def __init__(self,
fcrd,
fref,
box=0,
rnAmber=0,
pdbCode=None,
log=StdLog(),
verbose=0):
"""
@param fcrd: path to input coordinate file
@type fcrd: str
@param fref: PDB or pickled PDBModel with same atom content and order
@type fref: str
@param box: expect line with box info at the end of each frame
(default: 0)
@type box: 1|0
@param rnAmber: rename amber style residues into standard (default: 0)
@type rnAmber: 1|0
@param pdbCode: pdb code to be put into the model (default: None)
@type pdbCode: str
@param log: LogFile instance [Biskit.StdLog]
@type log: Biskit.LogFile
@param verbose: print progress to log [0]
@type verbose: int
"""
self.fcrd = T.absfile(fcrd)
self.crd = T.gzopen(self.fcrd)
self.ref = PDBModel(T.absfile(fref), pdbCode=pdbCode)
self.box = box
self.n = self.ref.lenAtoms()
self.log = log
self.verbose = verbose
if rnAmber:
self.ref.renameAmberRes()
## pre-compile pattern for line2numbers
xnumber = "-*\d+\.\d+" # optionally negtive number
xspace = ' *' # one or more space char
self.xnumbers = re.compile('(' + xspace + xnumber + ')')
## pre-compute lines expected per frame
self.lines_per_frame = self.n * 3 / 10
if self.n % 10 != 0: self.lines_per_frame += 1
if self.box: self.lines_per_frame += 1
def test_AmberCrdParser(self):
"""AmberCrdParser test"""
self.p = AmberCrdParser(self.finp,
self.fref,
box=True,
rnAmber=True,
log=self.log,
verbose=self.local)
self.t = self.p.crd2traj()
self.t.removeAtoms(
lambda a: a['residue_name'] in ['WAT', 'Na+', 'Cl-'])
self.t.removeAtoms(lambda a: a['element'] == 'H')
if self.local:
print "Dumping result to ", self.fout
T.dump(self.t, T.absfile(self.fout))
if self.local:
print "Dumped Trajectory with %i frames and %i atoms." % \
(len(self.t), self.t.lenAtoms() )
self.assertEqual(len(self.t), 10)
self.assertEqual(self.t.lenAtoms(), 440)
def writeCrd( self, fcrd, append=1, lastAtom=None ):
"""
Write/Append Amber-formatted block of coordinates to a file.
If a file handle is given, the file will not be closed.
@param fcrd: file to write to
@type fcrd: str or file object
@param append: append to existing file (default: 1)
@type append: 0|1
@param lastAtom: skip all atoms beyond this one (default: None)
@type lastAtom: int
"""
if not self.xyz:
self.getXyz()
if type( fcrd ) == file:
## take file handle
f = fcrd
else:
## create new file handle
mode = 'w'
if append:
mode = 'a'
f = open( T.absfile( fcrd ), mode )
newf = (mode=='w' or not os.path.exists( T.absfile(fcrd) ))
if newf:
f.write("\n")
i = 0
for x in N.ravel( self.xyz ):
i = i + 1
f.write( "%8.3f" % x )
if (i % 10) == 0:
f.write("\n")
if lastAtom and i / 3.0 == lastAtom:
break
if ((i % 10) != 0):
f.write("\n")
if type( fcrd ) != file:
## don't close file that was already given
f.close()
def writeCrd(self, fcrd, append=1, lastAtom=None):
"""
Write/Append Amber-formatted block of coordinates to a file.
If a file handle is given, the file will not be closed.
@param fcrd: file to write to
@type fcrd: str or file object
@param append: append to existing file (default: 1)
@type append: 0|1
@param lastAtom: skip all atoms beyond this one (default: None)
@type lastAtom: int
"""
if not self.xyz:
self.getXyz()
if type(fcrd) == file:
## take file handle
f = fcrd
else:
## create new file handle
mode = 'w'
if append:
mode = 'a'
f = open(T.absfile(fcrd), mode)
newf = (mode == 'w' or not os.path.exists(T.absfile(fcrd)))
if newf:
f.write("\n")
i = 0
for x in N0.ravel(self.xyz):
i = i + 1
f.write("%8.3f" % x)
if (i % 10) == 0:
f.write("\n")
if lastAtom and i / 3.0 == lastAtom:
break
if ((i % 10) != 0):
f.write("\n")
if type(fcrd) != file:
## don't close file that was already given
f.close()
def __init__(self, path):
"""
Take chains from ChainCleaner and write pdb files.
File names are created from segid of each chain + '_seg.pdb'
@param path: output path for PDB files
@type path: string
"""
self.path = T.absfile(path)
def __init__(self, path):
"""
Take chains from ChainCleaner and write pdb files.
File names are created from segid of each chain + '_seg.pdb'
@param path: output path for PDB files
@type path: string
"""
self.path = T.absfile( path )
def redirect_output():
import tempfile, os, sys
f_out = open( tempfile.mktemp( '.out', 'slave_', T.absfile('~')),'w')
sys.stdout = f_out
sys.stderr = f_out
flusher = Flusher( f_out )
flusher.start()
def redirect_output():
import tempfile, os, sys
f_out = open(tempfile.mktemp('.out', 'slave_', T.absfile('~')), 'w')
sys.stdout = f_out
sys.stderr = f_out
flusher = Flusher(f_out)
flusher.start()
def __getDatabase(self, db=None, createEmpty=False):
"""
Select and return database (which is actually a dictionary type) for which the user has writing permisions.
By default, the package database will be used but if the user cannot write there,
a new database will be created under the users home directory: $HOME/.mdmix/SOLVENTS.db
which will also contain all solvents from the package db.
:arg None|str db: If *db* != None:
- Check if this DB filename is writtable and return full path. Create it otherwise.
If None:
- Check if user has writing permisions in package DB and return the path.
- If not, create a user-spacific database and return the path.
:arg bool createEmpty: If the database has to be created, ignore solvents from the package DB.
Will create an empty DB.
:return: Path to a db for which the user should have writting permisions.
:type: string
"""
import shutil
# Try to use specified db
if db:
if osp.exists(db) and T.filePermission(db)['WRITE']:
return T.absfile(db)
else:
if createEmpty: T.dump({}, db)
else: shutil.copy(S.SOLVENTDB, db)
return T.absfile(db)
else:
# USE USER DATABASE IF IT EXISTS
if osp.exists(S.USER_SOLVENT_DB):
return T.absfile(S.USER_SOLVENT_DB)
else:
db = S.SOLVENTDB
# Create USER DB from package if user cannot write to package directory
if not T.filePermission(db)['WRITE']:
# User cannot write to package DB so create a custom one
if createEmpty: T.dump({}, S.USER_SOLVENT_DB)
else:
shutil.copy(db, S.USER_SOLVENT_DB
) # Make a copy to user's home mdmix folder
db = S.USER_SOLVENT_DB
return T.absfile(db)
def __init__( self, fcrd, fref, box=0, rnAmber=0, pdbCode=None,
log=StdLog(), verbose=0 ):
"""
@param fcrd: path to input coordinate file
@type fcrd: str
@param fref: PDB or pickled PDBModel with same atom content and order
@type fref: str
@param box: expect line with box info at the end of each frame
(default: 0)
@type box: 1|0
@param rnAmber: rename amber style residues into standard (default: 0)
@type rnAmber: 1|0
@param pdbCode: pdb code to be put into the model (default: None)
@type pdbCode: str
@param log: LogFile instance [Biskit.StdLog]
@type log: Biskit.LogFile
@param verbose: print progress to log [0]
@type verbose: int
"""
self.fcrd = T.absfile( fcrd )
self.crd = T.gzopen( self.fcrd )
self.ref = PDBModel( T.absfile(fref), pdbCode=pdbCode )
self.box = box
self.n = self.ref.lenAtoms()
self.log = log
self.verbose = verbose
if rnAmber:
self.ref.renameAmberRes()
## pre-compile pattern for line2numbers
xnumber = "-*\d+\.\d+" # optionally negtive number
xspace = ' *' # one or more space char
self.xnumbers = re.compile('('+xspace+xnumber+')')
## pre-compute lines expected per frame
self.lines_per_frame = self.n * 3 / 10
if self.n % 10 != 0: self.lines_per_frame += 1
if self.box: self.lines_per_frame += 1
def loadTraj(self, ftraj):
"""
Load trajectories from disc.
@param ftraj: path to trajectory
@type ftraj: str
@return: ensemble trajectory object
@rtype: EnsembleTraj
"""
t = T.load(T.absfile(ftraj))
return traj2ensemble(t)
def loadTraj( self, ftraj ):
"""
Load trajectories from disc.
@param ftraj: path to trajectory
@type ftraj: str
@return: ensemble trajectory object
@rtype: EnsembleTraj
"""
t = T.load( T.absfile( ftraj ) )
return traj2ensemble( t )
def __init__( self, frst ):
"""
@param frst: input restart file
@type frst: str
"""
self.frst = T.absfile( frst )
self.crd = open( self.frst )
self.n = 0 #: number of atoms
self.lines_per_frame = 0
self.xyz = None #: will hold coordinate array
self.box = None #: will hold box array if any
## pre-compile pattern for line2numbers
xnumber = "-*\d+\.\d+" # optionally negtive number
xspace = ' *' # one or more space char
self.xnumbers = re.compile('('+xspace+xnumber+')')
def __init__(self, frst):
"""
@param frst: input restart file
@type frst: str
"""
self.frst = T.absfile(frst)
self.crd = open(self.frst)
self.n = 0 #: number of atoms
self.lines_per_frame = 0
self.xyz = None #: will hold coordinate array
self.box = None #: will hold box array if any
## pre-compile pattern for line2numbers
xnumber = "-*\d+\.\d+" # optionally negtive number
xspace = ' *' # one or more space char
self.xnumbers = re.compile('(' + xspace + xnumber + ')')
def __init__(self, fdefault, fuser, createmissing=False, verbose=1):
"""
@param fdefault: default configuration file
@type fdedault: str
@param fuser: user configuration file
@type fuser: str
@param createmissing: create user config file if missing
@type createmissing: bool
@param verbose: verbosity level (default: 1)
@type verbose: 1|0
"""
self.log = logging.getLogger("SettingsManager")
self.verbose = verbose
self.fdefault = fdefault
self.fuser = fuser
self.createmissing = createmissing
self.fusermissing = not os.path.exists(T.absfile(fuser))
self.settings = [] #: will hold extracted Setting's
def test_AmberCrdParser(self):
"""AmberCrdParser test"""
self.p = AmberCrdParser( self.finp, self.fref, box=True, rnAmber=True,
log=self.log, verbose=self.local )
self.t = self.p.crd2traj()
self.t.removeAtoms(lambda a: a['residue_name'] in ['WAT','Na+','Cl-'] )
self.t.removeAtoms(lambda a: a['element'] == 'H' )
if self.local:
print "Dumping result to ", self.fout
T.dump( self.t, T.absfile(self.fout) )
if self.local:
print "Dumped Trajectory with %i frames and %i atoms." % \
(len(self.t), self.t.lenAtoms() )
self.assertEqual( len(self.t), 10 )
self.assertEqual( self.t.lenAtoms(), 440 )
def writeCrd(self, fname, frames=None):
"""
Write frames to Amber crd file (w/o box info).
@param fname: output file name
@type fname: str
@param frames: frame indices (default: all)
@type frames: [int]
"""
if frames == None:
frames = range(self.lenFrames())
template = " %7.3f" * 10 + '\n'
## open new file
out = open(T.absfile(fname), 'w')
__write = out.write ## cache function address for speed
__write('\n')
n_lines = None
for fi in frames:
f = N.ravel(self.frames[fi])
if n_lines is None:
n_lines = n_lines or len(f) / 10
overhang = (0 != len(f) % 10)
i_lines = range(n_lines)
for i in i_lines:
__write(template % tuple(f[10 * i:10 * i + 10]))
if overhang:
for x in f[i * 10 + 10:]:
__write(" %7.3f" % x)
__write('\n')
out.close()
def writeCrd( self, fname, frames=None ):
"""
Write frames to Amber crd file (w/o box info).
@param fname: output file name
@type fname: str
@param frames: frame indices (default: all)
@type frames: [int]
"""
if frames == None:
frames = range( self.lenFrames() )
template = " %7.3f" * 10 + '\n'
## open new file
out = open( T.absfile(fname), 'w')
__write = out.write ## cache function address for speed
__write('\n')
n_lines = None
for fi in frames:
f = N.ravel( self.frames[ fi ] )
if n_lines is None:
n_lines = n_lines or len( f ) / 10
overhang= ( 0 != len( f ) % 10 )
i_lines = range( n_lines )
for i in i_lines:
__write( template % tuple( f[10*i:10*i+10] ) )
if overhang:
for x in f[i*10+10:]:
__write(" %7.3f" % x )
__write('\n')
out.close()
def __init__( self, source=None ):
"""
@param source: path to EZD file
@type source: str OR file handle
"""
## Raik says: this is always overridden by the "self.source=source"
if type( source ) is str and os.path.isfile( source ):
self.source = LocalPath( source )
self.source = source
## my suggestion (LocalPath is a bit overkill here):
self.source = tools.absfile( source )
#try :
f=tools.gzopen(self.source)
self.__jumpComment(f)
cell=self.__readCell(f)
self.a=cell[0]
self.b=cell[1]
self.c=cell[2]
self.alpha=cell[3]
self.beta=cell[4]
self.gamma=cell[5]
self.origin=self.__readOrigin(f)
self.extent=self.__readExtent(f)
self.gridsize=self.__readGridSize(f)
self.scale=self.__readScale(f)
self.EDGrid=self.__readGrid(f)
self.__setCartesianCoords()
self.sd=npy.std(self.EDGrid)
self.mean=npy.mean(self.EDGrid)
f.close()
def __init__(self, source=None):
"""
@param source: path to EZD file
@type source: str OR file handle
"""
## Raik says: this is always overridden by the "self.source=source"
if type(source) is str and os.path.isfile(source):
self.source = LocalPath(source)
self.source = source
## my suggestion (LocalPath is a bit overkill here):
self.source = tools.absfile(source)
#try :
f = tools.gzopen(self.source)
self.__jumpComment(f)
cell = self.__readCell(f)
self.a = cell[0]
self.b = cell[1]
self.c = cell[2]
self.alpha = cell[3]
self.beta = cell[4]
self.gamma = cell[5]
self.origin = self.__readOrigin(f)
self.extent = self.__readExtent(f)
self.gridsize = self.__readGridSize(f)
self.scale = self.__readScale(f)
self.EDGrid = self.__readGrid(f)
self.__setCartesianCoords()
self.sd = npy.std(self.EDGrid)
self.mean = npy.mean(self.EDGrid)
f.close()
def __parseConfig(self, configFile):
"""
Read in a solvent configuration file and process the data to
create a new solvent in the main or local solvent database.
Templates for the configuration file can be obtained through
the user interface.
:arg str configFile: Solvent configuration filename to read and parse.
It should contain all mandatory fields.
"""
import SettingsParser as P
file = T.absfile(configFile)
config = P.SettingsParser(file)
result = config.parse(keepsections=True)
d = {}
# GENERAL SECTION
generalSection = self.__getSection(result, 'GENERAL')
name = self.__getOption(generalSection, 'name').value
info = self.__getOption(generalSection, 'info').value
off = self.__getOption(generalSection, 'objectfile').value
boxunit = self.__getOption(generalSection, 'boxunit').value
if generalSection.get('watermodel'):
watermodel = generalSection.get('watermodel').value
else:
watermodel = S.DEF_AMBER_WATBOX
d.update({
'name': name,
'info': info,
'boxunit': boxunit,
'watermodel': watermodel
})
# Check off file exists and can find it
if not osp.exists(off):
# Trye to search it in configfile directory
off = osp.join(osp.dirname(file), off)
if not osp.exists(off): raise P.InvalidPath
# This one is optional. If present, will be loaded along the off file in tleap
# Usually parameters will be saved inside the off file.
# If frcmod was given, convert to list and check all files exist
frcmod = generalSection.get('frcmod')
frcmodlist = []
if frcmod:
frcmod.typeCast(list)
frcmod = frcmod.value
frcmodlist = []
for f in frcmod:
if not osp.exists(f):
# Trye to search it in configfile directory
f = osp.join(osp.dirname(file), f)
if not osp.exists(f):
raise P.InvalidPath, "%f frcmod file not found" % f
frcmodlist.append(f)
else:
frcmodlist.append(f)
# PROBES SECTION
probesmap = self.__todict(self.__getSection(result, 'PROBES'))
# TYPES section -- Will contain chemical type mapping to probenames
typesmap = self.__todict(self.__getSection(result, 'TYPES'))
d.update({
'offpath': off,
'probesmap': probesmap,
'typesmap': typesmap,
'frcmodpaths': frcmodlist
})
# Check typesMapping and probesMapping have same keys
if not set(probesmap.keys()) == set(typesmap.keys()):
typesSet = set(typesmap.keys())
probesSet = set(probesmap.keys())
miss = typesSet - probesSet
self.log.error(
"Missmatch between probes in [PROBES] section and chemical types in [TYPES] section: %s"
% miss)
raise MappingError
# OPTIONAL SECTIONS BEGIN HERE
# CORRECTION SECTION IF MODULES ARE IMPLEMENTED THESE SECTIONS ARE NECESSARY
# TODO fix this mess of correction parsing
correctionSect = result.get('CORRECTION')
corrections = {}
if correctionSect:
corr = self.__todict(correctionSect)
for type, val in corr.iteritems():
type = type.upper()
corrections[type] = dict(
[[el.strip().upper() for el in probe.split(':')]
for probe in val.strip().split(',')])
# transform to float the numbers
for k, val in corrections.iteritems():
corrections[k] = dict(zip(val.keys(), map(float,
val.values())))
del correctionSect, type, k, val
d.update({'corrections': corrections})
# EXTRA SECTION. OPTIONAL.
# Specific pairs attribute to add to the solvent instances.
# Implemented for further development.
extra = result.get('EXTRA') or {}
if extra:
self.log.info(
"Solvent has EXTRA field. Will add each flag to attributes.")
extra = self.__todict(extra)
d.update(extra)
return d
def __init__(self, ini):
self.log = logging.getLogger("SettingsParser")
self.f_ini = T.absfile(ini)
self.result = {}
