def generatePNG():
lsmi = listdir(pathFolder.PR_SMI)
for smi in lsmi:
psmi = pathFolder.PR_SMI + smi
ppng = pathFolder.PR_PNG + smi[:-3] + "png"
runExternalSoft.molconvert(psmi, ppng)
def generatePNG(self):
pathFolder.createFolder(self.prPNG)
lnSMIs = listdir(self.prSMIclean)
for nSMI in lnSMIs:
runExternalSoft.molconvert(self.prSMIclean + nSMI,
self.prPNG + nSMI[:-3] + "png")
def drawMolecules(self, prpng):
if not "prsdf" in dir(self):
self.splitSDF()
pathFolder.createFolder(prpng)
self.prpng = prpng
if len(listdir(self.prsdf)) == len(listdir(self.prpng)):
return
lfsdf = listdir(self.prsdf)
for sdf in lfsdf:
runExternalSoft.molconvert(self.prsdf + sdf,
self.prpng + sdf[:-3] + "png")
def get_PNGAndSMI(p_desc, pr_results):
# load the ddesc to have SMILES cleanned
ddesc = toolbox.loadMatrix(p_desc)
pr_smi = pathFolder.createFolder(pr_results + "SMI/")
pr_png = pathFolder.createFolder(pr_results + "PNG/")
for chemID in ddesc.keys():
print chemID
SMILES = ddesc[chemID]["SMILES"]
p_fsmi = pr_smi + chemID + ".smi"
fsmi = open(p_fsmi, "w")
fsmi.write(SMILES)
fsmi.close()
p_fpng = pr_png + chemID + ".png"
runExternalSoft.molconvert(p_fsmi, p_fpng)
return
def extractByCluster(pcluster, prout, pdesc):
dcluster = toolbox.formatClusterTable(pcluster)
lcpddesc = toolbox.tableTolist(pdesc)
for cluster in dcluster.keys():
prcluster = pathFolder.createFolder(prout + "cluster" + str(cluster) + "/")
for compound in dcluster[cluster]:
for cpddec in lcpddesc:
if compound == cpddec["ID"]:
smile = cpddec["SMILES"]
psmi = prcluster + str(compound) + ".smi"
filesmi = open(psmi,"w")
filesmi.write(smile)
filesmi.close()
runExternalSoft.molconvert(psmi)
break
def runPNG(prSMI, prPNG):
if not path.exists(prSMI):
print ("ERROR: CREATE CLEAN SMI FIRST")
return
lSMI = listdir(prSMI)
shuffle(lSMI)
for SMI in lSMI:
#print prSMI + SMI
fSMI = open(prSMI + SMI, "r")
lelem = fSMI.readlines()
#print(lelem)
if len(lelem) == 0:
continue
lelem = lelem[0].split("\t")
#if len(lelem) == 1:
# print lelem
# print prSMI + SMI
if lelem[0] == "ERROR":
continue
else:
if len(lelem) < 3:
print (prSMI + SMI)
#remove(prSMI + SMI)
continue
inchikey = lelem[1]
DSSTOXid = lelem[2]
SMIclean = lelem[0]
if not path.exists(prPNG + inchikey + ".png"):
pSMIclean = prPNG + inchikey + ".smi"
fSMIcLean = open(pSMIclean, "w")
fSMIcLean.write(SMIclean)
fSMIcLean.close()
runExternalSoft.molconvert(pSMIclean)
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