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-rw-r--r--scripts/makeReport.py193
1 files changed, 129 insertions, 64 deletions
diff --git a/scripts/makeReport.py b/scripts/makeReport.py
index 79d9c70..fc53381 100644
--- a/scripts/makeReport.py
+++ b/scripts/makeReport.py
@@ -1,8 +1,8 @@
#!/usr/bin/python3
-import argparse
+import argparse
parser = argparse.ArgumentParser(description="Make Report Helper Script")
-parser.add_argument("-i","--input",help="Path to report folder")
+parser.add_argument("-i", "--input", help="Path to report folder")
args = parser.parse_args()
@@ -11,147 +11,160 @@ if args.input == None:
exit(1)
path = args.input
-#path = '/Users/navanchauhan/Desktop/nCOV-19/scripts/pymol/test/'
+# 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')
+# 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:
+ if ".png" in x and "UNL" in x:
image = x
import os
-fname = os.path.join(path,'report.xml')
+
+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
+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':
+ if x.identifiers.longname.cdata == "UNL":
break
else:
indexForUNL += 1
name = doc.report.pdbid.cdata
-#print(("# " + (name.replace("_"," ")).replace("PROTEIN","")), end="\n\n")
+# print(("# " + (name.replace("_"," ")).replace("PROTEIN","")), end="\n\n")
-print("## Visualisation", end="\n\n")
-print(f'![]({image})', 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 == '':
+ 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
+ fallback = 1
-if fallback==0:
- if doc.report.bindingsite[indexForUNL].interactions.hydrophobic_interactions.cdata == '':
+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 == '':
+ 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 == '':
+ 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 == '':
+ 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 == '':
+ 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 == '':
+ 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 == '':
+ 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")
+ 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 == '':
+ 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 == '':
+ 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 == '':
+ 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 == '':
+ 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 == '':
+ 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 == '':
+ 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 == '':
+ 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")
+ 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")
+ print("## Hydrophobic Interactions", end="\n\n")
tableBody = []
- tableHeaders = ['No.','Res.','AA','Dist','Ligand Atom','Proton Atom']
+ tableHeaders = ["No.", "Res.", "AA", "Dist", "Ligand Atom", "Proton Atom"]
i = 1
- for x in doc.report.bindingsite[indexForUNL].interactions.hydrophobic_interactions.hydrophobic_interaction:
+ for x in doc.report.bindingsite[
+ indexForUNL
+ ].interactions.hydrophobic_interactions.hydrophobic_interaction:
l = []
l.append(i)
l.append(x.resnr.cdata)
@@ -164,11 +177,24 @@ if fallback == 0:
print(tabulate(tableBody, headers=tableHeaders), end="\n\n")
if hb == 1:
- print("## Hydrogen Bonds",end="\n\n")
+ 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:
+ for x in doc.report.bindingsite[
+ indexForUNL
+ ].interactions.hydrogen_bonds.hydrogen_bond:
l = []
l.append(i)
l.append(x.resnr.cdata)
@@ -182,15 +208,25 @@ if fallback == 0:
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(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")
+ 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:
+ for x in doc.report.bindingsite[
+ indexForUNL
+ ].interactions.salt_bridges.salt_bridge:
l = []
l.append(i)
l.append(x.resnr.cdata)
@@ -206,12 +242,14 @@ if fallback == 0:
tableBody.append(l)
print(tabulate(tableBody, headers=tableHeaders), end="\n\n")
- if pc==1:
- print("## Pi Cation Interactions",end="\n\n")
+ if pc == 1:
+ print("## Pi Cation Interactions", end="\n\n")
tableBody = []
- tableHeaders = ['Index','Residue','AA','Distance','Prot charged?','Atoms']
+ tableHeaders = ["Index", "Residue", "AA", "Distance", "Prot charged?", "Atoms"]
i = 1
- for x in doc.report.bindingsite[indexForUNL].interactions.pi_cation_interactions.pi_cation_interaction:
+ for x in doc.report.bindingsite[
+ indexForUNL
+ ].interactions.pi_cation_interactions.pi_cation_interaction:
l = []
l.append(i)
l.append(x.resnr.cdata)
@@ -228,11 +266,15 @@ if fallback == 0:
print(tabulate(tableBody, headers=tableHeaders), end="\n\n")
elif fallback == 1:
if hi == 1:
- print("## Hydrophobic Interactions",end="\n\n")
+ print("## Hydrophobic Interactions", end="\n\n")
tableBody = []
- tableHeaders = ['No.','Res.','AA','Dist','Ligand Atom','Proton Atom']
+ tableHeaders = ["No.", "Res.", "AA", "Dist", "Ligand Atom", "Proton Atom"]
i = 1
- for x in doc.report.bindingsite.interactions.hydrophobic_interactions.hydrophobic_interaction:
+ for (
+ x
+ ) in (
+ doc.report.bindingsite.interactions.hydrophobic_interactions.hydrophobic_interaction
+ ):
l = []
l.append(i)
l.append(x.resnr.cdata)
@@ -245,9 +287,20 @@ elif fallback == 1:
print(tabulate(tableBody, headers=tableHeaders), end="\n\n")
if hb == 1:
- print("## Hydrogen Bonds",end="\n\n")
+ 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 = []
@@ -263,13 +316,21 @@ elif fallback == 1:
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(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")
+ 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 = []
@@ -287,12 +348,16 @@ elif fallback == 1:
tableBody.append(l)
print(tabulate(tableBody, headers=tableHeaders), end="\n\n")
- if pc==1:
- print("## Pi Cation Interactions",end="\n\n")
+ if pc == 1:
+ print("## Pi Cation Interactions", end="\n\n")
tableBody = []
- tableHeaders = ['Index','Residue','AA','Distance','Prot charged?','Atoms']
+ tableHeaders = ["Index", "Residue", "AA", "Distance", "Prot charged?", "Atoms"]
i = 1
- for x in doc.report.bindingsite.interactions.pi_cation_interactions.pi_cation_interaction:
+ for (
+ x
+ ) in (
+ doc.report.bindingsite.interactions.pi_cation_interactions.pi_cation_interaction
+ ):
l = []
l.append(i)
l.append(x.resnr.cdata)
@@ -310,7 +375,7 @@ elif fallback == 1:
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")
+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")
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-09 16:24:22 +0000