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-rw-r--r--scripts/makeReport.py196
1 files changed, 26 insertions, 170 deletions
diff --git a/scripts/makeReport.py b/scripts/makeReport.py
index 2a32d29..cab6b78 100644
--- a/scripts/makeReport.py
+++ b/scripts/makeReport.py
@@ -74,16 +74,8 @@ 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 = []
- l.append(i)
- l.append(x.resnr.cdata)
- l.append(x.restype.cdata)
- l.append(x.dist.cdata)
- l.append(x.ligcarbonidx.cdata)
- l.append(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")
@@ -92,31 +84,10 @@ 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 = []
- l.append(i)
- l.append(x.resnr.cdata)
- l.append(x.restype.cdata)
- l.append(x.dist_h_a.cdata)
- l.append(x.dist_d_a.cdata)
- l.append(x.don_angle.cdata)
- l.append(x.protisdon.cdata)
- l.append(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
@@ -127,10 +98,7 @@ 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")
@@ -139,10 +107,7 @@ 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")
@@ -167,10 +132,7 @@ 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")
@@ -234,16 +196,8 @@ 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 = []
- l.append(i)
- l.append(x.resnr.cdata)
- l.append(x.restype.cdata)
- l.append(x.dist.cdata)
- l.append(x.ligcarbonidx.cdata)
- l.append(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")
@@ -251,31 +205,10 @@ 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 = []
- l.append(i)
- l.append(x.resnr.cdata)
- l.append(x.restype.cdata)
- l.append(x.dist_h_a.cdata)
- l.append(x.dist_d_a.cdata)
- l.append(x.don_angle.cdata)
- l.append(x.protisdon.cdata)
- l.append(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
@@ -286,26 +219,10 @@ 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 = []
- l.append(i)
- l.append(x.resnr.cdata)
- l.append(x.restype.cdata)
- l.append(x.dist.cdata)
- l.append(x.protispos.cdata)
- l.append(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)
@@ -319,16 +236,8 @@ 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 = []
- l.append(i)
- l.append(x.resnr.cdata)
- l.append(x.restype.cdata)
- l.append(x.dist.cdata)
- l.append(x.offset.cdata)
- l.append(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)
@@ -342,18 +251,8 @@ 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 = []
- l.append(i)
- l.append(x.resnr.cdata)
- l.append(x.restype.cdata)
- l.append(x.dist.cdata)
- l.append(x.ligcarbonidx.cdata)
- l.append(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")
@@ -361,29 +260,10 @@ 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 = []
- l.append(i)
- l.append(x.resnr.cdata)
- l.append(x.restype.cdata)
- l.append(x.dist_h_a.cdata)
- l.append(x.dist_d_a.cdata)
- l.append(x.don_angle.cdata)
- l.append(x.protisdon.cdata)
- l.append(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
@@ -394,24 +274,10 @@ 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 = []
- l.append(i)
- l.append(x.resnr.cdata)
- l.append(x.restype.cdata)
- l.append(x.dist.cdata)
- l.append(x.protispos.cdata)
- l.append(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)
@@ -425,18 +291,8 @@ 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 = []
- l.append(i)
- l.append(x.resnr.cdata)
- l.append(x.restype.cdata)
- l.append(x.dist.cdata)
- l.append(x.offset.cdata)
- l.append(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 2024-11-09 17:15:12 +0000