## Automatically adapted for numpy.oldnumeric Mar 26, 2007 by alter_code1.py
#!/usr/bin/env python
## Biskit, a toolkit for the manipulation of macromolecular structures
## Copyright (C) 2004-2012 Raik Gruenberg & Johan Leckner
## This program is free software; you can redistribute it and/or
## modify it under the terms of the GNU General Public License as
## published by the Free Software Foundation; either version 3 of the
## License, or any later version.
## This program is distributed in the hope that it will be useful,
## but WITHOUT ANY WARRANTY; without even the implied warranty of
## General Public License for more details.
## You find a copy of the GNU General Public License in the file
## license.txt along with this program; if not, write to the Free
## Software Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
## last $Author: graik $
## last $Date: 2012-02-23 19:10:59 -0500 (Thu, 23 Feb 2012) $
## $Revision: 1086 $
Prepare and run a HEX docking.
from Biskit import PDBModel, PDBDope, molUtils
import Biskit.tools as t
from HexParser import HexParser
from ComplexList import ComplexList
import hexTools 
import settings
import re
import os.path
from time import localtime, sleep
from threading import Thread, RLock, Condition
import numpy.oldnumeric as N
class DockerError( Exception ):
class Docker:
    Prepare and run a hex docking for one or several models
    of a receptor and ligand pair. Collect docking results
    into a growing ComplexList.
    The docking runs are started in seperate Threads. External objects
    can register a method with call_when_done() that is called whenever
    a docking has finished. The waitForLastHex() method can be called
    to wait until all currently running dockings are finished.
    The models in the 2 given dictionaries might get different chainIds but
    Docker doesn't save them.
    @todo: implement that as JobMaster / JobSlave instead, so that also the
           Hex-file parsing is distributed.
    def __init__( self, recDic, ligDic, recPdb=None, ligPdb=None,
                  comPdb=None, out='hex_%s', soln=512,
                  recChainId=None, ligChainId=None, macDock=None,
                  bin=settings.hex_bin, verbose=1 ):
        @param recDic: receptor dictionary
        @type  recDic: dict
        @param ligDic: ligand dictionary
        @type  ligDic: dict
        @param recPdb: hex-formatted PDB with rec models
        @type  recPdb: str
        @param ligPdb: hex-formatted PDB with lig models
        @type  ligPdb: str
        @param comPdb: hex-formatted PDB with com models
        @type  comPdb: str
        @param soln: number of solutions to keep from HEX (default 512)
        @type  soln: int
        @param recChainId: force chain IDs only for HEX
        @type  recChainId: [str]
        @param ligChainId: force chain IDs only for HEX
        @type  ligChainId: [str]
        @param out: out folder name, will be formatted against date
        @type  out: str
        @param macDock: force macro docking ON or OFF (default: size decides)
        @type  macDock: 1|0
        @param bin: path to HEX binary
        @type  bin: str
        @param verbose: verbosity level (default: 1)
        @type  verbose: 1|0
        self.lock = RLock()
        self.lockMsg = Condition( self.lock )
        t.ensure( macDock, int, [None] )
        t.ensure( recDic, dict, )
        t.ensure( ligDic, dict, )
        self.verbose = verbose
        self.recDic = recDic
        self.ligDic = ligDic
        ## force chain IDs
        self.recChainId = recChainId
        self.ligChainId = ligChainId
        ## create folder if necessary
        self.out = self.prepareOutFolder( out )
        self.comPdb = None
        if comPdb:
            self.comPdb = t.absfile( comPdb )
        ## remember which HEX PDB was created for which model
        self.recHexPdbs = {}
        self.ligHexPdbs = {}
        ## remember which macrofile uses which models and which out file
        self.runDic = {}
        if recPdb:
            ## HEX PDB provided externally
            for k in self.recDic:
                self.recHexPdbs[ k ] = t.absfile( recPdb )
            ## HEX PDB has to be created
            self.recHexPdbs = self.prepareHexPdbs( self.recDic,
                                                   self.recChainId, 'rec')
        if ligPdb:
            for k in self.ligDic:
                self.ligHexPdbs[ k ] = t.absfile( recPdb )
            self.ligHexPdbs = self.prepareHexPdbs( self.ligDic,
                                                   self.ligChainId, 'lig')
        self.bin = bin
        self.call_when_done = None
        ## remember whether macro dock was used
        self.macroDock = macDock
        self.running = []
        self.hexDone = 0
        self.result = ComplexList()
        self.soln = soln
    def prepareOutFolder( self, fout ):
        Setup an output folder
        @param fout: outfile name
        @type  fout: str
        @return: out path
        @rtype: str
        ## date stamp in folder name
            datestr = "%02i%02i" % (localtime()[1], localtime()[2])
            fout = fout % ( datestr )
            if not os.path.exists( t.absfile( fout ) ):
                os.mkdir( t.absfile( fout ) )
        ## user provided folder name -> formatting fails
            if not os.path.exists( t.absfile( fout ) ):
                os.mkdir( t.absfile( fout ) )
        ## create folders for rec / lig HEX pdbs
        if not os.path.exists( t.absfile( fout ) + '/rec' ):
            os.mkdir( t.absfile( fout ) + '/rec' )
        if not os.path.exists( t.absfile( fout ) + '/lig' ):
            os.mkdir( t.absfile( fout ) + '/lig' )
        return t.absfile( fout )
    def __setChainID( self, m, ids ):
        set chaiID for Hex pdb files
        @param m: model
        @type  m: PDBModel
        @param ids: chain id, len(ids) == m.lenChains
        @type  ids: [str]
        @return: m is changed directly
        @rtype: PDBModel
        if ids:
            ids = t.toList( ids )
            cMap = m.chainMap()
            for chain in range( m.lenChains() ):
                idx = N.nonzero( cMap == chain )
                for i in idx:
                    m.atoms['chain_id'][i] = ids[chain]
    def prepareHexPdbs( self, modelDic, idList, subDir ):
        create HEX-formatted PDB for each model
        @param modelDic: model dictionary to be prepared for HEX
        @type  modelDic: dict
        @param idList: force chain IDs for HEX pdb files
        @type  idList: [str]
        @param subDir: 'rec' or 'lig'
        @type  subDir: str
        @return: model dictionary, { modelNumber : file_name_created, .. }
        @rtype: dict
        result = {}
        for k in modelDic:
            m = modelDic[k].clone()
            fhex = self.out + '/%s/%s_%03d_hex.pdb' % (subDir, m.pdbCode, k)
            if os.path.exists( fhex ) and self.verbose:
                print "using old ", os.path.split( fhex )[1]
                m.remove( m.maskH() )
                m = molUtils.sortAtomsOfModel(m)
                self.__setChainID( m, idList )
                hexTools.createHexPdb_single( m, fhex )
                if self.verbose: print "created ", fhex
            result[ k ] = fhex
        return result
    def createHexInp( self, nRec, nLig ):
        Create a HEX macro file for docking a rec lig pair.
        @param nRec: model number rec in model dictionaries
        @type  nRec: int
        @param nLig: model number lig in model dictionaries
        @type  nLig: int
        @return: macro file name, future out file name
        @rtype: (str, str)
        @raise DockerError: if macro dock option is different from previous
        ## fetch PDB file names for given model numbers
        recPdb, ligPdb = self.recHexPdbs[nRec], self.ligHexPdbs[nLig]
        ## fetch the according PDBModels
        rec, lig = self.recDic[ nRec ], self.ligDic[ nLig ]
        fout_base = self.out+'/%s_%i-%s_%i' % (rec.pdbCode, nRec,
                                               lig.pdbCode, nLig)
        if os.path.exists( t.absfile( fout_base + '_hex.mac' ) ) and self.verbose:
            fmac = t.absfile( fout_base + '_hex.mac' )
            fout = t.absfile( fout_base + '_hex.out' )
            macro = self.macroDock
            print "Dock setup: using old ", os.path.split( fmac )[1]
            if self.verbose: silent=0
            fmac, fout, macro = hexTools.createHexInp(recPdb,rec, ligPdb,lig,
                                                      self.comPdb, outFile=fout_base,
                                                      macDock=self.macroDock, sol=self.soln,
        if self.macroDock == None:
            self.macroDock = macro
            if self.macroDock != macro:
                raise DockerError('MacroDock setting changed to %i: %i : %i' %\
                                  ( macro, nRec, nLig) )
        ## remember which models and which out file are used
        self.runDic[ fmac ] = ( nRec, nLig, fout )
        return fmac, fout
    def runHex( self, finp, log=0, ncpu=2, nice=0, host=os.uname()[1] ):
        @param finp: hex macro file
        @type  finp: str
        @param log: write log file
        @type  log: 1|0
        @param ncpu: number of cpus to use
        @type  ncpu: int
        @param nice: nice value for HEX job (default: 0)
        @type  nice: int
        @param host: host to run jon on
        @type  host: str
        flog = finp + '.log'
        cmd = "%s -ncpu %i -nice %i -noexec -e %s > %s"
        cmd = cmd % (self.bin, ncpu, nice, finp, flog )
        if host != os.uname()[1]:
            cmd = "ssh %s %s" % (host, cmd)
        runner = RunThread( cmd, self, finp=finp, host=host,
                            log=log, verbose=self.verbose )
        self.lastCmd = cmd
        self.running += [runner]
    def countDifferentModels( self, lst ):
        mrec = []
        mlig = []
        for c in lst:
            if c.rec_model not in mrec:
                mrec += [ c.rec_model ]
            if c.lig_model not in mlig:
                mlig += [ c.lig_model ]
        return len( mrec ), len( mlig )
    def doneHex( self, runner ):
        Do something after hex has finished. Notify all threads waiting
        on self.lockMsg
        ## append ComplexList
        self.result += runner.result
        if self.call_when_done:
            self.call_when_done( runner )
        self.running.remove( runner )
        self.hexDone += 1
    def failedHex( self, runner ):
        notify of failed hex run.
        self.running.remove( runner )
        if self.call_when_failed:
            self.call_when_failed( runner )
    def waitForLastHex( self ):
        Return after the last hex thread has finished.
        while len( self.running ) > 0:
    def set_call_when_done( self, funct ):
        funct( RunThread )
        self.call_when_done = funct
    def set_call_when_failed( self, funct ):
        funct( RunThread )
        self.call_when_failed = funct
class RunThread( Thread ):
    @todo: implement that as JobSlave instead
    def __init__( self, cmd, owner, finp=None, log=0,
                  host=None, verbose=1, **kw ):
        @param cmd: command to execute
        @type  cmd: str
        @param owner: Docker job to run to run
        @type  owner: Docker instance
        @param finp: hex macro file (default: None)
        @type  finp: str
        @param log: write log file (default: 0)
        @type  log: 1|0
        @param host: host to run jon on (default: None, localhost)
        @type  host: str
        @param kw: optional key/value pairs
        @type  kw: key=value
        Thread.__init__( self, name=(host or 'local'), **kw )
        self.cmd = cmd
        self.owner = owner
        self.finp = finp
        self.log = log
        self.host = host or os.uname()[1]
        self.nRec, self.nLig, self.fout = self.owner.runDic[ self.finp ]
        self.output = None
        self.status = 0
        self.result = None
        self.verbose = verbose
    def run( self ):
        Run HEX job.
        @raise DockerError: if HEX exists with error
            if not os.path.exists( self.fout ):
                if self.verbose:
                    print "Executing on ", self.host, ' with ', \
                    print "Command: ", self.cmd
                cmd_lst = self.cmd.split()
                self.status = os.spawnvp(os.P_WAIT, cmd_lst[0], cmd_lst )
                if self.status != 0:
                    raise DockerError,\
                          'Hex returned exit status %i' % self.status
                waited = 0
                while waited < 25 and not os.path.exists( self.fout ):
                    sleep( 5 )
                    waited += 5
            ## replace model numbers in HEX output file
            self.__hackHexOut( self.nRec, self.nLig, self.fout )
            parser = HexParser(self.fout, self.owner.recDic,
            ## generate ComplexList from hex output
            self.result = parser.parseHex()
    def done( self ):
        HEX job done.
        self.owner.doneHex( self )
    def failed( self ):
        If HEX job fails
        print "FAILED: ", self.host, ' ', t.stripFilename(self.finp)
        print "\tJob details:"
        print "\tCommand: ", self.cmd
        print "\tinput:   ", self.finp
        print "\tHex log: ", self.log
        print "\tHex out: ", self.fout
        print "\t", t.lastError()
        self.owner.failedHex( self )
    def __hackHexOut( self, nRec, nLig, fout ):
        Replace current model numbers in HEX out file by given nRec and nLig.
        Only to be used with one-against-one dockings because all
        ReceptorModel and LigandModel entries are replaced by nRec, nLig.
        @param nRec: receptor number
        @type  nRec: int
        @param nLig: ligand number
        @type  nLig: int
        @param fout: name of existing  out file, is overwritten
        @type  fout: str
        old_out = open( fout, 'r' )
        contents = old_out.readlines()
        oldRec = 'ReceptorModel: \d+$'
        oldLig = 'LigandModel: \d+$'
        correctRec = 'ReceptorModel: %i' % nRec
        correctLig = 'LigandModel: %i'   % nLig
        contents = [re.sub(oldRec, correctRec, i ) for i in contents]
        contents = [re.sub(oldLig, correctLig, i ) for i in contents]
        new_out = open( fout, 'w')
        new_out.writelines(contents )
##  TESTING        
import Biskit.test as BT
class TestCore(BT.BiskitTest):
    """Base class for short and long Test case"""
    def prepare(self):
        import tempfile
        self.out_folder = tempfile.mktemp('_test_docker_%s')
    def cleanUp(self):
        t.tryRemove( self.out_folder, tree=1 )
    def dry_or_wet_run( self, run=True ):
        """ """
        import time, os
        import os.path
        ligDic = t.load( t.testRoot() + '/multidock/lig/1A19_models.dic' )
        ## in the test root the directories "multidock/rec" and
        ## "multidock/com" are symbolic links from "dock/rec" and
        ## "dock/com". If this is a fleshly checked out project
        ## they will not exist, so we will have to create them.
        rec_dir = t.testRoot() + '/dock/rec'
        com_dir = t.testRoot() + '/dock/com'
        if not os.path.exists( rec_dir ):
            ## remove old invalid links
            if os.path.lexists( rec_dir ):
                os.unlink( rec_dir )
            os.symlink( t.testRoot() + '/dock/rec', rec_dir )
        if not os.path.exists( com_dir ):
            ## remove old invalid links
            if os.path.lexists( com_dir ):
                os.unlink( com_dir )
            os.symlink( t.testRoot() + '/dock/com', com_dir )
        recDic = t.load( t.testRoot() + '/dock/rec/1A2P_model.dic' )
        self.d = Docker( recDic, ligDic, out=self.out_folder,
                         verbose=self.local  )
        # dock rec 1 vs. lig 2 on localhost
        fmac1, fout = self.d.createHexInp( 1, 2 )
        if run:
            self.d.runHex( fmac1, log=1, ncpu=2, host='localhost' )
        ## dock receptor 1 vs. ligand one on remote host
        # fmac2, fout2= d.createHexInp( 1, 1 )
        # d.runHex( fmac2, log=0, ncpu=2, host='remote_host_name' )
        if self.local: print "ALL jobs submitted."
class TestLong(TestCore):
    """Test case running a complete hex docking (ca. 30 min/CPU)"""
    TAGS = [ BT.EXE, BT.LONG ]
    def test_DockerLong(self):
        """Dock.Docker real test (20-30min/CPU)"""
        self.dry_or_wet_run( run=True )
class TestShort(TestCore):
    TAGS = [ BT.EXE ]
    def test_DockerShort(self):
        """Dock.Docker dry run test"""
        self.dry_or_wet_run( run=False )
if __name__ == '__main__':