Increased Speed by 50%

1 files changed, 458 insertions, 0 deletions

diff --git a/app/scripts/makeReport.py b/app/scripts/makeReport.py
new file mode 100644
index 0000000..4f693ac
--- /dev/null
+++ b/app/scripts/makeReport.py
@@ -0,0 +1,458 @@
+#!/usr/bin/python3
+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")
+fallback = 0
+
+print("## Visualisation", end="\n\n")
+print(f"![]({image})", end="\n\n")
+
+natural_ligands = []
+showNaturalLigands = True
+
+try:
+    for x in range(len(doc.report.bindingsite)):
+        if doc.report.bindingsite[x]["has_interactions"] == "True" and x != indexForUNL:
+            natural_ligands.append(x)
+except:
+    fallback == 1
+
+if natural_ligands == []:
+    showNaturalLigands == False
+
+for ligand in natural_ligands:
+    print("### Natural Ligand " + str(ligand+1), end="\n\n")
+    if doc.report.bindingsite[ligand].interactions.hydrophobic_interactions.cdata == "":
+        print("No Hydrophobic Interactions Found", end="\n\n")
+    else:
+        print("#### Hydrophobic Interactions", end="\n\n")
+        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 = [
+                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")
+    if doc.report.bindingsite[ligand].interactions.hydrogen_bonds.cdata == "":
+        print("No Hydrogen Bonds Found", end="\n\n")
+    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",
+        ]
+        i = 1
+        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
+            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")
+
+print("## Docked Ligand Interactions", end="\n\n")
+
+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 = [
+                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")
+
+    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 = [
+                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
+            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 = [
+                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)
+            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 = [
+                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)
+            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 = [
+                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")
+
+    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 = [
+                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
+            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 = [
+                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)
+            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 = [
+                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)
+            l.append(atoms)
+            i += 1
+            tableBody.append(l)
+        print(tabulate(tableBody, headers=tableHeaders), end="\n\n")
+
+