Fixed ANM testing

.gitignore

@@ -9,3 +9,5 @@ out_pca_test_trj\.xtc/
 .DS_Store
 
 data/.DS_Store
+
+src/ANM

src/ANM.cpp

@@ -36,10 +36,10 @@ using namespace std;
 using namespace alglib;
 
 
-int countAtoms()//counts Carbon Atoms (Beta carbons for all residues but Alpha carbons for Glycine)
-{
-	vector< vector<int> > row;
-}//countAtoms
+//int countAtoms()//counts Carbon Atoms (Beta carbons for all residues but Alpha carbons for Glycine)
+//{
+//	vector< vector<int> > row;
+//}//countAtoms
 
 
 vector< vector<double> > getCoOrds(string pdbInput,string atype)// gets the x,y,z cordinates for all the carbon atoms in PDB file. Returns 3 X numAtoms Matrix

tests/test_anm.sh

@@ -10,7 +10,7 @@ cd ../src
 
 ./coarseGrain.py --pdb ../tests/${prot}.pdb --cg 4 --atomType CB --outdir ../output/
 
-g++ -I cpp/src/ ANM.cpp -o ANM
+g++ -I ../src/cpp/src/ ../src/ANM.cpp -o ../src/ANM
 
 ../src/ANM --pdb ../output/ComplexCG4.pdb --cutoff 24 --atomType CB