def import_contact_map_from_pdb (self ,
pdb = None ,
cutoff = 6.0 ,
log = False):
""" Gera o mapa de contato a patir de um PDB (estrutura de referencia) """
system = Molecule()
system.load_PDB_to_system (filename = pdb )
cmap = 0*np.random.rand(len(system.residues),len(system.residues))
self.number_of_contacts = 0
for index_i in range(0, len(system.residues)):
for index_j in range(index_i+2, len(system.residues)):
name_i = system.residues[index_i].name
for atom in system.residues[index_i].atoms:
if atom.name == 'CA':
atom_i = atom
name_j = system.residues[index_j].name
for atom in system.residues[index_j].atoms:
if atom.name == 'CA':
atom_j = atom
R_ab = distance_ab (atom_i, atom_j)
if R_ab <= cutoff:
cmap[index_i][index_j] = 1
self.number_of_contacts += 1
if log:
print index_i, name_i, index_j, name_j, R_ab, 'contact'
else:
pass
if log:
print '\ncmap matrix:'
print cmap
print '\n---------------------------------------------'
print 'total number of residues = ', len(system.residues)
print 'Cutoff size = ', cutoff
print 'number of contacts = ', self.number_of_contacts
print '---------------------------------------------\n'
self.cmap = cmap
self.cutoff = cutoff
minimize(molecule = system,
imin = 1 ,
maxcyc= 1000 ,
ncyc = 100 ,
cut = 10 ,
rgbmax= 999 ,
igb = 1 ,
ntb = 0 ,
ntpr = 100 ,
ntr = 0 )
#restraintmask = ':1-50 & @CA,N,C,O=',
#restraint_wt = 50.0 )
save_PDB_to_file(system, os.path.join(PEPDICE_EXAMPLES , 'example02.1_fragments_extended_min.pdb'))
system.load_PDB_to_system (filename = os.path.join( PEPDICE_EXAMPLES , 'LABIO_set/'+PDB+'/'+PDB+'_A_AMBER_minimized.pdb' ))
minimize(molecule = system,
imin = 1 ,
maxcyc= 1000 ,
ncyc = 100 ,
cut = 10 ,
rgbmax= 999 ,
igb = 1 ,
ntb = 0 ,
ntpr = 100 ,
ntr = 0 )
#restraintmask = ':1-50 & @CA,N,C,O=',
#restraint_wt = 50.0 )
save_PDB_to_file(system, os.path.join(PEPDICE_EXAMPLES , 'example02.1_fragments_template_min.pdb'))
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') )
#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') )
#
PDB = pdb
sequence = get_sequence_from_segFile(seqFile = os.path.join(PEPDICE_EXAMPLES , '') )
TRAJECTORY = PDB+'trajectory'
# 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')
system.load_PDB_to_system (filename = os.path.join(PEPDICE_EXAMPLES , 'new_method_example02.1_fragments_extended_min.pdb'))
'''
minimize(molecule = system,
imin = 1 ,
maxcyc= 1000 ,
ncyc = 100 ,
cut = 10 ,
rgbmax= 999 ,
igb = 1 ,
ntb = 0 ,
ntpr = 100 ,
ntr = 0 )
#restraintmask = ':1-50 & @CA,N,C,O=',
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
#pprint(RMSD_list)
try:
cutoff = 6.0
contacts = []
#saltcon = 0.00
#EGBs = []
#
#for i in range(0, 6):
logtext.append(code + ' wget_pdb......Ok\n')
except Exception as error:
print 'failed wget pdb'
print error
logtext.append(code + ' wget_pdb......failed\n')
try:
# ------------------------------------------------------------------
build_AMBER_system_from_PDB(
pdbin=code+'_A.pdb',
basename=code+'_A_AMBER',
force_field='ff03ua.labio',
overwrite=True
)
system = Molecule()
system.load_PDB_to_system(filename=code + '_A_AMBER.pdb')
system.import_AMBER_parameters(
top=code + '_A_AMBER.top',
torsions=os.path.join(
PEPDICE_PARAMETER, 'amber/AMBER_rotamers.dat'),
)
save_PDB_to_file(system, code+'_A.pdb')
logtext.append(code + ' tleap......Ok\n')
except:
print 'failed wget pdb'
logtext.append(code + ' tleap......failed\n')
try:
minimize(
molecule=system,