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############################################################################
#
# Authors: Ruth Huey, William Lindstrom
#
# Copyright: A. Olson TSRI 2006
#
#############################################################################
#
# $Id: trilinterp_scorer.py,v 1.7.10.1 2016/02/12 08:01:40 annao Exp $
#
import numpy
from PyAutoDock.scorer import ScoringStrategy
from PyAutoDock.MolecularSystem import MolecularSystem
class TrilinterpScorer(ScoringStrategy):
def __init__(self, stem, atomtypes, ms=None, value_outside_grid=1000000.,
atoms_to_ignore=[], readMaps=True):
"""
based on AD4 scoring function:
stem and atomtypes list specify filenames for maps
value_outside_grid is energy penalty for pts outside box
atoms_to_ignore are assigned 0.0 energy: specifically
added to avoid huge energies from atoms bonded to flexible residues
"""
ScoringStrategy.__init__(self, None)
self.stem = stem
self.atomtypes = atomtypes
self.map_data = {}
#eg: stem = 'hsg1', atomtypes= ['C','A','HD','N','S']
if readMaps:
self.read_maps(stem, atomtypes)
if ms is not None:
self.set_molecular_system(ms)
# add the required attributes of this subclass to the dict
self.required_attr_dictA = {}
self.required_attr_dictA.setdefault('coords', False)
self.required_attr_dictA.setdefault('charge', False)
self.required_attr_dictA.setdefault('autodock_element', False)
self.required_attr_dictB = {}
self.value_outside_grid = value_outside_grid
self.atoms_to_ignore = atoms_to_ignore
## def set_map(self, map_type, grid_obj):
## """
## eg map_type=HD, grid_obj, instance of Pmv.Grid class
## """
## self.grid_obj = grid_obj
## cen = grid_obj.CENTER
## spacing = grid_obj.SPACING
## npts = grid_obj.NELEMENTS
## self.inv_spacing = 1.0/spacing
## #setup the lowvalues for each dimension
## #assume even number of pts?
## x_extent = spacing * (npts[0]-1)
## self.map_data[map_type] = grid_obj.array
## self.x_low = cen[0] - x_extent/2.
## self.x_high = cen[0] + x_extent/2.
## y_extent = spacing * (npts[1]-1)
## self.y_low = cen[1] - y_extent/2.
## self.y_high = cen[1] + y_extent/2.
## z_extent = spacing * (npts[2]-1)
## self.z_low = cen[2] - z_extent/2.
## self.z_high = cen[2] + z_extent/2.
## if not hasattr(grid_obj,'scorers'):
## grid_obj.scorers = []
## grid_obj.scorers.append(self)
## print "x_low,y_low,z_low=", self.x_low, self.y_low, self.z_low
## print "x_high,y_high,z_high=", self.x_high, self.y_high, self.z_high
def add_maps(self,stem,atomtypes):
"""
read a map for each specified atom type
stem: string
atomtypes: [] i.e ['C','HD']
"""
for t in atomtypes:
filename = "%s.%s.map" %(stem, t)
self.read_map(filename)
return True
def read_maps(self, stem, atomtypes):
"""
read one map for each specified atom type plus
desolvation and electrostatics maps...
"""
self.add_maps(stem, atomtypes)
#next read the desolvation map
dsolvmapname = "%s.d.map" %(stem)
self.read_map(dsolvmapname)
#finally read the electrostatics map
elecmapname = "%s.e.map" %(stem)
self.read_map(elecmapname)
def read_map(self, filename):
mapfileptr = open(filename)
maplines = mapfileptr.readlines()
gpf = maplines[0].split()[1]
grid_data_file = maplines[1].split()[1]
macromolecule = maplines[2].split()[1]
spacing = self.spacing = float(maplines[3].split()[1])
npts = self.npts = map(int, maplines[4].split()[1:])
for i in range(3):
if npts[i]%2==0: npts[i]+=1
cen = self.cen = map(float, maplines[5].split()[1:])
keys = ['gpf','grid_data_file','macromolecule','spacing','npts','cen']
values= [gpf,grid_data_file,macromolecule,spacing,npts,cen]
#make sure all maps have the same info
for k, new_val in zip(keys, values):
old_val = getattr(self, k, new_val)
assert old_val== new_val
self.inv_spacing = 1.0/self.spacing
#setup the lowvalues for each dimension
#assume even number of pts?
x_extent = spacing * (npts[0]-1)
self.x_low = cen[0] - x_extent/2.
self.x_high = cen[0] + x_extent/2.
y_extent = spacing * (npts[1]-1)
self.y_low = cen[1] - y_extent/2.
self.y_high = cen[1] + y_extent/2.
z_extent = spacing * (npts[2]-1)
self.z_low = cen[2] - z_extent/2.
self.z_high = cen[2] + z_extent/2.
##print "x_low,y_low,z_low=", self.x_low, self.y_low, self.z_low
#parse the data
data = []
for line in maplines[6:]:
data.append(float(line[:-1]))
#keep data for this map
map_type = filename.split('.')[1]
data_array = numpy.array(data)
data_array.shape = (npts[0], npts[1], npts[2])
self.map_data[map_type] = data_array
def set_molecular_system(self, ms):
"""
ms, a MolecularSystem, manages which of its entity_sets is 'receptor'
and which 'ligand' via its configuration tuple and
maintains the corresponding pairwise distance matrix.
'set_molecular_system' checks that the currently designated entity_sets have
attributes required by this scorer class (required_attr_dicts
manage only checking a required attr once per entity_sets.)
@@FIX THIS: if change ms configuration, reset required_attr_dicts
"""
# check the required attribute for both subsets before going on
listA = []
for k,v in self.required_attr_dictA.items():
if not v:
listA.append(k)
self.required_attr_dictA[k] = True
ms.check_required_attributes( ms.configuration[0], listA)
# now set the molecular system
self.ms = ms
for at in self.atoms_to_ignore:
at.ignore = 1
# check that all the atom type in the ligan have a corresponding map loaded
# get uniq atoms type in ligand
atom_type = {}
ligand = ms.get_entities(ms.configuration[0])
for x in ligand:
atom_type[x.autodock_element] =''
for type in atom_type.keys():
if type not in self.map_data.keys():
# try to load map from previously define stem
status = self.add_maps(self.stem,[type])
if not status:raise RuntimeError("grid map missing for atomtype %s"%type)
def get_score_array(self):
array = []
for at_a in self.ms.get_entities(self.ms.configuration[0]):
if hasattr(at_a, 'ignore'):
atom_score = 0
else:
atom_score = self._f(at_a)
array.append(atom_score)
self.array = numpy.array(array)
return self.array
def get_score(self):
if self.ms is None:
raise RuntimeError("no molecular system available in scorer")
array = self.get_score_array()
return numpy.add.reduce(array)
def is_out_grid_info(self, x, y,z):
if x<self.x_low or x>self.x_high or y<self.y_low or y>self.y_high or z<self.z_low or z>self.z_high :
return True
def _f_1map(self, at1):
# simple f using only 1 map for scoring
# for example, one built from sum of coordinates
x, y, z = at1.coords
if (self.is_out_grid_info(x,y,z)):
return self.value_outside_grid
inv_spacing = self.inv_spacing
##print "inv_spacing=", inv_spacing
#sample pt [0,0,0], x_low=y_low=z_low=-20, spacing=.25
u = (x - self.x_low)*inv_spacing # 0- -20*4 = 80
u0 = int(u) #80
u1 = u0 + 1 #81
p0u = u - float(u0) #-1
p1u = 1.0 - p0u #0.9
##print "u=",u, " u0=", u0, " u1=", u1, " p0u=", p0u, ' p1u=', p1u
v = (y - self.y_low)*inv_spacing
v0 = int(v)
v1 = v0 + 1
p0v = v - float(v0)
p1v = 1.0 - p0v
##print "v=",v, " v0=", v0, " v1=", v1, " p0v=", p0v, ' p1v=', p1v
w = (z - self.z_low)*inv_spacing
w0 = int(w)
w1 = w0 + 1
p0w = w - float(w0)
p1w = 1.0 - p0w
##print "w=",w, " w0=", w0, " w1=", w1, " p0w=", p0w, ' p1w=', p1w
e = m = d = 0.0
at_data = self.map_data[at1.autodock_element]
m += p1u * p1v * p1w * at_data[w0][v0][u0]
m += p0u * p1v * p1w * at_data[ w0 ][ v0 ][ u1 ]
m += p1u * p0v * p1w * at_data[ w0 ][ v1 ][ u0 ]
m += p0u * p0v * p1w * at_data[ w0 ][ v1 ][ u1 ]
m += p1u * p1v * p0w * at_data[ w1 ][ v0 ][ u0 ]
m += p0u * p1v * p0w * at_data[ w1 ][ v0 ][ u1 ]
m += p1u * p0v * p0w * at_data[ w1 ][ v1 ][ u0 ]
m += p0u * p0v * p0w * at_data[ w1 ][ v1 ][ u1 ]
return m
#def _f(self, at1, at2): scorers which inherit from pairwise need two atom input
def _f(self, at1):
#find index into list of data for this atoms coords
x, y, z = at1.coords
if (self.is_out_grid_info(x,y,z)):
return self.value_outside_grid
inv_spacing = self.inv_spacing
u = (x - self.x_low)*inv_spacing
u0 = int(u)
u1 = u0 + 1
p0u = u - float(u0)
p1u = 1.0 - p0u
#print "u=",u, " u0=", u0, " u1=", u1, " p0u=", p0u, ' p1u=', p1u
v = (y - self.y_low)*inv_spacing
v0 = int(v)
v1 = v0 + 1
p0v = v - float(v0)
p1v = 1.0 - p0v
#print "v=",v, " v0=", v0, " v1=", v1, " p0v=", p0v, ' p1v=', p1v
w = (z - self.z_low)*inv_spacing
w0 = int(w)
w1 = w0 + 1
p0w = w - float(w0)
p1w = 1.0 - p0w
#print "w=",w, " w0=", w0, " w1=", w1, " p0w=", p0w, ' p1w=', p1w
#add code to deal with pts outside grid and on edges
e = m = d = 0.0
#look up this atom in the appropriate map
at_data = self.map_data[at1.autodock_element]
#desolvation energy map
d_data = self.map_data['d']
#electrostatics energy map
e_data = self.map_data['e']
#e += p1u * p1v * p1w * map[ w0 ][ v0 ][ u0 ][ElecMap];
e += p1u * p1v * p1w * e_data[w0][v0][u0]
#m += p1u * p1v * p1w * map[ w0 ][ v0 ][ u0 ][AtomType];
##debug only##m += p1u * p1v * p1w * at_data[w0][v0][u0]
m += p1u * p1v * p1w * at_data[w0][v0][u0]
#d += p1u * p1v * p1w * map[ w0 ][ v0 ][ u0 ][DesolvMap];
d += p1u * p1v * p1w * d_data[w0][v0][ u0 ]
#d += p0u * p1v * p1w * map[ w0 ][ v0 ][ u1 ][DesolvMap];
d += p0u * p1v * p1w * d_data[ w0 ][ v0 ][ u1 ]
#m += p0u * p1v * p1w * map[ w0 ][ v0 ][ u1 ][AtomType];
##debug only##m += p0u * p1v * p1w * at_data[ w0 ][ v0 ][ u1 ]
m += p0u * p1v * p1w * at_data[ w0 ][ v0 ][ u1 ]
#e += p0u * p1v * p1w * map[ w0 ][ v0 ][ u1 ][ElecMap];
e += p0u * p1v * p1w * e_data[ w0 ][ v0 ][ u1 ]
#e += p1u * p0v * p1w * map[ w0 ][ v1 ][ u0 ][ElecMap];
e += p1u * p0v * p1w * e_data[ w0 ][ v1 ][ u0 ]
#m += p1u * p0v * p1w * map[ w0 ][ v1 ][ u0 ][AtomType];
##debug only##m += p1u * p0v * p1w * at_data[ w0 ][ v1 ][ u0 ]
m += p1u * p0v * p1w * at_data[ w0 ][ v1 ][ u0 ]
#d += p1u * p0v * p1w * map[ w0 ][ v1 ][ u0 ][DesolvMap];
d += p1u * p0v * p1w * d_data[ w0 ][ v1 ][ u0 ]
#d += p0u * p0v * p1w * map[ w0 ][ v1 ][ u1 ][DesolvMap];
d += p0u * p0v * p1w * d_data[ w0 ][ v1 ][ u1 ]
#m += p0u * p0v * p1w * map[ w0 ][ v1 ][ u1 ][AtomType];
##debug only##m += p0u * p0v * p1w * at_data[ w0 ][ v1 ][ u1 ]
m += p0u * p0v * p1w * at_data[ w0 ][ v1 ][ u1 ]
#e += p0u * p0v * p1w * map[ w0 ][ v1 ][ u1 ][ElecMap];
e += p0u * p0v * p1w * e_data[ w0 ][ v1 ][ u1 ]
#e += p1u * p1v * p0w * map[ w1 ][ v0 ][ u0 ][ElecMap];
e += p1u * p1v * p0w * e_data[ w1 ][ v0 ][ u0 ]
#m += p1u * p1v * p0w * map[ w1 ][ v0 ][ u0 ][AtomType];
##debug only##m += p1u * p1v * p0w * at_data[ w1 ][ v0 ][ u0 ]
m += p1u * p1v * p0w * at_data[ w1 ][ v0 ][ u0 ]
#d += p1u * p1v * p0w * map[ w1 ][ v0 ][ u0 ][DesolvMap];
d += p1u * p1v * p0w * d_data[ w1 ][ v0 ][ u0 ]
#d += p0u * p1v * p0w * map[ w1 ][ v0 ][ u1 ][DesolvMap];
d += p0u * p1v * p0w * d_data[ w1 ][ v0 ][ u1 ]
#m += p0u * p1v * p0w * map[ w1 ][ v0 ][ u1 ][AtomType];
##debug only##m += p0u * p1v * p0w * at_data[ w1 ][ v0 ][ u1 ]
m += p0u * p1v * p0w * at_data[ w1 ][ v0 ][ u1 ]
#e += p0u * p1v * p0w * map[ w1 ][ v0 ][ u1 ][ElecMap];
e += p0u * p1v * p0w * e_data[ w1 ][ v0 ][ u1 ]
#e += p1u * p0v * p0w * map[ w1 ][ v1 ][ u0 ][ElecMap];
e += p1u * p0v * p0w * e_data[ w1 ][ v1 ][ u0 ]
#m += p1u * p0v * p0w * map[ w1 ][ v1 ][ u0 ][AtomType];
##debug only## m += p1u * p0v * p0w * at_data[ w1 ][ v1 ][ u0 ]
m += p1u * p0v * p0w * at_data[ w1 ][ v1 ][ u0 ]
#d += p1u * p0v * p0w * map[ w1 ][ v1 ][ u0 ][DesolvMap];
d += p1u * p0v * p0w * d_data[ w1 ][ v1 ][ u0 ]
#d += p0u * p0v * p0w * map[ w1 ][ v1 ][ u1 ][DesolvMap];
d += p0u * p0v * p0w * d_data[ w1 ][ v1 ][ u1 ]
#m += p0u * p0v * p0w * map[ w1 ][ v1 ][ u1 ][AtomType];
##debug only##m += p0u * p0v * p0w * at_data[ w1 ][ v1 ][ u1 ]
m += p0u * p0v * p0w * at_data[ w1 ][ v1 ][ u1 ]
#e += p0u * p0v * p0w * map[ w1 ][ v1 ][ u1 ][ElecMap];
e += p0u * p0v * p0w * e_data[ w1 ][ v1 ][ u1 ]
charge = at1.charge
return e*charge + m + d*abs(charge)
class TrilinterpScorer_AD3(TrilinterpScorer):
def __init__(self, stem, atomtypes, ms=None, value_outside_grid=1000000.,
atoms_to_ignore=[]):
"""
stem and atomtypes list specify filenames for maps
"""
TrilinterpScorer.__init__(self, stem, atomtypes, ms, value_outside_grid,
atoms_to_ignore)
def read_maps(self, stem, atomtypes):
for t in atomtypes:
filename = "%s.%s.map" %(stem, t)
self.read_map(filename)
#dsolvmapname = "%s.d.map" %(stem)
#self.read_map(dsolvmapname)
elecmapname = "%s.e.map" %(stem)
self.read_map(elecmapname)
def _f_1map(self, at1):
# simple f using only 1 map for scoring
# for example, one built from sum of coordinates
x, y, z = at1.coords
if (self.is_out_grid_info(x,y,z)):
return self.value_outside_grid
inv_spacing = self.inv_spacing
##print "inv_spacing=", inv_spacing
#sample pt [0,0,0], x_low=y_low=z_low=-20, spacing=.25
u = (x - self.x_low)*inv_spacing # 0- -20*4 = 80
u0 = int(u) #80
u1 = u0 + 1 #81
p0u = u - float(u0) #-1
p1u = 1.0 - p0u #0.9
##print "u=",u, " u0=", u0, " u1=", u1, " p0u=", p0u, ' p1u=', p1u
v = (y - self.y_low)*inv_spacing
v0 = int(v)
v1 = v0 + 1
p0v = v - float(v0)
p1v = 1.0 - p0v
##print "v=",v, " v0=", v0, " v1=", v1, " p0v=", p0v, ' p1v=', p1v
w = (z - self.z_low)*inv_spacing
w0 = int(w)
w1 = w0 + 1
p0w = w - float(w0)
p1w = 1.0 - p0w
##print "w=",w, " w0=", w0, " w1=", w1, " p0w=", p0w, ' p1w=', p1w
e = m = d = 0.0
at_data = self.map_data[at1.autodock_element]
m += p1u * p1v * p1w * at_data[w0][v0][u0]
m += p0u * p1v * p1w * at_data[ w0 ][ v0 ][ u1 ]
m += p1u * p0v * p1w * at_data[ w0 ][ v1 ][ u0 ]
m += p0u * p0v * p1w * at_data[ w0 ][ v1 ][ u1 ]
m += p1u * p1v * p0w * at_data[ w1 ][ v0 ][ u0 ]
m += p0u * p1v * p0w * at_data[ w1 ][ v0 ][ u1 ]
m += p1u * p0v * p0w * at_data[ w1 ][ v1 ][ u0 ]
m += p0u * p0v * p0w * at_data[ w1 ][ v1 ][ u1 ]
return m
def _f(self, at1):
#find index into list of data for this atoms coords
x, y, z = at1.coords
if (self.is_out_grid_info(x,y,z)):
return self.value_outside_grid
inv_spacing = self.inv_spacing
u = (x - self.x_low)*inv_spacing
u0 = int(u)
u1 = u0 + 1
p0u = u - float(u0)
p1u = 1.0 - p0u
#print "u=",u, " u0=", u0, " u1=", u1, " p0u=", p0u, ' p1u=', p1u
v = (y - self.y_low)*inv_spacing
v0 = int(v)
v1 = v0 + 1
p0v = v - float(v0)
p1v = 1.0 - p0v
#print "v=",v, " v0=", v0, " v1=", v1, " p0v=", p0v, ' p1v=', p1v
w = (z - self.z_low)*inv_spacing
w0 = int(w)
w1 = w0 + 1
p0w = w - float(w0)
p1w = 1.0 - p0w
#print "w=",w, " w0=", w0, " w1=", w1, " p0w=", p0w, ' p1w=', p1w
#add code to deal with pts outside grid and on edges
e = m = 0.0
#e = m = d = 0.0
#look up this atom in the appropriate map
at_data = self.map_data[at1.autodock_element]
##desolvation energy map
#d_data = self.map_data['d']
#electrostatics energy map
e_data = self.map_data['e']
#e += p1u * p1v * p1w * map[ w0 ][ v0 ][ u0 ][ElecMap];
e += p1u * p1v * p1w * e_data[w0][v0][u0]
#m += p1u * p1v * p1w * map[ w0 ][ v0 ][ u0 ][AtomType];
##debug only##m += p1u * p1v * p1w * at_data[w0][v0][u0]
m += p1u * p1v * p1w * at_data[w0][v0][u0]
##d += p1u * p1v * p1w * map[ w0 ][ v0 ][ u0 ][DesolvMap];
#d += p1u * p1v * p1w * d_data[w0][v0][ u0 ]
##d += p0u * p1v * p1w * map[ w0 ][ v0 ][ u1 ][DesolvMap];
#d += p0u * p1v * p1w * d_data[ w0 ][ v0 ][ u1 ]
#m += p0u * p1v * p1w * map[ w0 ][ v0 ][ u1 ][AtomType];
##debug only##m += p0u * p1v * p1w * at_data[ w0 ][ v0 ][ u1 ]
m += p0u * p1v * p1w * at_data[ w0 ][ v0 ][ u1 ]
#e += p0u * p1v * p1w * map[ w0 ][ v0 ][ u1 ][ElecMap];
e += p0u * p1v * p1w * e_data[ w0 ][ v0 ][ u1 ]
#e += p1u * p0v * p1w * map[ w0 ][ v1 ][ u0 ][ElecMap];
e += p1u * p0v * p1w * e_data[ w0 ][ v1 ][ u0 ]
#m += p1u * p0v * p1w * map[ w0 ][ v1 ][ u0 ][AtomType];
##debug only##m += p1u * p0v * p1w * at_data[ w0 ][ v1 ][ u0 ]
m += p1u * p0v * p1w * at_data[ w0 ][ v1 ][ u0 ]
##d += p1u * p0v * p1w * map[ w0 ][ v1 ][ u0 ][DesolvMap];
#d += p1u * p0v * p1w * d_data[ w0 ][ v1 ][ u0 ]
##d += p0u * p0v * p1w * map[ w0 ][ v1 ][ u1 ][DesolvMap];
#d += p0u * p0v * p1w * d_data[ w0 ][ v1 ][ u1 ]
#m += p0u * p0v * p1w * map[ w0 ][ v1 ][ u1 ][AtomType];
##debug only##m += p0u * p0v * p1w * at_data[ w0 ][ v1 ][ u1 ]
m += p0u * p0v * p1w * at_data[ w0 ][ v1 ][ u1 ]
#e += p0u * p0v * p1w * map[ w0 ][ v1 ][ u1 ][ElecMap];
e += p0u * p0v * p1w * e_data[ w0 ][ v1 ][ u1 ]
#e += p1u * p1v * p0w * map[ w1 ][ v0 ][ u0 ][ElecMap];
e += p1u * p1v * p0w * e_data[ w1 ][ v0 ][ u0 ]
#m += p1u * p1v * p0w * map[ w1 ][ v0 ][ u0 ][AtomType];
##debug only##m += p1u * p1v * p0w * at_data[ w1 ][ v0 ][ u0 ]
m += p1u * p1v * p0w * at_data[ w1 ][ v0 ][ u0 ]
##d += p1u * p1v * p0w * map[ w1 ][ v0 ][ u0 ][DesolvMap];
#d += p1u * p1v * p0w * d_data[ w1 ][ v0 ][ u0 ]
##d += p0u * p1v * p0w * map[ w1 ][ v0 ][ u1 ][DesolvMap];
#d += p0u * p1v * p0w * d_data[ w1 ][ v0 ][ u1 ]
#m += p0u * p1v * p0w * map[ w1 ][ v0 ][ u1 ][AtomType];
##debug only##m += p0u * p1v * p0w * at_data[ w1 ][ v0 ][ u1 ]
m += p0u * p1v * p0w * at_data[ w1 ][ v0 ][ u1 ]
#e += p0u * p1v * p0w * map[ w1 ][ v0 ][ u1 ][ElecMap];
e += p0u * p1v * p0w * e_data[ w1 ][ v0 ][ u1 ]
#e += p1u * p0v * p0w * map[ w1 ][ v1 ][ u0 ][ElecMap];
e += p1u * p0v * p0w * e_data[ w1 ][ v1 ][ u0 ]
#m += p1u * p0v * p0w * map[ w1 ][ v1 ][ u0 ][AtomType];
##debug only## m += p1u * p0v * p0w * at_data[ w1 ][ v1 ][ u0 ]
m += p1u * p0v * p0w * at_data[ w1 ][ v1 ][ u0 ]
##d += p1u * p0v * p0w * map[ w1 ][ v1 ][ u0 ][DesolvMap];
#d += p1u * p0v * p0w * d_data[ w1 ][ v1 ][ u0 ]
##d += p0u * p0v * p0w * map[ w1 ][ v1 ][ u1 ][DesolvMap];
#d += p0u * p0v * p0w * d_data[ w1 ][ v1 ][ u1 ]
#m += p0u * p0v * p0w * map[ w1 ][ v1 ][ u1 ][AtomType];
##debug only##m += p0u * p0v * p0w * at_data[ w1 ][ v1 ][ u1 ]
m += p0u * p0v * p0w * at_data[ w1 ][ v1 ][ u1 ]
#e += p0u * p0v * p0w * map[ w1 ][ v1 ][ u1 ][ElecMap];
e += p0u * p0v * p0w * e_data[ w1 ][ v1 ][ u1 ]
charge = at1.charge
#return e*charge + m + d*abs(charge)
return e*charge + m
if __name__ == '__main__':
print 'in main'
tls = TrilinterpScorer('test', ['C'])
from MolKit import Read
m = Read("test.pdb")[0]
#crds= [4.083,6.527,-3.152], [2.737,6.793,-3.728], [1.900,5.679,-4.323]
ms = MolecularSystem()
ms.add_entities(m.allAtoms)
tls.set_molecular_system(ms)
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