initial commit

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diff --git a/scripts/makeReport.py b/scripts/makeReport.py
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+++ b/scripts/makeReport.py
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+import argparse 
+
+parser = argparse.ArgumentParser(description="Make Report Helper Script")
+parser.add_argument("-i","--input",help="Path to report folder")
+
+args = parser.parse_args()
+
+if args.input == None:
+    print("Error: Please specify path")
+    exit(1)
+
+path = args.input
+#path = '/Users/navanchauhan/Desktop/nCOV-19/scripts/pymol/test/'
+
+import untangle
+from tabulate import tabulate
+
+#import sys
+#report = path + "report.md"
+#sys.stdout = open(report, 'w')
+
+from os import listdir
+from os.path import isfile, join
+onlyfiles = [f for f in listdir(path) if isfile(join(path, f))]
+image = ""
+for x in onlyfiles:
+    if '.png' in x and 'UNL' in x:
+        image = x
+import os
+fname = os.path.join(path,'report.xml')
+
+doc = untangle.parse(fname)
+
+hi, hb, wb, sb, ps, pc, hab, mc = 0,0,0,0,0,0,0,0
+
+indexForUNL = 0
+
+for x in doc.report.bindingsite:
+    if x.identifiers.longname.cdata == 'UNL':
+        break
+    else:
+        indexForUNL += 1
+
+
+name = doc.report.pdbid.cdata
+print(("# " + (name.replace("_"," ")).replace("PROTEIN","")), end="\n\n")
+
+print("## Visualisation", end="\n\n")    
+print(f'![]({image})', end="\n\n")
+
+print("## Interactions", end="\n\n")
+
+fallback = 0
+try:
+    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")
+        hi = 1
+except AttributeError:
+    fallback=1
+
+if fallback==0:
+    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")
+        hi = 1
+    if doc.report.bindingsite[indexForUNL].interactions.hydrogen_bonds.cdata == '':
+        print("No Hydrogen Bonds Found", end="\n\n")
+    else:
+        print("**Hydrogen Bonds Found**", end="\n\n")
+        hb = 1
+    if doc.report.bindingsite[indexForUNL].interactions.water_bridges.cdata == '':
+        print("No Water Bridges Found", end="\n\n")
+    else:
+        print("**Water Bridges Found**", end="\n\n")
+        wb = 1
+    if doc.report.bindingsite[indexForUNL].interactions.salt_bridges.cdata == '':
+        print("No Salt Bridges Found", end="\n\n")
+    else:
+        print("**Salt Bridges Found**", end="\n\n")
+        sb = 1
+    if doc.report.bindingsite[indexForUNL].interactions.pi_stacks.cdata == '':
+        print("No Pi Stacks Found", end="\n\n")
+    else:
+        print("**Pi Stacks Found**", end="\n\n")
+        ps = 1
+    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")
+        pc = 1
+    if doc.report.bindingsite[indexForUNL].interactions.halogen_bonds.cdata == '':
+        print("No Halogen Bonds Found", end="\n\n")
+    else:
+        print("** Halogen Bonds Found**", end="\n\n")
+        hab = 1
+    if doc.report.bindingsite[indexForUNL].interactions.metal_complexes.cdata == '':
+        print("No Metal Complexes Found", end="\n\n")    
+    else:
+        print("**Metal Complexes Found**", end="\n\n")
+        mc = 1
+
+if fallback == 1:
+    if doc.report.bindingsite.interactions.hydrophobic_interactions.cdata == '':
+        print("No Hydrophobic Interactions Found", end="\n\n")
+    else:
+        print("**Hydrophobic Interactions Found**", end="\n\n")
+        hi = 1
+    if doc.report.bindingsite.interactions.hydrogen_bonds.cdata == '':
+        print("No Hydrogen Bonds Found", end="\n\n")
+    else:
+        print("**Hydrogen Bonds Found**", end="\n\n")
+        hb = 1
+    if doc.report.bindingsite.interactions.water_bridges.cdata == '':
+        print("No Water Bridges Found", end="\n\n")
+    else:
+        print("**Water Bridges Found**", end="\n\n")
+        wb = 1
+    if doc.report.bindingsite.interactions.salt_bridges.cdata == '':
+        print("No Salt Bridges Found", end="\n\n")
+    else:
+        print("**Salt Bridges Found**", end="\n\n")
+        sb = 1
+    if doc.report.bindingsite.interactions.pi_stacks.cdata == '':
+        print("No Pi Stacks Found", end="\n\n")
+    else:
+        print("**Pi Stacks Found**", end="\n\n")
+        ps = 1
+    if doc.report.bindingsite.interactions.pi_cation_interactions.cdata == '':
+        print("No Pi Cation Interactions Found", end="\n\n")
+    else:
+        print("**Pi Cation Interactions Found**", end="\n\n")
+        pc = 1
+    if doc.report.bindingsite.interactions.halogen_bonds.cdata == '':
+        print("No Halogen Bonds Found", end="\n\n")
+    else:
+        print("** Halogen Bonds Found**", end="\n\n")
+        hab = 1
+    if doc.report.bindingsite.interactions.metal_complexes.cdata == '':
+        print("No Metal Complexes Found", end="\n\n")    
+    else:
+        print("**Metal Complexes Found**", end="\n\n")
+        mc = 1
+
+if fallback == 0:
+    if hi == 1:
+        print("## Hydrophobic Interactions",end="\n\n")
+        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)
+            i += 1
+            tableBody.append(l)
+        print(tabulate(tableBody, headers=tableHeaders), end="\n\n")
+
+    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']
+        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)
+            l.append((x.donoridx.cdata + "[" + x.donortype.cdata + "]"))
+            l.append((x.acceptoridx.cdata + "[" + x.acceptortype.cdata + "]"))
+            i += 1
+            tableBody.append(l)
+            #print(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, (x.donoridx.cdata + "[" + x.donortype.cdata + "]"), (x.acceptoridx.cdata + "[" + x.acceptortype.cdata + "]"))
+        print(tabulate(tableBody, headers=tableHeaders), end="\n\n")
+
+    if sb == 1:
+        print("## Salt Bridges",end="\n\n")
+        tableBody = []
+        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)
+            atoms = []
+            for y in x.lig_idx_list.idx:
+                atoms.append(y.cdata)
+            l.append(atoms)
+            i += 1
+            tableBody.append(l)
+        print(tabulate(tableBody, headers=tableHeaders), end="\n\n")
+
+    if pc==1:
+        print("## Pi Cation Interactions",end="\n\n")
+        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)
+            atoms = []
+            for y in x.lig_idx_list.idx:
+                atoms.append(y.cdata)
+            l.append(atoms)
+            i += 1
+            tableBody.append(l)
+        print(tabulate(tableBody, headers=tableHeaders), end="\n\n")
+elif fallback == 1:
+    if hi == 1:
+        print("## Hydrophobic Interactions",end="\n\n")
+        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)
+            i += 1
+            tableBody.append(l)
+        print(tabulate(tableBody, headers=tableHeaders), end="\n\n")
+
+    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']
+        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.append((x.donoridx.cdata + "[" + x.donortype.cdata + "]"))
+            l.append((x.acceptoridx.cdata + "[" + x.acceptortype.cdata + "]"))
+            i += 1
+            tableBody.append(l)
+            #print(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, (x.donoridx.cdata + "[" + x.donortype.cdata + "]"), (x.acceptoridx.cdata + "[" + x.acceptortype.cdata + "]"))
+        print(tabulate(tableBody, headers=tableHeaders), end="\n\n")
+
+    if sb == 1:
+        print("## Salt Bridges",end="\n\n")
+        tableBody = []
+        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)
+            atoms = []
+            for y in x.lig_idx_list.idx:
+                atoms.append(y.cdata)
+            l.append(atoms)
+            i += 1
+            tableBody.append(l)
+        print(tabulate(tableBody, headers=tableHeaders), end="\n\n")
+
+    if pc==1:
+        print("## Pi Cation Interactions",end="\n\n")
+        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)
+            atoms = []
+            for y in x.lig_idx_list.idx:
+                atoms.append(y.cdata)
+            l.append(atoms)
+            i += 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")