def __find_nearest_nodes(self, num, signal, mahar=True):
#if mahar: return self.__find_nearest_nodes_by_mahar(num, signal)
n = self.nodes.shape[0]
indexes = [0.0] * num
sq_dists = [0.0] * num
D = util.calc_distance(self.nodes, np.asarray([signal] * n))
for i in range(num):
indexes[i] = np.nanargmin(D)
sq_dists[i] = D[indexes[i]]
D[indexes[i]] = float('nan')
return indexes, sq_dists
def monster_act(monster, level, game):
if monster.get(InFOV).in_fov:
player = level.player
monster_pos = monster.get(Position)
player_pos = player.get(Position)
distance = calc_distance(monster_pos.x, monster_pos.y, player_pos.x, player_pos.y)
if distance < 2:
return AttackAction(player)
else:
dx = int(round((player_pos.x - monster_pos.x) / distance))
dy = int(round((player_pos.y - monster_pos.y) / distance))
return MoveAction(dx, dy)
return WaitAction()
def calculate_similarity_thresholds(self, node_indexes):
sim_thresholds = []
for i in node_indexes:
pals = self.adjacent_mat[i, :]
if len(pals) == 0:
idx, sq_dists = self.__find_nearest_nodes(2, self.nodes[i, :])
sim_thresholds.append(sq_dists[1])
else:
pal_indexes = []
for k in pals.keys():
pal_indexes.append(k[1])
sq_dists = util.calc_distance(self.nodes[pal_indexes], np.asarray([self.nodes[i]] * len(pal_indexes)))
sim_thresholds.append(np.max(sq_dists))
return sim_thresholds
def monster_act(monster, level, game):
if monster.get(InFOV).in_fov:
player = level.player
monster_pos = monster.get(Position)
player_pos = player.get(Position)
distance = calc_distance(monster_pos.x, monster_pos.y, player_pos.x,
player_pos.y)
if distance < 2:
return AttackAction(player)
else:
dx = int(round((player_pos.x - monster_pos.x) / distance))
dy = int(round((player_pos.y - monster_pos.y) / distance))
return MoveAction(dx, dy)
return WaitAction()
def get_activesite( self, cutoff ):
# overall activesite dictionary
# key: unique protein name (resname_reschain_resnum), value: list of ATOM lines per residue
self.activesite_dict = {}
# unique ligand name (resname_reschain_resnum)
#value: list of 3-letter amino acid names
self.activesite_lig_pro_res_dict = {}
# unique ligand name (resname_reschain_resnum)
#value: list of atom_line for each AA ( to get atom count later )
self.activesite_lig_pro_atoms_dict = {}
# activesite data holders
self.num_activesite_res = 0
self.activesite_residues = []
self.num_activesite_atms = 0
self.num_activesite_nonpolar_atoms = 0
self.num_activesite_polar_atoms = 0
self.num_activesite_unk_atom_types = 0
self.activesite_num_nonpolar_atoms = {}
self.activesite_num_polar_atoms = {}
self.activesite_num_unk_atoms = {}
for uniq_lig_name in self.ligand.keys():
# list to store the 3 letter names of all of the protein residues within the cutoff distance of each ligand residue (by unique name)
AS_names_in_activesite = []
AS_atms_in_activesite = []
for hetatm_line in self.ligand[ uniq_lig_name ]:
# extract coordinates
x_lig = hetatm_line.x_coord
y_lig = hetatm_line.y_coord
z_lig = hetatm_line.z_coord
lig_xyz = [ x_lig, y_lig, z_lig ]
# for each unique protein residue
for uniq_pro_name in self.protein.keys():
# for each atom in the residue
for atom_line in self.protein[ uniq_pro_name ]:
# extract coordinates
x_pro = atom_line.x_coord
y_pro = atom_line.y_coord
z_pro = atom_line.z_coord
pro_xyz = [ x_pro, y_pro, z_pro ]
# check the distance
if calc_distance( lig_xyz, pro_xyz ) <= cutoff:
# append the line if the unique protein residue has already been counted
if uniq_pro_name in self.activesite_residues:
if atom_line not in self.activesite_dict[ uniq_pro_name ]:
self.activesite_dict[ uniq_pro_name ].append( atom_line )
# store all of the unique names of the protein residues within the activesite
# also, store all of the atom_lines for each unique protein residue in the activesite
else:
self.activesite_residues.append( uniq_pro_name )
self.activesite_dict[ uniq_pro_name ] = []
self.activesite_dict[ uniq_pro_name ].append( atom_line )
# store the 3 letter name of the amino acid within the activesite
three_letter_name = uniq_pro_name[0:3]
AS_names_in_activesite.append( three_letter_name )
# store atom_line for each unique amino acid within the activesite to get an atom count later
if atom_line not in AS_atms_in_activesite:
AS_atms_in_activesite.append( atom_line )
# store the list of the 3 letter names for the amino acid within the self.activesite_lig_pro_dict according to which ligand it is near
self.activesite_lig_pro_res_dict[ uniq_lig_name ] = AS_names_in_activesite
self.activesite_lig_pro_atoms_dict[ uniq_lig_name ] = AS_atms_in_activesite
# get number of activesite residues
self.num_activesite_res = len( self.activesite_dict.keys() )
# count the number of activesite atoms
for uniq_lig_name in self.activesite_lig_pro_atoms_dict.keys():
self.num_activesite_atms += len( self.activesite_lig_pro_atoms_dict[ uniq_lig_name ] )
# prepare the counter for nonpolar, polar, and unknown atom types for each unique activesite residue
self.activesite_num_nonpolar_atoms[ uniq_lig_name ] = 0
self.activesite_num_polar_atoms[ uniq_lig_name ] = 0
self.activesite_num_unk_atoms[ uniq_lig_name ] = 0
# count the number of nonpolar and polar atoms
for pdb_line in self.activesite_lig_pro_atoms_dict[ uniq_lig_name ]:
# if element is nonpolar
if pdb_line.element in nonpolar_atoms:
# total nonpolar activesite atoms
self.num_activesite_nonpolar_atoms += 1
# number of nonpolar atoms for this activesite residue
self.activesite_num_nonpolar_atoms[ uniq_lig_name ] += 1
# if element is polar
elif pdb_line.element in polar_atoms:
# total polar activesite atoms
self.num_activesite_polar_atoms += 1
# number of polar atoms for this activesite residue
self.activesite_num_polar_atoms[ uniq_lig_name ] += 1
# else I don't know what this is
else:
print " * I didn't know what type of atom", "'%s'" %pdb_line.element(), "is. Please add it to the list"
# total unkown activesite atoms
self.num_activesite_unk_atom_types += 1
# number of unknown atoms for this activesite residue
self.activesite_num_unk_atoms[ uniq_lig_name ] += 1
# return information
# if this ligand has no activesite for some reason
if len( self.activesite_dict.keys() ) == 0:
print "## Skipping", self.name, "because it had no activesite residues within", cutoff, "Angstroms of the ligand residue(s) ##"
return False
# otherwise print relevant information
else:
print " ", self.name, "has", self.num_activesite_res, "activesite residues",
print "and", self.num_activesite_atms, "non-hydrogen activesite atoms"
return True
def count_contacts( self, cutoff ):
# must have already found all residues within the activesite
# counted as ligand to protein!!
self.polar_polar = 0
self.polar_nonpolar = 0
self.nonpolar_polar = 0
self.nonpolar_nonpolar = 0
self.unk_contact = 0
# ligxyz_proxyz xyz coordinates unique for every atom, best way to collect unique contacts made
self.uniq_contact_list = []
for uniq_lig_name in self.ligand.keys():
# add pdb name and ligand name to list
self.CC_per_lig_pdb_names.append( self.name )
self.CC_per_lig_lig_names.append( uniq_lig_name )
self.CC_per_lig_lig_atms.append( len( self.ligand[ uniq_lig_name ] ) )
self.CC_per_lig_activesite_atms.append( len( self.activesite_lig_pro_atoms_dict[ uniq_lig_name ] ) )
# make empty counters - used for counting contacts per ligand
lig_polar_polar = 0
lig_polar_nonpolar = 0
lig_nonpolar_polar = 0
lig_nonpolar_nonpolar = 0
lig_unk_contact = 0
# for every ligand residue
for lig_pdb_line in self.ligand[ uniq_lig_name ]:
# get ligand atom xyz
x_lig = lig_pdb_line.x_coord
y_lig = lig_pdb_line.y_coord
z_lig = lig_pdb_line.z_coord
lig_xyz = [ x_lig, y_lig, z_lig ]
lig_xyz_str = str( x_lig ) + '_' + str( y_lig ) + '_' + str( z_lig )
for pro_pdb_line in self.activesite_lig_pro_atoms_dict[ uniq_lig_name ]:
# get protein atom xyz
x_pro = pro_pdb_line.x_coord
y_pro = pro_pdb_line.y_coord
z_pro = pro_pdb_line.z_coord
pro_xyz = [ x_pro, y_pro, z_pro ]
pro_xyz_str = str( x_pro ) + '_' + str( y_pro ) + '_' + str( z_pro )
# check atomic distance
contact_distance = calc_distance( lig_xyz, pro_xyz )
if contact_distance < cutoff:
# check to see that this contact has not yet been counted
uniq_contact = lig_xyz_str + '.' + pro_xyz_str
if uniq_contact not in self.uniq_contact_list:
# append unique contact to list
self.uniq_contact_list.append( uniq_contact )
# check contact type
if lig_pdb_line.element in polar_atoms or lig_pdb_line.element in metal_atoms:
# polar polar
if pro_pdb_line.element in polar_atoms or pro_pdb_line.element in metal_atoms:
lig_polar_polar += 1
# polar nonpolar
elif pro_pdb_line.element in nonpolar_atoms:
lig_polar_nonpolar += 1
# unknown
else:
lig_unk_contact += 1
elif lig_pdb_line.element in nonpolar_atoms:
# nonpolar polar
if pro_pdb_line.element in polar_atoms or pro_pdb_line.element in metal_atoms:
lig_nonpolar_polar += 1
# nonpolar nonpolar
elif pro_pdb_line.element in nonpolar_atoms:
lig_nonpolar_nonpolar += 1
# unknown
else:
lig_unk_contact += 1
# both unknown
else:
lig_unk_contact += 1
# append this info to the per ligand data frame lists
self.CC_per_lig_pp_contacts.append( lig_polar_polar )
self.CC_per_lig_pn_contacts.append( lig_polar_nonpolar )
self.CC_per_lig_np_contacts.append( lig_nonpolar_polar )
self.CC_per_lig_nn_contacts.append( lig_nonpolar_nonpolar )
self.CC_per_lig_unk_contacts.append( lig_unk_contact )
# add the counts for this particular ligand to the total count
self.polar_polar += lig_polar_polar
self.polar_nonpolar += lig_polar_nonpolar
self.nonpolar_polar += lig_nonpolar_polar
self.nonpolar_nonpolar += lig_nonpolar_nonpolar
self.unk_contact += lig_unk_contact
# store all data in global list
# because if it got here, all of the data existed
self.CC_pdb_names.append( self.name )
self.CC_lig_atms.append( self.num_lig_atoms )
self.CC_activesite_atms.append( self.num_activesite_atms )
self.CC_pp_contacts.append( self.polar_polar )
self.CC_pn_contacts.append( self.polar_nonpolar )
self.CC_np_contacts.append( self.nonpolar_polar )
self.CC_nn_contacts.append( self.nonpolar_nonpolar )
self.CC_unk_contacts.append( self.unk_contact )
return True
def goto(self, next_city):
here = self.city_map.here
self.meter += calc_distance(here["X"], here["Y"], next_city["X"],
next_city["Y"])
self.city_map.here = next_city