diff options
Diffstat (limited to 'scripts')
| -rw-r--r-- | scripts/get-best.py | 17 | ||||
| -rw-r--r-- | scripts/get_dock_score.py | 20 | ||||
| -rw-r--r-- | scripts/makeReport.py | 193 | ||||
| -rw-r--r-- | scripts/quick-ligand-protein.py | 69 |
4 files changed, 195 insertions, 104 deletions
diff --git a/scripts/get-best.py b/scripts/get-best.py index a10c2d2..c0185e4 100644 --- a/scripts/get-best.py +++ b/scripts/get-best.py @@ -11,13 +11,14 @@ version = "1.0" desc_text = "PyMol Quick Visualtion " + version parser = argparse.ArgumentParser(description=desc_text) -parser.add_argument("-p","--protein",help="Path to protein file") -parser.add_argument("-l","--ligand",help="Path to ligand_out file") +parser.add_argument("-p", "--protein", help="Path to protein file") +parser.add_argument("-l", "--ligand", help="Path to ligand_out file") args = parser.parse_args() + def li(s): - #log.info(s) + # log.info(s) None @@ -35,10 +36,10 @@ ligand = args.ligand session = pymol2.PyMOL() session.start() cmd = session.cmd -cmd.load(protein,'pro') -cmd.load(ligand,'lig') -cmd.split_states('lig') +cmd.load(protein, "pro") +cmd.load(ligand, "lig") +cmd.split_states("lig") -#fname = re.sub(r'^.*?/', '', protein.replace(".pdbqt","")) + "-" + re.sub(r'^.*?/', '', ligand.replace(".pdbqt","")) + ".pdb" +# fname = re.sub(r'^.*?/', '', protein.replace(".pdbqt","")) + "-" + re.sub(r'^.*?/', '', ligand.replace(".pdbqt","")) + ".pdb" -cmd.save("best.pdb","pro lig_0001") +cmd.save("best.pdb", "pro lig_0001") diff --git a/scripts/get_dock_score.py b/scripts/get_dock_score.py index c8b87d5..1cc0412 100644 --- a/scripts/get_dock_score.py +++ b/scripts/get_dock_score.py @@ -3,8 +3,8 @@ import argparse parser = argparse.ArgumentParser(description="Get Docking Score") -parser.add_argument("-p","--protein",help="Path to protein file") -parser.add_argument("-l","--ligand",help="Path to ligand_out file") +parser.add_argument("-p", "--protein", help="Path to protein file") +parser.add_argument("-l", "--ligand", help="Path to ligand_out file") args = parser.parse_args() @@ -21,7 +21,13 @@ ligand = args.ligand from os.path import basename -print("# " + str(basename(protein)).replace(".pdbqt","") + "-" + str(basename(ligand)).replace("_out.pdbqt",""), end="\n\n") +print( + "# " + + str(basename(protein)).replace(".pdbqt", "") + + "-" + + str(basename(ligand)).replace("_out.pdbqt", ""), + end="\n\n", +) from tabulate import tabulate @@ -31,7 +37,7 @@ results = [] i = 1 for line in lines: ta = [] - if line.find('REMARK VINA') == 0 and line.split()[3] != "": + if line.find("REMARK VINA") == 0 and line.split()[3] != "": l = line.split() ta.append(i) ta.append(l[3]) @@ -41,6 +47,6 @@ for line in lines: if ta != []: results.append(ta) -print("## Docking Scores",end="\n\n") -print(tabulate(results,headers=["No.","Affinity","rmsd l.b","rmsd u.b"])) -print("",end="\n\n") +print("## Docking Scores", end="\n\n") +print(tabulate(results, headers=["No.", "Affinity", "rmsd l.b", "rmsd u.b"])) +print("", end="\n\n") 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'', end="\n\n") +print("## Visualisation", end="\n\n") +print(f"", 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'', end="\n\n") -print(f'', end="\n\n") -print(f'', end="\n\n") -print(f'', end="\n\n") +print(f"", end="\n\n") +print(f"", end="\n\n") +print(f"", end="\n\n") +print(f"", end="\n\n") diff --git a/scripts/quick-ligand-protein.py b/scripts/quick-ligand-protein.py index faff403..e211844 100644 --- a/scripts/quick-ligand-protein.py +++ b/scripts/quick-ligand-protein.py @@ -1,12 +1,14 @@ #!/usr/bin/python3 import argparse -#import logzero -#import logging -#from logzero import logger as log + +# import logzero +# import logging +# from logzero import logger as log import pymol2 import time import os + print(os.getcwd()) ################# @@ -17,7 +19,7 @@ startTime = time.time() version = "1.0" desc_text = "PyMol Quick Visualtion " + version ligandColor = "red" -#logzero.loglevel(logging.INFO) +# logzero.loglevel(logging.INFO) height = 1000 width = 800 dpi = 300 @@ -28,9 +30,9 @@ m1 = "target" m2 = "ligand" parser = argparse.ArgumentParser(description=desc_text) -parser.add_argument("-p","--protein",help="Path to protein file") -parser.add_argument("-l","--ligand",help="Path to ligand_out file") -parser.add_argument("-c","--color",help="Color for ligand in visualisation") +parser.add_argument("-p", "--protein", help="Path to protein file") +parser.add_argument("-l", "--ligand", help="Path to ligand_out file") +parser.add_argument("-c", "--color", help="Color for ligand in visualisation") args = parser.parse_args() @@ -47,38 +49,55 @@ protein = args.protein print("Protein: ", protein) ligand = args.ligand + def loadMol(filename, name): print("Loading " + filename + " as " + name) - cmd.load(filename,name) + cmd.load(filename, name) + + def changeColor(name, colorName): print("Changed " + name + "'s color to " + colorName) - cmd.color(colorName,name) + cmd.color(colorName, name) + + def orientEtZoom(): cmd.orient() cmd.zoom() + + def showSurface(name): - cmd.show("surface",name) + cmd.show("surface", name) + + def surfaceTransparency(amount): - print("Changed surface transparency to " + str(amount*100) + "%") - cmd.set("transparency",amount) -def generatePNG(filename,height=height,width=width,dpi=dpi,ray=ray): + print("Changed surface transparency to " + str(amount * 100) + "%") + cmd.set("transparency", amount) + + +def generatePNG(filename, height=height, width=width, dpi=dpi, ray=ray): print("Generating " + filename + ".png") - cmd.png(filename,height,width,dpi=dpi,ray=ray) + cmd.png(filename, height, width, dpi=dpi, ray=ray) + + def flipHorizontal(): - cmd.rotate("y",180) + cmd.rotate("y", 180) + + def zoomTo(name): cmd.zoom(name) + + def generatePictures(): - generatePNG('output-front') + generatePNG("output-front") flipHorizontal() - generatePNG('output-back') + generatePNG("output-back") zoomTo(m2) - generatePNG('closeup-back') + generatePNG("closeup-back") orientEtZoom() flipHorizontal() zoomTo(m2) - generatePNG('closeup-front') - + generatePNG("closeup-front") + print("Initialising PyMol") session = pymol2.PyMOL() @@ -86,10 +105,10 @@ print("Starting PyMol Session") session.start() cmd = session.cmd -loadMol(protein,m1) -loadMol(ligand,m2) -changeColor(m1,"grey60") -changeColor(m2,ligandColor) +loadMol(protein, m1) +loadMol(ligand, m2) +changeColor(m1, "grey60") +changeColor(m2, ligandColor) orientEtZoom() showSurface(m1) surfaceTransparency(0.6) @@ -97,4 +116,4 @@ surfaceTransparency(0.6) generatePictures() endTime = time.time() -print("Finished Execution in " + str(round((endTime - startTime),2)) + " seconds.") +print("Finished Execution in " + str(round((endTime - startTime), 2)) + " seconds.") |