class SceneFile:
def __init__(self, filename, mode='r'):
if mode == 'r':
raise TypeError, 'Not implemented.'
self.file = TextFile(filename, 'w')
self.file.write('#VRML V2.0 utf8\n')
self.file.write('Transform { children [\n')
self.memo = {}
self.name_counter = 0
def __del__(self):
self.close()
def writeString(self, data):
self.file.write(data)
def close(self):
if self.file is not None:
self.file.write(']}\n')
self.file.close()
self.file = None
def write(self, object):
object.writeToFile(self)
def uniqueName(self):
self.name_counter = self.name_counter + 1
return 'i' + ` self.name_counter `
class SceneFile:
def __init__(self, filename, mode = 'r'):
if mode == 'r':
raise TypeError('Not yet implemented.')
self.file = TextFile(filename, 'w')
self.file.write('#VRML V1.0 ascii\n')
self.file.write('Separator {\n')
self.memo = {}
self.name_counter = 0
def __del__(self):
self.close()
def writeString(self, data):
self.file.write(data)
def close(self):
if self.file is not None:
self.file.write('}\n')
self.file.close()
self.file = None
def write(self, object):
object.writeToFile(self)
def uniqueName(self):
self.name_counter = self.name_counter + 1
return 'i' + `self.name_counter`
class SceneFile:
def __init__(self, filename, mode='r'):
if mode == 'r':
raise TypeError('Not yet implemented.')
self.file = TextFile(filename, 'w')
self.file.write('#VRML V1.0 ascii\n')
self.file.write('Separator {\n')
self.memo = {}
self.name_counter = 0
def __del__(self):
self.close()
def writeString(self, data):
self.file.write(data)
def close(self):
if self.file is not None:
self.file.write('}\n')
self.file.close()
self.file = None
def write(self, object):
object.writeToFile(self)
def uniqueName(self):
self.name_counter = self.name_counter + 1
return 'i' + ` self.name_counter `
class SceneFile(object):
def __init__(self, filename, mode='r', scale=1.):
if mode == 'r':
raise TypeError('Not yet implemented.')
self.file = TextFile(filename, 'w')
self.filename = filename
self._init(scale)
def _init(self, scale):
self.memo = {}
self.scale = scale
def __del__(self):
self.close()
def writeString(self, data):
self.file.write(data)
def writeVector(self, v):
self.writeString(" %g %g %g " % tuple(v))
def close(self):
self.file.close()
def write(self, object):
object.writeToFile(self)
def getData(filename):
"""
reads columns of data stored in an ASCII file and
return an multidimensional array with it
"""
try:
f = TextFile(filename, "r")
except:
return None
lines = f.readlines()
i = 0
data = []
ole = 0
for ia in lines:
data.append([])
if ia[0] != '#':
try:
ie = index(ia, '#')
except ValueError:
ie = len(ia)
for ib in split(ia[:ie]):
data[i].append(float(ib))
i = i + 1
ile = len(split(ia[:ie]))
if ile > ole: ole = ile
res = zeros((i, ole), N.Float)
for item in range(len(data)):
if len(data[item]) != 0:
for num in range(len(data[item])):
res[item, num] = data[item][num]
return res
class SceneFile:
def __init__(self, filename, mode = 'r'):
if mode == 'r':
raise TypeError, 'Not implemented.'
self.file = TextFile(filename, 'w')
self.file.write('#VRML V2.0 utf8\n')
self.file.write('Transform { children [\n')
self.memo = {}
self.name_counter = 0
def __del__(self):
self.close()
def writeString(self, data):
self.file.write(data)
def close(self):
if self.file is not None:
self.file.write(']}\n')
self.file.close()
self.file = None
def write(self, object):
object.writeToFile(self)
def uniqueName(self):
self.name_counter = self.name_counter + 1
return 'i' + `self.name_counter`
class SceneFile:
def __init__(self, filename, mode = 'r', scale = 1., delete = 0):
if mode == 'r':
raise TypeError, 'Not yet implemented.'
self.file = TextFile(filename, 'w')
self.memo = {}
self.delete = delete
self.scale = scale
self.filename = filename
self.writeString('proc mmtk_graphics {} {\n')
self.writeString('mol new graphics {MMTK Graphics}\n')
def __del__(self):
self.close()
def writeString(self, data):
self.file.write(data)
def writeVector(self, v):
self.writeString(" {%g %g %g}" % tuple(v))
def close(self):
if self.file is not None:
self.writeString('}\nmmtk_graphics\n')
self.writeString('display resetview\n')
if self.delete:
self.writeString('file delete ' + self.filename)
self.file.close()
self.file = None
def write(self, object):
object.writeToFile(self)
class SceneFile:
def __init__(self, filename, mode='r', scale=1., delete=0):
if mode == 'r':
raise TypeError, 'Not yet implemented.'
self.file = TextFile(filename, 'w')
self.memo = {}
self.delete = delete
self.scale = scale
self.filename = filename
self.writeString('proc mara_graphics {} {\n')
self.writeString('mol new\n')
self.writeString('mol rename top mara\n')
def __del__(self):
self.close()
def writeString(self, data):
self.file.write(data)
def writeVector(self, v):
self.writeString(" {%g %g %g}" % tuple(v))
def close(self):
if self.file is not None:
self.writeString('}\nmara_graphics\n')
self.writeString('display resetview\n')
if self.delete:
self.writeString('file delete ' + self.filename)
self.file.close()
self.file = None
def write(self, object):
object.writeToFile(self)
def __init__(self, filename, mode='r'):
if mode == 'r':
raise TypeError, 'Not implemented.'
self.file = TextFile(filename, 'w')
self.file.write('#VRML V2.0 utf8\n')
self.file.write('Transform { children [\n')
self.memo = {}
self.name_counter = 0
def __init__(self, filename, mode='r'):
if mode == 'r':
raise TypeError('Not yet implemented.')
self.file = TextFile(filename, 'w')
self.file.write('#VRML V1.0 ascii\n')
self.file.write('Separator {\n')
self.memo = {}
self.name_counter = 0
def __init__(self, filename, mode='r', scale=1., delete=False):
if mode == 'r':
raise TypeError('Not yet implemented.')
self.file = TextFile(filename, 'w')
self.memo = {}
self.delete = delete
self.scale = scale
self.filename = filename
self.writeString('proc python_graphics {} {\n')
self.writeString('mol new\n')
self.writeString('graphics 0 color 35\n')
def __init__(self, filename, mode='r', scale=1., delete=0):
if mode == 'r':
raise TypeError, 'Not yet implemented.'
self.file = TextFile(filename, 'w')
self.memo = {}
self.delete = delete
self.scale = scale
self.filename = filename
self.writeString('proc mara_graphics {} {\n')
self.writeString('mol new\n')
self.writeString('mol rename top mara\n')
def saveText(master=None, data=None, filename=None, title=None):
if not filename:
if master:
from nMoldyn.gui import FileDialog
fd = FileDialog.SaveFileDialog(master)
filename = fd.go(key='SaveText', pattern='*.txt')
else:
raise "Undetectable_System_Error",\
"No master for a slave"
if data is None:
raise ValueError, "no data to be saved"
if title is None: title = "pMoldyn data"
if filename:
file = TextFile(filename, 'w')
line = '#\n# ' + title + '\n#\n'
file.write(line)
for i in range(len(data)):
line = ''
for ia in range(len(data[i])):
line = line + str(data[i][ia]) + ' '
line = line + '\n'
file.write(line)
file.close()
return filename
def writeDataSets(datasets, filename, separator=''):
"""
Write multiple datasets to a text file.
@param datasets: a sequence of datasets describing a curve to be
plotted. Each dataset is either a 1d-array
(list of values) or a 2d-array of shape N x 2
(list of (x, y) pairs). Nested lists can be used
instead of arrays.
@param filename: the name of the output file
@type filename: C{str}
@param separator: the contents of the line that is written between
two datasets
@type separator: C{str}
"""
file = TextFile(filename, 'w')
nsets = len(datasets)
for i in range(nsets):
d = Numeric.array(list(datasets[i]))
if len(d.shape) == 1:
d = d[:, Numeric.NewAxis]
for point in d:
for number in point:
file.write( ` number ` + ' ')
file.write('\n')
if (i < nsets - 1):
file.write(separator + '\n')
file.close()
def readArray(filename):
"""
Read array data from a file
This function works for arbitrary data types (every array element can be
given by an arbitrary Python expression), but at the price of being
slow. For large arrays, use L{readFloatArray} or L{readIntegerArray}
if possible.
@param filename: the name of the file to read
@type filename: C{str}
@returns: an array containing the data from the file
@rtype: C{Numeric.array}
"""
data = []
for line in TextFile(filename):
if len(line) == 0 and len(data) > 0:
break
if line[0] != '#':
data.append(map(eval, string.split(line)))
a = Numeric.array(data)
if a.shape[0] == 1 or a.shape[1] == 1:
a = Numeric.ravel(a)
return a
def __init__(self, filename, mode = 'r'):
if mode == 'r':
raise TypeError, 'Not yet implemented.'
self.file = TextFile(filename, 'w')
self.file.write('#VRML V1.0 ascii\n')
self.file.write('Separator {\n')
self.memo = {}
self.name_counter = 0
def __init__(self, filename, mode = 'r'):
if mode == 'r':
raise TypeError, 'Not implemented.'
self.file = TextFile(filename, 'w')
self.file.write('#VRML V2.0 utf8\n')
self.file.write('Transform { children [\n')
self.memo = {}
self.name_counter = 0
def __init__(self, filename, mode='r', subformat=None):
self.file = TextFile(filename, mode)
self.output = string.lower(mode[0]) == 'w'
self.export_filter = None
if subformat is not None:
export = export_filters.get(subformat, None)
if export is not None:
self.export_filter = export()
self.open = 1
if self.output:
self.data = {
'serial_number': 0,
'residue_number': 0,
'chain_id': '',
'segment_id': ''
}
self.het_flag = 0
self.chain_number = -1
def __init__(self, filename, mode = 'r', scale = 1., delete = 0):
if mode == 'r':
raise TypeError, 'Not yet implemented.'
self.file = TextFile(filename, 'w')
self.memo = {}
self.delete = delete
self.scale = scale
self.filename = filename
self.writeString('proc mmtk_graphics {} {\n')
self.writeString('mol new graphics {MMTK Graphics}\n')
def readIntegerArray(filename):
"Return an integer array containing the data from file |filename|."
data = []
for line in TextFile(filename):
if line[0] != '#':
data.append(map(string.atoi, string.split(line)))
a = Numeric.array(data)
if a.shape[0] == 1 or a.shape[1] == 1:
a = Numeric.ravel(a)
return a
def __init__(self, filename, mode = 'r', scale = 1., delete = False):
if mode == 'r':
raise TypeError('Not yet implemented.')
self.file = TextFile(filename, 'w')
self.memo = {}
self.delete = delete
self.scale = scale
self.filename = filename
self.writeString('proc python_graphics {} {\n')
self.writeString('mol new\n')
self.writeString('graphics 0 color 35\n')
def getProgress():
""" Provide info about currently running calculations.
The name of a job (eg. the module name), a job ID,
a job owner, the date of starting
and a progress in percents are shown """
list = listdir(gettempdir())
list2 = []
owner = getpass.getuser()
for file in list:
try:
a = split(file, '.')
if a[-1] == 'moldyn' and a[-4] == owner:
jobID = int(a[-3])
try:
kill(jobID, 0)
list2.append(file)
except:
unlink(file)
except:
pass
if len(list2) == 0:
print "\n There are no currently running calculations\n"
else:
print '\n Progress indicator'
print ' --------------------'
print ' Module . Job ID . Job Owner .'+\
' Started . Progress'
print ' ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~'+\
'~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~'
for file in list2:
record = split(file, '.')
mod = record[-2]
jobID = int(record[-3])
jobOwner = record[-4]
temp = gettempdir()
filename = path.join(temp, file)
f = TextFile(filename, 'r')
l = []
for line in f:
l.append(line[:-1])
if len(l) > 1:
try:
t = l[0]
prog = l[len(l) - 1] + ' %'
print ' ' + rjust(mod,9),'.' + rjust(str(jobID),7),'.' +\
rjust(jobOwner,12),'.' + rjust(t,31),'.' + \
rjust(prog,8)
except:
pass
print
def writeArray(array, filename, mode='w'):
"""Write array |a| to file |filename|. |mode| can be 'w' (new file)
or 'a' (append)."""
file = TextFile(filename, mode)
if len(array.shape) == 1:
array = array[:, Numeric.NewAxis]
for line in array:
for element in line:
file.write(`element` + ' ')
file.write('\n')
file.close()
def writeDataSets(datasets, filename, separator = ''):
"""Write each of the items in the sequence |datasets|
to the file |filename|, separating the datasets by a line
containing |separator|. The items in the data sets can be
one- or two-dimensional arrays or equivalent nested sequences.
The output file format is understood by many plot programs.
"""
file = TextFile(filename, 'w')
nsets = len(datasets)
for i in range(nsets):
d = Numeric.array(datasets[i])
if len(d.shape) == 1:
d = d[:, Numeric.NewAxis]
for point in d:
for number in point:
file.write(`number` + ' ')
file.write('\n')
if (i < nsets-1):
file.write(separator + '\n')
file.close()
def readArray(filename):
"""Return an array containing the data from file |filename|. This
function works for arbitrary data types (every array element can be
given by an arbitrary Python expression), but at the price of being
slow. For large arrays, use readFloatArray or readIntegerArray
if possible."""
data = []
for line in TextFile(filename):
if len(line) == 0 and len(data) > 0:
break
if line[0] != '#':
data.append(map(eval, string.split(line)))
a = Numeric.array(data)
if a.shape[0] == 1 or a.shape[1] == 1:
a = Numeric.ravel(a)
return a
def __init__(self, filename, mode = 'r', subformat = None):
self.file = TextFile(filename, mode)
self.output = string.lower(mode[0]) == 'w'
self.export_filter = None
if subformat is not None:
export = export_filters.get(subformat, None)
if export is not None:
self.export_filter = export()
self.open = 1
if self.output:
self.data = {'serial_number': 0,
'residue_number': 0,
'chain_id': '',
'segment_id': ''}
self.het_flag = 0
self.chain_number = -1
def writeArray(array, filename, mode='w'):
"""Write array |a| to file |filename|. |mode| can be 'w' (new file)
or 'a' (append)."""
file = TextFile(filename, mode)
if len(array.shape) == 1:
array = array[:, Numeric.NewAxis]
for line in array:
for element in line:
file.write(`element` + ' ')
file.write('\n')
file.close()
def logfileInit(modName):
""" create a file with information about currently running calculations
(progress, start date, etc.) """
t1 = asctime(localtime(time())) + '\n0\n'
owner = getpass.getuser()
pid = getpid()
filename = join([mktemp(), owner, str(pid), modName, 'moldyn'], '.')
file = TextFile(filename, 'w')
file.write(t1)
file.flush()
return file, filename
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)
elif atom_name == 'OXT':
positions = []
chains.append(positions)
if len(chains[-1]) == 0:
del chains[-1]
return chains
def readIntegerArray(filename):
"""
Read array data from a file into an array of integers
@param filename: the name of the file to read
@type filename: C{str}
@returns: an array containing the data from the file
@rtype: C{Numeric.array} of C{int}
"""
data = []
for line in TextFile(filename):
if line[0] != '#':
data.append(map(string.atoi, string.split(line)))
a = Numeric.array(data)
if a.shape[0] == 1 or a.shape[1] == 1:
a = Numeric.ravel(a)
return a
def writeDataSets(datasets, filename, separator = ''):
"""Write each of the items in the sequence |datasets|
to the file |filename|, separating the datasets by a line
containing |separator|. The items in the data sets can be
one- or two-dimensional arrays or equivalent nested sequences.
The output file format is understood by many plot programs.
"""
file = TextFile(filename, 'w')
nsets = len(datasets)
for i in range(nsets):
d = Numeric.array(datasets[i])
if len(d.shape) == 1:
d = d[:, Numeric.NewAxis]
for point in d:
for number in point:
file.write(`number` + ' ')
file.write('\n')
if (i < nsets-1):
file.write(separator + '\n')
file.close()
def __init__(self, filename, model = 1, alternate_code = 'A'):
self.filename = filename
self.model = model
self.alternate = alternate_code
self.residues = []
self.objects = []
self.peptide_chains = []
self.nucleotide_chains = []
self.molecules = {}
self.prefix = None
self.chem_comp = None
self.entity_names = None
self.entities = None
self.chain_entities = None
self.chains = None
self.nonchains = None
self.atoms = {}
self.parseFile(TextFile(filename))
self._numberAtoms()
def __init__(self,
file_name=None,
file_object=None,
pdb_code=None,
pdb_sf_code=None):
"""
Specify the mmCIF file to be loaded. Only one of the four
keyword parameters may be given a value.
:param file_name: the name of a file. Compressed or gzipped files
can be handled directly
:type file_name: str
:param file_object: a file object
:type file_object: file
:param pdb_code: the PDB code for a structure file, which is
taken from a public or local PDB repository (see CDTK.PDBRepository)
:type pdb_code: str
:param pdb_sf_code: the PDB code for a structure factor file, which
is taken from a public or local PDB repository
(see CDTK.PDBRepository)
:type pdb_sf_code: str
"""
self.line_number = 0
if file_name is not None:
assert file_object is None
assert pdb_code is None
assert pdb_sf_code is None
self.file_object = TextFile(file_name)
elif file_object is not None:
assert pdb_code is None
assert pdb_sf_code is None
self.file_object = file_object
elif pdb_code is not None:
assert pdb_sf_code is None
from CDTK.PDBRepository import mmcif_files
self.file_object = mmcif_files.getFile(pdb_code)
elif pdb_sf_code is not None:
from CDTK.PDBRepository import sf_files
self.file_object = sf_files.getFile(pdb_sf_code)
else:
raise ValueError("No input file given")
def writeArray(array, filename, mode='w'):
"""
Write a text representation of an array to a file.
@param array: the array to be written
@type array: C{Numeric.array}
@param filename: the name of the output file
@type filename: C{str}
@param mode: the file access mode, 'w' (new file) or 'a' (append)
@type mode: C{str}
"""
file = TextFile(filename, mode)
if len(array.shape) == 1:
array = array[:, Numeric.NewAxis]
for line in array:
for element in line:
file.write( ` element ` + ' ')
file.write('\n')
file.close()
def __init__(self,
sf_file=None,
structure_file=None,
pdb_code=None,
fill=False,
load_model_sf=True,
require_sigma=True):
"""
Specify the data to be loaded. The following combinations
are valid:
- pdb_code only: the data is taken from a public or local
PDB repository
- sf_file only: the data is taken from the structure
factor file
- sf_file and structure_file: cell and/or symmetry information
is read from structure_file if it is missing in sf_file
:param sf_file: the name of the structure factor mmCIF file
:type sf_file: str
:param structure_file: the name of the structure mmCIF file
:type structure_file: str
:param pdb_code: a four-letter PDB code
:type pdb_code: str
:param fill: True if the reflection set should contain all
reflections in the resolution sphere. With the default value
of False, only the reflections listed in the mmCIF file
will be present in the reflection set.
:type fill: bool
:param load_model_sf: True if model structure factors (F_calc)
should be loaded if present in the file
:type load_model_sf: bool
:param require_sigma: if True, ignore experimental data points
without sigma. If False, set sigma to zero
if it is not given.
:type require_sigma: bool
"""
if pdb_code is not None:
self.pdb_code = pdb_code
assert sf_file is None
assert structure_file is None
elif sf_file is not None:
self.pdb_code = None
if isinstance(sf_file, str):
sf_file = TextFile(sf_file)
self.sf_file = sf_file
if structure_file is not None:
if isinstance(structure_file, str):
structure_file = TextFile(structure_file)
self.structure_file = structure_file
else:
raise MMCIFError("No structure factor data given")
self.load_model_sf = load_model_sf
self.require_sigma = require_sigma
self.cell = {}
self.symmetry = {}
self.reflections = None
self.parseSFFile()
self.finalize(fill)
# [xyz_atomFile]: Contains the xyz coordinates of each atom of each molecule # [xyz_CMEAFile]: Contains the xyz coordinates of the centre of mass (CM) and Euler Angles (EA) of each molecule ########### # Output: Returns the RMS difference between the two different configurations ############################################################################################### from MMTK import * import sys import ClathIO as CIO from Scientific.IO.TextFile import TextFile import numpy as np universe = InfiniteUniverse() #universe = OrthorhombicPeriodicUniverse((2,2,2)) xyz_atomFile = TextFile(sys.argv[1]) xyz_CMEAFile = TextFile(sys.argv[2]) #Set positions of O and H atoms from original xyz file CIO.readClathrate_xyz(xyz_atomFile, universe) #universe.view() conf_xyz = copy(universe.configuration()) # Empty the universe #universe = OrthorhombicPeriodicUniverse((2,2,2)) #universe = InfiniteUniverse() #Set water molecule positions from ZY'Z'' Euler Angles and Centre of Mass data CIO.readClathrate104_ZYZ_oneBead(xyz_CMEAFile, universe)
def __init__(self, file, modifications=[]):
if isinstance(file, basestring):
file = TextFile(file)
title = file.readline()[:-1]
self.atom_types = DictWithDefault(None)
self._readAtomTypes(file)
format = FortranFormat('20(A2,2X)')
done = False
while not done:
l = FortranLine(file.readline()[:-1], format)
for entry in l:
name = _normalizeName(entry)
if len(name) == 0:
done = True
break
try: # ignore errors for now
self.atom_types[name].hydrophylic = True
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 True:
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 True:
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, basestring):
file = TextFile(mod)
else:
file = mod
title = file.readline()[:-1]
blank = file.readline()[:-1]
while True:
keyword = file.readline()
if not keyword: break
keyword = keyword.strip()[: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])
"""argon.py"""
# Constant-temperature constant-pressure MD simulation of Argon
from MMTK import *
from MMTK.ForceFields import LennardJonesForceField
from MMTK.Environment import NoseThermostat, AndersenBarostat
from MMTK.Trajectory import Trajectory, TrajectoryOutput, LogOutput
from MMTK.Dynamics import VelocityVerletIntegrator, Velocity Scaler, \
TranslationRemover, BarostatReset
import string
from Scientific.IO.TextFile import TextFile
# Open the config file and read box size
conf_file = TextFile('argon.conf.gz')
lx, ly, lz = map(string.atof, string.split(conf_file.readline()))
# Construct periodic universe using Lennard-Jones (noble gas) force field
# with cutoff of 15 Angstroms
universe = OrthorhombicPeriodicUniverse((lx*Units.Ang, ly*Units.Ang, lz*Units.Ang),
LennardJonesForceField(15.*Units.Ang))
# Read the atom positions and construct the atoms
while 1:
line = conf_file.readline()
if not line:
break
x, y, z, = map(string.atof, string.split(line))
universe.addObject(Atom('Ar', position=Vector(x*Units.Ang, y*Units.Ang, z*Units.Ang)))
# Define thermodynamic parameters
out_dict = Clath_xyz.readWaterAtoms(xyz_atomFilename)
Hyd = out_dict["H"]
Oxy = out_dict["O"]
print "Read in atom positions. There are %d H atoms and %s O atoms." % (len(Hyd), len(Oxy))
###############################################################################
# Read in the Cage Centre locations
###############################################################################
large_cages = []
small_cages = []
# Open input file
xyz_file = TextFile(xyz_cageFilename)
# Ignore first two lines of the file
junk = xyz_file.readline()
junk = xyz_file.readline()
while 1:
line = xyz_file.readline()
if not line:
break
x, y, z = map(float, string.split(line)[1:]) # ignore atom label
cage_type = string.split(line)[0] # get the atom type
# Convert coordinates based on atom type
# Constant-temperature constant-pressure MD simulation of Argon.
#
from MMTK import *
from MMTK.ForceFields import LennardJonesForceField
from MMTK.Environment import NoseThermostat, AndersenBarostat
from MMTK.Trajectory import Trajectory, TrajectoryOutput, LogOutput
from MMTK.Dynamics import VelocityVerletIntegrator, VelocityScaler, \
TranslationRemover, BarostatReset
import string
from Scientific.IO.TextFile import TextFile
# Open the configuration file and read the box size.
conf_file = TextFile('argon.conf.gz')
lx, ly, lz = map(string.atof, string.split(conf_file.readline()))
# Construct a periodic universe using a Lennard-Jones (noble gas) force field
# with a cutoff of 15 Angstrom.
universe = OrthorhombicPeriodicUniverse(
(lx * Units.Ang, ly * Units.Ang, lz * Units.Ang),
LennardJonesForceField(15. * Units.Ang))
# Read the atom positions and construct the atoms.
while 1:
line = conf_file.readline()
if not line: break
x, y, z = map(string.atof, string.split(line))
universe.addObject(
Atom('Ar',
position=Vector(x * Units.Ang, y * Units.Ang, z * Units.Ang)))
# Define thermodynamic parameters.
def __init__(self, filename, mode='r', scale=1.):
if mode == 'r':
raise TypeError('Not yet implemented.')
self.file = TextFile(filename, 'w')
self.filename = filename
self._init(scale)
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])
class PDBFile:
"""PDB file with access at the record level
Constructor: PDBFile(|filename|, |mode|='"r"'), where |filename|
is the file name and |mode| is '"r"' for reading and '"w"' for writing,
The low-level file access is handled by the module
Scientific.IO.TextFile, therefore compressed files and URLs
(for reading) can be used as well.
"""
def __init__(self, filename, mode='r', subformat=None):
self.file = TextFile(filename, mode)
self.output = string.lower(mode[0]) == 'w'
self.export_filter = None
if subformat is not None:
export = export_filters.get(subformat, None)
if export is not None:
self.export_filter = export()
self.open = 1
if self.output:
self.data = {
'serial_number': 0,
'residue_number': 0,
'chain_id': '',
'segment_id': ''
}
self.het_flag = 0
self.chain_number = -1
def readLine(self):
"""Returns the contents of the next non-blank line (= record).
The return value is a tuple whose first element (a string)
contains the record type. For supported record types (HEADER,
ATOM, HETATM, ANISOU, TERM, MODEL, CONECT), the items from the
remaining fields are put into a dictionary which is returned
as the second tuple element. Most dictionary elements are
strings or numbers; atom positions are returned as a vector,
and anisotropic temperature factors are returned as a rank-2
tensor, already multiplied by 1.e-4. White space is stripped
from all strings except for atom names, whose correct
interpretation can depend on an initial space. For unsupported
record types, the second tuple element is a string containing
the remaining part of the record.
"""
while 1:
line = self.file.readline()
if not line: return ('END', '')
if line[-1] == '\n': line = line[:-1]
line = string.strip(line)
if line: break
line = string.ljust(line, 80)
type = string.strip(line[:6])
if type == 'ATOM' or type == 'HETATM':
line = FortranLine(line, atom_format)
data = {
'serial_number': line[1],
'name': line[2],
'alternate': string.strip(line[3]),
'residue_name': string.strip(line[4]),
'chain_id': string.strip(line[5]),
'residue_number': line[6],
'insertion_code': string.strip(line[7]),
'position': Vector(line[8:11]),
'occupancy': line[11],
'temperature_factor': line[12],
'segment_id': string.strip(line[13]),
'element': string.strip(line[14]),
'charge': string.strip(line[15])
}
return type, data
elif type == 'ANISOU':
line = FortranLine(line, anisou_format)
data = {
'serial_number':
line[1],
'name':
line[2],
'alternate':
string.strip(line[3]),
'residue_name':
string.strip(line[4]),
'chain_id':
string.strip(line[5]),
'residue_number':
line[6],
'insertion_code':
string.strip(line[7]),
'u':
1.e-4 * Tensor([[line[8], line[11], line[12]],
[line[11], line[9], line[13]],
[line[12], line[13], line[10]]]),
'segment_id':
string.strip(line[14]),
'element':
string.strip(line[15]),
'charge':
string.strip(line[16])
}
return type, data
elif type == 'TER':
line = FortranLine(line, ter_format)
data = {
'serial_number': line[1],
'residue_name': string.strip(line[2]),
'chain_id': string.strip(line[3]),
'residue_number': line[4],
'insertion_code': string.strip(line[5])
}
return type, data
elif type == 'CONECT':
line = FortranLine(line, conect_format)
data = {
'serial_number': line[1],
'bonded': filter(lambda i: i > 0, line[2:6]),
'hydrogen_bonded': filter(lambda i: i > 0, line[6:10]),
'salt_bridged': filter(lambda i: i > 0, line[10:12])
}
return type, data
elif type == 'MODEL':
line = FortranLine(line, model_format)
data = {'serial_number': line[1]}
return type, data
elif type == 'HEADER':
line = FortranLine(line, header_format)
data = {'compound': line[1], 'date': line[2], 'pdb_code': line[3]}
return type, data
else:
return type, line[6:]
def writeLine(self, type, data):
"""Writes a line using record type and data dictionary in the
same format as returned by readLine(). Default values are
provided for non-essential information, so the data dictionary
need not contain all entries.
"""
if self.export_filter is not None:
type, data = self.export_filter.processLine(type, data)
if type is None:
return
line = [type]
if type == 'ATOM' or type == 'HETATM':
format = atom_format
position = data['position']
line = line + [
data.get('serial_number', 1),
data.get('name'),
data.get('alternate', ''),
string.rjust(data.get('residue_name', ''), 3),
data.get('chain_id', ''),
data.get('residue_number', 1),
data.get('insertion_code', ''), position[0], position[1],
position[2],
data.get('occupancy', 0.),
data.get('temperature_factor', 0.),
data.get('segment_id', ''),
string.rjust(data.get('element', ''), 2),
data.get('charge', '')
]
elif type == 'ANISOU':
format = anisou_format
u = 1.e4 * data['u']
u = [
int(u[0, 0]),
int(u[1, 1]),
int(u[2, 2]),
int(u[0, 1]),
int(u[0, 2]),
int(u[1, 2])
]
line = line + [data.get('serial_number', 1),
data.get('name'),
data.get('alternate', ''),
string.rjust(data.get('residue_name'), 3),
data.get('chain_id', ''),
data.get('residue_number', 1),
data.get('insertion_code', '')] \
+ u \
+ [data.get('segment_id', ''),
string.rjust(data.get('element', ''), 2),
data.get('charge', '')]
elif type == 'TER':
format = ter_format
line = line + [
data.get('serial_number', 1),
string.rjust(data.get('residue_name'), 3),
data.get('chain_id', ''),
data.get('residue_number', 1),
data.get('insertion_code', '')
]
elif type == 'CONECT':
format = conect_format
line = line + [data.get('serial_number')]
line = line + (data.get('bonded', []) + 4 * [None])[:4]
line = line + (data.get('hydrogen_bonded', []) + 4 * [None])[:4]
line = line + (data.get('salt_bridged', []) + 2 * [None])[:2]
elif type == 'MODEL':
format = model_format
line = line + [data.get('serial_number')]
elif type == 'HEADER':
format = header_format
line = line + [
data.get('compound', ''),
data.get('date', ''),
data.get('pdb_code')
]
else:
format = generic_format
line = line + [data]
self.file.write(str(FortranLine(line, format)) + '\n')
def writeComment(self, text):
"""Writes |text| into one or several comment lines.
Each line of the text is prefixed with 'REMARK' and written
to the file.
"""
while text:
eol = string.find(text, '\n')
if eol == -1:
eol = len(text)
self.file.write('REMARK %s \n' % text[:eol])
text = text[eol + 1:]
def writeAtom(self,
name,
position,
occupancy=0.0,
temperature_factor=0.0,
element=''):
"""Writes an ATOM or HETATM record using the |name|, |occupancy|,
|temperature| and |element| information supplied. The residue and
chain information is taken from the last calls to the methods
nextResidue() and nextChain().
"""
if self.het_flag:
type = 'HETATM'
else:
type = 'ATOM'
name = string.upper(name)
if element != '' and len(element) == 1 and name and name[0] == element:
name = ' ' + name
self.data['name'] = name
self.data['position'] = position
self.data['serial_number'] = (self.data['serial_number'] + 1) % 100000
self.data['occupancy'] = occupancy
self.data['temperature_factor'] = temperature_factor
self.data['element'] = element
self.writeLine(type, self.data)
def nextResidue(self, name, number=None, terminus=None):
"""Signals the beginning of a new residue, starting with the
next call to writeAtom(). The residue name is |name|, and a
|number| can be supplied optionally; by default residues in a
chain will be numbered sequentially starting from 1. The
value of |terminus| can be 'None', '"C"', or '"N"'; it is passed
to export filters that can use this information in order to
use different atom or residue names in terminal residues.
"""
name = string.upper(name)
if self.export_filter is not None:
name, number = self.export_filter.processResidue(
name, number, terminus)
self.het_flag = not (name in amino_acids or name in nucleic_acids)
self.data['residue_name'] = name
self.data['residue_number'] = (self.data['residue_number'] + 1) % 10000
self.data['insertion_code'] = ''
if number is not None:
if type(number) is type(0):
self.data['residue_number'] = number % 10000
else:
self.data['residue_number'] = number.number % 10000
self.data['insertion_code'] = number.insertion_code
def nextChain(self, chain_id=None, segment_id=''):
"""Signals the beginning of a new chain. A chain identifier
(string of length one) can be supplied as |chain_id|, by
default consecutive letters from the alphabet are used.
The equally optional |segment_id| defaults to an empty string.
"""
if chain_id is None:
self.chain_number = (self.chain_number + 1) % len(self._chain_ids)
chain_id = self._chain_ids[self.chain_number]
if self.export_filter is not None:
chain_id, segment_id = \
self.export_filter.processChain(chain_id, segment_id)
self.data['chain_id'] = (chain_id + ' ')[:1]
self.data['segment_id'] = (segment_id + ' ')[:4]
self.data['residue_number'] = 0
_chain_ids = 'ABCDEFGHIJKLMNOPQRSTUVWXYZ'
def terminateChain(self):
"Signals the end of a chain."
if self.export_filter is not None:
self.export_filter.terminateChain()
self.data['serial_number'] = (self.data['serial_number'] + 1) % 100000
self.writeLine('TER', self.data)
self.data['chain_id'] = ''
self.data['segment_id'] = ''
def close(self):
"""Closes the file. This method *must* be called for write mode
because otherwise the file will be incomplete.
"""
if self.open:
if self.output:
self.file.write('END\n')
self.file.close()
self.open = 0
def __del__(self):
self.close()
class PDBFile:
"""PDB file with access at the record level
Constructor: PDBFile(|filename|, |mode|='"r"'), where |filename|
is the file name and |mode| is '"r"' for reading and '"w"' for writing,
The low-level file access is handled by the module
Scientific.IO.TextFile, therefore compressed files and URLs
(for reading) can be used as well.
"""
def __init__(self, filename, mode = 'r', subformat = None):
self.file = TextFile(filename, mode)
self.output = string.lower(mode[0]) == 'w'
self.export_filter = None
if subformat is not None:
export = export_filters.get(subformat, None)
if export is not None:
self.export_filter = export()
self.open = 1
if self.output:
self.data = {'serial_number': 0,
'residue_number': 0,
'chain_id': '',
'segment_id': ''}
self.het_flag = 0
self.chain_number = -1
def readLine(self):
"""Returns the contents of the next non-blank line (= record).
The return value is a tuple whose first element (a string)
contains the record type. For supported record types (HEADER,
ATOM, HETATM, ANISOU, TERM, MODEL, CONECT), the items from the
remaining fields are put into a dictionary which is returned
as the second tuple element. Most dictionary elements are
strings or numbers; atom positions are returned as a vector,
and anisotropic temperature factors are returned as a rank-2
tensor, already multiplied by 1.e-4. White space is stripped
from all strings except for atom names, whose correct
interpretation can depend on an initial space. For unsupported
record types, the second tuple element is a string containing
the remaining part of the record.
"""
while 1:
line = self.file.readline()
if not line: return ('END','')
if line[-1] == '\n': line = line[:-1]
line = string.strip(line)
if line: break
line = string.ljust(line, 80)
type = string.strip(line[:6])
if type == 'ATOM' or type == 'HETATM':
line = FortranLine(line, atom_format)
data = {'serial_number': line[1],
'name': line[2],
'alternate': string.strip(line[3]),
'residue_name': string.strip(line[4]),
'chain_id': string.strip(line[5]),
'residue_number': line[6],
'insertion_code': string.strip(line[7]),
'position': Vector(line[8:11]),
'occupancy': line[11],
'temperature_factor': line[12],
'segment_id': string.strip(line[13]),
'element': string.strip(line[14]),
'charge': string.strip(line[15])}
return type, data
elif type == 'ANISOU':
line = FortranLine(line, anisou_format)
data = {'serial_number': line[1],
'name': line[2],
'alternate': string.strip(line[3]),
'residue_name': string.strip(line[4]),
'chain_id': string.strip(line[5]),
'residue_number': line[6],
'insertion_code': string.strip(line[7]),
'u': 1.e-4*Tensor([[line[8], line[11], line[12]],
[line[11], line[9] , line[13]],
[line[12], line[13], line[10]]]),
'segment_id': string.strip(line[14]),
'element': string.strip(line[15]),
'charge': string.strip(line[16])}
return type, data
elif type == 'TER':
line = FortranLine(line, ter_format)
data = {'serial_number': line[1],
'residue_name': string.strip(line[2]),
'chain_id': string.strip(line[3]),
'residue_number': line[4],
'insertion_code': string.strip(line[5])}
return type, data
elif type == 'CONECT':
line = FortranLine(line, conect_format)
data = {'serial_number': line[1],
'bonded': filter(lambda i: i > 0, line[2:6]),
'hydrogen_bonded': filter(lambda i: i > 0, line[6:10]),
'salt_bridged': filter(lambda i: i > 0, line[10:12])}
return type, data
elif type == 'MODEL':
line = FortranLine(line, model_format)
data = {'serial_number': line[1]}
return type, data
elif type == 'HEADER':
line = FortranLine(line, header_format)
data = {'compound': line[1],
'date': line[2],
'pdb_code': line[3]}
return type, data
else:
return type, line[6:]
def writeLine(self, type, data):
"""Writes a line using record type and data dictionary in the
same format as returned by readLine(). Default values are
provided for non-essential information, so the data dictionary
need not contain all entries.
"""
if self.export_filter is not None:
type, data = self.export_filter.processLine(type, data)
if type is None:
return
line = [type]
if type == 'ATOM' or type == 'HETATM':
format = atom_format
position = data['position']
line = line + [data.get('serial_number', 1),
data.get('name'),
data.get('alternate', ''),
string.rjust(data.get('residue_name', ''), 3),
data.get('chain_id', ''),
data.get('residue_number', 1),
data.get('insertion_code', ''),
position[0], position[1], position[2],
data.get('occupancy', 0.),
data.get('temperature_factor', 0.),
data.get('segment_id', ''),
string.rjust(data.get('element', ''), 2),
data.get('charge', '')]
elif type == 'ANISOU':
format = anisou_format
u = 1.e4*data['u']
u = [int(u[0,0]), int(u[1,1]), int(u[2,2]),
int(u[0,1]), int(u[0,2]), int(u[1,2])]
line = line + [data.get('serial_number', 1),
data.get('name'),
data.get('alternate', ''),
string.rjust(data.get('residue_name'), 3),
data.get('chain_id', ''),
data.get('residue_number', 1),
data.get('insertion_code', '')] \
+ u \
+ [data.get('segment_id', ''),
string.rjust(data.get('element', ''), 2),
data.get('charge', '')]
elif type == 'TER':
format = ter_format
line = line + [data.get('serial_number', 1),
string.rjust(data.get('residue_name'), 3),
data.get('chain_id', ''),
data.get('residue_number', 1),
data.get('insertion_code', '')]
elif type == 'CONECT':
format = conect_format
line = line + [data.get('serial_number')]
line = line + (data.get('bonded', [])+4*[None])[:4]
line = line + (data.get('hydrogen_bonded', [])+4*[None])[:4]
line = line + (data.get('salt_bridged', [])+2*[None])[:2]
elif type == 'MODEL':
format = model_format
line = line + [data.get('serial_number')]
elif type == 'HEADER':
format = header_format
line = line + [data.get('compound', ''), data.get('date', ''),
data.get('pdb_code')]
else:
format = generic_format
line = line + [data]
self.file.write(str(FortranLine(line, format)) + '\n')
def writeComment(self, text):
"""Writes |text| into one or several comment lines.
Each line of the text is prefixed with 'REMARK' and written
to the file.
"""
while text:
eol = string.find(text,'\n')
if eol == -1:
eol = len(text)
self.file.write('REMARK %s \n' % text[:eol])
text = text[eol+1:]
def writeAtom(self, name, position, occupancy=0.0, temperature_factor=0.0,
element=''):
"""Writes an ATOM or HETATM record using the |name|, |occupancy|,
|temperature| and |element| information supplied. The residue and
chain information is taken from the last calls to the methods
nextResidue() and nextChain().
"""
if self.het_flag:
type = 'HETATM'
else:
type = 'ATOM'
name = string.upper(name)
if element != '' and len(element) == 1 and name and name[0] == element:
name = ' ' + name
self.data['name'] = name
self.data['position'] = position
self.data['serial_number'] = (self.data['serial_number'] + 1) % 100000
self.data['occupancy'] = occupancy
self.data['temperature_factor'] = temperature_factor
self.data['element'] = element
self.writeLine(type, self.data)
def nextResidue(self, name, number = None, terminus = None):
"""Signals the beginning of a new residue, starting with the
next call to writeAtom(). The residue name is |name|, and a
|number| can be supplied optionally; by default residues in a
chain will be numbered sequentially starting from 1. The
value of |terminus| can be 'None', '"C"', or '"N"'; it is passed
to export filters that can use this information in order to
use different atom or residue names in terminal residues.
"""
name = string.upper(name)
if self.export_filter is not None:
name, number = self.export_filter.processResidue(name, number,
terminus)
self.het_flag = not (name in amino_acids or name in nucleic_acids)
self.data['residue_name'] = name
self.data['residue_number'] = (self.data['residue_number'] + 1) % 10000
self.data['insertion_code'] = ''
if number is not None:
if type(number) is type(0):
self.data['residue_number'] = number % 10000
else:
self.data['residue_number'] = number.number % 10000
self.data['insertion_code'] = number.insertion_code
def nextChain(self, chain_id = None, segment_id = ''):
"""Signals the beginning of a new chain. A chain identifier
(string of length one) can be supplied as |chain_id|, by
default consecutive letters from the alphabet are used.
The equally optional |segment_id| defaults to an empty string.
"""
if chain_id is None:
self.chain_number = (self.chain_number + 1) % len(self._chain_ids)
chain_id = self._chain_ids[self.chain_number]
if self.export_filter is not None:
chain_id, segment_id = \
self.export_filter.processChain(chain_id, segment_id)
self.data['chain_id'] = (chain_id+' ')[:1]
self.data['segment_id'] = (segment_id+' ')[:4]
self.data['residue_number'] = 0
_chain_ids = 'ABCDEFGHIJKLMNOPQRSTUVWXYZ'
def terminateChain(self):
"Signals the end of a chain."
if self.export_filter is not None:
self.export_filter.terminateChain()
self.data['serial_number'] = (self.data['serial_number'] + 1) % 100000
self.writeLine('TER', self.data)
self.data['chain_id'] = ''
self.data['segment_id'] = ''
def close(self):
"""Closes the file. This method *must* be called for write mode
because otherwise the file will be incomplete.
"""
if self.open:
if self.output:
self.file.write('END\n')
self.file.close()
self.open = 0
def __del__(self):
self.close()