459 lines
15 KiB
Python
459 lines
15 KiB
Python
#!/usr/bin/python3
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import argparse
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parser = argparse.ArgumentParser(description="Make Report Helper Script")
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parser.add_argument("-i", "--input", help="Path to report folder")
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args = parser.parse_args()
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if args.input == None:
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print("Error: Please specify path")
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exit(1)
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path = args.input
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# path = '/Users/navanchauhan/Desktop/nCOV-19/scripts/pymol/test/'
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import untangle
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from tabulate import tabulate
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# import sys
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# report = path + "report.md"
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# sys.stdout = open(report, 'w')
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from os import listdir
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from os.path import isfile, join
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onlyfiles = [f for f in listdir(path) if isfile(join(path, f))]
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image = ""
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for x in onlyfiles:
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if ".png" in x and "UNL" in x:
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image = x
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import os
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fname = os.path.join(path, "report.xml")
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doc = untangle.parse(fname)
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hi, hb, wb, sb, ps, pc, hab, mc = 0, 0, 0, 0, 0, 0, 0, 0
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indexForUNL = 0
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for x in doc.report.bindingsite:
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if x.identifiers.longname.cdata == "UNL":
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break
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else:
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indexForUNL += 1
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name = doc.report.pdbid.cdata
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# print(("# " + (name.replace("_"," ")).replace("PROTEIN","")), end="\n\n")
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fallback = 0
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print("## Visualisation", end="\n\n")
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print(f"", end="\n\n")
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natural_ligands = []
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showNaturalLigands = True
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try:
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for x in range(len(doc.report.bindingsite)):
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if doc.report.bindingsite[x]["has_interactions"] == "True" and x != indexForUNL:
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natural_ligands.append(x)
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except:
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fallback == 1
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if natural_ligands == []:
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showNaturalLigands == False
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for ligand in natural_ligands:
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print("### Natural Ligand " + str(ligand+1), end="\n\n")
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if doc.report.bindingsite[ligand].interactions.hydrophobic_interactions.cdata == "":
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print("No Hydrophobic Interactions Found", end="\n\n")
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else:
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print("#### Hydrophobic Interactions", end="\n\n")
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tableBody = []
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tableHeaders = ["No.", "Res.", "AA", "Dist", "Ligand Atom", "Proton Atom"]
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i = 1
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for x in doc.report.bindingsite[
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ligand
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].interactions.hydrophobic_interactions.hydrophobic_interaction:
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l = [
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i,
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x.resnr.cdata,
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x.restype.cdata,
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x.dist.cdata,
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x.ligcarbonidx.cdata,
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x.protcarbonidx.cdata,
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]
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i += 1
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tableBody.append(l)
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print(tabulate(tableBody, headers=tableHeaders), end="\n\n")
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if doc.report.bindingsite[ligand].interactions.hydrogen_bonds.cdata == "":
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print("No Hydrogen Bonds Found", end="\n\n")
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else:
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print("## Hydrogen Bonds", end="\n\n")
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tableBody = []
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tableHeaders = [
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"No.",
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"Res.",
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"AA",
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"Dist H-A",
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"Dist D-A",
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"Don Angle",
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"Protisdon?",
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"Sidechain?",
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"D. Atom",
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"A. Atom",
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]
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i = 1
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for x in doc.report.bindingsite[
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ligand
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].interactions.hydrogen_bonds.hydrogen_bond:
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l = [
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i,
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x.resnr.cdata,
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x.restype.cdata,
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x.dist_h_a.cdata,
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x.dist_d_a.cdata,
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x.don_angle.cdata,
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x.protisdon.cdata,
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x.sidechain.cdata,
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]
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l.append((x.donoridx.cdata + "[" + x.donortype.cdata + "]"))
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l.append((x.acceptoridx.cdata + "[" + x.acceptortype.cdata + "]"))
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i += 1
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tableBody.append(l)
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# 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 + "]"))
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print(tabulate(tableBody, headers=tableHeaders), end="\n\n")
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print("## Docked Ligand Interactions", end="\n\n")
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try:
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if (
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doc.report.bindingsite[indexForUNL].interactions.hydrophobic_interactions.cdata
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== ""
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):
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print("No Hydrophobic Interactions Found", end="\n\n")
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else:
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print("**Hydrophobic Interactions Found**", end="\n\n")
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hi = 1
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except AttributeError:
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fallback = 1
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if fallback == 0:
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if (
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doc.report.bindingsite[indexForUNL].interactions.hydrophobic_interactions.cdata
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== ""
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):
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print("No Hydrophobic Interactions Found", end="\n\n")
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else:
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print("**Hydrophobic Interactions Found**", end="\n\n")
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hi = 1
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if doc.report.bindingsite[indexForUNL].interactions.hydrogen_bonds.cdata == "":
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print("No Hydrogen Bonds Found", end="\n\n")
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else:
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print("**Hydrogen Bonds Found**", end="\n\n")
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hb = 1
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if doc.report.bindingsite[indexForUNL].interactions.water_bridges.cdata == "":
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print("No Water Bridges Found", end="\n\n")
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else:
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print("**Water Bridges Found**", end="\n\n")
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wb = 1
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if doc.report.bindingsite[indexForUNL].interactions.salt_bridges.cdata == "":
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print("No Salt Bridges Found", end="\n\n")
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else:
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print("**Salt Bridges Found**", end="\n\n")
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sb = 1
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if doc.report.bindingsite[indexForUNL].interactions.pi_stacks.cdata == "":
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print("No Pi Stacks Found", end="\n\n")
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else:
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print("**Pi Stacks Found**", end="\n\n")
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ps = 1
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if (
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doc.report.bindingsite[indexForUNL].interactions.pi_cation_interactions.cdata
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== ""
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):
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print("No Pi Cation Interactions Found", end="\n\n")
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else:
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print("**Pi Cation Interactions Found**", end="\n\n")
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pc = 1
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if doc.report.bindingsite[indexForUNL].interactions.halogen_bonds.cdata == "":
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print("No Halogen Bonds Found", end="\n\n")
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else:
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print("** Halogen Bonds Found**", end="\n\n")
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hab = 1
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if doc.report.bindingsite[indexForUNL].interactions.metal_complexes.cdata == "":
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print("No Metal Complexes Found", end="\n\n")
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else:
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print("**Metal Complexes Found**", end="\n\n")
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mc = 1
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if fallback == 1:
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if doc.report.bindingsite.interactions.hydrophobic_interactions.cdata == "":
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print("No Hydrophobic Interactions Found", end="\n\n")
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else:
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print("**Hydrophobic Interactions Found**", end="\n\n")
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hi = 1
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if doc.report.bindingsite.interactions.hydrogen_bonds.cdata == "":
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print("No Hydrogen Bonds Found", end="\n\n")
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else:
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print("**Hydrogen Bonds Found**", end="\n\n")
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hb = 1
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if doc.report.bindingsite.interactions.water_bridges.cdata == "":
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print("No Water Bridges Found", end="\n\n")
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else:
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print("**Water Bridges Found**", end="\n\n")
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wb = 1
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if doc.report.bindingsite.interactions.salt_bridges.cdata == "":
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print("No Salt Bridges Found", end="\n\n")
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else:
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print("**Salt Bridges Found**", end="\n\n")
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sb = 1
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if doc.report.bindingsite.interactions.pi_stacks.cdata == "":
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print("No Pi Stacks Found", end="\n\n")
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else:
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print("**Pi Stacks Found**", end="\n\n")
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ps = 1
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if doc.report.bindingsite.interactions.pi_cation_interactions.cdata == "":
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print("No Pi Cation Interactions Found", end="\n\n")
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else:
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print("**Pi Cation Interactions Found**", end="\n\n")
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pc = 1
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if doc.report.bindingsite.interactions.halogen_bonds.cdata == "":
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print("No Halogen Bonds Found", end="\n\n")
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else:
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print("** Halogen Bonds Found**", end="\n\n")
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hab = 1
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if doc.report.bindingsite.interactions.metal_complexes.cdata == "":
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print("No Metal Complexes Found", end="\n\n")
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else:
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print("**Metal Complexes Found**", end="\n\n")
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mc = 1
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if fallback == 0:
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if hi == 1:
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print("## Hydrophobic Interactions", end="\n\n")
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tableBody = []
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tableHeaders = ["No.", "Res.", "AA", "Dist", "Ligand Atom", "Proton Atom"]
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i = 1
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for x in doc.report.bindingsite[
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indexForUNL
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].interactions.hydrophobic_interactions.hydrophobic_interaction:
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l = [
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i,
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x.resnr.cdata,
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x.restype.cdata,
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x.dist.cdata,
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x.ligcarbonidx.cdata,
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x.protcarbonidx.cdata,
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]
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i += 1
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tableBody.append(l)
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print(tabulate(tableBody, headers=tableHeaders), end="\n\n")
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if hb == 1:
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print("## Hydrogen Bonds", end="\n\n")
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tableBody = []
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tableHeaders = [
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"No.",
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"Res.",
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"AA",
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"Dist H-A",
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"Dist D-A",
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"Don Angle",
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"Protisdon?",
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"Sidechain?",
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"D. Atom",
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"A. Atom",
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]
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i = 1
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for x in doc.report.bindingsite[
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indexForUNL
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].interactions.hydrogen_bonds.hydrogen_bond:
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l = [
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i,
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x.resnr.cdata,
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x.restype.cdata,
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x.dist_h_a.cdata,
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x.dist_d_a.cdata,
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x.don_angle.cdata,
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x.protisdon.cdata,
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x.sidechain.cdata,
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]
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l.append((x.donoridx.cdata + "[" + x.donortype.cdata + "]"))
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l.append((x.acceptoridx.cdata + "[" + x.acceptortype.cdata + "]"))
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i += 1
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tableBody.append(l)
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# 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 + "]"))
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print(tabulate(tableBody, headers=tableHeaders), end="\n\n")
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if sb == 1:
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print("## Salt Bridges", end="\n\n")
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tableBody = []
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tableHeaders = [
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"Index",
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"Residue",
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"AA",
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"Distance",
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"Protein positive?",
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"Ligand Group",
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"Ligand Atoms",
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]
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i = 1
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for x in doc.report.bindingsite[
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indexForUNL
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].interactions.salt_bridges.salt_bridge:
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l = [
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i,
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x.resnr.cdata,
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x.restype.cdata,
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x.dist.cdata,
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x.protispos.cdata,
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x.lig_group.cdata,
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]
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atoms = []
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for y in x.lig_idx_list.idx:
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atoms.append(y.cdata)
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l.append(atoms)
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i += 1
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tableBody.append(l)
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print(tabulate(tableBody, headers=tableHeaders), end="\n\n")
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if pc == 1:
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print("## Pi Cation Interactions", end="\n\n")
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tableBody = []
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tableHeaders = ["Index", "Residue", "AA", "Distance", "Prot charged?", "Atoms"]
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i = 1
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for x in doc.report.bindingsite[
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indexForUNL
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].interactions.pi_cation_interactions.pi_cation_interaction:
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l = [
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i,
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x.resnr.cdata,
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x.restype.cdata,
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x.dist.cdata,
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x.offset.cdata,
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x.protcharged.cdata,
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]
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atoms = []
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for y in x.lig_idx_list.idx:
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atoms.append(y.cdata)
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l.append(atoms)
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i += 1
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tableBody.append(l)
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print(tabulate(tableBody, headers=tableHeaders), end="\n\n")
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elif fallback == 1:
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if hi == 1:
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print("## Hydrophobic Interactions", end="\n\n")
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tableBody = []
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tableHeaders = ["No.", "Res.", "AA", "Dist", "Ligand Atom", "Proton Atom"]
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i = 1
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for (
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x
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) in (
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doc.report.bindingsite.interactions.hydrophobic_interactions.hydrophobic_interaction
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):
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l = [
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i,
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x.resnr.cdata,
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x.restype.cdata,
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x.dist.cdata,
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x.ligcarbonidx.cdata,
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x.protcarbonidx.cdata,
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]
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i += 1
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tableBody.append(l)
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print(tabulate(tableBody, headers=tableHeaders), end="\n\n")
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if hb == 1:
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print("## Hydrogen Bonds", end="\n\n")
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tableBody = []
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tableHeaders = [
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"No.",
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"Res.",
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"AA",
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"Dist H-A",
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"Dist D-A",
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"Don Angle",
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"Protisdon?",
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"Sidechain?",
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"D. Atom",
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"A. Atom",
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]
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i = 1
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for x in doc.report.bindingsite.interactions.hydrogen_bonds.hydrogen_bond:
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l = [
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i,
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x.resnr.cdata,
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x.restype.cdata,
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x.dist_h_a.cdata,
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x.dist_d_a.cdata,
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x.don_angle.cdata,
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x.protisdon.cdata,
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x.sidechain.cdata,
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]
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l.append((x.donoridx.cdata + "[" + x.donortype.cdata + "]"))
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l.append((x.acceptoridx.cdata + "[" + x.acceptortype.cdata + "]"))
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i += 1
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tableBody.append(l)
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# 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 + "]"))
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print(tabulate(tableBody, headers=tableHeaders), end="\n\n")
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if sb == 1:
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print("## Salt Bridges", end="\n\n")
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tableBody = []
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tableHeaders = [
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"Index",
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"Residue",
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"AA",
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"Distance",
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"Protein positive?",
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"Ligand Group",
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"Ligand Atoms",
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]
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i = 1
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for x in doc.report.bindingsite.interactions.salt_bridges.salt_bridge:
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l = [
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i,
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x.resnr.cdata,
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x.restype.cdata,
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x.dist.cdata,
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x.protispos.cdata,
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x.lig_group.cdata,
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]
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atoms = []
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for y in x.lig_idx_list.idx:
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atoms.append(y.cdata)
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l.append(atoms)
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i += 1
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tableBody.append(l)
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print(tabulate(tableBody, headers=tableHeaders), end="\n\n")
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if pc == 1:
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print("## Pi Cation Interactions", end="\n\n")
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tableBody = []
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tableHeaders = ["Index", "Residue", "AA", "Distance", "Prot charged?", "Atoms"]
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i = 1
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for (
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x
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) in (
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doc.report.bindingsite.interactions.pi_cation_interactions.pi_cation_interaction
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):
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l = [
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i,
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x.resnr.cdata,
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x.restype.cdata,
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x.dist.cdata,
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x.offset.cdata,
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x.protcharged.cdata,
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]
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atoms = []
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for y in x.lig_idx_list.idx:
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atoms.append(y.cdata)
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l.append(atoms)
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i += 1
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tableBody.append(l)
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print(tabulate(tableBody, headers=tableHeaders), end="\n\n")
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