def computeRMSFresBS(self, pr_MDout):
# load BS in frame 0
l_pBS = listdir(pr_MDout + "BSs/")
l_res = []
for pBS in l_pBS:
cBS = PDB.PDB(pr_MDout + "BSs/" + pBS)
dres = cBS.get_byres()
for res in dres.keys():
nRes = res.split("_")[1]
if not nRes in l_res:
l_res.append(nRes)
# rewrite RMSF with binding site
presRMSF = pr_MDout + "RMSDs/residues/resRMSD"
ldresRMSF = toolbox.matrixToList(presRMSF)
# rewrting
pfilout = pr_MDout + "RMSDs/residues/resRMSD_BS"
filout = open(pfilout, "w")
filout.write("NameRes\tall\tCa\tDmax\tBS\n")
for dresRMSF in ldresRMSF:
if dresRMSF["NameRes"] in l_res:
BS = 1
else:
BS = 0
filout.write("%s\t%s\t%s\t%s\t%s\n" %
(dresRMSF["NameRes"], dresRMSF["all"], dresRMSF["Ca"],
dresRMSF["Dmax"], BS))
filout.close()
return pfilout
def buildRMDSSheets(self):
"""
Function use to build a pdf by chemicals with RMSD prot, ligand, BS and RMSF by residues of protein
Need 3 files, RMSD for prot, RMSD for ligand and RMSF
"""
l_fMDout = listdir(self.pr_MDout)
# load ChEMBL table
ldchem = toolbox.matrixToList(self.p_dataset)
for dchem in ldchem:
dfile = {}
dfile["prot RMSD"] = ""
dfile["lig RMSD"] = ""
dfile["RMSF residue"] = ""
ChEMBL_id = dchem["CMPD_CHEMBLID"]
typeAff = dchem["STANDARD_TYPE"]
# extract RMSD files
for fMDout in l_fMDout:
ChEMBL_id_folder = fMDout.split("_")[0]
if ChEMBL_id == ChEMBL_id_folder:
# protein
p_RMSD_prot = self.pr_MDout + fMDout + "/RMSDs/protein/protRMSD"
if path.exists(p_RMSD_prot):
dfile["prot RMSD"] = p_RMSD_prot
else:
print "Error in " + fMDout + ": prot RMSD missing"
self.computeRMSDProt(self.pr_MDout + fMDout + "/")
# lig need to define here
p_RMSD_lig = self.pr_MDout + fMDout + "/RMSDs/ligand/ligRMSD"
if path.exists(p_RMSD_lig):
dfile["lig RMSD"] = p_RMSD_lig
else:
print "Error in " + fMDout + ": lig RMSD missing"
p_RMSD_lig = self.computeRMSDLig(self.pr_MDout +
fMDout + "/")
dfile["lig RMSD"] = p_RMSD_lig
# RMSF with the binding site represented
p_RMSF_res = self.pr_MDout + fMDout + "/RMSDs/residues/resRMSD_BS"
if path.exists(p_RMSF_res):
dfile["RMSF residue"] = p_RMSF_res
else:
print "Error in " + fMDout + ": lig RMSF BS missing"
p_RMSF_res = self.computeRMSFresBS(self.pr_MDout +
fMDout + "/")
dfile["lig RMSD"] = p_RMSF_res
# build figure 3 panels
runExternalSoft.RMSD3panels(
dfile["prot RMSD"], dfile["lig RMSD"],
dfile["RMSF residue"], ChEMBL_id,
pathFolder.createFolder(self.pr_out + typeAff + "/"))
def loadRMSDs(self, lload=["ligand", "protein", "residues"]):
for typeRMSD in lload:
if typeRMSD == "ligand":
dlig = {}
dlig["RMSF"] = {}
pRMSF = self.prin + typeRMSD + "/ligRMSF"
dlig["RMSF"] = toolbox.loadMatrixToDict(pRMSF)
pShaEP = self.prin + typeRMSD + "/ligShaEP"
dlig["ShaEP"] = toolbox.matrixToList(pShaEP)
self.lig = dlig
if typeRMSD == "protein":
pRMSD = self.prin + typeRMSD + "/protRMSD"
dprot = toolbox.matrixToList(pRMSD)
self.prot = dprot
if typeRMSD == "residues":
pRes = self.prin + typeRMSD + "/resRMSD"
dres = toolbox.loadMatrixToDict(pRes)
self.res = dres
def CleanCHEMBLFileProtAff(self):
# if filout already exist
pfilout = self.pr_out + "tab_filtered_" + "-".join(self.ltypeAff) + ".csv"
if path.exists(pfilout):
ltable = toolbox.matrixToList(pfilout)
print len(ltable), "Nb selected compounds"
print ltable[0].keys()
self.table = ltable
return ltable
self.parseCHEMBLFile()
print len(self.table), "Init cleaning"
self.selectConfidencecore(cutoff=9)
print len(self.table), "prot confidence"
self.getOnlyExactConstant()
print len(self.table), "strict value"
self.getByTypeOfAff(self.ltypeAff)
print len(self.table), self.ltypeAff
self.MergeIdenticCHEMBLIDforACtivity()
print len(self.table), "Repetition"
self.selectAssayType("B")
print len(self.table), "Type assay"
# remove some biassay
self.removeBA(self.outlier)
print len(self.table), "remove bioassay"
self.checkIdenticSMI()
print len(self.table), "Identic SMI"
self.writeTable(pfilout)
# return the table in list
return self.table
def plot_dockScoreVSActivity(self, ptableCHEMBL):
pfilout = self.pr_out + "ScoreVSAff.txt"
if path.exists(pfilout):
return pfilout
# load ChEMBL dataset
ldchem = toolbox.matrixToList(ptableCHEMBL)
filout = open(pfilout, "w")
filout.write("IDCHEMBL\tDock_score\temodel_score\tAff\ttypeAff\tNB poses\n")
self.dscores
for dchem in ldchem:
print(chemID)
filout.write("%s\t%s\t%s\t%s\t%s\t%s\n"%(dchem["CMPD_CHEMBLID"], self.dscores[chemID]["r_i_docking_score"], self.dscores[chemID]["r_i_glide_emodel"], dchem[chemID]["PCHEMBL_VALUE"], dchem[chemID]["STANDARD_TYPE"], self.dscores[chemID]["count"]))
filout.close()
runExternalSoft.corPlot(pfilout, ptableCHEMBL, prout)
def get_TopRanking(self, ptableCHEMBL, nrank = 5):
pr_topChem = pathFolder.createFolder(self.pr_out + "top-" + str(nrank) + "/")
# load dock score
if not "dscores" in self.__dict__:
self.get_bestdockingscore()
# load dataset
ldchem = toolbox.matrixToList(ptableCHEMBL)
dbytypeAct = {}
for dchem in ldchem:
typeAff = dchem["STANDARD_TYPE"]
if not typeAff in dbytypeAct.keys():
dbytypeAct[typeAff] = {}
nameChem = dchem["CMPD_CHEMBLID"]
dbytypeAct[typeAff][nameChem] = dchem
# extract top 10 dock score
for typeAff in dbytypeAct.keys():
print typeAff
laff = []
for pose in self.cPoses.lc:
pose_chem = pose["s_m_entry_name"].split(".")[0]
if pose_chem in dbytypeAct[typeAff].keys():
laff.append(float(pose["r_i_docking_score"]))
# order
laff.sort()
i = 0
irank = 1
l_chem_image = []
while irank <= nrank:
for pose in self.cPoses.lc:
pose_chem = pose["s_m_entry_name"].split(".")[0]
try:score_dock = float(pose["r_i_docking_score"])
except:continue
if score_dock == laff[i]:
if pose_chem in l_chem_image:
continue
else:
l_chem_image.append(pose_chem)
# path png and sdf
p_image = "%s%s_%s-%s.png"%(pr_topChem, irank, pose_chem, typeAff)
p_smiout = "%s%s_%s-%s.smi"%(pr_topChem, irank, pose_chem, typeAff)
# to write on figure
lw = ["ChEMBL ID: " + str(pose_chem)]
lw.append("Rank: " + str(irank))
lw.append("p" + typeAff + ": " + str(dbytypeAct[typeAff][pose_chem]["PCHEMBL_VALUE"]))
lw.append("Docking score: {:0.2f}".format(float(pose["r_i_docking_score"])))
lw.append("Emodel score: {:0.2f}".format(float(pose["r_i_glide_emodel"])))
# generate png
f_smiout = open(p_smiout, "w")
f_smiout.write(dbytypeAct[typeAff][pose_chem]["CANONICAL_SMILES"])
f_smiout.close()
# png
runExternalSoft.molconvert(p_smiout, p_image)
img = Image.open(p_image)
imgnew = Image.new("RGBA", (580, 775), (250, 250, 250))
imgnew.paste(img, (0,0))
draw = ImageDraw.Draw(imgnew)
draw.text((10, 600), lw[0], (0, 0, 0), font=font)
draw.text((10, 625), lw[1], (0, 0, 0), font=font)
draw.text((10, 650), lw[2], (0, 0, 0), font=font)
draw.text((10, 675), lw[3], (0, 0, 0), font=font)
draw.text((10, 700), lw[4], (0, 0, 0), font=font)
imgnew.save(p_image)
irank = irank + 1
break
i = i + 1