def write_bgf(atoms,description=None):
uc = atoms.get_cell()
a,b,c = [Vector(x) for x in uc]
A = a.length()
B = b.length()
C = c.length()
rad2deg = 360./(2*math.pi)
alpha = b.angle(c)*rad2deg
beta = a.angle(c)*rad2deg
gamma = a.angle(b)*rad2deg
crstx = str(FortranLine(('CRYSTX',
A,
B,
C,
alpha,
beta,
gamma),
FortranFormat('a6,1x,6f11.5')))
atom_lines = []
fmt = FortranFormat('a6,1x,i5,1x,a5,1x,a3,1x,a1,1x,a5,3f10.5,1x,a5,i3,i2,1x,f8.5')
for i,atom in enumerate(atoms):
line = str(FortranLine(('HETATM',
i,
atom.symbol,
'',
'',
'',
atom.x,
atom.y,
atom.z,
atom.symbol,
1,
1,
0.0),
fmt))
atom_lines.append(line)
# energy in kcal
energy = atoms.get_potential_energy()*23.061
bgf = Template(bgf_template, searchList=[locals()])
return bgf.respond()
def _readLJParameters(self, file, ljpar_set):
format = FortranFormat('2X,A2,6X,3F10.6')
while 1:
l = FortranLine(file.readline()[:-1], format)
if l.isBlank(): break
name = _normalizeName(l[0])
ljpar_set.addEntry(name, l[1], l[2], l[3])
def _readImproperParameters(self, file):
format = FortranFormat('A2,1X,A2,1X,A2,1X,A2,I4,3F15.2')
while 1:
l = FortranLine(file.readline()[:-1], format)
if l.isBlank(): break
name1 = _normalizeName(l[0])
name2 = _normalizeName(l[1])
name3 = _normalizeName(l[2])
name4 = _normalizeName(l[3])
if name1 == 'X':
if name2 == 'X':
name1 = name3
name2 = name4
name3 = 'X'
name4 = 'X'
else:
name1 = name3
name2, name3 = _sort(name2, name4)
name4 = 'X'
else:
name1, name2, name3, name4 = \
(name3, ) + _sort3(name1, name2, name4)
p = AmberImproperParameters(self.atom_types[name1],
self.atom_types[name2],
self.atom_types[name3],
self.atom_types[name4], l[4], l[5],
l[6], l[7])
if name4 == 'X':
if name3 == 'X':
self.impropers_2[(name1, name2)] = p
else:
self.impropers_1[(name1, name2, name3)] = p
else:
self.impropers[(name1, name2, name3, name4)] = p
def _readDihedralParameters(self, file):
format = FortranFormat('A2,1X,A2,1X,A2,1X,A2,I4,3F15.2')
append = None
while 1:
l = FortranLine(file.readline()[:-1], format)
if l.isBlank(): break
name1 = _normalizeName(l[0])
name2 = _normalizeName(l[1])
name3 = _normalizeName(l[2])
name4 = _normalizeName(l[3])
name1, name2, name3, name4 = _sort4(name1, name2, name3, name4)
if append is not None:
append.addTerm(l[4], l[5], l[6], l[7])
if l[7] >= 0: append = None
else:
p = AmberDihedralParameters(self.atom_types[name1],
self.atom_types[name2],
self.atom_types[name3],
self.atom_types[name4], l[4], l[5],
l[6], l[7])
if name1 == 'X' and name4 == 'X':
self.dihedrals_2[(name2, name3)] = p
else:
self.dihedrals[(name1, name2, name3, name4)] = p
if l[7] < 0: append = p
def _readAtomTypes(self, file):
format = FortranFormat('A2,1X,F10.2')
while 1:
l = FortranLine(file.readline()[:-1], format)
if l.isBlank(): break
name = _normalizeName(l[0])
self.atom_types[name] = AmberAtomType(name, l[1])
def _readHbondParameters(self, file):
format = FortranFormat('2X,A2,2X,A2,2X,2F10.2')
while 1:
l = FortranLine(file.readline()[:-1], format)
if l.isBlank(): break
name1 = _normalizeName(l[0])
name2 = _normalizeName(l[1])
name1, name2 = _sort(name1, name2)
self.hbonds[(name1, name2)] = \
AmberHbondParameters(self.atom_types[name1],
self.atom_types[name2],
l[2], l[3])
def _readAngleParameters(self, file):
format = FortranFormat('A2,1X,A2,1X,A2,2F10.2')
while 1:
l = FortranLine(file.readline()[:-1], format)
if l.isBlank(): break
name1 = _normalizeName(l[0])
name2 = _normalizeName(l[1])
name3 = _normalizeName(l[2])
name1, name3 = _sort(name1, name3)
self.bond_angles[(name1, name2, name3)] = \
AmberBondAngleParameters(self.atom_types[name1],
self.atom_types[name2],
self.atom_types[name3],
l[3], l[4])
def __init__(self,atoms,outfile=None):
unitcell = atoms.get_cell()
A = Vector(unitcell[0])
B = Vector(unitcell[1])
C = Vector(unitcell[2])
# lengths of the vectors
a = A.length()#*angstroms2bohr
b = B.length()#*angstroms2bohr
c = C.length()#*angstroms2bohr
# angles between the vectors
rad2deg = 360./(2.*math.pi)
alpha = B.angle(C)*rad2deg
beta = A.angle(C)*rad2deg
gamma = A.angle(B)*rad2deg
# scaledpositions = atoms.get_scaled_positions()
# chemicalsymbols = [atom.get_symbol() for atom in atoms]
input = ''
input += '%1.3f %1.3f %1.3f %1.3f %1.3f %1.3f\n' % (a,b,c,
alpha,beta,gamma)
input += '1 1 0.1 0.1\n'
for atom in atoms:
sym = atom.get_symbol()
group = 1
x,y,z = atom.get_position()
#format(a6,i2,6f9.5)
input += str(FortranLine((sym,
group,
x,y,z),
FortranFormat('a6,i2,3f9.5')))+'\n'
pin,pout = os.popen2('symmol')
pin.writelines(input)
pin.close()
self.output = pout.readlines()
pout.close()
if outfile:
f = open(outfile,'w')
f.writelines(self.output)
f.close()
if os.path.exists('symmol.log'):
os.remove('symmol.log')
dy = event.y() - self.click3y
except AttributeError:
return
if dy != 0:
ratio = -dy/self.plotbox_size[1]
self.scale = self.scale * (1.+ratio)
self.update()
if __name__ == '__main__':
from Scientific.IO.TextFile import TextFile
from Scientific.IO.FortranFormat import FortranFormat, FortranLine
import string
generic_format = FortranFormat('A6')
atom_format = FortranFormat('A6,I5,1X,A4,A1,A3,1X,A1,I4,A1,' +
'3X,3F8.3,2F6.2,7X,A4,2A2')
# Read the PDB file and make a list of all C-alpha positions
def readCAlphaPositions(filename):
positions = []
chains = [positions]
for line in TextFile(filename):
record_type = FortranLine(line, generic_format)[0]
if record_type == 'ATOM ' or record_type == 'HETATM':
data = FortranLine(line, atom_format)
atom_name = string.strip(data[2])
position = N.array(data[8:11])
if atom_name == 'CA':
positions.append(position)
>>>print conf
>>>for residue in conf.residues:
>>> for atom in residue:
>>> print atom
"""
from Scientific.IO.TextFile import TextFile
from Scientific.IO.FortranFormat import FortranFormat, FortranLine
from Scientific.Geometry import Vector, Tensor
from PDBExportFilters import export_filters
import copy, string
#
# Fortran formats for PDB entries
#
atom_format = FortranFormat('A6,I5,1X,A4,A1,A4,A1,I4,A1,3X,3F8.3,2F6.2,' +
'6X,A4,2A2')
anisou_format = FortranFormat('A6,I5,1X,A4,A1,A4,A1,I4,A1,1X,6I7,2X,A4,2A2')
conect_format = FortranFormat('A6,11I5')
ter_format = FortranFormat('A6,I5,6X,A4,A1,I4,A1')
model_format = FortranFormat('A6,4X,I4')
header_format = FortranFormat('A6,4X,A40,A9,3X,A4')
generic_format = FortranFormat('A6,A74')
#
# Amino acid and nucleic acid residues
#
amino_acids = [
'ALA', 'ARG', 'ASN', 'ASP', 'CYS', 'CYX', 'GLN', 'GLU', 'GLY', 'HIS',
'HID', 'HIE', 'HIP', 'HSD', 'HSE', 'HSP', 'ILE', 'LEU', 'LYS', 'MET',
'PHE', 'PRO', 'SER', 'THR', 'TRP', 'TYR', 'VAL', 'ACE', 'NME', 'NHE'
]
def __init__(self, file, modifications=[]):
if isinstance(file, str):
file = TextFile(file)
title = file.readline()[:-1]
self.atom_types = DictWithDefault(None)
self._readAtomTypes(file)
format = FortranFormat('20(A2,2X)')
done = 0
while not done:
l = FortranLine(file.readline()[:-1], format)
for entry in l:
name = _normalizeName(entry)
if len(name) == 0:
done = 1
break
try: # ignore errors for now
self.atom_types[name].hydrophylic = 1
except:
pass
self.bonds = {}
self._readBondParameters(file)
self.bond_angles = {}
self._readAngleParameters(file)
self.dihedrals = {}
self.dihedrals_2 = {}
self._readDihedralParameters(file)
self.impropers = {}
self.impropers_1 = {}
self.impropers_2 = {}
self._readImproperParameters(file)
self.hbonds = {}
self._readHbondParameters(file)
self.lj_equivalent = {}
format = FortranFormat('20(A2,2X)')
while 1:
l = FortranLine(file.readline()[:-1], format)
if l.isBlank(): break
name1 = _normalizeName(l[0])
for s in l[1:]:
name2 = _normalizeName(s)
self.lj_equivalent[name2] = name1
self.ljpar_sets = {}
while 1:
l = FortranLine(file.readline()[:-1], 'A4,6X,A2')
if l[0] == 'END ': break
set_name = _normalizeName(l[0])
ljpar_set = AmberLJParameterSet(set_name, l[1])
self.ljpar_sets[set_name] = ljpar_set
self._readLJParameters(file, ljpar_set)
file.close()
for mod, ljname in modifications:
if isinstance(mod, str):
file = TextFile(mod)
else:
file = mod
title = file.readline()[:-1]
blank = file.readline()[:-1]
while 1:
keyword = file.readline()
if not keyword: break
keyword = string.strip(keyword)[:4]
if keyword == 'MASS':
self._readAtomTypes(file)
elif keyword == 'BOND':
self._readBondParameters(file)
elif keyword == 'ANGL':
self._readAngleParameters(file)
elif keyword == 'DIHE':
self._readDihedralParameters(file)
elif keyword == 'IMPR':
self._readImproperParameters(file)
elif keyword == 'HBON':
self._readHbondParameters(file)
elif keyword == 'NONB':
self._readLJParameters(file, self.ljpar_sets[ljname])
1) Type 'mkfifo HISTORY' in dlpoly_directory.
2) Start dlpoly_to_nc.
3) Start DLPOLY.
"""
_elements2 = [
'cl', 'as', 'in', 'tb', 'tl', 'he', 'ar', 'se', 'sn', 'dy', 'pb', 'li',
'br', 'sb', 'ho', 'bi', 'be', 'ca', 'kr', 'te', 'er', 'po', 'sc', 'rb',
'tm', 'at', 'ti', 'sr', 'xe', 'yb', 'rn', 'cs', 'lu', 'fr', 'cr', 'zr',
'ba', 'hf', 'ra', 'mn', 'nb', 'la', 'ta', 'ac', 'ne', 'fe', 'mo', 'ce',
'th', 'na', 'co', 'tc', 'pr', 're', 'pa', 'mg', 'ni', 'ru', 'nd', 'os',
'al', 'cu', 'rh', 'pm', 'ir', 'np', 'si', 'zn', 'pd', 'sm', 'pt', 'pu',
'ga', 'ag', 'eu', 'au', 'am', 'ge', 'cd', 'gd', 'hg', 'cm', 'cf'
]
field_atom_line = FortranFormat('A8,2F12,3I5')
history_timestep_line = FortranFormat('A8,4I10,F12.6')
history_pbc_line = FortranFormat('3G12.4')
class DLPOLYData:
def __init__(self, directory):
self.directory = directory
self.history = open(os.path.join(self.directory, 'HISTORY'))
self.title = string.strip(self.history.readline())
info = FortranLine(self.history.readline(), '2I10')
if info[1] > 3:
raise ValueError, "box shape not implemented"
nvectors = info[0] + 1
self.makeUniverse(info[1], self.readField())
if nvectors > 1:
def write_bgf(atoms, geofile=None):
'''
prepares a bgf entry from an atoms object and writes it to the geofile
'''
if geofile is None:
geofile = 'geo'
# create the geofile if it does not already exist
if not os.path.exists(geofile):
f = open(geofile, 'w')
f.close()
# get descriptions to make sure they are all unique.
f = open(geofile, 'r')
DESCRIPTIONS = []
for line in f.readlines():
if line.startswith('DESCRP'):
DESCRIPTIONS.append(line[6:].strip())
f.close()
# we need a hash of something to check for uniqueness of the atoms.
description = reax_hash(atoms)
if description in DESCRIPTIONS:
raise Exception, 'Non-unique description "%s" in geofile' % description
# now prepare the unit cell information for the CRYSTX line
uc = atoms.get_cell()
a, b, c = [Vector(x) for x in uc]
A = a.length()
B = b.length()
C = c.length()
rad2deg = 360. / (2 * math.pi)
alpha = b.angle(c) * rad2deg
beta = a.angle(c) * rad2deg
gamma = a.angle(b) * rad2deg
crstx = str(
FortranLine(('CRYSTX', A, B, C, alpha, beta, gamma),
FortranFormat('a6,1x,6f11.5')))
# now we prepare each atom line. These are printed in the template.
atom_lines = []
reax_coords = reax_coordinates(atoms)
fmt = FortranFormat(
'a6,1x,i5,1x,a5,1x,a3,1x,a1,1x,a5,3f10.5,1x,a5,i3,i2,1x,f8.5')
for i, atom in enumerate(atoms):
x, y, z = reax_coords[i]
line = FortranLine(('HETATM', i, atom.symbol, '', '', '', x, y, z,
atom.symbol, 1, 1, 0.0), fmt)
atom_lines.append(line)
# energy in kcal
calc = atoms.get_calculator()
if calc is not None:
directory = os.path.abspath(calc.vaspdir)
energy = atoms.get_potential_energy() * 23.061
else:
directory = 'None'
energy = 'None'
bgf = Template(bgf_template, searchList=[locals()])
entry = bgf.respond()
if geofile is None:
geofile = 'geo'
f = open(geofile, 'a')
f.write(entry)
f.close()
from Scientific import N as Num
# The MMTK distribution modules
from MMTK.PDB import PDBOutputFile
from MMTK import Units
from MMTK.Trajectory import Trajectory
# The nMOLDYN modules
from nMOLDYN.GlobalVariables import GVAR
from nMOLDYN.Preferences import PREFERENCES
from nMOLDYN.Core.Error import Error
from nMOLDYN.Core.IO import load_trajectory_file
from nMOLDYN.Core.Logger import LogMessage
from nMOLDYN.GUI.Widgets import *
atom_format = FortranFormat(
'A6,I5,1X,A4,A1,A4,A1,I4,A1,3X,3F8.3,2F6.2,6X,A4,2A2')
class PDBSnapshotGeneratorDialog(PortableToplevel):
"""Sets up a dialog used to export one or several trajectory frames into a PDB file.
@note: if a trajectory has been previously loaded in nMOLDYN this will be the one proposed for extraction
by default. Otherwise, the user can still choose a trajectory to visualize from the dialog.
"""
def __init__(self, parent, title=None):
"""The constructor.
@param parent: the parent widget.
@param title: a string specifying the title of the dialog.
@type title: string
