def __init__(self, PDBlines, parent, atoms): Molecule.__init__(self, PDBlines) self.parent = parent self.atoms = atoms for atom in atoms: atom.parent = self line = PDBlines[0] self.res_type1 = string.strip(line[17:20]) self.res_number = string.atoi(line[23:26]) self.is_Nterm = 0 self.is_Cterm = 0 self.has_central_pt = 0 self.atoms_dict = {} for atom in self.atoms: self.atoms_dict[atom.atom_type] = atom if atom.atom_type[:2] == 'C3': self.central_pt = Point(atom.x, atom.y, atom.z) self.central_atom = atom self.x = atom.x self.y = atom.y self.z = atom.z self.has_central_pt = 1 self.is_Nterm = 0 self.is_Cterm = 0 self.vtk_arg_list = {} trace_args = {'color': [0.1, 0.1, 1.0], 'opacity': 1.0} self.vtk_arg_list['trace'] = trace_args self.visible = 0 self.transparent = 0
def __init__(self, PDBlines, parent, atoms): Molecule.__init__(self, PDBlines) self.parent = parent self.atoms = atoms for atom in atoms: atom.parent = self line = PDBlines[0] self.res_type1 = string.strip(line[17:20]) self.res_number = string.atoi(line[23:26]) self.is_Nterm = 0 self.is_Cterm = 0 self.has_central_pt = 0 self.atoms_dict = {} for atom in self.atoms: self.atoms_dict[atom.atom_type] = atom if atom.atom_type[:2] == 'C3': self.central_pt = Point(atom.x, atom.y, atom.z) self.central_atom = atom self.x=atom.x self.y=atom.y self.z=atom.z self.has_central_pt = 1 self.is_Nterm = 0 self.is_Cterm = 0 self.vtk_arg_list = {} trace_args = {'color':[0.1,0.1,1.0], 'opacity':1.0} self.vtk_arg_list['trace'] = trace_args self.visible = 0 self.transparent = 0
def __init__(self, PDBlines, parent): Molecule.__init__(self, PDBlines) self.parent = parent for atom in self.atoms: atom.parent = self self.res_number = string.atoi(PDBlines[0][23:26]) self.key = '%s%s' % (self.res_number, self.chain_name)
def __init__(self, PDBlines, parent): Molecule.__init__(self, PDBlines) self.parent = parent for atom in self.atoms: atom.parent = self self.res_number = string.atoi(PDBlines[0][23:26]) self.key = '%s%s'%(self.res_number, self.chain_name)
def __init__(self, parent, PDBlines, atoms): Molecule.__init__(self, PDBlines) self.atoms = atoms for atom in self.atoms: atom.parent = self self.parent = parent # load amino acid properties types = {'ALA':'A', 'CYS':'C','CYD':'C','CYX':'C','CYZ':'C', 'ASP':'D','GLU':'E','PHE':'F','GLY':'G', 'HIS':'H','HID':'H','HIE':'H', 'ILE':'I','LYS':'K','LEU':'L', 'MET':'M','ASN':'N','PRO':'P','GLN':'Q','ARG':'R', 'SER':'S','THR':'T','VAL':'V','TRP':'W','TYR':'Y'} self.res_type1 = types[self.res_type] line = PDBlines[0] self.res_number = string.atoi(line[23:26]) # store alpha carbon coordinates self.has_central_pt = 0 self.atoms_dict = {} for atom in self.atoms: self.atoms_dict[atom.atom_type] = atom if atom.atom_type == 'CA': self.central_pt = Point(atom.x, atom.y, atom.z) self.central_atom = atom self.x=atom.x self.y=atom.y self.z=atom.z self.has_central_pt = 1 try: self.atoms_dict['CA'] except KeyError: print "Warning: %s%d has no apparent alpha carbon"%(self.res_type, self.res_number) types = {'ALA':71.09,'CYS':103.15,'CYD':103.15,'CYX':103.15,'CYZ':103.15, 'ASP':115.09,'GLU':129.12,'PHE':147.18, 'GLY':57.05,'HIS':137.14,'HID':137.14,'HIE':137.14,'ILE':113.16,'LYS':128.17,'LEU':113.16, 'MET':131.19,'ASN':114.11,'PRO':97.12,'GLN':128.14,'ARG':156.19, 'SER':87.08,'THR':101.11,'VAL':99.14,'TRP':186.21,'TYR':163.18} self.mw = types[self.res_type] # these get fixed later on in initialization by class Protein self.is_Nterm = 0 self.is_Cterm = 0 # create the vtk_args_list # [onoff, width, color, splines, sides, specular, specularpower] self.vtk_arg_list = {} # this gets overridden because residue doesnt need everything in Molecule trace_args = {'color':[0.1,0.1,1.0], 'opacity':1.0} self.vtk_arg_list['trace'] = trace_args self.visible = 0 self.transparent = 0
def __init__(self, PDBlines, parent): Molecule.__init__(self, PDBlines) self.parent = parent self.residues = [] self.residue_dict = {} self.selected = 1 self.key = self.chain_name self.default_chain_color = self.get_chain_color_word() trace_args = {'visualize':1, 'currently_on':0, 'representation':'tube', 'width':0.4, 'splines':6, 'sides':5, 'specular':0.1, 'specular_power':10} self.vtk_arg_list['trace'] = trace_args
def __init__(self, PDBlines, parent): Molecule.__init__(self, PDBlines) self.parent = parent self.residues = [] self.residue_dict = {} self.selected = 1 self.key = self.chain_name self.default_chain_color = self.get_chain_color_word() trace_args = { 'visualize': 1, 'currently_on': 0, 'representation': 'tube', 'width': 0.4, 'splines': 6, 'sides': 5, 'specular': 0.1, 'specular_power': 10 } self.vtk_arg_list['trace'] = trace_args
def __init__(self, PDBlines): Molecule.__init__(self, PDBlines) self.res_number = string.atoi(PDBlines[0][23:26]) self.key = '%s%s'%(self.res_number, self.chain_name)
def deselect(self): Molecule.deselect(self) self.selected = 0 for rez in self.residues: rez.deselect()
def select(self): Molecule.select(self) self.selected = 1 for rez in self.residues: rez.select()
def __init__(self, parent, PDBlines, atoms): Molecule.__init__(self, PDBlines) self.atoms = atoms for atom in self.atoms: atom.parent = self self.parent = parent # load amino acid properties types = { 'ALA': 'A', 'CYS': 'C', 'CYD': 'C', 'CYX': 'C', 'CYZ': 'C', 'ASP': 'D', 'GLU': 'E', 'PHE': 'F', 'GLY': 'G', 'HIS': 'H', 'HID': 'H', 'HIE': 'H', 'ILE': 'I', 'LYS': 'K', 'LEU': 'L', 'MET': 'M', 'ASN': 'N', 'PRO': 'P', 'GLN': 'Q', 'ARG': 'R', 'SER': 'S', 'THR': 'T', 'VAL': 'V', 'TRP': 'W', 'TYR': 'Y' } self.res_type1 = types[self.res_type] line = PDBlines[0] self.res_number = string.atoi(line[23:26]) # store alpha carbon coordinates self.has_central_pt = 0 self.atoms_dict = {} for atom in self.atoms: self.atoms_dict[atom.atom_type] = atom if atom.atom_type == 'CA': self.central_pt = Point(atom.x, atom.y, atom.z) self.central_atom = atom self.x = atom.x self.y = atom.y self.z = atom.z self.has_central_pt = 1 try: self.atoms_dict['CA'] except KeyError: print "Warning: %s%d has no apparent alpha carbon" % ( self.res_type, self.res_number) types = { 'ALA': 71.09, 'CYS': 103.15, 'CYD': 103.15, 'CYX': 103.15, 'CYZ': 103.15, 'ASP': 115.09, 'GLU': 129.12, 'PHE': 147.18, 'GLY': 57.05, 'HIS': 137.14, 'HID': 137.14, 'HIE': 137.14, 'ILE': 113.16, 'LYS': 128.17, 'LEU': 113.16, 'MET': 131.19, 'ASN': 114.11, 'PRO': 97.12, 'GLN': 128.14, 'ARG': 156.19, 'SER': 87.08, 'THR': 101.11, 'VAL': 99.14, 'TRP': 186.21, 'TYR': 163.18 } self.mw = types[self.res_type] # these get fixed later on in initialization by class Protein self.is_Nterm = 0 self.is_Cterm = 0 # create the vtk_args_list # [onoff, width, color, splines, sides, specular, specularpower] self.vtk_arg_list = { } # this gets overridden because residue doesnt need everything in Molecule trace_args = {'color': [0.1, 0.1, 1.0], 'opacity': 1.0} self.vtk_arg_list['trace'] = trace_args self.visible = 0 self.transparent = 0