Merge lp:~pierrepo/ptools/bug539468 into lp:ptools

[Pierre Poulain]

- fix bug 53946: add options to attract.py
- nicer timing message
- updated tutorial

[Adrien Saladin (adrien-saladin)]

review: Approve

=== modified file 'PyAttract/attract.py'
--- PyAttract/attract.py	2010-03-29 07:43:24 +0000
+++ PyAttract/attract.py	2010-06-03 17:08:23 +0000
@@ -3,7 +3,7 @@
 from ptools import *
 import sys
 import os
-import time
+#import time
 import datetime
 import math
 import string
@@ -168,70 +168,80 @@
 
 # check if a required file is found
 def checkFile(name, comment):
-	flag = os.path.exists(name)
-	if  not flag :
-		print "ERROR: file %s is missing" %(name)
-		print "ERROR: %s" %(comment)
-		exit(2)	
+    flag = os.path.exists(name)
+    if not flag :
+        msg =  "ERROR: file %s not found\n" %(name)
+        if comment != "":
+            msg += "ERROR: %s" %(comment)
+        sys.exit(msg)	
 
 
 ###########################
 ##  MAIN ATTRACT PROGRAM  #
 ###########################
 from optparse import OptionParser
-parser = OptionParser()
-parser.add_option("-s", "--single", action="store_true", dest="single",default=False,help="single minimization mode")
+parser = OptionParser(usage="%prog -r receptor_file -l ligand_file [-h] [-s] [-t] [--ref]")
+parser.add_option("-r", "--receptor", action="store", type="string", dest="receptor_name", help="name of the receptor file")
+parser.add_option("-l", "--ligand", action="store", type="string", dest="ligand_name", help="name of the ligand file")
+parser.add_option("-s", "--single", action="store_true", dest="single", default=False, help="single minimization mode")
 parser.add_option("--ref", action="store", type="string", dest="reffile", help="reference ligand for rmsd" )
 parser.add_option("-t", "--translation", action="store", type="int", dest="transnb", help="translation number (distributed mode) starting from 0 for the first one!")
 (options, args) = parser.parse_args()
 
-receptor_name=args[0]
-ligand_name=args[1]
+
+#receptor_name=args[0]
+#ligand_name=args[1]
 
 print """
 **********************************************************************
+**                                                                  **
 **                ATTRACT  (Python edition)                         **
-**                version: this is a development version,           **
-**                         see below for details                    **
+**                based on the PTools library                       **
+**                                                                  **
 **********************************************************************
-Attract.py
-using PTools revision %s, from branch %s, unique id %s
+PTools revision %s
+from branch %s
+unique id %s
 """%(Version().revstr, Version().branchnick, Version().revid)
 
-
-
 import locale
-import datetime
-
 
 #locale.setlocale(locale.LC_ALL, 'fr_FR')
-now = datetime.datetime.now()
-print now,"(",now.strftime("%A %B %d %Y, %H:%M"),")"
+time_start = datetime.datetime.now()
+#print now,"(",now.strftime("%A %B %d %Y, %H:%M"),")"
+print "Start time:", time_start
 
 #==========================
 # check required files
 #==========================
 # receptor
-checkFile(receptor_name, "A receptor file is needed.")
+if not options.receptor_name:
+    parser.print_help()
+    parser.error("option -r is mandatory")
+checkFile(options.receptor_name, "")
 # ligand
-checkFile(ligand_name, "A ligand file is needed.")
+if not options.ligand_name:
+    parser.print_help()
+    parser.error("option -l is mandatory")
+checkFile(options.ligand_name, "")
 # attract.inp
-checkFile("attract.inp", "A parameters file is needed.")
+checkFile("attract.inp", "parameters file is required.")
 # aminon.par
-checkFile("aminon.par", "A forcefield file is needed.")
+checkFile("aminon.par", "forcefield file is required.")
 
 #==========================
 # read parameter file
 #==========================
 
+print "Reading parameters file: attract.inp"
 (nbminim,lignames,minimlist,rstk) = readParams("attract.inp")
 print "rstk = ",rstk
-rec=Rigidbody(receptor_name)
-lig=Rigidbody(ligand_name)
+rec=Rigidbody(options.receptor_name)
+lig=Rigidbody(options.ligand_name)
 rec=AttractRigidbody(rec)
 lig=AttractRigidbody(lig)
-print "Receptor (fixed) %s  has %d particules" %(receptor_name,rec.Size())
-print "Ligand (mobile) %s  has %d particules" %(ligand_name,lig.Size())
+print "Reading receptor (fixed): %s with %d particules" %( options.receptor_name, rec.Size() )
+print "Reading  ligand (mobile): %s with %d particules" %( options.ligand_name,   lig.Size() )
 
 if (options.single and options.transnb):
     parser.error("options -s and -t are mutually exclusive")
@@ -242,28 +252,28 @@
     ftraj = open(trjname, "w")
 
 if (options.reffile):
-    print "using reference file: %s"%options.reffile
+    checkFile(options.reffile, "")
     ref=Rigidbody(options.reffile)
+    print "Reading reference file: %s with %d particules" %( options.reffile, ref.Size() )
     refca = ref.CA()
     if refca.Size() == 0:  #No C alpha atom, ligand is probably a dna
         Rmsd_alias = Rmsd
-        print "No Calpha atom found for ligand (dna ?), I will calculate rmsd on all grains"
+        print "No Calpha atom found for ligand (DNA?). RMSD will be calculated on all grains"
     else:
         Rmsd_alias = rmsdca
 
-
 if (not options.single):
     #systematic docking with default translations and rotations
     # check for rotation.dat and translation.dat
-    checkFile("rotation.dat", "A rotation file is needed.")
-    checkFile("translation.dat", "A translation file is needed.\nFormer users may rename translat.dat into translation.dat.")
+    checkFile("rotation.dat", "rotation file is required.")
+    checkFile("translation.dat", "translation file is required.\nFormer users can rename translat.dat into translation.dat.")
     translations=Translation()
     rotations=Rotation()
 else: #(single mode)
     #creates dummy translation and rotation
     translations=[[1,lig.FindCenter()]]
     rotations=[(0,0,0)]
-    print "Single mode"
+    print "Single mode simulation"
 
 
 
@@ -272,8 +282,8 @@
 transnb=0
 if (options.transnb!=None):
     # check for rotation.dat and translation.dat
-    checkFile("rotation.dat", "A rotation file is needed.")
-    checkFile("translation.dat", "A translation file is needed.\nFormer users may rename translat.dat into translation.dat.")
+    checkFile("rotation.dat", "rotation file is required.")
+    checkFile("translation.dat", "translation file is required.\nFormer users may rename translat.dat into translation.dat.")
     trans=Rigidbody("translation.dat")
     co=trans.GetCoords(options.transnb)
     translations=[[options.transnb+1,co]]
@@ -356,8 +366,8 @@
 
 #output compressed ligand and receptor:
 if ( not options.single and printFiles==True): 
-    print compress_file(receptor_name)
-    print compress_file(ligand_name)
+    print compress_file(options.receptor_name)
+    print compress_file(options.ligand_name)
     print compress_file("aminon.par")
     print compress_file("translation.dat")
     print compress_file("rotation.dat")
@@ -368,8 +378,9 @@
     ftraj.close()
     print "Saved all minimization variables (translations/rotations) in %s" %(trjname)
 
-
-now = datetime.datetime.now()
-print "Finished at: ",now.strftime("%A %B %d %Y, %H:%M")
-
+# print end and elapsed time
+time_end = datetime.datetime.now()
+#print "Finished at: ",now.strftime("%A %B %d %Y, %H:%M")
+print "End time:", time_end
+print "Elapsed time:", time_end - time_start
 
 
=== modified file 'Tutorial/doc/tutorial.tex'
--- Tutorial/doc/tutorial.tex	2010-04-23 07:33:13 +0000
+++ Tutorial/doc/tutorial.tex	2010-06-03 17:08:23 +0000
@@ -90,7 +90,7 @@
 \subsubsection{On Debian or Debian-like systems (Ubuntu)}
 
 \begin{verbatim}
-apt-get install scons libboost-dev libbost-python-dev gccxml
+apt-get install scons libboost-dev libboost-python-dev gccxml
 \end{verbatim}
 %
 See \ref{pyplusplus} for installing necessary tools for building python bindings.
@@ -720,17 +720,20 @@
 \item docking parameters ({\tt attract.inp})
 \end{itemize}
 
-ATTRACT can be used with different options:
+ATTRACT can be used with different options.
 \begin{itemize}
-\item {\tt -s}, performs one single serie of minimisations with the ligand in its initial position.
+\item \verb@-r@ or \verb@--receptor@ (mandatory): defines the receptor file.
+\item \verb@-l@ or \verb@--ligand@ (mandatory): defines the ligand file.
+\item \verb@ -s@ (optional): performs one single serie of minimisations with the ligand in its initial position.
 \item \verb@--ref@, (optional) provides a ligand PDB file as a reference (reduced). After each docking, the RMSD is calculated between this reference structure and the simulated ligand.
-\item \verb!--t transnb!, loads only the translation number {\tt transnb} (and all its associated rotations). This option is very usefull for dispatching a simulation over a cluster of computers.
+\item \verb@--t transnb@ (optional): loads only the translation number {\tt transnb} (and all its associated rotations). This option is very usefull for dispatching a simulation over a cluster of computers.
+\item \verb@-h@ or \verb@--help@ (optional): reminds possible options.
 \end{itemize}
 
 
 A single ATTRACT simulation (optimization) may thus be obtained by:
 \begin{verbatim}
-attract.py receptor.red ligand.red --ref=ligand.red -s > single.att
+attract.py -r receptor.red -l ligand.red --ref=ligand.red -s > single.att
 \end{verbatim}
 
 The first PDB file provided must be the receptor file (and the second the ligand).
@@ -739,72 +742,79 @@
 \newpage
 \linenumbers*
 \begin{verbatim}
-
 **********************************************************************
+**                                                                  **
 **                ATTRACT  (Python edition)                         **
-**                version: 0.3                                      **
+**                based on the PTools library                       **
+**                                                                  **
 **********************************************************************
-Attract.py: $Id: Attract.py 616 2008-11-25 12:42:39Z asaladin $
-using PTools: 614
+PTools revision 437
+from branch bug539468
+unique id pierre_poulain-20100603130128-awuyfelj7avtls54
 
-2008-12-11 00:08:18.212859 ( Thursday December 11 2008, 00:08 )
+Start time: 2010-06-03 18:50:57.506277
+Reading parameters file: attract.inp
 6 series of minimizations
 rstk =  0.0005
-Receptor (fixed) receptor.red  has 522 particules
-Ligand (mobile) ligand.red  has 126 particules
-using reference file: ligand.red
-Single mode
+Reading receptor (fixed): receptor.red with 246 particules
+Reading  ligand (mobile): ligand.red with 162 particules
+Reading reference file: ligand.red with 162 particules
+Single mode simulation
 @@@@@@@ Translation nb 1 @@@@@@@
 ----- Rotation nb 1 -----
 {{ minimization nb 1 of 6 ; cutoff= 99.50 (A) ; maxiter= 100
 number of free variables for the minimizer: 6
-CONVERGENCE: REL_REDUCTION_OF_F <= FACTR*EPSMCH             |  72 iterations
+CONVERGENCE: REL_REDUCTION_OF_F <= FACTR*EPSMCH             |  69 iterations
 {{ minimization nb 2 of 6 ; cutoff= 38.73 (A) ; maxiter= 100
 number of free variables for the minimizer: 6
-CONVERGENCE: REL_REDUCTION_OF_F <= FACTR*EPSMCH             |  2 iterations
+CONVERGENCE: REL_REDUCTION_OF_F <= FACTR*EPSMCH             |  9 iterations
 {{ minimization nb 3 of 6 ; cutoff= 31.62 (A) ; maxiter= 100
 number of free variables for the minimizer: 6
-CONVERGENCE: REL_REDUCTION_OF_F <= FACTR*EPSMCH             |  3 iterations
+CONVERGENCE: REL_REDUCTION_OF_F <= FACTR*EPSMCH             |  13 iterations
 {{ minimization nb 4 of 6 ; cutoff= 22.36 (A) ; maxiter= 50
 number of free variables for the minimizer: 6
-CONVERGENCE: REL_REDUCTION_OF_F <= FACTR*EPSMCH             |  10 iterations
+CONVERGENCE: REL_REDUCTION_OF_F <= FACTR*EPSMCH             |  11 iterations
 {{ minimization nb 5 of 6 ; cutoff= 22.36 (A) ; maxiter= 50
 number of free variables for the minimizer: 6
-CONVERGENCE: REL_REDUCTION_OF_F <= FACTR*EPSMCH             |  1 iterations
+CONVERGENCE: REL_REDUCTION_OF_F <= FACTR*EPSMCH             |  3 iterations
 {{ minimization nb 6 of 6 ; cutoff= 22.36 (A) ; maxiter= 50
 number of free variables for the minimizer: 6
 CONVERGENCE: REL_REDUCTION_OF_F <= FACTR*EPSMCH             |  1 iterations
       Trans    Rot          Ener    RmsdCA_ref
-==        1      1   -58.3541422 1.19455904733
+==        1      1   -58.4463779 1.23525236672
 ### MAT BEGIN
-MAT        0.9973001      0.0414787     -0.0605965      0.4545131 
-MAT       -0.0430245      0.9987753     -0.0244310      1.9814388 
-MAT        0.0595089      0.0269722      0.9978633     -2.8603610 
+MAT        0.9941915     -0.0969983      0.0466331      0.4410928 
+MAT        0.0984211      0.9947151     -0.0292441     -1.1030090 
+MAT       -0.0435501      0.0336639      0.9984839      0.5793707 
 MAT        0.0000000      0.0000000      0.0000000      1.0000000 
 ### MAT END
 
-Finished at:  Thursday December 11 2008, 00:08
-
+Saved all minimization variables (translations/rotations) in minimization.trj
+End time: 2010-06-03 18:50:58.031199
+Elapsed time: 0:00:00.524922
 \end{verbatim}
 \nolinenumbers
 
 \begin{itemize}
-\item{\bf line 9:} starting date and time of the simulation
-\item{\bf lines 18--20:} minimization 1. Minimization index, cutoff 
-in \AA\ and maximum number of iterations (line~18). 
-Number of variables (line~19). End of minimization (line~20), either 
+\item{\bf lines 1--6:} header
+\item{\bf lines 7--9:} PTools library revision, branch and unique id
+\item{\bf line 11:} starting date and time of the simulation
+\item{\bf lines 21--23:} minimization 1. Minimization index, cutoff 
+in \AA\ and maximum number of iterations (line~21). 
+Number of variables (line~22). End of minimization (line~23), either 
 convergence is achieved (the number of performed iterations is specified), 
 either maximum number of steps is reached.
-\item{\bf lines 21--23:} minimization 2.
-\item{\bf lines 24--26:} minimization 3.
-\item{\bf lines 27--29:} minimization 4.
-\item{\bf lines 30--32:} minimization 5.
-\item{\bf lines 33--35:} minimization 6.
-\item{\bf lines 36--37:} final result after the 6 minimizations. With a single series of minimization, the default translation ({\tt Trans}) is 1 and the default rotation ({\tt Rot}) is 1. 
+\item{\bf lines 24--26:} minimization 2.
+\item{\bf lines 27--29:} minimization 3.
+\item{\bf lines 30--32:} minimization 4.
+\item{\bf lines 33--35:} minimization 5.
+\item{\bf lines 36--38:} minimization 6.
+\item{\bf lines 39--40:} final result after the 6 minimizations. With a single series of minimization, the default translation ({\tt Trans}) is 1 and the default rotation ({\tt Rot}) is 1. 
 Energy ({\tt Ener}) is given in RT unit and the C$_{\alpha}$-RMSD 
 ({\tt RmsdCA\_ref}) in \AA\ if the \verb@--ref@ option is specified.
-\item{\bf lines 38--43:} rotation/translation matrix of the ligand compared to its initial position.
-\item{\bf line 45:} end date and time of the simulation.
+\item{\bf lines 41--46:} rotation/translation matrix of the ligand compared to its initial position.
+\item{\bf line 49:} end date and time of the simulation.
+\item{\bf line 50:} elapsed time for the simulation
 \end{itemize}
 
 Here, the final energy is -58.4~RT unit and the RMSD is 1.2~\AA, which is pretty close from the initial position. (In a \emph{perfect} simulation, RMSD would be, of course, 0.0~\AA).
@@ -813,7 +823,7 @@
 
 For a full systematic docking in the translational and rotational space (using both {\tt translation.dat} and {\tt rotation.dat} files), the command line is:
 \begin{verbatim}
-attract.py receptor.red ligand.red --ref=ligand.red > docking.att &
+attract.py -r receptor.red -l ligand.red --ref=ligand.red > docking.att &
 \end{verbatim}
 
 The output file {\tt docking.att} contains all informations on the docking simulation. 
@@ -1074,7 +1084,7 @@
 
 An ATTRACT optimization is done with:
 \begin{verbatim}
-attract.py receptor.red ligand.red --ref=ligand.red -s > single.att
+attract.py -r receptor.red -l ligand.red --ref=ligand.red -s > single.att
 \end{verbatim}
 
 Here, the final energy is -38.4~RT unit and the RMSD is 1.3~\AA\ which is very close
@@ -1087,7 +1097,7 @@
 
 A systematic docking simulation is then:
 \begin{verbatim}
-attract.py receptor.red ligand.red --ref=ligand.red > docking.att &
+attract.py -r receptor.red -l ligand.red --ref=ligand.red > docking.att &
 \end{verbatim}
 
 The output file {\tt docking.att} contains all informations on the docking