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")