Repulsions again

tools/domain_sectioner/README.md

@@ -1,9 +1,20 @@
-divide_inrtamat.sh takes as input the atom defining the division between two domains and divide the second input (intramat) into four blocks setting to 0 all the inter-domain interaction
+##Workflow:
+
+1) Use divide_intramat.sh (or domain_intramat.py) on the md intramat. This will generate an intramat (split_intramat.ndx) divided in blocks (0 for inter-domain contact) to be used for the inter-domain random coil
+2) Use the rc intramat and the split_intramat.ndx to generate a mego ff with the intra-domain interaction on and the inter-domain interaction off. This will be the simulation of the inter-domain random coil.
+3) Calculate the intramat of the inter-domain random coil
+4) Use group_intramats.sh with rc intramat and inter-domain rc intramat. This will generate a new rc intramat with off diagonal blocks obtained from the inter-domain rc
+5) Use the new rc_intramat and the full md intramat for multi-eGO to generate a new ff for multi-domain proteins
+
+
+##Scrits:
+
+divide_intramat.sh takes as input the atom defining the division between two domains and divide the second input (intramat) into four blocks setting to 0 all the inter-domain interaction
 
 > bash divide_intramat.sh num(int) path_to_md_intramat
 
 group_inrtamat.sh takes as input the atom defining the division between two domains, the path of the random_coil intramat and the path of the inter-domain random coil. The script regroups the intramat so that the intra-domain matrix blocks are the random_coil ones and the inter_domain matrix blocks are the inter-domain "random coil" ones
 
 > bash group_intrmat.sh num(int) path_to_random_coil_intramat path_to_inter_domain_rc_intramat
 
-Alternatively the python code can be used in the same way
+Alternatively the python code (domain_intramat.py) can be used in the same way

tools/domain_sectioner/divide_intramat.sh

@@ -6,6 +6,6 @@ mat=$2
 echo "Dividing $2 at atom i = $i_block"
 echo 
 
-awk -v i=$i_block '{if(($2<=i && $4<=i) || ($2>i && $4>i)){print $0} else{print $1,$2,$3,$4,0.000000,0.000000,0.000000,0.000000 ,$9}}' $2 > split_intramat.ndx
+awk -v i=$i_block '{if(($2<=i && $4<=i) || ($2>i && $4>i)){print $0} else{print $1,$2,$3,$4,"0.000000","0.000000+e00" ,$7}}' $2 > split_intramat.ndx
 
-echo "finished job"
+echo "Finished job"

tools/domain_sectioner/domains_intramat.py

@@ -8,9 +8,8 @@
     exit()
 
 elif len(sys.argv)==3:
-    print("reading")
     intra_md = np.loadtxt(sys.argv[2], unpack=True)
-    print("read")
+    print(f"Dividing {intra_md} at atom {i_block}")
     dim = int(np.sqrt(len(intra_md[0])))
 
     map_i = np.array([ True if i <= i_block - 1 else False for i in range(dim)])
@@ -19,22 +18,20 @@
     map_j = map_j * map_j[:,np.newaxis]
     map = np.logical_or(map_j,map_i)
     map = map.reshape(dim**2)
-    intra_md[4] = np.where(map, intra_md[4], 0)
-    intra_md[5] = np.where(map, intra_md[5], 0)
-    intra_md[6] = np.where(map, intra_md[6], 0)
-    intra_md[7] = np.where(map, intra_md[7], 0)
-    #intra_md[8] = np.where(map, intra_md[8], 0)
 
-    np.savetxt("split_intramat.ndx",intra_md.T, delimiter=" ", fmt = ['%4i', '%4i', '%4i', '%4i', '%2.6f', '%2.6f', '%2.6f', '%2.6f', '%2.6f'])
+    intra_md[4] = np.where(map, intra_md[4], 0.)
+    intra_md[5] = np.where(map, intra_md[5], 0.)
+
+    np.savetxt("split_intramat.ndx",intra_md.T, delimiter=" ", fmt = ['%i', '%i', '%i', '%i', '%2.6f', '%.6e', '%2.6f' ])
+    print(f"Finished job ")
 
 elif len(sys.argv)==4:
-    print("reading")
     intra_rc = np.loadtxt(sys.argv[2], unpack=True)
     intra_domain_rc = np.loadtxt(sys.argv[3], unpack=True)
+    print("Group {intra_rc} with {intra_domain_rc} at atom {i_block}")
     if(intra_rc.shape != intra_domain_rc.shape): 
         print("input intramats have different dimensions")
         exit()
-    print("read")
     dim = int(np.sqrt(len(intra_rc[0])))
 
     map_i = np.array([ True if i <= i_block - 1 else False for i in range(dim)])
@@ -47,10 +44,7 @@
     intra_rc[4] = np.where(map, intra_rc[4], intra_domain_rc[4])
     intra_rc[5] = np.where(map, intra_rc[5], intra_domain_rc[5])
     intra_rc[6] = np.where(map, intra_rc[6], intra_domain_rc[6])
-    intra_rc[7] = np.where(map, intra_rc[7], intra_domain_rc[7])
-    #intra_rc[8] = np.where(map, intra_rc[8], intra_domain_rc[8])
 
-    np.savetxt("grouped_intramat.ndx",intra_rc.T, delimiter=" ",fmt = ['%4i', '%4i', '%4i', '%4i', '%2.6f', '%2.6f', '%2.6f', '%2.6f', '%2.6f'])
+    np.savetxt("grouped_intramat.ndx",intra_rc.T, delimiter=" ",fmt = ['%4i', '%4i', '%4i', '%4i', '%2.6f', '%.6e', '%2.6' ])
+    print("Finished job")
 
-print(i_block)
-print(len(sys.argv))

tools/domain_sectioner/group_intramats.sh

@@ -4,8 +4,8 @@ i_block=$1
 mat_1=$2
 mat_2=$3
 
-echo "Grouping $mat1 with $mat2 at atom $i_block"
+echo "Group $mat1 with $mat2 at atom $i_block"
 
-paste $mat_1 $mat_2 | awk -v i=$i_block '{if(($2<=i && $4<=i) || ($2>i && $4>i)){print $1,$2,$3,$4,$5,$6,$7,$8,$9} else{print $10,$11,$12,$13,$14,$15,$16,$17,$18}}' > grouped_intramat.ndx
+paste $mat_1 $mat_2 | awk -v i=$i_block '{if(($2<=i && $4<=i) || ($2>i && $4>i)){print $1,$2,$3,$4,$5,$6,$7} else{print $8,$9,$10,$11,$12,$13,$14}}' > grouped_intramat.ndx
 
-echo "Finished grouping"
+echo "Finished job"