Merge remote-tracking branch 'origin/master'

RUBi-ZA · Dec 12, 2017 · 49aa06e · 49aa06e
2 parents c1d8b17 + b08e4e8
commit 49aa06e
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Showing 12 changed files with 6 additions and 5 deletions.
diff --git a/.travis.yml b/.travis.yml
@@ -1,6 +1,7 @@
 branches:
     only:
         - master
+        - dev-michael
 
 language: python
 

diff --git a/README.md b/README.md
@@ -12,7 +12,7 @@ git clone https://github.com/RUBi-ZA/MODE-TASK.git
 cd MODE-TASK
 ```
 
-*Compile C++ binaries:*
+*C++ scripts are pre-compiled and can be called from within a python environment using their corresponding ANM.py and getEigenVectors.py scripts. To compile the C++ yourself, use the following commands:*
 ```
 sudo apt install g++
 g++ -I cpp/src/ ANM.cpp -o ANM

diff --git a/assemblyCovariance.py b/assemblyCovariance.py
diff --git a/coarseGrain.py b/coarseGrain.py
diff --git a/combinationMode.py b/combinationMode.py
diff --git a/conformationMode.py b/conformationMode.py
diff --git a/getEigenVectors b/getEigenVectors
diff --git a/getEigenVectors.py b/getEigenVectors.py
@@ -10,7 +10,7 @@
 parser = argparse.ArgumentParser()
 
 # custom arguments
-parser.add_argument("--vt", help="VT matrix file")
+parser.add_argument("--vtMatrix", help="VT matrix file")
 parser.add_argument("--mode", help="Specify the index of the mode you wish to target")
 parser.add_argument("--direction", help="Direction of overlap correction (Default -1)", default="-1")
 parser.add_argument("--outdir", help="Directory to generate output to", default="output")
@@ -33,7 +33,7 @@
             sys.exit()
 
     # Run getEigenVectors executable
-    os.system("./getEigenVectors --vt " + args.vt + " --mode " + args.mode + " --direction " + args.direction + " --outdir " + args.outdir)
+    os.system("./getEigenVectors --vtMatrix " + args.vtMatrix + " --mode " + args.mode + " --direction " + args.direction + " --outdir " + args.outdir)
 
 else:
     print ('No arguments provided. Use -h to view help')
diff --git a/meanSquareFluctuations.py b/meanSquareFluctuations.py
diff --git a/tests/test_eigen_vectors.sh b/tests/test_eigen_vectors.sh
@@ -3,4 +3,4 @@ cd ..
 
 g++ -I cpp/input/ getEigenVectors.cpp -o getEigenVectors
 
-./getEigenVectors --vt output/VT_values.txt --mode 1
+./getEigenVectors --vtMatrix output/VT_values.txt --mode 1
diff --git a/tests/test_eigen_vectors_wrapper.sh b/tests/test_eigen_vectors_wrapper.sh
@@ -1,4 +1,4 @@
 #!/bin/bash
 cd ..
 
-./getEigenVectors.py --vt output/VT_values.txt --mode 1
+./getEigenVectors.py --vtMatrix output/VT_values.txt --mode 1
diff --git a/visualiseVector.py b/visualiseVector.py
Original file line number	Diff line number	Diff line change
Expand Up		@@ -3,4 +3,4 @@ cd ..

		g++ -I cpp/input/ getEigenVectors.cpp -o getEigenVectors

		./getEigenVectors --vt output/VT_values.txt --mode 1
		./getEigenVectors --vtMatrix output/VT_values.txt --mode 1