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Hi everyone !
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Do you think that a singe page for all the cartoon_helix types would be better than separate pages? e.g. putting the fance, normal, and cylindrical all on one page --Adam Shea
  
I have created a script because I was tired of browsing the pdb for endless searches of structures relevant to my field. This scripts takes as input a text file in which you copied your favourite keywords, and the number of days you want to search back (by default, it will look at the structures added the last 50 days). It generates a report text file that contains the pdb id and name of the relevant structures that have been recently added. All you need to do is add 'run pdbsurvey.py' to your startup file, and create a text file called 'keywords.txt' with your keywords separated by an end-of-line character. Then you're ready to go. Just hit 'pdbsurvey' from within your PyMol instance, and the program returns the report file. The pdb ftp server is updated every tuesday.
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Yes I think it would be best to have all the cartoon_helix links of the settings page point to the same page. Do you know how to do that ? I think it would be less hairy/redundant than a 'related settings' section in multiple pages. --Philippe Garteiser
 
 
I am still new to wiki, so I don't know yet how to upload this script. Could someone help ?
 
 
 
P.S. Here's the script in raw text format :
 
 
 
<source lang="python">
 
from pymol import cmd
 
 
 
def pdbsurvey(days=50):
 
 
 
    """USAGE : pdbsurvey (<days>)
 
    Surveys the updates added to the PDB (ftp.rcsb.org) in the last
 
    50 days (or otherwise specified when calling this function) for
 
    entries that contain the words specified in the file
 
    keywords.txt.
 
    """
 
    print days
 
 
 
    import ftplib
 
    import time
 
    import os
 
    import string
 
 
 
 
 
 
 
    def todaymerge():
 
        """Puts today's date in a pdb format string.
 
        """
 
        date=time.localtime()
 
        fyear="%i" %(date[0])
 
        fmonth="%i" %(date[1])
 
        if date[1]<10:
 
            fmonth="0"+"%i" %(date[1])
 
        fday="%i" %(date[2])
 
        if date[2]<10:
 
            fday="0"+"%i" %(date[2])
 
        dateS=fyear+fmonth+fday
 
        return dateS
 
 
 
    def file2list(filename):
 
        """Low-level routine to brainlessly implement
 
        file.read().
 
        """
 
        fq=open(filename,'rb')
 
        linesS=fq.read()
 
        fq.close()
 
        LIST=linesS.splitlines()
 
        return LIST
 
 
 
    def connect2pdb():
 
        """Opens an anonymous socket to ftp://ftp.rcsb.org
 
        """
 
        f=ftplib.FTP()
 
        f.connect ('ftp.rcsb.org')
 
        f.login ()
 
        print "Remote connection established","\n"
 
        return f
 
 
 
    def decrementdate(dateS):
 
        """given a string date (pdb format yyyymmdd)
 
        this routine returns a string of the day before
 
        (sadly assuming that every month has 31 days, but
 
        no big deal here...).
 
        """
 
        #decompose dateS into components
 
        yearS=dateS[0]+dateS[1]+dateS[2]+dateS[3]
 
        monthS=dateS[4]+dateS[5]
 
        dayS=dateS[6]+dateS[7]
 
 
 
        #convert each into integers
 
        yearI=int(yearS)
 
        monthI=int(monthS)
 
        dayI=int(dayS)
 
 
 
        #actual stuff
 
        dayI=dayI-1
 
        if dayI==0:
 
            dayI=31
 
            monthI=monthI-1
 
            if monthI==0:
 
                monthI=12
 
                yearI=yearI-1
 
        dayS="%i" %(dayI)
 
        monthS="%i" %(monthI)
 
        yearS="%i" %(yearI)
 
        if dayI<10:
 
            dayS="0"+dayS
 
        if monthI<10:
 
            monthS="0"+monthS
 
        #and finally...
 
        dateS=yearS+monthS+dayS
 
        return dateS
 
 
 
    def findlastdir(dateS,f,days):
 
        """Puts the names of the "recent" directories in the
 
        list named "directoriesL".
 
        """
 
        directoriesL=['']
 
        j=p=0
 
        while p<days:
 
            dateS=decrementdate(dateS)
 
            attempt="/pub/pdb/data/status/"+dateS
 
            try :
 
                f.cwd(attempt)
 
                directoriesL[j:j]=[attempt]
 
                j=j+1
 
            except :
 
                pass
 
            p=p+1
 
        directoriesL.pop()
 
        return directoriesL
 
 
 
    def compilinfile(directoriesL,f):
 
        """lists all structures in the added.pdb files
 
        contained in the directories specified in directoriesL
 
        """
 
        command="RETR added.pdb"
 
        handle=open("donotedit.dat","wrb")
 
        for k in directoriesL:
 
            f.cwd(k)
 
            print "Currently in directory ",f.pwd()
 
            f.retrbinary(command,handle.write)
 
        handle.close()
 
        return len(directoriesL)
 
 
 
    def listparser():
 
        """Extracts the pdbids from donotedit.dat file,
 
        and stacks them into the list pdbidsL
 
        """
 
        linesL=file2list("donotedit.dat")
 
        pdbidsL=[]
 
        for iter in linesL:
 
            pdbidsL.append(iter[57:61])
 
        for iter in pdbidsL:
 
            iter=string.lower(iter)
 
        pdbidsL.sort()
 
        return pdbidsL
 
 
 
    def currentrelease(f):
 
        """Stores the content of cmpd_res.idx file
 
        This file contains the equivalencies pdbid<->title
 
        for all current entries of the PDB.
 
        """
 
        command="RETR cmpd_res.idx"
 
        f.cwd("/pub/pdb/derived_data/index/")
 
        print "Currently in directory ",f.pwd()
 
        fq=open("dictionnary.dat",'wrb')
 
        f.retrbinary(command,fq.write)
 
        fq.close()
 
        dictL=file2list("dictionnary.dat")
 
        return dictL
 
 
 
    def extract(pdbidsL,dictL):
 
        """Populates dictionnaryD with pdb entries found in the
 
        latest releases.
 
        """
 
        dictionnaryD={}
 
        problemL=[]
 
        extractL=[dictionnaryD,problemL]
 
        for i in dictL:
 
            tempS=string.lower(i[0:4])
 
            for ii in pdbidsL:
 
                if ii == tempS:
 
                    title=i[14:216]
 
                    extractL[0][ii]=title
 
        if len(extractL[0].keys()) != len(pdbidsL):
 
            print "Dimension mismatch, seeking troublemaker..."
 
            for i in pdbidsL:
 
                equiv=0
 
                for ii in extractL[0].keys():
 
                    if i==ii:
 
                        equiv=equiv+1
 
                if equiv==0:
 
                    extractL[1].append(i)
 
        return extractL
 
 
 
    def disconnectpdb(f):
 
        """Diconnects the current ftp session
 
        """
 
        f.quit()
 
        print "Remote connection terminated","\n"
 
        return f
 
 
 
    def releventries(dictionnaryD):
 
        """Generates a cleaned dictionnary with only entries
 
        that have one or more keywords specified in the local
 
        user-defined keywords.txt file
 
        """
 
        keywL=file2list("keywords.txt")
 
        relevdicD={}
 
        for i in keywL:
 
            for elem in dictionnaryD.keys():
 
                temp=dictionnaryD[elem]
 
                if temp.find(i) != -1:
 
                    relevdicD[elem]=temp
 
        return relevdicD
 
 
 
    def diskcleanup(filelist=["donotedit.dat","dictionnary.dat"]):
 
        """Lo-level disk cleanup to free up memory without the user
 
        """
 
        for filename in filelist:
 
            command='DEL '+filename
 
            os.system(command)
 
        return "clean"
 
 
 
 
 
 
 
 
 
    print "Welcome in the auto-PDB updater !"
 
 
 
    print "Survey of updates made since",days,"days ago."
 
   
 
    print "Acquisition of local time..."
 
    dateS=todaymerge()                                                #Initializes dateS
 
    print "today is ",dateS
 
    print "Connecting to remote ftp server..."
 
    f=connect2pdb()                                                    #Connect anonymously to ftp.rcsb.org
 
 
 
    print "Acquisition of latest added remote directories..."
 
    directoriesL=findlastdir(dateS,f,days)                            #Lists recent directories in directoriesL
 
    if len(directoriesL)==0:
 
        print "No updates have been found since",days,"ago. Starting over with 50 days ago."
 
        directoriesL=findlastdir(dateS,f,50)
 
 
 
    print "Acquisition of latest addedremote files..."
 
    updatesnumberI=compilinfile(directoriesL,f)                        #Concatenates the corresponding added.pdb into donotedit.dat
 
 
 
    print "Parsing of latest entries..."
 
    pdbidsL=listparser()                                              #Recent names now present in the pdbidsL list (one name per element)
 
 
 
    print "Acquisition of the current pdb distribution..."
 
    dictL=currentrelease(f)                                            #Populates dictL with the current entries of the PDB
 
 
 
    print "Parsing of the current pdb distribution into [code,title] tuples..."
 
    extractL=extract(pdbidsL,dictL)                                    #generates the dictionnary of latest releases key:PDBid ; definition:pdbtitle
 
 
 
    print "Disconnection from the remote ftp server..."
 
    f=disconnectpdb(f)                                                #Closes the ftp instance
 
 
 
    print "Extraction of the relevant entries..."
 
    relevdicD=releventries(extractL[0])                              #Generates a subset of dictionnary D with criterion being "has keywords contained in keywords.txt in its title"
 
 
 
    print "Cleaning program-generated temporary files..."
 
    clean=diskcleanup()                                                #Cleans the mess generated by the program
 
 
 
    reportL=[]
 
    reportL.append("\n")
 
    reportL.append("###############REPORT########################################\n")
 
    reportL.append("\n")
 
    lendictS="%i" %(len(dictL))
 
    chmilblik = 'The current pdb version (as of '+dateS+") has "+lendictS+" entries.\n"
 
    reportL.append(chmilblik)
 
    line="The most recent directory is : "+directoriesL[0]+".\n"
 
    reportL.append(line)
 
    updatesnumberS="%i" %(updatesnumberI)
 
    entriesnumber="%i" %(len(extractL[0].keys()))
 
    line="The "+updatesnumberS+" last updates ("+entriesnumber+" entries) have been examined.\n"
 
    reportL.append(line)
 
    diclengthS="%i" %(len(relevdicD.keys()))
 
    line=diclengthS+" are relevant to you :\n"
 
    reportL.append(line)
 
    for i in relevdicD.keys():
 
        entry=i+" : "+relevdicD[i]+"\n"
 
        reportL.append(entry)
 
    problemS=""
 
    for i in extractL[1]:
 
        problemS=i+";"+problemS
 
    problemS="["+problemS
 
    problemS=problemS.strip(";")
 
    problemS=problemS+"]"
 
    lineS="The entries "+problemS+" raised problems,"
 
    reportL.append(lineS)
 
    reportL.append("they should be examined manually.")
 
    reportL.append("\n")
 
    reportL.append("###############END OF REPORT#################################\n")
 
    report=open("report.aut","w")
 
    for elem in reportL:
 
        print elem
 
        elem=elem+'\n'
 
        report.writelines(elem)
 
    report.close()
 
    command2='start keywords.txt'
 
    command3='start report.aut'
 
    os.system(command2)
 
    os.system(command3)
 
 
 
cmd.extend("pdbsurvey",pdbsurvey)
 
</source>
 

Latest revision as of 04:13, 28 March 2014

Do you think that a singe page for all the cartoon_helix types would be better than separate pages? e.g. putting the fance, normal, and cylindrical all on one page --Adam Shea

Yes I think it would be best to have all the cartoon_helix links of the settings page point to the same page. Do you know how to do that ? I think it would be less hairy/redundant than a 'related settings' section in multiple pages. --Philippe Garteiser