#-------------------------------------------------------------------------------
# creating a new system
system = Molecule()
system.name = '1GAB - LABIO dataset'
# - setup energy model
system.set_energy_model('amber')
# importing coordinates and amber parameters
system.load_PDB_to_system (filename = os.path.join(PEPDICE_EXAMPLES , 'LABIO_set/1GAB/1GAB_A_AMBER_minimized.pdb' ) )
system.import_AMBER_parameters (top = os.path.join(PEPDICE_EXAMPLES , 'LABIO_set/1GAB/1GAB_A_AMBER.top') ,
torsions = os.path.join(PEPDICE_PARAMETER, 'amber/AMBER_rotamers.dat') )
print system.compute_R_gy_Calpha()
#print system.compute_SS_energy(log = True)
#cmap = CMAP(pdb = os.path.join(PEPDICE_EXAMPLES , 'Itasser_set/IT1af7__/native_A_AMBER_minimized.pdb'), cutoff = 6.5, log = True)
#system.load_PDB_to_system (filename = os.path.join(PEPDICE_EXAMPLES , 'Itasser_set/IT1af7__/native_A_AMBER_minimized.pdb') )
#system.import_AMBER_parameters (top = os.path.join(PEPDICE_EXAMPLES , 'Itasser_set/IT1af7__/native_A_AMBER.top') ,
# torsions = os.path.join(PEPDICE_PARAMETER, 'amber/AMBER_rotamers.dat') )
#
system.import_SS_restraints_from_string ( ss = 'CCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCHHHHHHHHHHHHHHCC',
w_ss = '00000123345553221111000000001234432100012342335556110', log= True)
print system.compute_SS_energy(log = True)
#os.path.join( PEPDICE_EXAMPLES , 'LABIO_set/1I6C/decoy1_17_A_AMBER_minimized.pdb'),
#os.path.join( PEPDICE_EXAMPLES , 'LABIO_set/1I6C/decoy1_23_A_AMBER_minimized.pdb'),
#os.path.join( PEPDICE_EXAMPLES , 'LABIO_set/1I6C/decoy1_24_A_AMBER_minimized.pdb'),
#os.path.join( PEPDICE_EXAMPLES , 'LABIO_set/1I6C/decoy1_30_A_AMBER_minimized.pdb'),
#os.path.join( PEPDICE_EXAMPLES , 'LABIO_set/1I6C/decoy1_31_A_AMBER_minimized.pdb'),
#os.path.join( PEPDICE_EXAMPLES , 'LABIO_set/1I6C/decoy2_14_A_AMBER_minimized.pdb'),
#os.path.join( PEPDICE_EXAMPLES , 'LABIO_set/1I6C/decoy2_35_A_AMBER_minimized.pdb')
]
template = Molecule()
template.load_PDB_to_system (filename = os.path.join(PEPDICE_EXAMPLES , 'example02.1_fragments_template_min.pdb'))
template.import_AMBER_parameters (top = None, #os.path.join(PEPDICE_EXAMPLES , 'LABIO_set/1I6C/1I6C_A_AMBER.top') ,
torsions = os.path.join(PEPDICE_PARAMETER, 'amber/AMBER_rotamers.dat') )
print template.torsions
from Fragments import *
fragment = import_fragments_from_pdb (molecule = template, residues = range(0,len(system.residues)), mainchain =True, sidechain = True)
#extended
system.load_PDB_to_system (filename = os.path.join(PEPDICE_EXAMPLES , 'example02.1_fragments_extended_min.pdb'))
insert_fragment_from_dic (molecule = system, fragment = fragment, sidechain = True)
save_PDB_to_file(system, os.path.join(PEPDICE_EXAMPLES , 'example02.1_fragments_after_insertion_EXT.pdb'))
#template
system.load_PDB_to_system (filename = os.path.join(PEPDICE_EXAMPLES , 'example02.1_fragments_after_insertion_EXT.pdb'))
logfile = open('logfile.txt', 'w')
logfile.writelines(text)
logfile.write('\n')
print text
for folder in folders:
path = os.path.join(cwd, folder)
os.chdir(os.path.join(cwd, folder))
#/home/fernando/programs/pepdice/Examples/LABIO_set/1I6C/1I6C_A_AMBER.top
RMSD_list = import_rmsd_from_file ( filein = 'list.txt')
system = Molecule()
system.set_energy_model('FULL')
system.import_AMBER_parameters (top = folder+'_A_AMBER.top' ,
torsions = os.path.join(PEPDICE_PARAMETER, 'amber/AMBER_rotamers.dat') )
for pdb in RMSD_list:
if pdb == 'NAME':
pass
else:
filename = pdb.replace('.', '_A_AMBER_minimized.')
system.load_PDB_to_system (filename = filename)
#print pdb , filename
