def calculate(self, atoms, properties, system_changes):
Calculator.calculate(self, atoms, properties, system_changes)
if system_changes:
if 'energy' in self.results:
del self.results['energy']
if 'forces' in self.results:
del self.results['forces']
if 'energy' not in self.results:
if self.permutation is None:
crd = np.reshape(atoms.get_positions(), (1, len(atoms), 3))
else:
crd = np.reshape(atoms.get_positions()
[self.permutation[0, :]], (1, len(atoms), 3))
sander.set_positions(crd)
e, f = sander.energy_forces()
self.results['energy'] = e.tot * units.kcal / units.mol
if self.permutation is None:
self.results['forces'] = (np.reshape(np.array(f),
(len(atoms), 3)) *
units.kcal / units.mol)
else:
ff = np.reshape(np.array(f), (len(atoms), 3)) * \
units.kcal / units.mol
self.results['forces'] = ff[self.permutation[1, :]]
if 'forces' not in self.results:
if self.permutation is None:
crd = np.reshape(atoms.get_positions(), (1, len(atoms), 3))
else:
crd = np.reshape(atoms.get_positions()[self.permutation[0, :]],
(1, len(atoms), 3))
sander.set_positions(crd)
e, f = sander.energy_forces()
self.results['energy'] = e.tot * units.kcal / units.mol
if self.permutation is None:
self.results['forces'] = (np.reshape(np.array(f),
(len(atoms), 3)) *
units.kcal / units.mol)
else:
ff = np.reshape(np.array(f), (len(atoms), 3)) * \
units.kcal / units.mol
self.results['forces'] = ff[self.permutation[1, :]]
def calculate(self, atoms, properties, system_changes):
Calculator.calculate(self, atoms, properties, system_changes)
if system_changes:
if 'energy' in self.results:
del self.results['energy']
if 'forces' in self.results:
del self.results['forces']
if 'energy' not in self.results:
if self.permutation is None:
crd = np.reshape(atoms.get_positions(), (1, len(atoms), 3))
else:
crd = np.reshape(atoms.get_positions()
[self.permutation[0, :]], (1, len(atoms), 3))
sander.set_positions(crd)
e, f = sander.energy_forces()
self.results['energy'] = e.tot * units.kcal / units.mol
if self.permutation is None:
self.results['forces'] = (np.reshape(np.array(f),
(len(atoms), 3)) *
units.kcal / units.mol)
else:
ff = np.reshape(np.array(f), (len(atoms), 3)) * \
units.kcal / units.mol
self.results['forces'] = ff[self.permutation[1, :]]
if 'forces' not in self.results:
if self.permutation is None:
crd = np.reshape(atoms.get_positions(), (1, len(atoms), 3))
else:
crd = np.reshape(atoms.get_positions()[self.permutation[0, :]],
(1, len(atoms), 3))
sander.set_positions(crd)
e, f = sander.energy_forces()
self.results['energy'] = e.tot * units.kcal / units.mol
if self.permutation is None:
self.results['forces'] = (np.reshape(np.array(f),
(len(atoms), 3)) *
units.kcal / units.mol)
else:
ff = np.reshape(np.array(f), (len(atoms), 3)) * \
units.kcal / units.mol
self.results['forces'] = ff[self.permutation[1, :]]
def test_update_dihedral_parm(self):
traj = pt.iterload("./data/Tc5b.crd", fn('Tc5b.top'))
p = pmd.load_file(traj.top.filename)
inp = sander.gas_input(8)
coords = traj[0].xyz
with pt.utils.context.tempfolder():
for k in range(20, 100):
p.bonds[3].type.k = k
p.remake_parm()
with sander.setup(p, coords, None, inp):
ene, frc = sander.energy_forces()
def test_update_dihedral_parm(self):
traj = pt.iterload("./data/Tc5b.crd", "./data/Tc5b.top")
p = pmd.load_file(traj.top.filename)
inp = sander.gas_input(8)
coords = traj[0].xyz
fname = "tmp.parm7"
with pt.utils.context.tempfolder():
for k in range(20, 100):
p.bonds[3].type.k = k
p.remake_parm()
with sander.setup(p, coords, None, inp):
ene, frc = sander.energy_forces()
def get_total_energy(agls):
# get the coor from pyrosetta
inp_coor=generate_coord(agls)
# initialize the object topology with coordinates
parm=AmberParm("tpp-1.prmtop",inp_coor)
# set up the input options
inp=sander.gas_input()
sander.setup (parm, parm.coordinates, None, inp)
# compute the energy and force
eney, frc=sander.energy_forces()
# print('sander',eney.tot,eney.gb,eney.vdw, eney.elec, eney.dihedral,eney.angle, eney.bond)
# clean and finish
sander.cleanup()
return eney.tot
def sanderforce(self,parmstr,atmlst,boxflag=False,pmeflag=False):
"""Calculates energy and forces for a provided
Amber parm string and set of coordinates using the Sander
API. Also takes box dimensions and a flag for use of PME.
Currently uses standard simulation options for gas phase or pme
based on pmeflag.
Only returns forces on first 2 atoms in atmlst
Returns a sander energy object and a 3 x 2 x traj length array
of forces with units"""
self.forces=[]
self.energies=[]
# sander.APPLY_UNITS = True # More bugs/inconsistencies in pysander in amber15, may be fixed later
indices = [a.idx for a in atmlst[:2]]
if pmeflag is True:
# These default options will be suitable in most cases
# PME,cut=8.0,ntb=1,ntf=1,ntc=1
# Should be adapted if shake is required (not important here for ele)
inp = sander.pme_input()
else:
inp = sander.gas_input()
for i in range(0,self.traj.frame):
coord = self.traj.coordinates[i]
if boxflag is True:
box = self.traj.box[i]
# print box
else:
box = None
with sander.setup(parmstr,coord,box=box,mm_options=inp): #Pass a string, else a temp parmfile is created that fills up tmp directory!
ene,frc = sander.energy_forces(as_numpy=False) # pysander __init__ bug/inconsistency, can't use as_numpy!
frc = np.asarray(frc)
frc = np.reshape(frc,((len(frc)/3.),3))
frcslice = frc[indices]
# Add units for forces: kcal mol-1 A-1
frcslice = frcslice * u.kilocalorie / (u.mole * u.angstroms)
self.forces.append(frcslice)
self.energies.append(ene)
def test_eneregy_and_force():
path = os.path.dirname(__file__)
prmtop = path + '/vAla3.prmtop'
rst7 = path + '/vAla3.rst7'
with mdgx.setup(prmtop, rst7) as context:
mdgx_energies, mdgx_forces = context.energy_forces()
pme_input = sander.pme_input()
parm = pmd.load_file(prmtop, rst7)
with sander.setup(prmtop, rst7, box=parm.box, mm_options=pme_input):
ene, sander_forces = sander.energy_forces()
sander_enegies = dict((att, getattr(ene, att)) for att in dir(ene) if not
att.startswith('_'))
print("")
print("potential energy")
print("sander_enegies")
print(sander_enegies['tot'])
print("mdgx_energies")
print(mdgx_energies['eptot'])
print("")
print('forces')
print('sander_forces, first 5 atoms')
print(sander_forces[:15])
print("")
print('mdgx_forces, first 5 atoms')
print(mdgx_forces.tolist()[:15])
aa_eq([sander_enegies['tot'],],
[mdgx_energies['eptot'],],
decimal=4)
help='OpenMM platform to use. Default is %(default)s')
args = parser.parse_args()
# Get the Amber forces and energies
if args.pbc:
inp = sander.pme_input()
inp.cut = args.cutoff
inp.ntc = inp.ntf = 1
else:
inp = sander.gas_input(args.igb)
inp.cut = 1000
inp.rgbmax = 1000
with sander.setup(args.prmtop, args.inpcrd, None, inp) as context:
e, f = sander.energy_forces()
f = np.array(f).reshape((context.natom, 3))
# Get the OpenMM forces and energies
parm = app.AmberPrmtopFile(args.prmtop)
inpcrd = app.AmberInpcrdFile(args.inpcrd)
gbmap = collections.defaultdict(lambda: None)
gbmap[1] = app.HCT
gbmap[2] = app.OBC1
gbmap[5] = app.OBC2
gbmap[7] = app.GBn
gbmap[8] = app.GBn2
if args.pbc:
nonbondedMethod = app.PME
#! /usr/bin/env python
import sander
from chemistry.amber.readparm import AmberParm, Rst7
import numpy as np
pdb = '3stl'
parm = AmberParm('4amber_%s.prmtop' % pdb) #topo
rst = Rst7.open('4amber_%s.rst7' % pdb) #box
sander.setup(parm, rst.coordinates, rst.box, sander.pme_input())
ene, frc = sander.energy_forces()
print ene.tot
print max(frc)
import code
code.interact(local=dict(globals(), **locals()))
sander.cleanup()
def energy(parm, args, output=sys.stdout):
"""
Compute a single-point energy using sander and print the result to the
desired output
Parameters
----------
parm : Structure
args : ArgumentList
output : file handler, default sys.stdout
"""
global HAS_SANDER
if not HAS_SANDER:
raise SimulationError('Could not import sander')
cutoff = args.get_key_float('cutoff', None)
igb = args.get_key_int('igb', 5)
saltcon = args.get_key_float('saltcon', 0.0)
do_ewald = args.has_key('Ewald')
vdw_longrange = not args.has_key('nodisper')
has_1264 = 'LENNARD_JONES_CCOEF' in parm.parm_data
# Get any unmarked arguments
unmarked_cmds = args.unmarked()
if len(unmarked_cmds) > 0:
warnings.warn("Un-handled arguments: " + ' '.join(unmarked_cmds),
UnhandledArgumentWarning)
if parm.ptr('ifbox') == 0:
if not igb in (0, 1, 2, 5, 6, 7, 8):
raise SimulationError('Bad igb value. Must be 0, 1, 2, 5, '
'6, 7, or 8')
# Force vacuum electrostatics down the GB code path
if igb == 0:
igb = 6
inp = sander.gas_input(igb)
if cutoff is None:
cutoff = 1000.0
if cutoff <= 0:
raise SimulationError('cutoff must be > 0')
inp.cut = cutoff
if saltcon < 0:
raise SimulationError('salt concentration must be >= 0')
inp.saltcon = saltcon
elif parm.ptr('ifbox') > 0:
inp = sander.pme_input()
if cutoff is None:
cutoff = 8.0
elif cutoff <= 0:
raise SimulationError('cutoff must be > 0')
inp.cut = cutoff
inp.ew_type = int(do_ewald)
inp.vdwmeth = int(vdw_longrange)
inp.lj1264 = int(has_1264)
if parm.coordinates is None:
raise SimulationError('No coordinates are loaded')
# Time to set up sander
with sander.setup(parm, parm.coordinates, parm.box, inp):
e, f = sander.energy_forces()
if parm.chamber:
output.write('Bond = %20.7f Angle = %20.7f\n'
'Dihedral = %20.7f Urey-Bradley = %20.7f\n'
'Improper = %20.7f ' %
(e.bond, e.angle, e.dihedral, e.angle_ub, e.imp))
if parm.has_cmap:
output.write('CMAP = %20.7f\n' % e.cmap)
output.write('1-4 vdW = %20.7f 1-4 Elec. = %20.7f\n'
'Lennard-Jones = %20.7f Electrostatic = %20.7f\n'
'TOTAL = %20.7f\n' %
(e.vdw_14, e.elec_14, e.vdw, e.elec, e.tot))
else:
output.write(
'Bond = %20.7f Angle = %20.7f\n'
'Dihedral = %20.7f 1-4 vdW = %20.7f\n'
'1-4 Elec = %20.7f vdWaals = %20.7f\n'
'Elec. = %20.7f' %
(e.bond, e.angle, e.dihedral, e.vdw_14, e.elec_14, e.vdw, e.elec))
if igb != 0 and inp.ntb == 0:
output.write(' Egb = %20.7f' % e.gb)
elif e.hbond != 0:
output.write(' EHbond = %20.7f' % e.hbond)
output.write('\nTOTAL = %20.7f\n' % e.tot)
def energy_function(xyz):
sander.set_positions(xyz)
e, f = sander.energy_forces()
return e.tot, -np.array(f)
def energy(parm, args, output=sys.stdout):
"""
Compute a single-point energy using sander and print the result to the
desired output
"""
global HAS_SANDER
if not HAS_SANDER:
raise SimulationError('Could not import sander')
cutoff = args.get_key_float('cutoff', None)
igb = args.get_key_int('igb', 5)
saltcon = args.get_key_float('saltcon', 0.0)
do_ewald = args.has_key('Ewald')
vdw_longrange = not args.has_key('nodisper')
has_1264 = 'LENNARD_JONES_CCOEF' in parm.parm_data
# Get any unmarked arguments
unmarked_cmds = args.unmarked()
if len(unmarked_cmds) > 0:
warnings.warn("Un-handled arguments: " + ' '.join(unmarked_cmds),
UnhandledArgumentWarning)
if parm.ptr('ifbox') == 0:
if not igb in (0, 1, 2, 5, 6, 7, 8):
raise SimulationError('Bad igb value. Must be 0, 1, 2, 5, '
'6, 7, or 8')
# Force vacuum electrostatics down the GB code path
if igb == 0:
igb = 6
inp = sander.gas_input(igb)
if cutoff is None:
cutoff = 1000.0
if cutoff <= 0:
raise SimulationError('cutoff must be > 0')
inp.cut = cutoff
if saltcon < 0:
raise SimulationError('salt concentration must be >= 0')
inp.saltcon = saltcon
elif parm.ptr('ifbox') > 0:
inp = sander.pme_input()
if cutoff is None:
cutoff = 8.0
elif cutoff <= 0:
raise SimulationError('cutoff must be > 0')
inp.cut = cutoff
inp.ew_type = int(do_ewald)
inp.vdwmeth = int(vdw_longrange)
inp.lj1264 = int(has_1264)
if parm.coordinates is None:
raise SimulationError('No coordinates are loaded')
# Time to set up sander
with sander.setup(parm, parm.coordinates, parm.box, inp):
e, f = sander.energy_forces()
if parm.chamber:
output.write('Bond = %20.7f Angle = %20.7f\n'
'Dihedral = %20.7f Urey-Bradley = %20.7f\n'
'Improper = %20.7f ' % (e.bond, e.angle,
e.dihedral, e.angle_ub, e.imp))
if parm.has_cmap:
output.write('CMAP = %20.7f\n' % e.cmap)
output.write('1-4 vdW = %20.7f 1-4 Elec. = %20.7f\n'
'Lennard-Jones = %20.7f Electrostatic = %20.7f\n'
'TOTAL = %20.7f\n' % (e.vdw_14, e.elec_14,
e.vdw, e.elec, e.tot))
else:
output.write('Bond = %20.7f Angle = %20.7f\n'
'Dihedral = %20.7f 1-4 vdW = %20.7f\n'
'1-4 Elec = %20.7f vdWaals = %20.7f\n'
'Elec. = %20.7f' % (e.bond, e.angle, e.dihedral,
e.vdw_14, e.elec_14, e.vdw, e.elec))
if igb != 0 and inp.ntb == 0:
output.write(' Egb = %20.7f' % e.gb)
elif e.hbond != 0:
output.write(' EHbond = %20.7f' % e.hbond)
output.write('\nTOTAL = %20.7f\n' % e.tot)
def energy_function(xyz):
sander.set_positions(xyz)
e, f = sander.energy_forces()
return e.tot, -np.array(f)
from parmed.amber.readparm import AmberParm, Rst7
import numpy as np
import os, sys
import pickle
base = '1nie'
# parm = AmberParm('4amber_%s.prmtop' %base) #topo
rst = Rst7.open('4amber_%s.rst7' %base) #box
coords1 = rst.coordinates
coords2 = np.around( np.array(pickle.load(open('tmp2','rb') ) ), 3) #2nd coordinate set
print coords1, coords1.shape
print coords2, coords2.shape
sander.setup('4amber_%s.prmtop' %base, rst.coordinates, rst.box, sander.pme_input())
ene, frc = sander.energy_forces()
print frc[0]
sander.set_positions(coords1)
ene, frc = sander.energy_forces()
print frc[0]
sander.set_positions(coords2)
ene, frc = sander.energy_forces()
print frc[0]
print max(frc)
print ene.tot, ene.elec, ene.vdw
# import code; code.interact(local=dict(globals(), **locals()))
import boost.python
sander.set_positions(rst.coordinates)
def energy_decomposition(traj=None,
prmtop=None,
igb=8,
mm_options=None,
qm_options=None,
mode=None,
dtype='dict',
frame_indices=None,
top=None):
"""energy decomposition by calling `libsander`
Parameters
----------
traj : Trajectory-like or iterables that produce Frame
if `traj` does not hold Topology information, `top` must be provided
prmtop : str or Structure from ParmEd, default=None, optional
To avoid any unexpected error, you should always provide original topology
filename. If prmtop is None, pytraj will load Topology from traj.top.filename.
- why do you need to load additional topology filename? Because cpptraj and sander
use different Topology object, can not convert from one to another.
igb : GB model, default=8 (GB-Neck2)
If specify `mm_options`, this `igb` input will be ignored
mm_options : InputOptions from `sander`, default=None, optional
if `mm_options` is None, use `gas_input` with given igb.
If `mm_options` is not None, use this
qm_options : InputOptions from `sander` for QMMM, optional
mode : str, default=None, optional
if mode='minimal', get only 'bond', 'angle', 'dihedral' and 'total' energies
top : pytraj.Topology or str, default=None, optional
only need to specify this ``top`` if ``traj`` does not hold Topology
dtype : str, {'dict', 'dataset', 'ndarray', 'dataframe'}, default='dict'
return data type
frame_indices : None or 1D array-like, default None
if not None, only perform calculation for given frames
Returns
-------
Dict of energies (to be used with DataFrame) or DatasetList
Examples
--------
Examples are adapted from $AMBERHOME/test/sanderapi
>>> import pytraj as pt
>>> # GB energy
>>> traj = pt.datafiles.load_ala3()
>>> traj.n_frames
1
>>> data = pt.energy_decomposition(traj, igb=8)
>>> data['gb']
array([-92.88577683])
>>> data['bond']
array([ 5.59350521])
>>> # PME
>>> import os
>>> from pytraj.testing import amberhome
>>> import sander
>>> topfile = os.path.join(amberhome, "test/4096wat/prmtop")
>>> rstfile = os.path.join(amberhome, "test/4096wat/eq1.x")
>>> traj = pt.iterload(rstfile, topfile)
>>> options = sander.pme_input()
>>> options.cut = 8.0
>>> edict = pt.energy_decomposition(traj=traj, mm_options=options)
>>> edict['vdw']
array([ 6028.95167558])
>>> # GB + QMMM
>>> topfile = os.path.join(amberhome, "test/qmmm2/lysine_PM3_qmgb2/prmtop")
>>> rstfile = os.path.join(amberhome, "test/qmmm2/lysine_PM3_qmgb2/lysine.crd")
>>> traj = pt.iterload(rstfile, topfile)
>>> options = sander.gas_input(8)
>>> options.cut = 99.0
>>> options.ifqnt = 1
>>> qm_options = sander.qm_input()
>>> qm_options.iqmatoms[:3] = [8, 9, 10]
>>> qm_options.qm_theory = "PM3"
>>> qm_options.qmcharge = 0
>>> qm_options.qmgb = 2
>>> qm_options.adjust_q = 0
>>> edict = pt.energy_decomposition(traj=traj, mm_options=options, qm_options=qm_options)
>>> edict['bond']
array([ 0.00160733])
>>> edict['scf']
array([-11.92177575])
Notes
-----
This method does not work with `pytraj.pmap` when you specify mm_options and
qm_options. Use `pytraj.pmap_mpi` with MPI instead.
Work with ``pytraj.pmap``::
pt.pmap(pt.energy_decomposition, traj, igb=8, dtype='dict')
Will NOT work with ``pytraj.pmap``::
import sander
inp = sander.gas_input(8)
pt.pmap(pt.energy_decomposition, traj, mm_options=inp, dtype='dict')
Why? Because Python need to pickle each object to send to different cores and Python
does not know how to pickle mm_options from sander.gas_input(8).
This works with ``pytraj.pmap_mpi`` because pytraj explicitly create ``mm_options``
in each core without pickling.
"""
from collections import defaultdict, OrderedDict
from pytraj.misc import get_atts
import numpy as np
try:
import sander
except ImportError:
raise ImportError("need both `pysander` installed. Check Ambertools15")
ddict = defaultdict(_default_func)
if mm_options is None:
inp = sander.gas_input(igb)
elif igb is not None:
inp = mm_options
if isinstance(inp, string_types):
# dangerous
local_dict = {'sander': sander}
exec(inp.lstrip(), local_dict)
inp = local_dict['mm_options']
if isinstance(qm_options, string_types):
# dangerous
local_dict = {'sander': sander}
exec(qm_options.lstrip(), local_dict)
qm_options = local_dict['qm_options']
if prmtop is None:
try:
# try to load from file by taking top.filename
prmtop_ = top.filename
except AttributeError:
raise ValueError("prmtop must be AmberParm object in ParmEd")
else:
# Structure, string
prmtop_ = prmtop
if not hasattr(prmtop_, 'coordinates') or prmtop_.coordinates is None:
try:
# if `traj` is Trajectory-like (not frame_iter), try to take 1st
# coords
coords = traj[0].xyz
except (TypeError, AttributeError):
# create fake list
coords = [0. for _ in range(top.n_atoms * 3)]
else:
# use default coords in `AmberParm`
coords = prmtop_.coordinates
if top.has_box():
box = top.box.tolist()
has_box = True
else:
box = None
has_box = False
with sander.setup(prmtop_, coords, box, inp, qm_options):
for frame in iterframe_master(traj):
if has_box:
sander.set_box(*frame.box.tolist())
sander.set_positions(frame.xyz)
ene, frc = sander.energy_forces()
# potentially slow
ene_atts = get_atts(ene)
for att in ene_atts:
ddict[att].append(getattr(ene, att))
new_dict = None
if mode == 'minimal':
new_dict = {}
for key in ['bond', 'angle', 'dihedral', 'tot']:
new_dict[key] = ddict[key]
else:
new_dict = ddict
for key in new_dict.keys():
new_dict[key] = np.asarray(new_dict[key])
if dtype == 'dict':
return OrderedDict(new_dict)
else:
from pytraj.datasets.c_datasetlist import DatasetList
dslist = DatasetList()
size = new_dict['tot'].__len__()
for key in new_dict.keys():
dslist.add('double')
dslist[-1].key = key
dslist[-1].resize(size)
dslist[-1].data[:] = new_dict[key]
return get_data_from_dtype(dslist, dtype)
always infinite for non-periodic systems''')
group.add_argument('--platform', dest='platform', default='Reference',
help='OpenMM platform to use. Default is %(default)s')
args = parser.parse_args()
# Get the Amber forces and energies
if args.pbc:
inp = sander.pme_input()
inp.cut = args.cutoff
else:
inp = sander.gas_input(args.igb)
inp.cut = 1000
with sander.setup(args.prmtop, args.inpcrd, None, inp) as context:
e, f = sander.energy_forces()
f = np.array(f).reshape((context.natom, 3))
# Get the OpenMM forces and energies
parm = app.AmberPrmtopFile(args.prmtop)
inpcrd = app.AmberInpcrdFile(args.inpcrd)
gbmap = collections.defaultdict(lambda: None)
gbmap[1] = app.HCT
gbmap[2] = app.OBC1
gbmap[5] = app.OBC2
gbmap[7] = app.GBn
gbmap[8] = app.GBn2
if args.pbc:
nonbondedMethod = app.PME
