Difference between revisions of "User talk:Philaltist"

From PyMOLWiki
Jump to navigation Jump to search
(pdbsurvey.py)
Line 4: Line 4:
  
 
I am still new to wiki, so I don't know yet how to upload this script. Could someone help ?
 
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 :
 +
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 ZONE###############
 +
    import ftplib
 +
    import time
 +
    import os
 +
    import string
 +
##################################################################
 +
 +
#####################################DEFINITIONS ZONE#############
 +
    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"
 +
 +
    ####################################################################
 +
 +
    ##########################################CALL ZONE#################
 +
    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)

Revision as of 18:15, 3 March 2005

Hi everyone !

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.

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 : 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
                                                                                1. IMPORT ZONE###############
   import ftplib
   import time
   import os
   import string
                                                                          1. DEFINITIONS ZONE#############
   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"

   ####################################################################

   ##########################################CALL ZONE#################
   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)

Retrieved from "http://pymolwiki.org/index.php?title=User_talk:Philaltist&oldid=450"