#----------------------------------------------------#
import random
random.seed(1234)
#-------------------------------------------------------------------------------
PEPDICE = os.environ.get('PEPDICE')
PEPDICE_EXAMPLES = os.path.join(PEPDICE, 'Examples')
PEPDICE_PARAMETER= os.path.join(PEPDICE, 'Parameters')
#-------------------------------------------------------------------------------
#/home/farminf/Programas/PepDice/Examples/outputs/1gab_amber_example04_extended.pdb
system = Molecule()
name = 'poliALa_1GAB_from_sequence_CMAP_SSrest_restraints'
TRAJECTORY = name+'_traj'
system.name = name
system.build_peptide_from_sequence (
sequence = 'TIDQWLLKNAKEDAIAELKKAGITSDFYFNAINKAKTVEEVNALKNEILKAHA',
_type = 'amber' ,
force_field = 'ff03ua.labio',
overwrite = True ,
)
system.set_energy_model('RAW')
#AAAAAAAA
system.import_SS_restraints_from_string ( ss = 'CCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCHHHHHHHHHHHHHHCC',
w_ss = '00023456788888654320000000034565400000023456789654000', log= True)
print system.compute_SS_energy(log = True)
system.energy_components['SS_RESTRAINT'] [1]= 1.0
system.energy_components['SIZE' ][1]= 0.0
# building a contact map - required for Contact model calculations
#-------------------------------------------------------------------------------
#from CMAP import CMAP
#cmap = CMAP(pdb = os.path.join(PEPDICE_EXAMPLES , 'LABIO_set/1I6C/1I6C_A_AMBER_minimized.pdb'), cutoff = 6.5, log = True)
#-------------------------------------------------------------------------------
PDB = '1GAB'
sequence = 'TIDQWLLKNAKEDAIAELKKAGITSDFYFNAINKAKTVEEVNALKNEILKAHA'
# creating a new system
system = Molecule()
system.name = PDB+'-from_sequence'
system.build_peptide_from_sequence (
sequence = sequence,
_type = 'amber' ,
force_field = 'ff03ua.labio',
overwrite = True ,
)
system.set_energy_model('RAW')
minimize(molecule = system,
imin = 1 ,
maxcyc= 1000 ,
ncyc = 100 ,
cut = 10 ,
rgbmax= 999 ,
# building a contact map - required for Contact model calculations
#-------------------------------------------------------------------------------
from CMAP import CMAP
cmap = CMAP(pdb = os.path.join(PEPDICE_EXAMPLES , 'LABIO_set/1GAB/1GAB_A_AMBER_minimized.pdb'), cutoff = 6.5, log = True)
#-------------------------------------------------------------------------------
# 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') )
# building a contact map - required for Contact model calculations
#-------------------------------------------------------------------------------
from CMAP import CMAP
cmap = CMAP(pdb = os.path.join(PEPDICE_EXAMPLES , 'LABIO_set/1I6C/1I6C_A_AMBER_minimized.pdb'), cutoff = 6.5, log = True)
#-------------------------------------------------------------------------------
# creating a new system
system = Molecule()
system.name = '1I6C - 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/1I6C/1I6C_A_AMBER_minimized.pdb' ) )
system.import_AMBER_parameters (top = os.path.join(PEPDICE_EXAMPLES , 'LABIO_set/1I6C/1I6C_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') )
#----------------------------------------------------#
from SideChainRefine import optimize_side_chain
#----------------------------------------------------#
import random
random.seed(1234)
#-------------------------------------------------------------------------------
PEPDICE = os.environ.get('PEPDICE')
PEPDICE_EXAMPLES = os.path.join(PEPDICE, 'Examples')
PEPDICE_PARAMETER= os.path.join(PEPDICE, 'Parameters')
#-------------------------------------------------------------------------------
#/home/farminf/Programas/PepDice/Examples/outputs/1gab_amber_example04_extended.pdb
system = Molecule()
system.name = '1gab_from_sequence'
system.build_peptide_from_sequence (
sequence = 'TIDQWLLKNAKEDAIAELKKAGITSDFYFNAINKAKTVEEVNALKNEILKAHA',
_type = 'amber' ,
force_field = 'ff03ua.labio',
overwrite = True ,
)
system.set_energy_model('RAW')
system.import_SS_restraints_from_string ( ss = 'CCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCHHHHHHHHHHHHHHCC',
w_ss = '00000123345553221111000000001234432100012342335556110', log= True)
print system.compute_SS_energy(log = True)
system.energy_components['SS_RESTRAINT'][1] = 0.01
system.Status()
