/usr/share/autodock/Tests/test

#! /usr/bin/env python
#
# $Id: test_autodock4.py,v 1.61 2012/12/13 06:44:43 mp Exp $
#

"""
Unit Tests for AutoDock 4.
"""

#______________________________________________________________________________

import sys
import os
import unittest
import getopt
import subprocess
from DlgParser import DlgParser

#______________________________________________________________________________
#
# Global variables

autodock_executable = "../autodock4" # where the AutoDock executable resides
dpf_directory = '.' # where the input DPF files reside
test_output_directory = '.' # where the DLG files will be written

try:
    opts, argv = getopt.getopt(sys.argv[1:], "d:e:o:",
    ["dpf-directory=","executable=","test-output-directory="]) 
except getopt.GetoptError, v:
    usage() 
    sys.exit(2)

for o,a in opts:
    if o in ("-d", "--dpf-directory"):
        dpf_directory = a
    if o in ("-e", "--executable"):
        autodock_executable = a
    if o in ("-o","--test-output-directory"):
        test_output_directory = a


#______________________________________________________________________________

def usage():
    """Print out the usage of this command."""
    print """Usage:  python test_autodock4.py [-d <string>] [-e <string>] [-o <string>]

where:
    -d, --dpf-directory
        specifies the directory containing the DPFs to be tested;
        this flag is optional; default is '.'
    -e, --executable
        specifies the path to the AutoDock executable to be tested;
        this flag is optional; default is '../autodock4'
    -o, --test-output-directory
        specifies the directory where the output DLGs will be written;
        this flag is optional; default is '.'

NOTE:  these may be relative to the directory where this script was invoked.
"""

#______________________________________________________________________________

def run_AutoDock( dpf_filename, dlg_filename ):
    """Launch AutoDock, using the specified AutoDock executable and DPF,
    create the specified DLG, and trap all the outputs from standard output
    and standard error."""
    dpf = dpf_directory + os.sep + dpf_filename
    dlg = test_output_directory + os.sep + dlg_filename
    rm( dlg )
    command =   [autodock_executable, '-p', dpf, '-l', dlg] 
    print '\nRunning ' + autodock_executable + ' using DPF "'+dpf+'", saving results in "'+dlg+'":'
    try:
        rc = subprocess.call( command )
	#print 'autodock returned ', rc  # DEBUG
        return find_success_in_DLG( dlg_filename )
    except OSError,e:
        print "\nUnable to run " + autodock_executable + " :", e
        return False

#______________________________________________________________________________

def parse_energy_from_DLG( dlg_filename, energy_list):
    """Parse the AutoDock DLG, and return the intermolecular and internal
    energies as a tuple."""
    parser = DlgParser()
    dlg = test_output_directory + os.sep + dlg_filename
    parser.parse( dlg )
    docked = parser.clist[0]  #dictionary of results
    result = []
    for energy_type in energy_list:
        newVal = docked.get(energy_type, 'ERROR')
        print energy_type, ' is now ', newVal
        result.append(docked.get(energy_type, 'ERROR'))
    #intermol_energy = docked['intermol_energy']  #-6.17
    #internal_energy = docked['total_internal']  # -1.58
    #print "docked[binding_energy]=", docked['binding_energy']
    #print "docked[electrostatic_energy]=", docked['electrostatic_energy']
    #print "docked[intermol_energy]=", docked['intermol_energy']
    #print "docked[total_internal]=", docked['total_internal']
    #unbound_energy = docked['unbound_energy']
    #print "unbound_energy=", unbound_energy
    #return ( intermol_energy, internal_energy )
    return result

#______________________________________________________________________________

def find_success_in_DLG( dlg_filename ):
    """Open the AutoDock DLG, and look for the string "Successful Completion"
    in the last 10 lines of the file."""
    dlg = test_output_directory + os.sep + dlg_filename
    try:
        fptr = open( dlg )
        lines = fptr.readlines()
        fptr.close()
        success = False
        for l in lines[-10:]:
            if l.find( "Successful Completion" ) > -1:
                success = True
        return success
    except:
        return False

#______________________________________________________________________________

def rm( filename ):
    """Remove single file """
    # no regular expression wildcards, e.g. * or ?, allowed
    if os.access(filename, os.F_OK) :
       try:
          os.remove( filename )
       except OSError,e:
         print 'unable to remove '+filename


#______________________________________________________________________________

class AutoDock_base_test( unittest.TestCase ):
    """Base Class for AutoDock testing."""
    """ do not instantiate this for a test, use simple_test or other subclass instead """
    dpf_stem = "BaseClass"
    computed = False
    def setUp( self ):
        """Set up for autodock4 tests. Locate the autodock binary now during setUp."""
        self.dlg_filename = "test_" + self.dpf_stem + ".dlg"
        self.computed = run_AutoDock( self.dpf_stem + ".dpf", self.dlg_filename )

    #def test_dlg_exists( self ):
    #    """Check that run finished and a new DLG has been computed."""
    #    # Check that run finished and a new DLG has been computed.
    #    if (self.expected_outcome == True ):
    #        print "Testing that DLG exists and AutoDock successfully completed."
    #    else:
    #        print "Testing that DLG exists and AutoDock did not complete."
    #    self.assertEqual( self.computed, self.expected_outcome )


#______________________________________________________________________________

class AutoDock_simple_test( unittest.TestCase ):
    """Base Class for AutoDock testing."""
    dpf_stem = "BaseClass"
    computed = False
    def setUp( self ):
        """Set up for autodock4 tests. Locate the autodock binary now during setUp."""
        self.dlg_filename = "test_" + self.dpf_stem + ".dlg"
        self.computed = run_AutoDock( self.dpf_stem + ".dpf", self.dlg_filename )

    def test_dlg_exists( self ):
        """Check that run finished and a new DLG has been computed."""
        # Check that run finished and a new DLG has been computed.
        if (self.expected_outcome == True ):
            print "Testing that DLG exists and AutoDock successfully completed."
        else:
            print "Testing that DLG exists and AutoDock did not complete."
        self.assertEqual( self.computed, self.expected_outcome )
#______________________________________________________________________________

class AutoDock4_1pgp_no_extension( AutoDock_simple_test ):
    """Test that autodock4 stops early if .dpf extension is missing
    keywords are specified."""
    dpf_stem = "1pgp_no_extension"
    print "in 1pgp_no_extension"
    expected_outcome = False # True means Successful Completion!
    def setUp( self ):
        """Set up for autodock4 tests. Locate the autodock binary now during setUp."""
        self.dlg_filename = "test_" + self.dpf_stem + ".dlg"
        self.computed = run_AutoDock( self.dpf_stem , self.dlg_filename )

#______________________________________________________________________________

class AutoDock4_1pgp_wrong_extension( AutoDock_simple_test ):
    """Test that autodock4 stops early if extension is not '.dpf'
    keywords are specified."""
    dpf_stem = "1pgp.fpd"
    print "in 1pgp_wrong_extension"
    expected_outcome = False # True means Successful Completion!
    def setUp( self ):
        """Set up for autodock4 tests. Locate the autodock binary now during setUp."""
        self.dlg_filename = "test_" + self.dpf_stem + ".dlg"
        self.computed = run_AutoDock( self.dpf_stem , self.dlg_filename )

#______________________________________________________________________________


class AutoDock4_1pgp_two_extensions( AutoDock_simple_test ):
    """Test that autodock4 stops early if dpf name includes two .dpf
    keywords are specified."""
    dpf_stem = "1pgp.dpf"
    print "in 1pgp_two_extensions"
    expected_outcome = False # True means Successful Completion!
    def setUp( self ):
        """Set up for autodock4 tests. Locate the autodock binary now during setUp."""
        self.dlg_filename = "test_" + self.dpf_stem + ".dlg"
        self.computed = run_AutoDock( self.dpf_stem +'.dpf', self.dlg_filename )


#______________________________________________________________________________


class AutoDock4_1pgp_ligand_types_map_mismatch( AutoDock_simple_test ):
    """Test that autodock4 stops early if number of maps do not equal number
    of ligand types"""
    dpf_stem = "1pgp_ligand_types_map_mismatch"
    expected_outcome = False # True means Successful Completion!
#______________________________________________________________________________

class AutoDock4_1pgp_illegal_keyword_test( AutoDock_simple_test ):
    """Test that autodock4 stops early if it finds an illegal keyword 
    in dpf """
    dpf_stem = "1pgp_illegal_keyword"
    expected_outcome = False # True means Successful Completion!
#______________________________________________________________________________

class AutoDock4_1pgp_no_elecmap_test( AutoDock_simple_test ):
    """Test that autodock4 stops early if no "elecmap" keyword is specified."""
    dpf_stem = "1pgp_no_elecmap"
    expected_outcome = False # True means Successful Completion!
#______________________________________________________________________________

class AutoDock4_1pgp_no_desolvmap_test( AutoDock_simple_test ):
    """Test that autodock4 stops early if no "desolvmap" keyword is specified."""
    dpf_stem = "1pgp_no_desolvmap"
    expected_outcome = False # True means Successful Completion!
#______________________________________________________________________________

class AutoDock4_1pgp_no_elec_desolv_maps_test( AutoDock_simple_test ):
    """Test that autodock4 stops early if no elecmap and no desolvmap 
    keywords are specified."""
    dpf_stem = "1pgp_no_elec_desolv_maps"
    expected_outcome = False # True means Successful Completion!
#______________________________________________________________________________

class AutoDock4_1pgp_too_many_torsions( AutoDock_simple_test ):
    """Test that autodock4 stops early if too many torsions 
    are specified. (current limit is 32)"""
    dpf_stem = "1pgp_too_many_torsions"
    expected_outcome = False # True means Successful Completion!
#______________________________________________________________________________

class AutoDock4_1pgp_just_right_number_torsions( AutoDock_simple_test ):
    """Test that autodock4 completes with current limit of number of  torsions 
    are specified. (current limit is 32)"""
    dpf_stem = "1pgp_just_right_number_torsions"
    expected_outcome = True # True means Successful Completion!
#______________________________________________________________________________


class AutoDock4_1pgp_too_many_ligand_types_test( AutoDock_simple_test ):
    """Test that autodock4 stops early if too many ligand types 
    are specified. (current limit is 14)"""
    dpf_stem = "1pgp_too_many_ligand_types"
    expected_outcome = False # True means Successful Completion!
#______________________________________________________________________________

class AutoDock4_1pgp_two_ligands_test( AutoDock_simple_test ):
    """Test that autodock4 can run dpf specifying two ligands."""
    dpf_stem = "1pgp_two_ligands"
    expected_outcome = True # True means Successful Completion!
#______________________________________________________________________________

class AutoDock4_1pgp_two_mapsets_test( AutoDock_simple_test ):
    """Test that autodock4 can run dpf specifying two sets of maps and one ligand."""
    dpf_stem = "1pgp_two_mapsets"
    expected_outcome = True # True means Successful Completion!
#______________________________________________________________________________

class AutoDock4_1pgp_unbound_set_illegal_test( AutoDock_simple_test ):
    """Test that autodock 4.1 works when unbound is set to 'foo' in the DPF."""
    dpf_stem = "1pgp_unbound_set_illegal"
    expected_outcome = False # True means Successful Completion!
#______________________________________________________________________________

class AutoDock4_1pgp_unbound_model_illegal_test( AutoDock_simple_test ):
    """Test that autodock4 stops early if it finds an illegal unbound_model 
    in dpf """
    dpf_stem = "1pgp_unbound_model_illegal"
    expected_outcome = False # True means Successful Completion!
#______________________________________________________________________________

class AutoDock4_1pgp_ga_run_maxruns_test( AutoDock_simple_test ):
    """Test that autodock 4 runs with max number of runs"""
    dpf_stem = "1pgp_ga_run_maxruns"
    expected_outcome = True # True means Successful Completion!

#______________________________________________________________________________

class AutoDock4_1pgp_ga_run_maxruns_analysis_test( AutoDock_simple_test ):
    """Test that autodock 4 runs with max number of runs followed by cluster analysis"""
    dpf_stem = "1pgp_ga_run_maxruns_analysis"
    expected_outcome = True # True means Successful Completion!

#______________________________________________________________________________

class AutoDock4_1pgp_ga_select_tournament_test( AutoDock_simple_test ):
    """Test that autodock 4.2 stops when ga_select_tournament is set in the DPF."""
    dpf_stem = "1pgp_ga_select_tournament"
    expected_outcome = False # True means Successful Completion!

#______________________________________________________________________________

class AutoDock4_1pgp_ga_select_linear_ranking_test( AutoDock_simple_test ):
    """Test that autodock 4.2 works when ga_select_linear_ranking is set in the DPF."""
    dpf_stem = "1pgp_ga_select_linear_ranking"
    expected_outcome = True # True means Successful Completion!

#______________________________________________________________________________

#print "docked[binding_energy]=", docked['binding_energy']
class AutoDock4_1pgp_ligrand_ga_only_test( AutoDock_simple_test ):
    """Test that autodock 4.2 works when ligand is randomized within autodock as set in the DPF."""
    dpf_stem = "1pgp_ligrand_ga_only"
    #print "in new ligrand_ga_only test"
        #expected_binding_energy = +843.59     -5.87
        #expected_intermol_energy = +21.00  -6.17
        #expected_internal_energy = +820.50 -3.23
    expected_outcome = True # True means Successful Completion!
#______________________________________________________________________________

class AutoDock4_1pgp_ga_only_test( AutoDock_simple_test ):
    """Test that autodock 4.2 works when ga_only is set in the DPF."""
    dpf_stem = "1pgp_ga_only"
    #print "in new ga_only test"
        #expected_binding_energy = +843.59     -5.87
        #expected_intermol_energy = +21.00  -6.17
        #expected_internal_energy = +820.50 -3.23
    expected_outcome = True # True means Successful Completion!

#______________________________________________________________________________

class AutoDock4_1pgp_about_only_test( AutoDock_simple_test ):
    """Test that autodock 4.2 works when about is set in the DPF but tran0,
    dihe0 and quat0 are missing."""
    dpf_stem = "1pgp_about_only"
    #print "in new ga_only test"
        #expected_binding_energy = +843.59     -5.87
        #expected_intermol_energy = +21.00  -6.17
        #expected_internal_energy = +820.50 -3.23
    expected_outcome = True # True means Successful Completion!

#______________________________________________________________________________

class AutoDock4_1pgp_multipleabouts_test( AutoDock_simple_test ):
    """Test that autodock 4.2 works when about appears multiple times"""
    dpf_stem = "1pgp_multipleabouts"
    #print "in new ga_only test"
        #expected_binding_energy = +843.59     -5.87
        #expected_intermol_energy = +21.00  -6.17
        #expected_internal_energy = +820.50 -3.23
    expected_outcome = True # True means Successful Completion!

#______________________________________________________________________________


class AutoDock4_1pgp_simanneal_small( AutoDock_simple_test ):
    """Test that autodock 4.2 simanneal works (at all). """
    dpf_stem = "1pgp_simanneal_small"
        #expected_binding_energy = +843.59     -5.87
        #expected_intermol_energy = +21.00  -6.17
        #expected_internal_energy = +820.50 -3.23
    expected_outcome = True # True means Successful Completion!

#______________________________________________________________________________

class AutoDock4_1pgp_simanneal_small_geometric_schedule( AutoDock_simple_test ):
    """Test that autodock 4.2 simanneal alternate cooling schedule """
    dpf_stem = "1pgp_simanneal_small_geometric_schedule"
        #expected_binding_energy = +843.59     -5.87
        #expected_intermol_energy = +21.00  -6.17
        #expected_internal_energy = +820.50 -3.23
    expected_outcome = True # True means Successful Completion!

#______________________________________________________________________________

class AutoDock4_1pgp_about_auto_simanneal( AutoDock_simple_test ):
    """Test that autodock 4.2 simanneal works when about, tran0, dihe0, and quat0 are missing."""
    dpf_stem = "1pgp_about_auto_simanneal"
        #expected_binding_energy = +843.59     -5.87
        #expected_intermol_energy = +21.00  -6.17
        #expected_internal_energy = +820.50 -3.23
    expected_outcome = True # True means Successful Completion!

#______________________________________________________________________________

class AutoDock4_1pgp_about_auto_ga_only( AutoDock_simple_test ):
    """Test that autodock 4.2 ga_only works when about, tran0, dihe0, and quat0 are missing."""
    dpf_stem = "1pgp_about_auto_ga_only"
        #expected_binding_energy = +843.59     -5.87
        #expected_intermol_energy = +21.00  -6.17
        #expected_internal_energy = +820.50 -3.23
    expected_outcome = True # True means Successful Completion!

#______________________________________________________________________________

class AutoDock4_1pgp_about_auto_gals( AutoDock_simple_test ):
    """Test that autodock 4.2 ga_ls works when about, tran0, dihe0, and quat0 are missing."""
    dpf_stem = "1pgp_about_auto_gals"
        #expected_binding_energy = +843.59     -5.87
        #expected_intermol_energy = +21.00  -6.17
        #expected_internal_energy = +820.50 -3.23
    expected_outcome = True # True means Successful Completion!

#______________________________________________________________________________

class AutoDock4_1pgp_about_auto_local_only( AutoDock_simple_test ):
    """Test that autodock 4.2 local_only works when about, tran0, dihe0, and quat0 are missing."""
    dpf_stem = "1pgp_about_auto_local_only"
        #expected_binding_energy = +843.59     -5.87
        #expected_intermol_energy = +21.00  -6.17
        #expected_internal_energy = +820.50 -3.23
    expected_outcome = True # True means Successful Completion!

#______________________________________________________________________________

class AutoDock4_1pgp_flexres_test( AutoDock_simple_test ):
    """Test that autodock 4.2 works when flexres is set in the DPF."""
    dpf_stem = "1pgp_flexres"
    #print "in new flexres test"
        #expected_binding_energy =  -4.22
        #expected_intermol_energy = -5.93
        #expected_internal_energy = -2.18
    expected_outcome = True # True means Successful Completion!

#______________________________________________________________________________

class AutoDock4_1pgp_rmsmode_heavy_atoms_only_noH_test( AutoDock_simple_test ):
    """Test that autodock4 works if noHs when using new keyword rmsmode heavy_atoms_only."""
    dpf_stem = "1pgp_rmsmode_heavy_atoms_only_noH"
    expected_outcome = True # True means Successful Completion!

#______________________________________________________________________________

class AutoDock4_1pgp_rmsmode_all_heavy_atom_pairs_only_test( AutoDock_simple_test ):
    """Test that autodock4 works if rms calc uses all pairs of heavy_atoms.
       Set by including these TWO rmsmode cmds in dpf:  
        rmsmode unique_pair       #sets B_unique_pair_flag to TRUE (default is FALSE)
        rmsmode heavy_atoms_only  #sets B_rms_heavy_atoms_only to TRUE (default is FALSE)
        """
    dpf_stem = "1pgp_rmsmode_all_heavy_atom_pairs_only"
    expected_outcome = True # True means Successful Completion!

#______________________________________________________________________________

class AutoDock4_1pgp_rmsmode_unique_heavy_atom_pairs_only_test( AutoDock_simple_test ):
    """Test that autodock4 works if rms calc uses only unique pairs of heavy_atoms specified 
          with two rmsmode cmds: unique_pair heavy_atoms_only."""
    dpf_stem = "1pgp_rmsmode_unique_heavy_atom_pairs_only"
    expected_outcome = True # True means Successful Completion!

#______________________________________________________________________________

class AutoDock_test( AutoDock_base_test ):
    """Class for AutoDock testing."""

    def test_dlg_exists_and_test_energy( self ):
        """Check that run finished and a new DLG has been computed.
        Also check the final energy is the expected value."""
        # Check that run finished and a new DLG has been computed.
        if (self.expected_outcome == True ):
            print "Testing that DLG exists and AutoDock successfully completed."
        else:
            print "Testing that DLG exists and AutoDock did not complete."
        self.assertEqual( self.computed, self.expected_outcome )
        # Check the final energy is expected value.
        expected_intermol_energy = -6.44  
        expected_internal_energy = -3.28  # 3.17? MP
        (intermol_energy, internal_energy) = parse_energy_from_DLG( self.dlg_filename, ['intermol_energy','total_internal'] )
        print "Testing that intermolecular energy = %.2f kcal/mol." % (expected_intermol_energy,)
        self.assertEqual( round(intermol_energy,6), round(expected_intermol_energy,6))
        print "Testing that internal energy = %.2f kcal/mol." % (expected_internal_energy,)
        self.assertEqual( round(internal_energy,6), round(expected_internal_energy,6))
#______________________________________________________________________________

class AutoDock4_1pgp_test( AutoDock_test ):
    """Test that autodock4 executes using an extremely short run."""
    dpf_stem = "1pgp"
    expected_outcome = True # True means Successful Completion!
#______________________________________________________________________________

# next test not installed yet as I do not have a way I know of to pass
# different expected values to the superclass - M Pique  July 2012
class AutoDock4_1pgp_intelec_off_test( AutoDock_test ):
    """Test autodock4.3 internal energy off option yields 4.2 value."""
    dpf_stem = "1pgp_intelec_off"
    expected_intermol = -7.72
    expected_outcome = True # True means Successful Completion!
#______________________________________________________________________________

class AutoDock4_1pgp_timepid_test( AutoDock_simple_test ):
    """Test that autodock4 executes using seed set by time and process-id"""
    dpf_stem = "1pgp_timepid"
    expected_outcome = True # True means Successful Completion!
#______________________________________________________________________________

class AutoDock4_1pgp_seed01_test( AutoDock_simple_test ):
    """Test that autodock4 executes using seeds  set to 0 1"""
    dpf_stem = "1pgp_seed01"
    expected_outcome = True # True means Successful Completion!
#______________________________________________________________________________

class AutoDock4_1pgp_seedinttime_test( AutoDock_simple_test ):
    """Test that autodock4 executes using seeds  set to integer and time"""
    dpf_stem = "1pgp_seedinttime"
    expected_outcome = True # True means Successful Completion!
#______________________________________________________________________________

class AutoDock4_1pgp_epdb_flexres_intelec_test( AutoDock_simple_test ):
    """Test autodock 4.3 epdb output flexres with intelec on."""
    dpf_stem = "1pgp_epdb_flexres_intelec"
    expected_outcome = True # True means Successful Completion!
#______________________________________________________________________________

class AutoDock4_1pgp_epdb_flexres_nointelec_test( AutoDock_simple_test ):
    """Test autodock 4.3 epdb output flexres with intelec off."""
    dpf_stem = "1pgp_epdb_flexres_nointelec"
    expected_outcome = True # True means Successful Completion!
#______________________________________________________________________________

class AutoDock4_1pgp_epdb_etables_test( AutoDock_simple_test ):
    """Test autodock 4.3 high outlev detail for epdb and energy tables."""
    dpf_stem = "1pgp_epdb_etables"
    expected_outcome = True # True means Successful Completion!
#______________________________________________________________________________

class AutoDock4_1pgp_numoutlev_test( AutoDock_simple_test ):
    """Test autodock 4.3 numeric outlev detail settings."""
    dpf_stem = "1pgp_numoutlev"
    expected_outcome = True # True means Successful Completion!
#______________________________________________________________________________

class AutoDock4_1pgp_no_outlev_test( AutoDock_simple_test ):
    """Test autodock 4.3 default outlev detail setting."""
    dpf_stem = "1pgp_no_outlev"
    expected_outcome = True # True means Successful Completion!
#______________________________________________________________________________

class AutoDock4_1pgp_illegal_outlev_test( AutoDock_simple_test ):
    """Test autodock 4.3 outlev with no argument setting."""
    dpf_stem = "1pgp_illegal_outlev"
    expected_outcome = False # True means Successful Completion!
#______________________________________________________________________________

class AutoDock4_1pgp_symoutlev_test( AutoDock_simple_test ):
    """Test autodock 4.3 symbolic and numeric outlev detail settings."""
    dpf_stem = "1pgp_symoutlev"
    expected_outcome = True # True means Successful Completion!
#______________________________________________________________________________

class AutoDock4_1pgp_illegal_symoutlev_test( AutoDock_simple_test ):
    """Test autodock 4.3 symbolic outlev incorrect setting."""
    dpf_stem = "1pgp_illegal_symoutlev"
    expected_outcome = False # True means Successful Completion!
#______________________________________________________________________________

class AutoDock4_1pgp_gals_set_sw1_test( AutoDock_simple_test ):
    """Test that autodock4 gals_run succeeds with older sw1 rather than psw1."""
    dpf_stem = "1pgp_gals_set_sw1"
    expected_outcome = True # True means Successful Completion!
#______________________________________________________________________________

class AutoDock4_1pgp_smaller_test( AutoDock_simple_test ):
    expected_intermol_energy = -6.17  
    expected_internal_energy = -3.23
    """Test that autodock4 executes using fewer parameters and an extremely short run."""
    dpf_stem = "1pgp_smaller"
    #expected_intermol_energy = -6.17  
    #expected_internal_energy = -3.23
    expected_outcome = True # True means Successful Completion!
#______________________________________________________________________________

class AutoDock4_1pgp_gals_use_defaults_test( AutoDock_test ):
    """Test that autodock4 executes using default gals parameters."""
    dpf_stem = "1pgp_gals_use_defaults"
    expected_outcome = True # True means Successful Completion!
#______________________________________________________________________________

class AutoDock4_1pgp_gals_no_set_ga_test( AutoDock_simple_test ):
    """Test that autodock4 ga_run fails when set_ga command is omitted."""
    dpf_stem = "1pgp_no_set_ga"
    expected_outcome = False # True means Successful Completion!
#______________________________________________________________________________

class AutoDock4_1pgp_gals_no_set_psw1_test( AutoDock_simple_test ):
    """Test that autodock4 gals_run fails when set_psw1 command is omitted."""
    dpf_stem = "1pgp_no_set_psw1"
    expected_outcome = False # True means Successful Completion!
#______________________________________________________________________________

class AutoDock4_1pgp_no_parameter_file_test( AutoDock_test ):
    """Test that autodock4 works using default parameter library."""
    dpf_stem = "1pgp_no_parameter_file"
    expected_outcome = True # True means Successful Completion!
#______________________________________________________________________________

class AutoDock4_1pgp_output_pop_file_test( AutoDock_simple_test ):
    """Test that autodock4 executes while writing out popfile"""
    dpf_stem = "1pgp_outpopfil"
    expected_outcome = True # True means Successful Completion!
#______________________________________________________________________________

class AutoDock4_1pgp_rmsmode_heavy_atoms_only_test( AutoDock_test ):
    """Test that autodock4 works using new keyword rmsmode heavy_atoms_only."""
    dpf_stem = "1pgp_rmsmode_heavy_atoms_only"
    expected_outcome = True # True means Successful Completion!
#______________________________________________________________________________
class AutoDock4_energy_test( AutoDock_base_test ):
    """Class for AutoDock testing free energy."""
    expected_binding_energy = None

    def test_dlg_exists_and_test_energy( self):
        """Check that run finished and a new DLG has been computed.
        Also check the final energy is the expected value."""
        # Check that run finished and a new DLG has been computed.
        if (self.expected_outcome == True ):
            print "Testing that DLG exists and AutoDock successfully completed."
        else:
            print "Testing that DLG exists and AutoDock did not complete."
        self.assertEqual( self.computed, self.expected_outcome )
        # Check the final energy is expected value.
        #expected_unbound_energy = -3.23
        #expected_binding_energy = +843.59     -5.87
        (binding_energy) = parse_energy_from_DLG( self.dlg_filename, ['binding_energy'])[0]
        print "Testing that binding energy = %.2f kcal/mol." % (self.expected_binding_energy,)
        print "binding_energy=", binding_energy
        self.assertEqual( round(binding_energy,6), round(self.expected_binding_energy,6))
#______________________________________________________________________________


class AutoDock4_unbound_test( AutoDock_base_test ):
    """Class for AutoDock testing unbound energy."""
    expected_unbound_energy = None

    def test_dlg_exists_and_test_energy( self):
        """Check that run finished and a new DLG has been computed.
        Also check the final energy is the expected value."""
        # Check that run finished and a new DLG has been computed.
        if (self.expected_outcome == True ):
            print "Testing that DLG exists and AutoDock successfully completed."
        else:
            print "Testing that DLG exists and AutoDock did not complete."
        self.assertEqual( self.computed, self.expected_outcome )
        # Check the final energy is expected value.
        #expected_unbound_energy = -3.23
        (unbound_energy) = parse_energy_from_DLG( self.dlg_filename, ['unbound_energy'])[0]
        print "Testing that unbound energy = %.2f kcal/mol." % (self.expected_unbound_energy,)
        print "unbound_energy=", unbound_energy
        self.assertEqual( round(unbound_energy,6), round(self.expected_unbound_energy,6))
#______________________________________________________________________________

class AutoDock4_1pgp_unbound_default_test( AutoDock4_unbound_test ):
    """Test that autodock 4.1 works when unbound is NOT set in the DPF."""
    dpf_stem = "1pgp_unbound_default"
    expected_unbound_energy = -3.23
    expected_outcome = True # True means Successful Completion!
#______________________________________________________________________________

class AutoDock4_1pgp_unbound_model_extended( AutoDock4_unbound_test ):
    """Test that autodock 4.1 works when unbound_model is set to extended."""
    dpf_stem = "1pgp_unbound_model_extended"
    expected_unbound_energy = -0.75
    expected_outcome = True # True means Successful Completion!
#______________________________________________________________________________

class AutoDock4_1pgp_unbound_compute_unbound_extended( AutoDock4_unbound_test ):
    """Test that autodock 4.1 works when unbound_model is set to extended."""
    dpf_stem = "1pgp_unbound_compute_unbound_extended"
    expected_unbound_energy = -0.75
    expected_outcome = True # True means Successful Completion!
#______________________________________________________________________________

class AutoDock4_1pgp_unbound_model_value( AutoDock4_unbound_test ):
    """Test that autodock 4.1 works when unbound_model is set to a value in the DPF."""
    dpf_stem = "1pgp_unbound_model_value"
    expected_unbound_energy = -3.12 
    expected_outcome = True # True means Successful Completion!
#______________________________________________________________________________

class AutoDock4_1pgp_unbound_model_compact( AutoDock4_unbound_test ):
    """Test that autodock 4.1 works when unbound_model is set to compact."""
    dpf_stem = "1pgp_unbound_model_compact"
    expected_unbound_energy =  0.00 #@FixMe 3/2009 do not know how to calc this
    expected_outcome = True # True means Successful Completion!
#______________________________________________________________________________

class AutoDock4_1pgp_unbound_model_bound( AutoDock4_unbound_test ):
    """Test that autodock 4.1 works when unbound_model is set to bound."""
    dpf_stem = "1pgp_unbound_model_bound"
    expected_unbound_energy = -3.23
    expected_outcome = True # True means Successful Completion!
#______________________________________________________________________________

class AutoDock4_1pgp_unbound_set0_test( AutoDock4_unbound_test ):
    """Test that autodock 4.1 works when unbound is set to 0 in the DPF."""
    dpf_stem = "1pgp_unbound_set0"
    expected_unbound_energy = 0.
    expected_outcome = True # True means Successful Completion!
#______________________________________________________________________________

class AutoDock4_1pgp_unbound_set10_test( AutoDock4_unbound_test ):
    """Test that autodock 4.1 works when unbound is set to 10 in the DPF."""
    dpf_stem = "1pgp_unbound_set10"
    expected_unbound_energy = 10.
    expected_outcome = True # True means Successful Completion!
#______________________________________________________________________________

class AutoDock4_1pgp_1_4_50_test( AutoDock4_energy_test ):
    """Test that autodock 4.2 works include_1_4 set to 50 in the DPF."""
    dpf_stem = "1pgp_1_4_50"
    #print "in new ga_only test"
        #expected_binding_energy = +843.59     -5.87
        #expected_intermol_energy = +21.00  -6.17
        #expected_internal_energy = +820.50 -3.23
    expected_binding_energy = -4.08
    expected_outcome = True # True means Successful Completion!

#______________________________________________________________________________


class AutoDock4_1pgp_1_4_100_test( AutoDock4_energy_test ):
    """Test that autodock 4.2 works include_1_4 set to 100 in the DPF."""
    dpf_stem = "1pgp_1_4_100"
    #print "in new ga_only test"
        #expected_binding_energy = +843.59     -5.87
        #expected_intermol_energy = +21.00  -6.17
        #expected_internal_energy = +820.50 -3.23
    #expected_binding_energy = -4.08
    expected_binding_energy = -3.49
    expected_outcome = True # True means Successful Completion!

#______________________________________________________________________________

#print "docked[binding_energy]=", docked['binding_energy']
class AutoDock4_1pgp_ligrand_ga_only_energy_test( AutoDock4_energy_test ):
    """Test that autodock 4.2 works when ligand is randomized within autodock as set in the DPF.
                 and that expected energy is found"""
    dpf_stem = "1pgp_ligrand_ga_only"
    expected_binding_energy = 1.39
    expected_outcome = True # True means Successful Completion!

#______________________________________________________________________________


class AutoDock4_1pgp_ga_only_energy_test( AutoDock4_energy_test ):
    """Test that autodock 4.2 works when ga_only is set in the DPF."""
    dpf_stem = "1pgp_ga_only"
    #print "in new ga_only test"
        #expected_binding_energy = +843.59     -5.87
        #expected_intermol_energy = +21.00  -6.17
        #expected_internal_energy = +820.50 -3.23
    expected_binding_energy = -4.08
    expected_outcome = True # True means Successful Completion!

#______________________________________________________________________________


class AutoDock4_1pgp_flexres_energy_test( AutoDock4_energy_test ):
    """Test that autodock 4.2 works when flexres is set in the DPF."""
    dpf_stem = "1pgp_flexres"
    #print "in new flexres test"
        #expected_binding_energy =  -4.22
        #expected_intermol_energy = -5.93
        #expected_internal_energy = -2.18
    expected_binding_energy = -4.33
    expected_outcome = True # True means Successful Completion!

#______________________________________________________________________________

class AutoDock4_1pgp_flexres_energy_1_4_50_test( AutoDock4_energy_test ):
    """Test that autodock 4.2 works when flexres is set in the DPF."""
    dpf_stem = "1pgp_flexres_1_4_50"
    #print "in new flexres test"
        #expected_binding_energy =  -4.22
        #expected_intermol_energy = -5.93
        #expected_internal_energy = -2.18
    #expected_binding_energy = -4.72
    expected_binding_energy = -4.33
    expected_outcome = True # True means Successful Completion!

#______________________________________________________________________________

class AutoDock4_1pgp_flexres_energy_1_4_100_test( AutoDock4_energy_test ):
    """Test that autodock 4.2 works when flexres is set in the DPF."""
    dpf_stem = "1pgp_flexres_1_4_100"
    #print "in new flexres test"
        #expected_binding_energy =  -4.22
        #expected_intermol_energy = -5.93
        #expected_internal_energy = -2.18
    expected_binding_energy = -4.33
    expected_outcome = True # True means Successful Completion!

#______________________________________________________________________________


class AutoDock4_1pgp_ga_smooth0_energy_test( AutoDock4_energy_test ):
    """Test that autodock 4.2 gives expected internal energy when smooth is set to 0 in the DPF."""
    dpf_stem = "1pgp_smooth0"
    #restores former values (less negative)
    expected_binding_energy =  -5.87
    expected_intermol_energy = -6.17
    expected_internal_energy = -1.78
    expected_outcome = True # True means Successful Completion!

#______________________________________________________________________________




if __name__ == '__main__':
    #  This syntax lets us run all the tests,
    #  or conveniently comment out tests we're not interested in.
    #  NOTE:  Remember to add new TestCase class names to the list "test_cases"
    test_cases = [
        # tests for .dpf extension:
        'AutoDock4_1pgp_no_extension',
        'AutoDock4_1pgp_wrong_extension',
        'AutoDock4_1pgp_two_extensions',
        # simple tests:
        'AutoDock4_1pgp_timepid_test',
	'AutoDock4_1pgp_seed01_test',
	'AutoDock4_1pgp_seedinttime_test',
        'AutoDock4_1pgp_epdb_flexres_intelec_test',
        'AutoDock4_1pgp_epdb_flexres_nointelec_test',
        'AutoDock4_1pgp_epdb_etables_test',
        'AutoDock4_1pgp_numoutlev_test',
        'AutoDock4_1pgp_symoutlev_test',
	'AutoDock4_1pgp_no_outlev_test',
	'AutoDock4_1pgp_illegal_outlev_test',
        'AutoDock4_1pgp_illegal_symoutlev_test',
        'AutoDock4_1pgp_ligand_types_map_mismatch',
        'AutoDock4_1pgp_illegal_keyword_test',
        'AutoDock4_1pgp_no_elecmap_test',
        'AutoDock4_1pgp_no_desolvmap_test',
        'AutoDock4_1pgp_no_elec_desolv_maps_test',
        'AutoDock4_1pgp_too_many_ligand_types_test',
        'AutoDock4_1pgp_too_many_torsions',
        'AutoDock4_1pgp_just_right_number_torsions',
        'AutoDock4_1pgp_two_ligands_test',
        'AutoDock4_1pgp_two_mapsets_test',
        'AutoDock4_1pgp_unbound_set_illegal_test',
        'AutoDock4_1pgp_unbound_model_illegal_test', #1
	'AutoDock4_1pgp_ga_run_maxruns_test',
	'AutoDock4_1pgp_ga_run_maxruns_analysis_test',
        'AutoDock4_1pgp_ga_select_tournament_test',
        'AutoDock4_1pgp_ga_select_linear_ranking_test',
        #'AutoDock4_1pgp_rmsmode_heavy_atoms_only_test',
        'AutoDock4_1pgp_rmsmode_heavy_atoms_only_noH_test',
        'AutoDock4_1pgp_rmsmode_all_heavy_atom_pairs_only_test',
        'AutoDock4_1pgp_rmsmode_unique_heavy_atom_pairs_only_test',
        'AutoDock4_1pgp_simanneal_small', 
        'AutoDock4_1pgp_simanneal_small_geometric_schedule', 
        #next dpf sets tran0,quaternion0,dihe0 to random
        'AutoDock4_1pgp_ligrand_ga_only_test', 
        'AutoDock4_1pgp_ga_only_test',
	'AutoDock4_1pgp_output_pop_file_test',
        # tests using flexible residues 
        'AutoDock4_1pgp_flexres_test',
        ## tests which check for specific value
        'AutoDock4_1pgp_test',
        'AutoDock4_1pgp_smaller_test',
## next test not installed yet as I do not have a way I know of to pass
## different expected values to the superclass - M Pique  July 2012
	# 'AutoDock4_1pgp_intelec_off_test',
        'AutoDock4_1pgp_no_parameter_file_test',
	'AutoDock4_1pgp_gals_set_sw1_test',
	'AutoDock4_1pgp_gals_no_set_psw1_test',
	'AutoDock4_1pgp_gals_no_set_ga_test',
	'AutoDock4_1pgp_gals_use_defaults_test',
        #'AutoDock4_1pgp_ga_only_value_test',
        ## tests for unbound values 
        'AutoDock4_1pgp_unbound_default_test',
        'AutoDock4_1pgp_unbound_set0_test',
        'AutoDock4_1pgp_unbound_set10_test',
        # tests for unbound_model choices
        'AutoDock4_1pgp_unbound_model_compact',
        'AutoDock4_1pgp_unbound_model_bound',
        'AutoDock4_1pgp_unbound_model_extended',
        'AutoDock4_1pgp_unbound_compute_unbound_extended',
        'AutoDock4_1pgp_unbound_model_value',
        # tests for ga_only and energy
        'AutoDock4_1pgp_ligrand_ga_only_energy_test',
        'AutoDock4_1pgp_ga_only_energy_test',
        'AutoDock4_1pgp_ga_smooth0_energy_test',
        # tests for energy with flexible residues 
        'AutoDock4_1pgp_flexres_energy_test',
        'AutoDock4_1pgp_flexres_energy_1_4_50_test',
        'AutoDock4_1pgp_flexres_energy_1_4_100_test',
        # tests for energy with 1_4_interactions
        'AutoDock4_1pgp_1_4_50_test',
        'AutoDock4_1pgp_1_4_100_test',
        # tests for setting tran0 from about
        'AutoDock4_1pgp_about_only_test', 
        'AutoDock4_1pgp_multipleabouts_test', 
        # tests for setting 'about' automatically
        'AutoDock4_1pgp_about_auto_simanneal', 
        'AutoDock4_1pgp_about_auto_ga_only', 
        'AutoDock4_1pgp_about_auto_local_only', 
        'AutoDock4_1pgp_about_auto_gals', 
    ]
    unittest.main( argv=( [__name__ ,] + test_cases ) )
    #  The call "unittest.main()" automatically runs all the TestCase classes in
    #  alphabetical order; calling with argv=([]), lets us specify the order.
    #  NOTE: "unittest.main()" saves us having to remember to add new tests to the 
    #  list of test cases.
    #unittest.main()
    #  For verbose output, use this:
    #unittest.main( argv=( [__name__, '-v'] + test_cases ) )
autodock-test 4.2.5.1-3ubuntu1 / usr / share / autodock / Tests / test_autodock4.py
