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-rw-r--r--scripts/makeReport.py206
1 files changed, 180 insertions, 26 deletions
diff --git a/scripts/makeReport.py b/scripts/makeReport.py
index cab6b78..c83928d 100644
--- a/scripts/makeReport.py
+++ b/scripts/makeReport.py
@@ -74,8 +74,17 @@ for ligand in natural_ligands:
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]
+ 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")
@@ -84,10 +93,32 @@ for ligand in natural_ligands:
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",]
+ 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]
+ 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
@@ -98,7 +129,10 @@ for ligand in natural_ligands:
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")
@@ -107,7 +141,10 @@ except AttributeError:
fallback = 1
if fallback == 0:
- 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")
@@ -132,7 +169,10 @@ if fallback == 0:
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")
@@ -196,8 +236,17 @@ if fallback == 0:
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]
+ 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")
@@ -205,10 +254,32 @@ if fallback == 0:
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"]
+ 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]
+ 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
@@ -219,10 +290,27 @@ if fallback == 0:
if sb == 1:
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:
- l = [i,x.resnr.cdata,x.restype.cdata,x.dist.cdata,x.protispos.cdata,x.lig_group.cdata]
+ 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)
@@ -236,8 +324,17 @@ if fallback == 0:
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]
+ 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)
@@ -251,8 +348,19 @@ elif fallback == 1:
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]
+ 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")
@@ -260,10 +368,30 @@ elif fallback == 1:
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"]
+ 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 = [
+ 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
@@ -274,10 +402,25 @@ elif fallback == 1:
if sb == 1:
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 = [i,x.resnr.cdata,x.restype.cdata,x.dist.cdata,x.protispos.cdata,x.lig_group.cdata]
+ 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)
@@ -291,8 +434,19 @@ elif fallback == 1:
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]
+ 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)
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-25 00:56:14 +0000