Update makeReport.py

1 files changed, 26 insertions, 170 deletions

diff --git a/scripts/makeReport.py b/scripts/makeReport.py
index 2a32d29..cab6b78 100644
--- a/scripts/makeReport.py
+++ b/scripts/makeReport.py
@@ -74,16 +74,8 @@ for ligand in natural_ligands:
         tableBody = []
         tableHeaders = ["No.", "Res.", "AA", "Dist", "Ligand Atom", "Proton Atom"]
         i = 1
-        for x in doc.report.bindingsite[
-            ligand
-        ].interactions.hydrophobic_interactions.hydrophobic_interaction:
-            l = []
-            l.append(i)
-            l.append(x.resnr.cdata)
-            l.append(x.restype.cdata)
-            l.append(x.dist.cdata)
-            l.append(x.ligcarbonidx.cdata)
-            l.append(x.protcarbonidx.cdata)
+        for x in doc.report.bindingsite[ligand].interactions.hydrophobic_interactions.hydrophobic_interaction:
+            l = [i,x.resnr.cdata,x.restype.cdata,x.dist.cdata,x.ligcarbonidx.cdata,x.protcarbonidx.cdata]
             i += 1
             tableBody.append(l)
         print(tabulate(tableBody, headers=tableHeaders), end="\n\n")
@@ -92,31 +84,10 @@ for ligand in natural_ligands:
     else:
         print("## Hydrogen Bonds", end="\n\n")
         tableBody = []
-        tableHeaders = [
-            "No.",
-            "Res.",
-            "AA",
-            "Dist H-A",
-            "Dist D-A",
-            "Don Angle",
-            "Protisdon?",
-            "Sidechain?",
-            "D. Atom",
-            "A. Atom",
-        ]
+        tableHeaders = ["No.","Res.","AA","Dist H-A","Dist D-A","Don Angle","Protisdon?","Sidechain?","D. Atom","A. Atom",]
         i = 1
-        for x in doc.report.bindingsite[
-            ligand
-        ].interactions.hydrogen_bonds.hydrogen_bond:
-            l = []
-            l.append(i)
-            l.append(x.resnr.cdata)
-            l.append(x.restype.cdata)
-            l.append(x.dist_h_a.cdata)
-            l.append(x.dist_d_a.cdata)
-            l.append(x.don_angle.cdata)
-            l.append(x.protisdon.cdata)
-            l.append(x.sidechain.cdata)
+        for x in doc.report.bindingsite[ligand].interactions.hydrogen_bonds.hydrogen_bond:
+            l = [i,x.resnr.cdata,x.restype.cdata,x.dist_h_a.cdata,x.dist_d_a.cdata,x.don_angle.cdata,x.protisdon.cdata,x.sidechain.cdata]
             l.append((x.donoridx.cdata + "[" + x.donortype.cdata + "]"))
             l.append((x.acceptoridx.cdata + "[" + x.acceptortype.cdata + "]"))
             i += 1
@@ -127,10 +98,7 @@ for ligand in natural_ligands:
 print("## Ligand Interactions", end="\n\n")
 
 try:
-    if (
-        doc.report.bindingsite[indexForUNL].interactions.hydrophobic_interactions.cdata
-        == ""
-    ):
+    if doc.report.bindingsite[indexForUNL].interactions.hydrophobic_interactions.cdata== "":
         print("No Hydrophobic Interactions Found", end="\n\n")
     else:
         print("**Hydrophobic Interactions Found**", end="\n\n")
@@ -139,10 +107,7 @@ except AttributeError:
     fallback = 1
 
 if fallback == 0:
-    if (
-        doc.report.bindingsite[indexForUNL].interactions.hydrophobic_interactions.cdata
-        == ""
-    ):
+    if doc.report.bindingsite[indexForUNL].interactions.hydrophobic_interactions.cdata== "":
         print("No Hydrophobic Interactions Found", end="\n\n")
     else:
         print("**Hydrophobic Interactions Found**", end="\n\n")
@@ -167,10 +132,7 @@ if fallback == 0:
     else:
         print("**Pi Stacks Found**", end="\n\n")
         ps = 1
-    if (
-        doc.report.bindingsite[indexForUNL].interactions.pi_cation_interactions.cdata
-        == ""
-    ):
+    if doc.report.bindingsite[indexForUNL].interactions.pi_cation_interactions.cdata== "":
         print("No Pi Cation Interactions Found", end="\n\n")
     else:
         print("**Pi Cation Interactions Found**", end="\n\n")
@@ -234,16 +196,8 @@ if fallback == 0:
         tableBody = []
         tableHeaders = ["No.", "Res.", "AA", "Dist", "Ligand Atom", "Proton Atom"]
         i = 1
-        for x in doc.report.bindingsite[
-            indexForUNL
-        ].interactions.hydrophobic_interactions.hydrophobic_interaction:
-            l = []
-            l.append(i)
-            l.append(x.resnr.cdata)
-            l.append(x.restype.cdata)
-            l.append(x.dist.cdata)
-            l.append(x.ligcarbonidx.cdata)
-            l.append(x.protcarbonidx.cdata)
+        for x in doc.report.bindingsite[indexForUNL].interactions.hydrophobic_interactions.hydrophobic_interaction:
+            l = [i,x.resnr.cdata,x.restype.cdata,x.dist.cdata,x.ligcarbonidx.cdata,x.protcarbonidx.cdata]
             i += 1
             tableBody.append(l)
         print(tabulate(tableBody, headers=tableHeaders), end="\n\n")
@@ -251,31 +205,10 @@ if fallback == 0:
     if hb == 1:
         print("## Hydrogen Bonds", end="\n\n")
         tableBody = []
-        tableHeaders = [
-            "No.",
-            "Res.",
-            "AA",
-            "Dist H-A",
-            "Dist D-A",
-            "Don Angle",
-            "Protisdon?",
-            "Sidechain?",
-            "D. Atom",
-            "A. Atom",
-        ]
+        tableHeaders = ["No.","Res.","AA","Dist H-A","Dist D-A","Don Angle","Protisdon?","Sidechain?","D. Atom","A. Atom"]
         i = 1
-        for x in doc.report.bindingsite[
-            indexForUNL
-        ].interactions.hydrogen_bonds.hydrogen_bond:
-            l = []
-            l.append(i)
-            l.append(x.resnr.cdata)
-            l.append(x.restype.cdata)
-            l.append(x.dist_h_a.cdata)
-            l.append(x.dist_d_a.cdata)
-            l.append(x.don_angle.cdata)
-            l.append(x.protisdon.cdata)
-            l.append(x.sidechain.cdata)
+        for x in doc.report.bindingsite[indexForUNL].interactions.hydrogen_bonds.hydrogen_bond:
+            l = [i,x.resnr.cdata,x.restype.cdata,x.dist_h_a.cdata,x.dist_d_a.cdata,x.don_angle.cdata,x.protisdon.cdata,x.sidechain.cdata]
             l.append((x.donoridx.cdata + "[" + x.donortype.cdata + "]"))
             l.append((x.acceptoridx.cdata + "[" + x.acceptortype.cdata + "]"))
             i += 1
@@ -286,26 +219,10 @@ if fallback == 0:
     if sb == 1:
         print("## Salt Bridges", end="\n\n")
         tableBody = []
-        tableHeaders = [
-            "Index",
-            "Residue",
-            "AA",
-            "Distance",
-            "Protein positive?",
-            "Ligand Group",
-            "Ligand Atoms",
-        ]
+        tableHeaders = ["Index","Residue","AA","Distance","Protein positive?","Ligand Group","Ligand Atoms"]
         i = 1
-        for x in doc.report.bindingsite[
-            indexForUNL
-        ].interactions.salt_bridges.salt_bridge:
-            l = []
-            l.append(i)
-            l.append(x.resnr.cdata)
-            l.append(x.restype.cdata)
-            l.append(x.dist.cdata)
-            l.append(x.protispos.cdata)
-            l.append(x.lig_group.cdata)
+        for x in doc.report.bindingsite[indexForUNL].interactions.salt_bridges.salt_bridge:
+            l = [i,x.resnr.cdata,x.restype.cdata,x.dist.cdata,x.protispos.cdata,x.lig_group.cdata]
             atoms = []
             for y in x.lig_idx_list.idx:
                 atoms.append(y.cdata)
@@ -319,16 +236,8 @@ if fallback == 0:
         tableBody = []
         tableHeaders = ["Index", "Residue", "AA", "Distance", "Prot charged?", "Atoms"]
         i = 1
-        for x in doc.report.bindingsite[
-            indexForUNL
-        ].interactions.pi_cation_interactions.pi_cation_interaction:
-            l = []
-            l.append(i)
-            l.append(x.resnr.cdata)
-            l.append(x.restype.cdata)
-            l.append(x.dist.cdata)
-            l.append(x.offset.cdata)
-            l.append(x.protcharged.cdata)
+        for x in doc.report.bindingsite[indexForUNL].interactions.pi_cation_interactions.pi_cation_interaction:
+            l = [i,x.resnr.cdata,x.restype.cdata,x.dist.cdata,x.offset.cdata,x.protcharged.cdata]
             atoms = []
             for y in x.lig_idx_list.idx:
                 atoms.append(y.cdata)
@@ -342,18 +251,8 @@ elif fallback == 1:
         tableBody = []
         tableHeaders = ["No.", "Res.", "AA", "Dist", "Ligand Atom", "Proton Atom"]
         i = 1
-        for (
-            x
-        ) in (
-            doc.report.bindingsite.interactions.hydrophobic_interactions.hydrophobic_interaction
-        ):
-            l = []
-            l.append(i)
-            l.append(x.resnr.cdata)
-            l.append(x.restype.cdata)
-            l.append(x.dist.cdata)
-            l.append(x.ligcarbonidx.cdata)
-            l.append(x.protcarbonidx.cdata)
+        for x in doc.report.bindingsite.interactions.hydrophobic_interactions.hydrophobic_interaction:
+            l = [i,x.resnr.cdata,x.restype.cdata,x.dist.cdata,x.ligcarbonidx.cdata,x.protcarbonidx.cdata]
             i += 1
             tableBody.append(l)
         print(tabulate(tableBody, headers=tableHeaders), end="\n\n")
@@ -361,29 +260,10 @@ elif fallback == 1:
     if hb == 1:
         print("## Hydrogen Bonds", end="\n\n")
         tableBody = []
-        tableHeaders = [
-            "No.",
-            "Res.",
-            "AA",
-            "Dist H-A",
-            "Dist D-A",
-            "Don Angle",
-            "Protisdon?",
-            "Sidechain?",
-            "D. Atom",
-            "A. Atom",
-        ]
+        tableHeaders = ["No.","Res.","AA","Dist H-A","Dist D-A","Don Angle","Protisdon?","Sidechain?","D. Atom","A. Atom"]
         i = 1
         for x in doc.report.bindingsite.interactions.hydrogen_bonds.hydrogen_bond:
-            l = []
-            l.append(i)
-            l.append(x.resnr.cdata)
-            l.append(x.restype.cdata)
-            l.append(x.dist_h_a.cdata)
-            l.append(x.dist_d_a.cdata)
-            l.append(x.don_angle.cdata)
-            l.append(x.protisdon.cdata)
-            l.append(x.sidechain.cdata)
+            l = [i,x.resnr.cdata,x.restype.cdata,x.dist_h_a.cdata,x.dist_d_a.cdata,x.don_angle.cdata,x.protisdon.cdata,x.sidechain.cdata]
             l.append((x.donoridx.cdata + "[" + x.donortype.cdata + "]"))
             l.append((x.acceptoridx.cdata + "[" + x.acceptortype.cdata + "]"))
             i += 1
@@ -394,24 +274,10 @@ elif fallback == 1:
     if sb == 1:
         print("## Salt Bridges", end="\n\n")
         tableBody = []
-        tableHeaders = [
-            "Index",
-            "Residue",
-            "AA",
-            "Distance",
-            "Protein positive?",
-            "Ligand Group",
-            "Ligand Atoms",
-        ]
+        tableHeaders = ["Index","Residue","AA","Distance","Protein positive?","Ligand Group","Ligand Atoms"]
         i = 1
         for x in doc.report.bindingsite.interactions.salt_bridges.salt_bridge:
-            l = []
-            l.append(i)
-            l.append(x.resnr.cdata)
-            l.append(x.restype.cdata)
-            l.append(x.dist.cdata)
-            l.append(x.protispos.cdata)
-            l.append(x.lig_group.cdata)
+            l = [i,x.resnr.cdata,x.restype.cdata,x.dist.cdata,x.protispos.cdata,x.lig_group.cdata]
             atoms = []
             for y in x.lig_idx_list.idx:
                 atoms.append(y.cdata)
@@ -425,18 +291,8 @@ elif fallback == 1:
         tableBody = []
         tableHeaders = ["Index", "Residue", "AA", "Distance", "Prot charged?", "Atoms"]
         i = 1
-        for (
-            x
-        ) in (
-            doc.report.bindingsite.interactions.pi_cation_interactions.pi_cation_interaction
-        ):
-            l = []
-            l.append(i)
-            l.append(x.resnr.cdata)
-            l.append(x.restype.cdata)
-            l.append(x.dist.cdata)
-            l.append(x.offset.cdata)
-            l.append(x.protcharged.cdata)
+        for x in doc.report.bindingsite.interactions.pi_cation_interactions.pi_cation_interaction:
+            l = [i,x.resnr.cdata,x.restype.cdata,x.dist.cdata,x.offset.cdata,x.protcharged.cdata]
             atoms = []
             for y in x.lig_idx_list.idx:
                 atoms.append(y.cdata)