From 004f4513c8cd5cfffbf69484fb39a3d7bc98bd49 Mon Sep 17 00:00:00 2001 From: Navan Chauhan Date: Fri, 11 Sep 2020 16:17:57 +0530 Subject: shifting hardcoded figures to another level --- scripts/add-pictures.py | 6 ++++++ scripts/main.sh | 10 ++++++---- scripts/makeReport.py | 5 ----- 3 files changed, 12 insertions(+), 9 deletions(-) create mode 100644 scripts/add-pictures.py (limited to 'scripts') diff --git a/scripts/add-pictures.py b/scripts/add-pictures.py new file mode 100644 index 0000000..95079f0 --- /dev/null +++ b/scripts/add-pictures.py @@ -0,0 +1,6 @@ +print("## Figures", end="\n\n") + +print("![Back View](output-back.png){width=100%}", end="\n\n") +print("![Front View](output-front.png){width=100%}", end="\n\n") +print("![Close Up View of the Back](closeup-back.png){width=100%}", end="\n\n") +print("![Close Up View of the Front](closeup-front.png){width=100%}", end="\n\n") \ No newline at end of file diff --git a/scripts/main.sh b/scripts/main.sh index 68397fb..a165994 100755 --- a/scripts/main.sh +++ b/scripts/main.sh @@ -137,16 +137,18 @@ if [[ $dockingCheck == "true" ]]; then vina --receptor $proteinPath --ligand $ligandPath --config $config fi -if [[ $visualisations == "true" ]]; then - file=$(echo "$ligandPath" | cut -f 1 -d '.') - python3 /src/scripts/quick-ligand-protein.py -p $proteinPath -l "$(echo $file)_out.pdbqt" -fi + if [[ $interactions == "true" ]]; then python3 /src/scripts/get-best.py -p $proteinPath -l "$(echo $file)_out.pdbqt" python3 /src/plip/plipcmd.py -f best.pdb -qpxy python3 /src/scripts/get_dock_score.py -l "$(echo $file)_out.pdbqt" -p $proteinPath > report.md python3 /src/scripts/makeReport.py --input . >> report.md + if [[ $visualisations == "true" ]]; then + file=$(echo "$ligandPath" | cut -f 1 -d '.') + python3 /src/scripts/quick-ligand-protein.py -p $proteinPath -l "$(echo $file)_out.pdbqt" + python3 /src/scripts/add-pictures.py + fi pandoc -V geometry:margin=1in report.md --pdf-engine=xelatex -o $name.pdf fi diff --git a/scripts/makeReport.py b/scripts/makeReport.py index c83928d..535da9b 100644 --- a/scripts/makeReport.py +++ b/scripts/makeReport.py @@ -455,9 +455,4 @@ elif fallback == 1: tableBody.append(l) print(tabulate(tableBody, headers=tableHeaders), end="\n\n") -print("## Figures", end="\n\n") -print(f"![](output-back.png)", end="\n\n") -print(f"![](output-front.png)", end="\n\n") -print(f"![](closeup-back.png)", end="\n\n") -print(f"![](closeup-front.png)", end="\n\n") -- cgit v1.2.3