def fill_LJ(self):
"""
Fills the LJ_radius, LJ_depth arrays and LJ_types dictionary with data
from LENNARD_JONES_ACOEF and LENNARD_JONES_BCOEF sections of the prmtop
files, by undoing the canonical combining rules.
"""
AmberParm.fill_LJ(self)
acoef = self.parm_data['LENNARD_JONES_14_ACOEF']
bcoef = self.parm_data['LENNARD_JONES_14_BCOEF']
ntypes = self.pointers['NTYPES']
self.LJ_14_radius = [] # empty LJ_radii so it can be re-filled
self.LJ_14_depth = [] # empty LJ_depths so it can be re-filled
one_sixth = 1.0 / 6.0 # we need to raise some numbers to the 1/6th power
for i in range(ntypes):
lj_index = self.parm_data["NONBONDED_PARM_INDEX"][ntypes * i +
i] - 1
if acoef[lj_index] < 1.0e-6:
self.LJ_14_radius.append(0)
self.LJ_14_depth.append(0)
else:
factor = 2 * acoef[lj_index] / bcoef[lj_index]
self.LJ_14_radius.append(pow(factor, one_sixth) * 0.5)
self.LJ_14_depth.append(bcoef[lj_index] / 2 / factor)
def fill_LJ(self):
"""
Fills the LJ_radius, LJ_depth arrays and LJ_types dictionary with data
from LENNARD_JONES_ACOEF and LENNARD_JONES_BCOEF sections of the prmtop
files, by undoing the canonical combining rules.
"""
AmberParm.fill_LJ(self)
acoef = self.parm_data['LENNARD_JONES_14_ACOEF']
bcoef = self.parm_data['LENNARD_JONES_14_BCOEF']
ntypes = self.pointers['NTYPES']
self.LJ_14_radius = [] # empty LJ_radii so it can be re-filled
self.LJ_14_depth = [] # empty LJ_depths so it can be re-filled
one_sixth = 1.0 / 6.0 # we need to raise some numbers to the 1/6th power
for i in range(ntypes):
lj_index = self.parm_data["NONBONDED_PARM_INDEX"][ntypes*i+i] - 1
if acoef[lj_index] < 1.0e-6:
self.LJ_14_radius.append(0)
self.LJ_14_depth.append(0)
else:
factor = 2 * acoef[lj_index] / bcoef[lj_index]
self.LJ_14_radius.append(pow(factor, one_sixth) * 0.5)
self.LJ_14_depth.append(bcoef[lj_index] / 2 / factor)
def initialize_topology(self, xyz=None, box=None):
"""
Initializes topology data structures, like the list of atoms, bonds,
etc., after the topology file has been read. The following methods are
called:
"""
self.LJ_14_radius = []
self.LJ_14_depth = []
AmberParm.initialize_topology(self, xyz, box)
def initialize_topology(self, xyz=None, box=None):
"""
Initializes topology data structures, like the list of atoms, bonds,
etc., after the topology file has been read. The following methods are
called:
"""
self.LJ_14_radius = []
self.LJ_14_depth = []
AmberParm.initialize_topology(self, xyz, box)
def load_pointers(self):
"""
Loads the data in POINTERS section into a pointers dictionary with each
key being the pointer name according to http://ambermd.org/formats.html
"""
AmberParm.load_pointers(self)
# Other pointers
nub, nubtypes = self.parm_data['CHARMM_UREY_BRADLEY_COUNT'][:2]
self.pointers['NUB'] = nub
self.pointers['NUBTYPES'] = nubtypes
self.pointers['NIMPHI'] = self.parm_data['CHARMM_NUM_IMPROPERS'][0]
self.pointers['NIMPRTYPES'] = self.parm_data['CHARMM_NUM_IMPR_TYPES'][0]
# If CMAP is not present, don't load the pointers
if self.has_cmap:
self.pointers['CMAP'] = self.parm_data['CHARMM_CMAP_COUNT'][0]
self.pointers['CMAP_TYPES'] = self.parm_data['CHARMM_CMAP_COUNT'][1]
def recalculate_LJ(self):
"""
Takes the values of the LJ_radius and LJ_depth arrays and recalculates
the LENNARD_JONES_A/BCOEF topology sections from the canonical
combining rules.
"""
AmberParm.recalculate_LJ(self)
ntypes = self.pointers['NTYPES']
acoef = self.parm_data['LENNARD_JONES_14_ACOEF']
bcoef = self.parm_data['LENNARD_JONES_14_BCOEF']
for i in range(ntypes):
for j in range(i, ntypes):
index = self.parm_data['NONBONDED_PARM_INDEX'][ntypes*i+j] - 1
rij = self.LJ_14_radius[i] + self.LJ_14_radius[j]
wdij = sqrt(self.LJ_14_depth[i] * self.LJ_14_depth[j])
acoef[index] = wdij * rij ** 12
bcoef[index] = 2 * wdij * rij**6
def recalculate_LJ(self):
"""
Takes the values of the LJ_radius and LJ_depth arrays and recalculates
the LENNARD_JONES_A/BCOEF topology sections from the canonical
combining rules.
"""
AmberParm.recalculate_LJ(self)
ntypes = self.pointers['NTYPES']
acoef = self.parm_data['LENNARD_JONES_14_ACOEF']
bcoef = self.parm_data['LENNARD_JONES_14_BCOEF']
for i in range(ntypes):
for j in range(i, ntypes):
index = self.parm_data['NONBONDED_PARM_INDEX'][ntypes * i +
j] - 1
rij = self.LJ_14_radius[i] + self.LJ_14_radius[j]
wdij = sqrt(self.LJ_14_depth[i] * self.LJ_14_depth[j])
acoef[index] = wdij * rij**12
bcoef[index] = 2 * wdij * rij**6
def load_pointers(self):
"""
Loads the data in POINTERS section into a pointers dictionary with each
key being the pointer name according to http://ambermd.org/formats.html
"""
AmberParm.load_pointers(self)
# Other pointers
nub, nubtypes = self.parm_data['CHARMM_UREY_BRADLEY_COUNT'][:2]
self.pointers['NUB'] = nub
self.pointers['NUBTYPES'] = nubtypes
self.pointers['NIMPHI'] = self.parm_data['CHARMM_NUM_IMPROPERS'][0]
self.pointers['NIMPRTYPES'] = self.parm_data['CHARMM_NUM_IMPR_TYPES'][
0]
# If CMAP is not present, don't load the pointers
if self.has_cmap:
self.pointers['CMAP'] = self.parm_data['CHARMM_CMAP_COUNT'][0]
self.pointers['CMAP_TYPES'] = self.parm_data['CHARMM_CMAP_COUNT'][
1]