def __init__(self,ballfn,stickfn):
self.orientdict = {} # stick orientation dict
self.typedict = {} # stick type dict
balldat = IO.read_balls(ballfn)
stickdat = IO.read_sticks(stickfn)
ball1s = stickdat['BALL1']
ball2s = stickdat['BALL2']
types = stickdat['TYPE']
# loop over sticks
for i in range(len(stickdat)):
# make sure 1st endball id always less than or eq to 2nd endball id
id1 = min(ball1s[i], ball2s[i])
id2 = max(ball1s[i], ball2s[i])
self.typedict[(id1,id2)] = types[i]
coord1 = balldat[id1].coords # ball1 coord
coord2 = balldat[id2].coords # ball2 coord
stick = coord1 - coord2 # stick vector
so = stick / np.linalg.norm(stick) # stick orientation
so = so.reshape((1,3))
# calculate sblock
# sblock(ijpair)=| ll lm ln |
# | lm mm mn |
# | ln mn nn |
self.orientdict[id1, id2] = np.dot(so.T,so)
def __init__(self, extballfn, extstickfn, forcevec, kassigner): self.ballfn = extballfn self.stickfn = extstickfn self.f = forcevec self.kassigner = kassigner self.balldat = IO.read_balls(extballfn) self.ballnum = len(self.balldat['COORDX']) self.stickdat = IO.read_sticks(extstickfn) self.sticknum = len(self.stickdat['BALL1']) self.k_mat = self.__get_k_matrix()
def __init__(self, ballfn='', stickfn='', dispdifffn='', forcevec = None, ktypeassinger=None): self.ballfn = ballfn self.stickfn = stickfn self.dispdifffn = dispdifffn self.f = forcevec self.ktypeassinger = ktypeassinger self.ba_mat = None if ballfn != '': self.balldat = IO.read_balls(self.ballfn) self.ballnum = len(self.balldat['COORDX']) self.ba_mat = self.__get_ba_matrix()
def ForceGen(ballfn, division, forceprofile):
balldat = IO.read_balls(ballfn)
freenum = sum(1 for facing in balldat["FACING"] if facing != "SP")
force = np.zeros((3 * freenum, 1))
for i in range(freenum):
secid = -1
for j in range(len(division)):
if i in division[j]:
secid = j
break
if secid != -1:
force[3 * i] = balldat[i].coords[0] * forceprofile[secid]
force[3 * i + 1] = balldat[i].coords[1] * forceprofile[secid]
return force
def __init__(self, ballfn, mempos):
""" Divide ball data into different sections according to their z coordinate.
Based on Wimley's Division. c.f. Jackups' paper
"""
self.dict = {0:[], 1:[], 2:[]}
self.sections = []
balldat = IO.read_balls(ballfn)
extra_z, peri_z, offset_z = mempos
coreupper_z = 6.5-offset_z
corelower_z = -6.5-offset_z
self.sections = [[extra_z, coreupper_z],[coreupper_z, corelower_z],[corelower_z, peri_z]]
for i in range(len(balldat)):
if balldat[i].facing == 'SP':
continue
if peri_z <= balldat[i].coords[2] and balldat[i].coords[2] < corelower_z:
self.dict[2].append(i)
elif corelower_z <= balldat[i].coords[2] and balldat[i].coords[2] < coreupper_z:
self.dict[1].append(i)
elif coreupper_z <= balldat[i].coords[2] and balldat[i].coords[2] <= extra_z:
self.dict[0].append(i)
def opm_mempos(opmpdbfn, geofn, ballfn):
""" get membrane position from opmdb pdb file
"""
geodat = IO.read_geo(geofn)
# an anchor residue used to find out the offset. it has no meaning
base_res_id = geodat['startingSNs'][0]
opmchain = IO.guess_chain(opmpdbfn, geodat)
for res in opmchain:
if res.get_id()[1] == base_res_id:
opm_base_z = res['CA'].get_coord()[2]
break
my_base_z = IO.read_balls(ballfn)[0].coords[2]
# offset from my ball coords to opm pdb coords
my_z_offset = opm_base_z - my_base_z
opm_half_thickness = abs( Bio.PDB.PDBParser().get_structure('MyStruct',opmpdbfn)[0] # structure and model
.get_list()[-1].get_list()[0] # last chain and first residue
.get_list()[0].get_coord()[2] ) # first atom and z coord
# my extracellular membrane position
my_extra_z = opm_half_thickness - my_z_offset
# my periplasm membrane position
my_peri_z = -opm_half_thickness - my_z_offset
return my_extra_z, my_peri_z, my_z_offset