def createRMSDdata(CASFyear, dockingMethod, scorFunc="para"):
proteinDir = os.path.join(OUTPUT_DIR, "RMSD", CASF_VERSION[CASFyear], dockingMethod)
if dockingMethod == "gold":
proteinDir = os.path.join(proteinDir, scorFunc)
for proteinID in os.listdir(proteinDir):
RMSDfile = os.path.join(OUTPUT_DIR, "RMSD", CASF_VERSION[CASFyear], "_pool", "{0}_RMSD.csv".format(proteinID))
# find reference ligand location (mol2)
refLigandPath = os.path.join(PDBBIND_DIR, CASF_VERSION[CASFyear], proteinID)
refLigandFile = proteinID+"_complex_prep_lig.mol2"
refLigand = os.path.join(refLigandPath, refLigandFile)
# only calculate the RMSD if its data still doesn't exist
if (not os.path.exists(RMSDfile)) or (not libRMSD.IsPoseExistsFromCSV(RMSDfile, typeOfPose=scorFunc)):
# spitting some outputs
print("Calculating RMSDs poses for {0} {1} {2}...".format(proteinID, scorFunc, dockingMethod))
poseDir = os.path.join(proteinDir, proteinID)
suffix = ".mol2"
if dockingMethod == "gold":
prefix = "gold_soln"
elif dockingMethod == "glide":
poseDir = os.path.join(poseDir, scorFunc)
#prefix = "_{0}".format(proteinID)
prefix = ""
elif dockingMethod == "paradocks":
prefix = "paradocks"
if os.path.exists(poseDir):
RMSDs = libRMSD.calcRMSDPoses(refLigand, poseDir, prefix, suffix)
libRMSD.writeRMSD2CSV(RMSDs, RMSDfile)
def samplingRMSDdata(CASFyear, numSamples = 100):
RMSDpath = os.path.join(OUTPUT_DIR, "RMSD", CASF_VERSION[CASFyear], "_pool")
samplingPath = os.path.join(OUTPUT_DIR, "RMSD", CASF_VERSION[CASFyear], "_sampling")
for RMSDfile in os.listdir(RMSDpath):
if os.path.getsize(os.path.join(RMSDpath, RMSDfile)) > 0:
baseFileName, ext = os.path.splitext(RMSDfile)
samplingFile = "{0}_sampling_clusters10.csv".format(baseFileName)
samplesRMSD = samplingRMSDtoCluster(os.path.join(RMSDpath, RMSDfile), numSamples=numSamples)
libRMSD.writeRMSD2CSV(samplesRMSD, os.path.join(samplingPath, samplingFile))
samplingFile = "{0}_sampling_100.csv".format(baseFileName)
samplesRMSD = samplingRMSDmixing(os.path.join(RMSDpath, RMSDfile), numSamples=numSamples)
libRMSD.writeRMSD2CSV(samplesRMSD, os.path.join(samplingPath, samplingFile))