((..((((.......)))).(((((((...))))))).....(((((.......))))))))))).....
->>__'GLUTAMINYL-TRNA_SYNTHETASE_MUTANT_C229R_WITH_BOUND_ANALOG_5\'-O-[N-(L-GLUTAMYL)-SULFAMOYL]ADENOSINE_'_(PDB_01259)
-GGGGUAUCGCCAAGCGGUAAGGCACCGGAUUCUGAUUCCGGCAUUCCGAGGUUCGAAUCCUCGUACCCCAGCCA
-((((((..((((.......))))((((((((...))))))))....(((((.......))))))))))).....

@@ -312,7 +312,7 @@ def launch_BayesPairing(module_type, seq_, header_, basename):
     rna.close()
 
 def launch_RNAMoIP_worker(x):
-    RNAMoIP = "../RNAMoIP/RNAMoIP.py"
+    RNAMoIP = biorseoDir + "/../RNAMoIP/Src/RNAMoIP.py"
     logfile = open("log_of_the_run.sh", 'a')
     logfile.write(" ".join(["gurobi.sh", RNAMoIP, "-s", '"' +x[1]+'"', "-ss", '"'+x[0].strip()+'"', "-d", descfolder]))
     logfile.write("\n")