aboutsummaryrefslogtreecommitdiff
diff options
context:
space:
mode:
authorNavan Chauhan <navanchauhan@gmail.com>2020-08-07 23:49:53 +0530
committerGitHub <noreply@github.com>2020-08-07 23:49:53 +0530
commitba9df5c3e7b518cde6db2a3d8ba0749299f8f127 (patch)
tree24edd9beab48a5a4f7ecaed55c865222b1b62331
parente3fc3363a20701a4c5bdd77b13665a1d539405ea (diff)
parent0ca4149acc0c69a327c72dd8528194d4b6383a28 (diff)
Merge pull request #4 from navanchauhan/deepsource-transform-b8729926
Format code with Black
-rw-r--r--scripts/makeReport.py234
1 files changed, 157 insertions, 77 deletions
diff --git a/scripts/makeReport.py b/scripts/makeReport.py
index 49b69f0..2a32d29 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()
@@ -11,68 +11,72 @@ 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")
fallback = 0
-print("## Visualisation", end="\n\n")
-print(f'![]({image})', end="\n\n")
+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:
+ if doc.report.bindingsite[x]["has_interactions"] == "True" and x != indexForUNL:
natural_ligands.append(x)
except:
- fallback==1
+ fallback == 1
if natural_ligands == []:
showNaturalLigands == False
for ligand in natural_ligands:
- print("### Natural Ligand " + str(x),end="\n\n")
- if doc.report.bindingsite[ligand].interactions.hydrophobic_interactions.cdata == '':
- print("No Hydrophobic Interactions Found",end="\n\n")
+ print("### Natural Ligand " + str(x), 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")
+ 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[ligand].interactions.hydrophobic_interactions.hydrophobic_interaction:
+ for x in doc.report.bindingsite[
+ ligand
+ ].interactions.hydrophobic_interactions.hydrophobic_interaction:
l = []
l.append(i)
l.append(x.resnr.cdata)
@@ -83,14 +87,27 @@ for ligand in natural_ligands:
i += 1
tableBody.append(l)
print(tabulate(tableBody, headers=tableHeaders), end="\n\n")
- if doc.report.bindingsite[ligand].interactions.hydrogen_bonds.cdata == '':
+ if doc.report.bindingsite[ligand].interactions.hydrogen_bonds.cdata == "":
print("No Hydrogen Bonds Found", end="\n\n")
else:
- 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[ligand].interactions.hydrogen_bonds.hydrogen_bond:
+ for x in doc.report.bindingsite[
+ ligand
+ ].interactions.hydrogen_bonds.hydrogen_bond:
l = []
l.append(i)
l.append(x.resnr.cdata)
@@ -104,111 +121,122 @@ for ligand in natural_ligands:
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")
print("## Ligand Interactions", end="\n\n")
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)
@@ -221,11 +249,24 @@ 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)
@@ -239,15 +280,25 @@ 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)
@@ -263,12 +314,14 @@ 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)
@@ -285,11 +338,15 @@ 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)
@@ -302,9 +359,20 @@ 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 = []
@@ -320,13 +388,21 @@ 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 = []
@@ -344,12 +420,16 @@ 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)
@@ -367,7 +447,7 @@ 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")