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
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, PDBlines):
Molecule.__init__(self, PDBlines)
self.res_number = string.atoi(PDBlines[0][23:26])
self.key = '%s%s'%(self.res_number, self.chain_name)
