def set_radii(self, igb=0, radius_set='mbondi'):
""" Sets the radius set to a new one using parmed """
# If someone sets an igb, change to the appropriate radius set
if igb:
if igb == 1: radius_set = 'mbondi'
elif igb == 2: radius_set = 'mbondi2'
elif igb == 5: radius_set = 'mbondi2'
elif igb == 7: radius_set = 'bondi'
elif igb == 8: radius_set = 'mbondi3'
if not radius_set in [
'mbondi', 'mbondi2', 'mbondi3', 'bondi', 'amber6'
]:
raise InputError('Bad radius set! Choose from ' +
'mbondi, mbondi2, mbondi3, bondi, and amber6')
parmed = which('parmed.py')
change_str = ("setOverwrite True\n" + "changeRadii %s\n" % radius_set +
"parmout %s\n" % self.prmtop + "go\n")
process = Popen(
[parmed, '-q', '-n', str(self.prmtop)],
stdin=PIPE,
stderr=PIPE,
stdout=PIPE)
(output, error) = process.communicate(change_str)
if process.wait():
raise ProgramError('parmed.py failed to change radii!')
# Reload our topology file now that we've changed radius sets
self.prmtop = AmberParm(str(self.prmtop))
def get_shrot_region(args, x, y, z, size):
with open(args.pdb) as f:
lines = f.readlines()
atoms = []
for l in lines:
if l.startswith('ATOM'):
l = l.split()
atoms.append(l[5:8])
atoms = np.array(atoms, dtype=float)
parm = AmberParm(args.prmtop)
radii = []
for atom in parm.atom_list:
nbidx = parm.LJ_types[atom.attype]
radii.append(float(parm.LJ_radius[nbidx - 1]))
# convert meshgrid to a matrix and find indexes of all points
# which are inside molecule
xyz = np.c_[x.flatten(), y.flatten(), z.flatten()]
ktree = cKDTree(xyz)
mask = []
for atom, r in zip(atoms, radii):
excluded_r = r * args.vdw_multiple
excl_indxs = ktree.query_ball_point(atom, excluded_r)
mask.extend(excl_indxs)
mask = list(set(mask))
# create shrot range from indexes
short_range = np.zeros(xyz.shape[0], dtype='bool') #all false array
short_range[mask] = True
return short_range.reshape(size)
def set_radii(self, igb=0, radius_set='mbondi'):
""" Sets the radius set to a new one using parmed """
# If someone sets an igb, change to the appropriate radius set
if igb:
if igb == 1: radius_set = 'mbondi'
elif igb == 2: radius_set = 'mbondi2'
elif igb == 5: radius_set = 'mbondi2'
elif igb == 7: radius_set = 'bondi'
elif igb == 8: radius_set = 'mbondi3'
if not radius_set in ['mbondi', 'mbondi2', 'mbondi3', 'bondi', 'amber6']:
raise InputError('Bad radius set! Choose from ' +
'mbondi, mbondi2, mbondi3, bondi, and amber6')
parmed = which('parmed.py')
change_str = ("setOverwrite True\n" +
"changeRadii %s\n" % radius_set +
"parmout %s\n" % self.prmtop +
"go\n")
process = Popen([parmed, '-q', '-n', str(self.prmtop)], stdin=PIPE,
stderr=PIPE, stdout=PIPE)
(output, error) = process.communicate(change_str)
if process.wait():
raise ProgramError('parmed.py failed to change radii!')
# Reload our topology file now that we've changed radius sets
self.prmtop = AmberParm(str(self.prmtop))
class AmberSystem(object):
""" An Amber system with a topology file and input coordinate file """
# ==============================
def __init__(self, prmtop, inpcrd):
# Only load the inpcrd file if it actually exists.
# if os.path.exists(inpcrd): self.prmtop = AmberParm(prmtop, inpcrd)
# else: self.prmtop = AmberParm(prmtop)
self.prmtop = AmberParm(prmtop)
self.inpcrd = inpcrd
# ==============================
def periodic(self):
""" Returns whether or not a topology file is set up for PBC """
# PBCs are indicated by a non-zero IFBOX pointer
return bool(self.prmtop.ptr('ifbox'))
# ==============================
def query_radii(self):
""" Returns the radii set in the topology file """
return self.prmtop.parm_data['RADIUS_SET'][0]
# ==============================
def set_radii(self, igb=0, radius_set='mbondi'):
""" Sets the radius set to a new one using parmed """
# If someone sets an igb, change to the appropriate radius set
if igb:
if igb == 1: radius_set = 'mbondi'
elif igb == 2: radius_set = 'mbondi2'
elif igb == 5: radius_set = 'mbondi2'
elif igb == 7: radius_set = 'bondi'
elif igb == 8: radius_set = 'mbondi3'
if not radius_set in ['mbondi', 'mbondi2', 'mbondi3', 'bondi', 'amber6']:
raise InputError('Bad radius set! Choose from ' +
'mbondi, mbondi2, mbondi3, bondi, and amber6')
parmed = which('parmed.py')
change_str = ("setOverwrite True\n" +
"changeRadii %s\n" % radius_set +
"parmout %s\n" % self.prmtop +
"go\n")
process = Popen([parmed, '-q', '-n', str(self.prmtop)], stdin=PIPE,
stderr=PIPE, stdout=PIPE)
(output, error) = process.communicate(change_str)
if process.wait():
raise ProgramError('parmed.py failed to change radii!')
# Reload our topology file now that we've changed radius sets
self.prmtop = AmberParm(str(self.prmtop))
def run(parm_file_name,
traj_file_name,
asu_prmtop_file_name,
asu_rst7_file_name,
prop_a,
prob_b,
prop_c,
target_unit_cell,
atoms_per_uc,
wrap,
buffer,
spacegroup=' '):
parm = AmberParm(parm_file_name)
traj = NetCDFTraj.open_old(traj_file_name)
n_frames = traj.frame
U, invU, UCbox = get_U_invU(asu_rst7_file_name)
start_atm, end_atm = calc_start_end_atm(atoms_per_uc, target_unit_cell,
prop_a, prop_b, prop_c)
# for frame in range(n_frames):
# parm = AmberParm(parm_file_name)
for frame in range(0, 1):
coords = traj.coordinates(frame)
frac_crds = get_frac_crds(coords, traj, U)
cntred_frac_crds = center_frac_coords(frac_crds, parm, start_atm,
end_atm)
# atom_selection1 = select_atoms(cntred_frac_crds, parm, buffer, solvent=True)
print frame
# print atom_selection1
# print frac_crds[9794]
# print cntred_frac_crds[9794]
# if wrap:
# wrap_coords(parm, frac_crds, cntred_frac_crds, prop_a, prop_b, prop_c, buffer, solvent=True)
atom_selection = select_atoms(cntred_frac_crds,
parm,
buffer,
solvent=True)
frac_crds = rev_translate_frac_crds(frac_crds, target_unit_cell,
prop_a, prop_b, prop_c)
coords = get_cart_crds(frac_crds, traj, invU).flatten()
# print atom_selection
# print cntred_frac_crds[9794]
write_pdb(coords, parm, atom_selection,
'uc%d_frame%d' % (target_unit_cell, frame), UCbox,
spacegroup)
# write_pdb(coords, parm, atom_selection1, 'uc%d_frame%d_nowrap' %(target_unit_cell,frame))
write_amber_files(coords, parm,
'uc%d_frame%d' % (target_unit_cell, frame),
atom_selection)
# import code; code.interact(local=dict(globals(), **locals()))
return atom_selection
def read_amber_prm(pfile, cfile):
prmtop = AmberParm(pfile)
crds = read_rstf(cfile)
atids = list(range(1, len(prmtop.parm_data['ATOM_NAME']) + 1))
resids = list(range(1, len(prmtop.parm_data['RESIDUE_LABEL']) + 1))
if len(prmtop.parm_data['ATOM_NAME']) != len(crds):
raise ReadError('The toplogy and coordinates file are not \
consistent in the atom numbers.')
residues = {}
atoms = {}
for i in range(0, len(prmtop.parm_data['RESIDUE_LABEL'])):
resid = i + 1
resname = prmtop.parm_data['RESIDUE_LABEL'][i]
if i < len(prmtop.parm_data['RESIDUE_LABEL']) - 1:
resconter = list(range(prmtop.parm_data['RESIDUE_POINTER'][i], \
prmtop.parm_data['RESIDUE_POINTER'][i+1]))
else:
resconter = list(range(prmtop.parm_data['RESIDUE_POINTER'][i], \
len(prmtop.parm_data['ATOM_NAME'])+1))
residues[resid] = Residue(resid, resname, resconter)
for j in resconter:
gtype = 'ATOM'
atid = j
atname = prmtop.parm_data['ATOM_NAME'][j - 1]
element = prmtop.parm_data['ATOMIC_NUMBER'][j - 1]
atomtype = prmtop.parm_data['AMBER_ATOM_TYPE'][j - 1]
crd = crds[j - 1]
charge = prmtop.parm_data['CHARGE'][j - 1]
try:
element = AtnumRev[element]
except:
print(resname, atname, atomtype)
element = 'X'
atoms[j] = Atom(gtype, atid, atname, element, atomtype, crd, charge, \
resid, resname)
mol = Molecule(atoms, residues)
return prmtop, mol, atids, resids
def get_rmin2_radii(prmtop):
""" Return a list of r_min/2 values """
try:
parm = AmberParm(prmtop)
radii = []
for atom in parm.atom_list:
nbidx = parm.LJ_types[atom.attype]
radii.append(float(parm.LJ_radius[nbidx - 1]))
except IndexError:
print('Couldnt open {} using AmberParm'.format(prmtop))
print('Assuming single atom topology')
with open(prmtop) as f:
for l in f:
if 'JONES_ACOEF' in l:
f.next()
acoef = float(f.next())
f.next()
f.next()
bcoef = float(f.next())
radii = [(acoef / bcoef * 2)**(1. / 6) / 2]
return radii
def visualize_molecule(args):
with open(args.pdb) as f:
lines = f.readlines()
names = []
atoms = []
for l in lines:
if l.startswith('ATOM'):
l = l.split()
names.append(l[2])
atoms.append(l[5:8])
atoms = np.array(atoms, dtype=float)
colours = paint_atoms(names)
#get vdw and plot
if args.prmtop:
parm = AmberParm(args.prmtop)
radii = []
for atom in parm.atom_list:
nbidx = parm.LJ_types[atom.attype]
radii.append(float(parm.LJ_radius[nbidx - 1]))
else:
radii = [1. for i in atoms]
for (x, y, z), r, c in zip(atoms, radii, colours):
#print('visualizing atom')
mlab.points3d(x, y, z, scale_factor=r * 1.25, resolution=20, color=c)
def natom(topfile):
parm = AmberParm(topfile)
return parm.ptr("NATOM")
#! /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 main(opt):
# Check all of the arguments
if not os.path.exists(opt.prmtop):
raise CpinInputError('prmtop file (%s) is missing' % opt.prmtop)
# Process the arguments that take multiple args
resstates = process_arglist(opt.resstates, int)
resnums = process_arglist(opt.resnums, int)
notresnums = process_arglist(opt.notresnums, int)
resnames = process_arglist(opt.resnames, str)
notresnames = process_arglist(opt.notresnames, str)
minpka = opt.minpka
maxpka = opt.maxpka
if not opt.igb in (2, 5, 8):
raise CpinInputError('-igb must be 2, 5, or 8!')
if resnums is not None and notresnums is not None:
raise CpinInputError(
'Cannot specify -resnums and -notresnums together')
if resnames is not None and notresnames is not None:
raise CpinInputError(
'Cannot specify -resnames and -notresnames together')
if opt.intdiel != 1 and opt.intdiel != 2:
raise CpinInputError('-intdiel must be either 1 or 2 currently')
# Set the list of residue names we will be willing to titrate
titratable_residues = []
if notresnames is not None:
for resname in residues.titratable_residues:
if resname in notresnames: continue
titratable_residues.append(resname)
elif resnames is not None:
for resname in resnames:
if not resname in residues.titratable_residues:
raise CpinInputError('%s is not a titratable residue!' %
resname)
titratable_residues.append(resname)
else:
titratable_residues = residues.titratable_residues[:]
solvent_ions = [
'WAT', 'Na+', 'Br-', 'Cl-', 'Cs+', 'F-', 'I-', 'K+', 'Li+', 'Mg+',
'Rb+', 'CIO', 'IB', 'MG2'
]
# Filter titratable residues based on min and max pKa
new_reslist = []
for res in titratable_residues:
if getattr(residues, res).pKa < minpka: continue
if getattr(residues, res).pKa > maxpka: continue
new_reslist.append(res)
titratable_residues = new_reslist
del new_reslist
# Make sure we still have a couple residues
if len(titratable_residues) == 0:
raise CpinInputError('No titratable residues fit your criteria!')
# Load the topology file
parm = AmberParm(opt.prmtop)
# Replace an un-set notresnums with an empty list so we get __contains__()
if notresnums is None:
notresnums = []
# If we have a list of residue numbers, check that they're all titratable
if resnums is not None:
for resnum in resnums:
if resnum > parm.ptr('nres'):
raise CpinInputError('%s only has %d residues. (%d chosen)' %
(parm, parm.ptr('nres'), resnum))
if resnum <= 0:
raise CpinInputError('Cannot select negative residue numbers.')
resname = parm.parm_data['RESIDUE_LABEL'][resnum - 1]
if not resname in titratable_residues:
raise CpinInputError(
'Residue number %s [%s] is not titratable' %
(resnum, resname))
else:
# Select every residue except those in notresnums
resnums = []
for resnum in range(1, parm.ptr('nres') + 1):
if resnum in notresnums: continue
resnums.append(resnum)
solvated = False
first_solvent = 0
if 'WAT' in parm.parm_data['RESIDUE_LABEL']:
solvated = True
for i, res in enumerate(parm.parm_data['RESIDUE_LABEL']):
if res in solvent_ions:
first_solvent = parm.parm_data['RESIDUE_POINTER'][i]
break
main_reslist = TitratableResidueList(system_name=opt.system,
solvated=solvated,
first_solvent=first_solvent)
for resnum in resnums:
resname = parm.parm_data['RESIDUE_LABEL'][resnum - 1]
if not resname in titratable_residues: continue
res = getattr(residues, resname)
# Filter out termini (make sure the residue in the prmtop has as many
# atoms as the titratable residue defined in residues.py)
if resnum == parm.ptr('nres'):
natoms = parm.ptr('natom') - parm.parm_data['RESIDUE_POINTER'][
resnum - 1]
else:
natoms = (parm.parm_data['RESIDUE_POINTER'][resnum] -
parm.parm_data['RESIDUE_POINTER'][resnum - 1])
if natoms != len(res.atom_list): continue
# If we have gotten this far, add it to the list.
main_reslist.add_residue(res, resnum,
parm.parm_data['RESIDUE_POINTER'][resnum - 1])
# Set the states if requested
if resstates is not None:
main_reslist.set_states(resstates)
# Open the output file
if opt.output is None:
output = sys.stdout
else:
output = open(opt.output, 'w', 0)
main_reslist.write_cpin(output, opt.igb, opt.intdiel)
if opt.output is not None:
output.close()
if solvated:
if opt.outparm is None:
has_carboxylate = False
for res in main_reslist:
if res is residues.AS4 or res is residues.GL4:
has_carboxylate = True
break
if has_carboxylate:
print >> sys.stderr, "Warning: Carboxylate residues in explicit ",
print >> sys.stderr, "solvent simulations require a modified"
print >> sys.stderr, "topology file! Use the -op flag to print one."
else:
changeradii(parm, 'mbondi2').execute()
change(parm, 'RADII', ':AS4,GL4@OD=,OE=', 1.3).execute()
parm.overwrite = True
parm.writeParm(opt.outparm)
else:
if opt.outparm is not None:
print >> sys.stderr, "A new prmtop is only necessary for explicit ",
print >> sys.stderr, "solvent CpHMD simulations."
sys.stderr.write('CPIN generation complete!\n')
def main(opt):
# Check all of the arguments
if not os.path.exists(opt.prmtop):
raise CpinInputError('prmtop file (%s) is missing' % opt.prmtop)
# Process the arguments that take multiple args
resstates = process_arglist(opt.resstates, int)
resnums = process_arglist(opt.resnums, int)
notresnums = process_arglist(opt.notresnums, int)
resnames = process_arglist(opt.resnames, str)
notresnames = process_arglist(opt.notresnames, str)
minpka = opt.minpka
maxpka = opt.maxpka
if not opt.igb in (2, 5, 8):
raise CpinInputError('-igb must be 2, 5, or 8!')
if resnums is not None and notresnums is not None:
raise CpinInputError('Cannot specify -resnums and -notresnums together')
if resnames is not None and notresnames is not None:
raise CpinInputError('Cannot specify -resnames and -notresnames together')
if opt.intdiel != 1 and opt.intdiel != 2:
raise CpinInputError('-intdiel must be either 1 or 2 currently')
# Set the list of residue names we will be willing to titrate
titratable_residues = []
if notresnames is not None:
for resname in residues.titratable_residues:
if resname in notresnames: continue
titratable_residues.append(resname)
elif resnames is not None:
for resname in resnames:
if not resname in residues.titratable_residues:
raise CpinInputError('%s is not a titratable residue!' % resname)
titratable_residues.append(resname)
else:
titratable_residues = residues.titratable_residues[:]
print str(titratable_residues)
solvent_ions = ['WAT', 'Na+', 'Br-', 'Cl-', 'Cs+', 'F-', 'I-', 'K+', 'Li+',
'Mg+', 'Rb+', 'CIO', 'IB', 'MG2']
# Filter titratable residues based on min and max pKa
new_reslist = []
for res in titratable_residues:
if getattr(residues, res).pKa < minpka: continue
if getattr(residues, res).pKa > maxpka: continue
new_reslist.append(res)
titratable_residues = new_reslist
del new_reslist
# Make sure we still have a couple residues
if len(titratable_residues) == 0:
raise CpinInputError('No titratable residues fit your criteria!')
# Load the topology file
parm = AmberParm(opt.prmtop)
# Replace an un-set notresnums with an empty list so we get __contains__()
if notresnums is None:
notresnums = []
# If we have a list of residue numbers, check that they're all titratable
if resnums is not None:
for resnum in resnums:
if resnum > parm.ptr('nres'):
raise CpinInputError('%s only has %d residues. (%d chosen)' % (parm,
parm.ptr('nres'), resnum))
if resnum <= 0:
raise CpinInputError('Cannot select negative residue numbers.')
resname = parm.parm_data['RESIDUE_LABEL'][resnum-1]
if not resname in titratable_residues:
raise CpinInputError('Residue number %s [%s] is not titratable' %
(resnum, resname))
else:
# Select every residue except those in notresnums
resnums = []
for resnum in range(1, parm.ptr('nres') + 1):
if resnum in notresnums: continue
resnums.append(resnum)
solvated = False
first_solvent = 0
if 'WAT' in parm.parm_data['RESIDUE_LABEL']:
solvated = True
for i, res in enumerate(parm.parm_data['RESIDUE_LABEL']):
if res in solvent_ions:
first_solvent = parm.parm_data['RESIDUE_POINTER'][i]
break
main_reslist = TitratableResidueList(system_name=opt.system,
solvated=solvated, first_solvent=first_solvent)
for resnum in resnums:
resname = parm.parm_data['RESIDUE_LABEL'][resnum-1]
if not resname in titratable_residues:
print resname
continue
res = getattr(residues, resname)
# Filter out termini (make sure the residue in the prmtop has as many
# atoms as the titratable residue defined in residues.py)
if resnum == parm.ptr('nres'):
natoms = parm.ptr('natom')-parm.parm_data['RESIDUE_POINTER'][resnum-1]
else:
natoms = (parm.parm_data['RESIDUE_POINTER'][resnum] -
parm.parm_data['RESIDUE_POINTER'][resnum-1])
if natoms != len(res.atom_list): continue
# If we have gotten this far, add it to the list.
main_reslist.add_residue(res, resnum,
parm.parm_data['RESIDUE_POINTER'][resnum-1])
# Set the states if requested
if resstates is not None:
main_reslist.set_states(resstates)
# Open the output file
if opt.output is None:
output = sys.stdout
else:
output = open(opt.output, 'w', 0)
main_reslist.write_cpin(output, opt.igb, opt.intdiel)
if opt.output is not None:
output.close()
if solvated:
if opt.outparm is None:
has_carboxylate = False
for res in main_reslist:
if res is residues.AS4 or res is residues.GL4:
has_carboxylate = True
break
if has_carboxylate:
print >> sys.stderr, "Warning: Carboxylate residues in explicit ",
print >> sys.stderr, "solvent simulations require a modified"
print >> sys.stderr, "topology file! Use the -op flag to print one."
else:
changeradii(parm, 'mbondi2').execute()
change(parm, 'RADII', ':AS4,GL4@OD=,OE=', 1.3).execute()
parm.overwrite = True
parm.writeParm(opt.outparm)
else:
if opt.outparm is not None:
print >> sys.stderr, "A new prmtop is only necessary for explicit ",
print >> sys.stderr, "solvent CpHMD simulations."
sys.stderr.write('CPIN generation complete!\n')
def __init__(self, prmtop, inpcrd):
# Only load the inpcrd file if it actually exists.
# if os.path.exists(inpcrd): self.prmtop = AmberParm(prmtop, inpcrd)
# else: self.prmtop = AmberParm(prmtop)
self.prmtop = AmberParm(prmtop)
self.inpcrd = inpcrd
def __init__(self, prmtop, inpcrd):
# Only load the inpcrd file if it actually exists.
# if os.path.exists(inpcrd): self.prmtop = AmberParm(prmtop, inpcrd)
# else: self.prmtop = AmberParm(prmtop)
self.prmtop = AmberParm(prmtop)
self.inpcrd = inpcrd
class AmberSystem(object):
""" An Amber system with a topology file and input coordinate file """
# ==============================
def __init__(self, prmtop, inpcrd):
# Only load the inpcrd file if it actually exists.
# if os.path.exists(inpcrd): self.prmtop = AmberParm(prmtop, inpcrd)
# else: self.prmtop = AmberParm(prmtop)
self.prmtop = AmberParm(prmtop)
self.inpcrd = inpcrd
# ==============================
def periodic(self):
""" Returns whether or not a topology file is set up for PBC """
# PBCs are indicated by a non-zero IFBOX pointer
return bool(self.prmtop.ptr('ifbox'))
# ==============================
def query_radii(self):
""" Returns the radii set in the topology file """
return self.prmtop.parm_data['RADIUS_SET'][0]
# ==============================
def set_radii(self, igb=0, radius_set='mbondi'):
""" Sets the radius set to a new one using parmed """
# If someone sets an igb, change to the appropriate radius set
if igb:
if igb == 1: radius_set = 'mbondi'
elif igb == 2: radius_set = 'mbondi2'
elif igb == 5: radius_set = 'mbondi2'
elif igb == 7: radius_set = 'bondi'
elif igb == 8: radius_set = 'mbondi3'
if not radius_set in [
'mbondi', 'mbondi2', 'mbondi3', 'bondi', 'amber6'
]:
raise InputError('Bad radius set! Choose from ' +
'mbondi, mbondi2, mbondi3, bondi, and amber6')
parmed = which('parmed.py')
change_str = ("setOverwrite True\n" + "changeRadii %s\n" % radius_set +
"parmout %s\n" % self.prmtop + "go\n")
process = Popen(
[parmed, '-q', '-n', str(self.prmtop)],
stdin=PIPE,
stderr=PIPE,
stdout=PIPE)
(output, error) = process.communicate(change_str)
if process.wait():
raise ProgramError('parmed.py failed to change radii!')
# Reload our topology file now that we've changed radius sets
self.prmtop = AmberParm(str(self.prmtop))
quit
""" % (extras, prev_str, resname, next_str, resname.lower(), resname.lower())
if igb == 1:
tleap_script = tleap_script % 'mbondi'
elif igb == 7:
tleap_script = tleap_script % 'bondi'
elif igb == 8:
tleap_script = tleap_script % 'mbondi3'
else:
tleap_script = tleap_script % 'mbondi2'
open("tleap.in","w").write(tleap_script)
os.system(tleap + " -f tleap.in > tleap.log")
prm = AmberParm("%s0.prmtop" % resname.lower())
prm.overwrite = True # allow the prmtop to be overwritten
# check validity of prmtop
if not prm.valid:
sys.exit('Error: Invalid prmtop (%s)!' % prm)
if isolated or not prev_str:
act = changeprotstate(prm, ':1 %s' % opt.state0)
else:
act = changeprotstate(prm, ':2 %s' % opt.state0)
act.execute()
prm.writeParm(str(prm))
chg1 = netcharge(prm, '*').execute()
group = OptionGroup(parser, 'Output Files',
'Files that are made by this script')
group.add_option('-o',
'--outtraj',
dest='outtraj',
metavar='FILE',
default='mutant.mdcrd',
help='Name of mutant trajectory '
'file to generate. Default %default')
parser.add_option_group(group)
opt, arg = parser.parse_args()
if opt.norm_prm is None or opt.mut_prm is None:
sys.stderr.write('Please provide a normal and mutated topology file\n')
parser.print_help()
sys.exit(1)
if opt.inptraj is None:
sys.stderr.write('Please provide a trajectory to mutate!\n')
parser.print_help()
sys.exit(1)
norm_prm = AmberParm(opt.norm_prm)
mut_prm = AmberParm(opt.mut_prm)
mut_traj = GlyMutantMdcrd(opt.inptraj, norm_prm, mut_prm)
mut_traj.MutateTraj(opt.outtraj)
print 'FINALLY DONE!'
def resnum(topfile):
parm = AmberParm(topfile)
return parm.ptr("NRES")
from chemistry.amber.mask import AmberMask
from chemistry.amber.readparm import AmberParm
l = AmberParm('asu.prmtop')
k = AmberMask(l, ':12,41,119,125,126')
sel = k.Selected()
sel2 = k.Selection()
print sum(sel2)
for i in sel:
print 'Selected atom %d: %s' % (i + 1, l.atoms[i])
at = l.atoms[0]
at.residue
at.residue.name
at.residue.number
at.residue.idx
at.atomic_number
at.name
at.type
