def __init__(self, params):
self.params = params
print("\n> Input DATA:")
print(">> protein receptor: %s" % params.receptor)
print(">> ligand: %s" % params.ligand)
#import protein structures - get receptor and ligand
print(">> importing PDB files...")
self.M1 = bb.Molecule()
self.M2 = bb.Molecule()
self.M1.import_pdb(params.receptor)
self.M2.import_pdb(params.ligand)
print(">> importing density files...")
self.E2 = bb.Density()
self.E2._import_dx(params.ligand_map)
self.E1 = bb.Density()
self.E1._import_dx(params.receptor_map)
# Build the jabber maps so we save computation time (essentially just the chosen isosurface from dx)
self.J1 = jd.Jabber(params.receptor_map, params.iso_cutoff)
self.J2 = jd.Jabber(params.ligand_map, params.iso_cutoff)
# The structures are already in the correct positions as that was part of the parsing process
trans_M1 = deepcopy(self.M1.get_center())
trans_M2 = deepcopy(self.M2.get_center())
self.E1.write_dx('./models/initial_%s' % (params.receptor_map))
self.E2.write_dx('./models/initial_%s' % (params.ligand_map))
self.M1.write_pdb('./models/initial_%s' % (params.receptor))
self.M2.write_pdb('./models/initial_%s' % (params.ligand))
self.J1.write_jabber('./models/initial_receptormap.pdb')
self.J2.write_jabber('./models/initial_ligandmap.pdb')
def __init__(self, params):
self.params = params
print("\n> Input DATA:")
print(">> protein receptor: %s" % params.receptor)
print(">> ligand: %s" % params.ligand)
#import protein structures - get receptor and ligand
print(">> importing PDB files...")
self.M1 = bb.Molecule()
self.M2 = bb.Molecule()
self.M1.import_pdb(params.receptor)
self.M2.import_pdb(params.ligand)
print(">> importing density files...")
self.E2 = bb.Density()
self.E2._import_dx(params.ligand_map)
self.E1 = bb.Density()
self.E1._import_dx(params.receptor_map)
# Build the jabber maps so we save computation time (essentially just the chosen isosurface from dx)
self.J1 = jd.Jabber(params.receptor_map, params.iso_cutoff)
self.J2 = jd.Jabber(params.ligand_map, params.iso_cutoff)
# move the structures to the geometric center (so they're overlapping)
trans_M1 = deepcopy(self.M1.get_center())
trans_M2 = deepcopy(self.M2.get_center())
self.M1.translate(-trans_M1[0], -trans_M1[1], -trans_M1[2])
self.M2.translate(-trans_M2[0], -trans_M2[1], -trans_M2[2])
jd.geometry.translate_map(self.E1, -trans_M1[0], -trans_M1[1],
-trans_M1[2])
jd.geometry.translate_map(self.E2, -trans_M2[0], -trans_M2[1],
-trans_M2[2])
self.J1.translate(-trans_M1)
self.J2.translate(-trans_M2)
self.E1.write_dx('./models/initial_%s' % (params.receptor_map))
self.E2.write_dx('./models/initial_%s' % (params.ligand_map))
self.M1.write_pdb('./models/initial_%s' % (params.receptor))
self.M2.write_pdb('./models/initial_%s' % (params.ligand))
self.J1.write_jabber('./models/initial_receptormap.pdb')
self.J2.write_jabber('./models/initial_ligandmap.pdb')
def match_residue(name1, name2):
"""
Match residues of two pdbs, similar to bb.match_residue, but better with biopython
"""
# Import structures
R1 = bb.Molecule()
R2 = bb.Molecule()
R1.import_pdb(name1)
R2.import_pdb(name2)
# Assign atomtypes just in case
R1.assign_atomtype()
R2.assign_atomtype()
# we need to align to the pdb with more residues (otherwise we might get funky matching answers)
# check the length of each first
R1_CA = R1.atomselect("*", "*", "CA", get_index=True)[1]
R2_CA = R2.atomselect("*", "*", "CA", get_index=True)[1]
if len(R1_CA) > len(R2_CA):
# get alignment
ali = get_alignment(R1, R2)
R1_seq, lines, R2_seq = ali.split('\n')[:3]
else:
ali = get_alignment(R2, R1)
R2_seq, lines, R1_seq = ali.split('\n')[:3]
# now only get resid matches which works for both
matches = np.asarray(["|" in a for a in lines])
matches1 = condense_sequence(R1_seq, matches)
matches2 = condense_sequence(R2_seq, matches)
# need to match where there is a line and a letter in each
return matches1, matches2
logger = logging.getLogger("dipole")
fh = logging.FileHandler(logname)
ch = logging.StreamHandler()
logger.addHandler(fh)
logger.addHandler(ch)
if not args["v"]:
logger.setLevel(logging.DEBUG)
else:
logger.setLevel(logging.INFO)
logger.info("> Loading in files...")
R = jd.Dipole()
L = jd.Dipole()
L_pdb = bb.Molecule()
R.import_dipole(receptor_tcl)
L.import_dipole(ligand_tcl)
L_pdb.import_pdb(ligand_pdb)
data = np.loadtxt(data_file)
COM = L_pdb.get_center()
S = []
no_samples = np.shape(data)[0]
logger.info("> Assessing the dipole alignment...")
for i in range(no_samples):
else:
logger.setLevel(logging.INFO)
logger.info(cmd_output)
# Run error checks if time is too short / long
if time_start >= time_end:
raise Exception('ERROR: time_end must be at least 1 frame more than time_start')
if time_end != -1:
time_end += 1 # shift by 1 to account for python counting
# Begin building grid map
logger.info("> Building the voxel map...")
M = bb.Molecule()
M.import_pdb(pdb)
window_size = vox * width # resolution, in angstroms
crds = M.coordinates[time_start:time_end, :]
if ac == 1:
M_pqr = M.pdb2pqr(ff=ff)
else:
M_pqr = M.pdb2pqr(ff=ff, amber_convert=False)
M.assign_atomtype()
mass = M.get_mass_by_atom()
# Find the max / min boundaries of our box and add buffer regions to use desired resolutions and get a complete picture
maxmin = []
def __init__(self, params):
self.params = params
print("\n> Input DATA:")
print(">> protein receptor: %s" % params.receptor)
print(">> ligand: %s" % params.ligand)
#import protein structures - get receptor and ligand
print(">> importing PDB files...")
self.M1 = bb.Molecule()
self.M2 = bb.Molecule()
self.M1.import_pdb(params.receptor)
self.M2.import_pdb(params.ligand)
print(">> importing density files...")
self.E2 = bb.Density()
self.E2._import_dx(params.ligand_map)
self.E1 = bb.Density()
self.E1._import_dx(params.receptor_map)
# Import dipole maps to get initial positions (if necessary)
if params.receptor_dip != 'None':
if not os.path.isfile(params.receptor_dip):
raise Exception("ERROR: receptor tcl file %s not found!" %
params.receptor_dip)
sys.exit(0)
if not os.path.isfile(params.ligand_dip):
raise Exception("ERROR: ligand tcl file %s not found!" %
params.ligand_dip)
sys.exit(0)
self.D1 = jd.Dipole()
self.D1.import_dipole(params.receptor_dip)
self.D2 = jd.Dipole()
self.D2.import_dipole(params.ligand_dip)
dip = True
else:
dip = False
# Build the jabber maps so we save computation time (essentially just the chosen isosurface from dx)
self.J1 = jd.Jabber(params.receptor_map, params.iso_cutoff)
self.J2 = jd.Jabber(params.ligand_map, params.iso_cutoff)
# move the structures to the geometric center (so they're overlapping)
trans_M1 = deepcopy(self.M1.get_center())
trans_M2 = deepcopy(self.M2.get_center())
self.M1.translate(-trans_M1[0], -trans_M1[1], -trans_M1[2])
self.M2.translate(-trans_M2[0], -trans_M2[1], -trans_M2[2])
jd.geometry.translate_map(self.E1, -trans_M1[0], -trans_M1[1],
-trans_M1[2])
jd.geometry.translate_map(self.E2, -trans_M2[0], -trans_M2[1],
-trans_M2[2])
self.J1.translate(-trans_M1)
self.J2.translate(-trans_M2)
if dip:
self.D1.translate_dipole(-trans_M1)
self.D2.translate_dipole(-trans_M2)
self.D1.write_dipole('./models/initial_%s' % (params.receptor_dip))
self.D2.write_dipole('./models/initial_%s' % (params.ligand_dip))
self.E1.write_dx('./models/initial_%s' % (params.receptor_map))
self.E2.write_dx('./models/initial_%s' % (params.ligand_map))
self.M1.write_pdb('./models/initial_%s' % (params.receptor))
self.M2.write_pdb('./models/initial_%s' % (params.ligand))
self.J1.write_jabber('./models/initial_receptormap.pdb')
self.J2.write_jabber('./models/initial_ligandmap.pdb')