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7 changed files
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25 additions
and
5 deletions
... | @@ -24,6 +24,7 @@ log_of_the_run.sh | ... | @@ -24,6 +24,7 @@ log_of_the_run.sh |
24 | logBadDesc.txt | 24 | logBadDesc.txt |
25 | gurobi.log | 25 | gurobi.log |
26 | temp/* | 26 | temp/* |
27 | +test_on_RNAstrand.py | ||
27 | 28 | ||
28 | # data | 29 | # data |
29 | data/modules/BGSU/HL/3.2/diagnostic/* | 30 | data/modules/BGSU/HL/3.2/diagnostic/* | ... | ... |
... | @@ -36,8 +36,19 @@ $(OBJECTS): $(OBJDIR)/%.o : $(SRCDIR)/%.cpp $(INCLUDES) | ... | @@ -36,8 +36,19 @@ $(OBJECTS): $(OBJDIR)/%.o : $(SRCDIR)/%.cpp $(INCLUDES) |
36 | $(CC) -c $(CFLAGS) $(CXXFLAGS) $< -o $@ | 36 | $(CC) -c $(CFLAGS) $(CXXFLAGS) $< -o $@ |
37 | @echo "\033[00;32mCompiled "$<".\033[00m" | 37 | @echo "\033[00;32mCompiled "$<".\033[00m" |
38 | 38 | ||
39 | +doc: mainpdf supppdf | ||
40 | + | ||
41 | +mainpdf: doc/main_bioinformatics.tex doc/references.bib doc/bioinfo.cls doc/natbib.bst | ||
42 | + cd doc; pdflatex -synctex=1 -interaction=nonstopmode -file-line-error main_bioinformatics | ||
43 | + cd doc; bibtex main_bioinformatics | ||
44 | + cd doc; pdflatex -synctex=1 -interaction=nonstopmode -file-line-error main_bioinformatics | ||
45 | + cd doc; pdflatex -synctex=1 -interaction=nonstopmode -file-line-error main_bioinformatics | ||
46 | + | ||
47 | +supppdf: doc/supplementary_material.tex | ||
48 | + cd doc; pdflatex -synctex=1 -interaction=nonstopmode -file-line-error supplementary_material | ||
49 | + | ||
39 | .PHONY: all | 50 | .PHONY: all |
40 | -all: $(BINDIR)/$(TARGET) | 51 | +all: $(BINDIR)/$(TARGET) doc |
41 | 52 | ||
42 | .PHONY: re | 53 | .PHONY: re |
43 | re: remove clean all | 54 | re: remove clean all |
... | @@ -45,9 +56,12 @@ re: remove clean all | ... | @@ -45,9 +56,12 @@ re: remove clean all |
45 | .PHONY: clean | 56 | .PHONY: clean |
46 | clean: | 57 | clean: |
47 | $(rm) $(OBJECTS) | 58 | $(rm) $(OBJECTS) |
59 | + $(rm) doc/supplementary_material.bbl doc/supplementary_material.blg doc/supplementary_material.synctex.gz doc/supplementary_material.log doc/supplementary_material.aux | ||
60 | + $(rm) doc/main_bioinformatics.bbl doc/main_bioinformatics.blg doc/main_bioinformatics.synctex.gz doc/main_bioinformatics.log doc/main_bioinformatics.aux doc/OUP_First_SBk_Bot_8401-eps-converted-to.pdf | ||
48 | @echo "\033[00;32mCleanup completed.\033[00m" | 61 | @echo "\033[00;32mCleanup completed.\033[00m" |
49 | 62 | ||
50 | .PHONY: remove | 63 | .PHONY: remove |
51 | -remove: clean | 64 | +remove: |
52 | @$(rm) $(BINDIR)/$(TARGET) | 65 | @$(rm) $(BINDIR)/$(TARGET) |
53 | - @echo "\033[00;32mExecutable removed!\033[00m" | 66 | + @$(rm) doc/main_bioinformatics.pdf doc/supplementary_material.pdf |
67 | + @echo "\033[00;32mExecutable and docs removed!\033[00m" | ... | ... |
data/fasta/applications.fa
0 → 100644
1 | +>__'CRYSTAL_STRUCTURE_OF_A_TIGHT-BINDING_GLUTAMINE_TRNA_BOUND_TO_GLUTAMINE_AMINOACYL_TRNA_SYNTHETASE_'_(PDB_00376) | ||
2 | +GGGGUAUCGCCAAGCGGUAAGGCACCGGAUUCUGAUUCCGGAGGUCGAGGUUCGAAUCCUCGUACCCCAGCCA | ||
3 | +>__'GUANINE_RIBOSWITCH_U22C,_A52G_MUTANT_BOUND_TO_HYPOXANTHINE_'_(PDB_01023) | ||
4 | +GGACAUACAAUCGCGUGGAUAUGGCACGCAAGUUUCUGCCGGGCACCGUAAAUGUCCGACUAUGUCCa | ||
5 | +>__'SOLUTION_STRUCTURE_OF_THE_P2B-P3_PSEUDOKNOT_FROM_HUMAN_TELOMERASE_RNA_'_(PDB_00857) | ||
6 | +GGGCUGUUUUUCUCGCUGACUUUCAGCCCCAAACAAAAAAGUCAGCA |
data/sec_structs/article_dataset.dbn
deleted
100644 → 0
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data/sec_structs/rna1999.dG
deleted
100644 → 0
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... | @@ -498,8 +498,7 @@ | ... | @@ -498,8 +498,7 @@ |
498 | % Vol. 00\ no. 00 \@pubyear\\ | 498 | % Vol. 00\ no. 00 \@pubyear\\ |
499 | % \hfill Pages \thepagerange | 499 | % \hfill Pages \thepagerange |
500 | % } | 500 | % } |
501 | - \vspace{-2cm} | 501 | + \hfill\includegraphics{OUP_First_SBk_Bot_8401.eps}} |
502 | - \hfill\includegraphics{fig/oxford.png}} | ||
503 | \vskip2pt | 502 | \vskip2pt |
504 | \rule{415pt}{2\p@}\par% | 503 | \rule{415pt}{2\p@}\par% |
505 | \helvetica | 504 | \helvetica | ... | ... |
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