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__init__.py
Xavier Robin authored
__init__.py 21.43 KiB
#------------------------------------------------------------------------------
# This file is part of the OpenStructure project <www.openstructure.org>
#
# Copyright (C) 2008-2020 by the OpenStructure authors
#
# This library is free software; you can redistribute it and/or modify it under
# the terms of the GNU Lesser General Public License as published by the Free
# Software Foundation; either version 3.0 of the License, or (at your option)
# any later version.
# This library is distributed in the hope that it will be useful, but WITHOUT
# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
# FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
#
# You should have received a copy of the GNU Lesser General Public License
# along with this library; if not, write to the Free Software Foundation, Inc.,
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
#------------------------------------------------------------------------------
import os, tempfile, ftplib, http.client
from ._ost_io import *
from ost import mol, geom, conop, seq
class IOProfiles:
def __init__(self):
self._dict={}
if conop.GetDefaultLib():
processor = conop.RuleBasedProcessor(conop.GetDefaultLib())
else:
processor = conop.HeuristicProcessor()
self['STRICT'] = IOProfile(dialect='PDB', fault_tolerant=False,
quack_mode=False, processor=processor.Copy())
self['SLOPPY'] = IOProfile(dialect='PDB', fault_tolerant=True,
quack_mode=True, processor=processor.Copy())
self['CHARMM'] = IOProfile(dialect='CHARMM', fault_tolerant=True,
quack_mode=False, processor=processor.Copy())
self['DEFAULT'] = 'STRICT'
def __getitem__(self, key):
return IOProfileRegistry.Instance().Get(key)
def __setitem__(self, key, value):
if isinstance(value, str):
value=self[value].Copy()
IOProfileRegistry.Instance().Set(key, value)
self._dict[key]=value
def Get(self, key):
""" Getter which keeps compound library up to date
Keeps compound library for default profiles up to date. Reason for that is
that conop.SetDefaultLib() after importing io has no effect. Processors
(and the associated compound library) are set at import. Custom profiles,
i.e. profiles that are not defined in constructor of this class, are
returned as is without any update.
"""
if key not in ['STRICT', 'SLOPPY', 'CHARMM', 'DEFAULT']:
return self[key].Copy()
prof = self[key].Copy()
if conop.GetDefaultLib():
processor = conop.RuleBasedProcessor(conop.GetDefaultLib())
else:
processor = conop.HeuristicProcessor()
prof.processor = processor
return prof
def __len__(self):
return len(self._dict)
def __iter__(self):
return self._dict.__iter__()
profiles = IOProfiles()
def _override(val1, val2):
if val2!=None:
return val2
else:
return val1
def LoadPDB(filename, restrict_chains="", no_hetatms=None,
fault_tolerant=None, load_multi=False, quack_mode=None,
join_spread_atom_records=None, calpha_only=None,
profile='DEFAULT', remote=False, remote_repo='pdb',
dialect=None, seqres=False, bond_feasibility_check=None,
read_conect=False):
"""
Load PDB file from disk and return one or more entities. Several options
allow to customize the exact behaviour of the PDB import. For more information
on these options, see :doc:`profile`.
Residues are flagged as ligand if they are mentioned in a HET record.
:param filename: File to be loaded
:type filename: :class:`str`
:param restrict_chains: If not an empty string, only chains listed in the
string will be imported.
:type restrict_chains: :class:`str`
:param no_hetatms: If set to True, HETATM records will be ignored. Overrides
the value of :attr:`IOProfile.no_hetatms`
:type no_hetatms: :class:`bool`
:param fault_tolerant: Enable/disable fault-tolerant import. If set, overrides
the value of :attr:`IOProfile.fault_tolerant`.
:type fault_tolerant: :class:`bool`
:param load_multi: If set to True, a list of entities will be returned instead
of only the first. This is useful when dealing with
multi-PDB files.
:type load_multi: :class:`bool`
:param quack_mode: Guess the chemical class for unknown residues based on its
atoms and connectivity. If set, overrides the value of
:attr:`IOProfile.quack_mode`.
:type quack_mode: :class:`bool`
:param join_spread_atom_records: If set, overrides the value of
:attr:`IOProfile.join_spread_atom_records`.
:type join_spread_atom_records: :class:`bool`
:param calpha_only: When set to true, forces the importer to only load atoms
named CA. If set, overrides the value of
:attr:`IOProfile.calpha_only`.
:type calpha_only: :class:`bool`
:param profile: Aggregation of flags and algorithms to control import and
processing of molecular structures. Can either be a
:class:`str` specifying one of the default profiles
['DEFAULT', 'SLOPPY', 'CHARMM', 'STRICT'] or an actual object
of type :class:`ost.io.IOProfile`. If a :class:`str` defines
a default profile, :attr:`IOProfile.processor` is set to
:class:`ost.conop.RuleBasedProcessor` with the currently
set :class:`ost.conop.CompoundLib` available as
:func:`ost.conop.GetDefaultLib()`. If no
:class:`ost.conop.CompoundLib` is available,
:class:`ost.conop.HeuristicProcessor` is used instead. See
:doc:`profile` for more info.
:type profile: :class:`str`/:class:`ost.io.IOProfile`
:param remote: If set to True, the method tries to load the pdb from the remote
repository given as *remote_repo*. The filename is then
interpreted as the entry id as further specified for the
*remote_repo* parameter.
:type remote: :class:`bool`
:param remote_repo: Remote repository to fetch structure if *remote* is True.
Must be one in ['pdb', 'smtl', 'pdb_redo']. In case of
'pdb' and 'pdb_redo', the entry must be given as lower
case pdb id, which loads the deposited assymetric unit
(e.g. '1ake'). In case of 'smtl', the entry must also
specify the desired biounit (e.g. '1ake.1').
:type remote_repo: :class:`str`
:param dialect: Specifies the particular dialect to use. If set, overrides
the value of :attr:`IOProfile.dialect`
:type dialect: :class:`str`
:param seqres: Whether to read SEQRES records. If set to True, the loaded
entity and seqres entry will be returned as a tuple.
:type seqres: :class:`bool`
:param bond_feasibility_check: Flag for :attr:`IOProfile.processor`. If
turned on, atoms are only connected by
bonds if they are within a reasonable distance
(as defined by
:func:`ost.conop.IsBondFeasible`).
If set, overrides the value of
:attr:`ost.conop.Processor.check_bond_feasibility`
:type bond_feasibility_check: :class:`bool`
:param read_conect: By default, OpenStructure doesn't read CONECT statements in
a pdb file. Reason is that they're often missing and we prefer
to rely on the chemical component dictionary from the PDB.
However, there may be cases where you really want these CONECT
statements. For example novel compounds with no entry in
the chemical component dictionary. Setting this to True has
two effects: 1) CONECT statements are read and blindly applied
2) The processor does not connect any pair of HETATOM atoms in
order to not interfer with the CONECT statements.
:type read_conect: :class:`bool`
:rtype: :class:`~ost.mol.EntityHandle` or a list thereof if `load_multi` is
True.
:raises: :exc:`~ost.io.IOException` if the import fails due to an erroneous or
inexistent file
"""
def _override(val1, val2):
if val2!=None:
return val2
else:
return val1
if isinstance(profile, str):
prof=profiles.Get(profile)
elif isinstance(profile, IOProfile):
prof=profile.Copy()
else:
raise TypeError('profile must be of type string or IOProfile, '+\
'instead of %s'%type(profile))
if dialect not in (None, 'PDB', 'CHARMM',):
raise ValueError('dialect must be PDB or CHARMM')
prof.calpha_only=_override(prof.calpha_only, calpha_only)
prof.no_hetatms=_override(prof.no_hetatms, no_hetatms)
prof.dialect=_override(prof.dialect, dialect)
prof.quack_mode=_override(prof.quack_mode, quack_mode)
prof.read_conect=_override(prof.read_conect, read_conect)
if prof.processor:
prof.processor.check_bond_feasibility=_override(prof.processor.check_bond_feasibility,
bond_feasibility_check)
prof.processor.connect_hetatm=_override(prof.processor.connect_hetatm,
not read_conect)
prof.fault_tolerant=_override(prof.fault_tolerant, fault_tolerant)
prof.join_spread_atom_records=_override(prof.join_spread_atom_records,
join_spread_atom_records)
tmp_file = None # avoid getting out of scope
if remote:
if remote_repo not in ['pdb', 'smtl', 'pdb_redo']:
raise IOError("remote_repo must be in ['pdb', 'smtl', 'pdb_redo']")
from ost.io.remote import RemoteGet
tmp_file =RemoteGet(filename, from_repo=remote_repo)
filename = tmp_file.name
conop_inst=conop.Conopology.Instance()
if prof.processor:
if prof.dialect=='PDB':
prof.processor.dialect=conop.PDB_DIALECT
elif prof.dialect=='CHARMM':
prof.processor.dialect=conop.CHARMM_DIALECT
reader=PDBReader(filename, prof)
reader.read_seqres=seqres
try:
if load_multi:
ent_list=[]
while reader.HasNext():
ent=mol.CreateEntity()
reader.Import(ent, restrict_chains)
if prof.processor:
prof.processor.Process(ent)
ent_list.append(ent)
if len(ent_list)==0:
raise IOError("File '%s' doesn't contain any entities" % filename)
return ent_list
else:
ent=mol.CreateEntity()
if reader.HasNext():
reader.Import(ent, restrict_chains)
if prof.processor:
prof.processor.Process(ent)
else:
raise IOError("File '%s' doesn't contain any entities" % filename)
if seqres:
return ent, reader.seqres
return ent
except:
raise
def SavePDB(models, filename, dialect=None, pqr=False, profile='DEFAULT'):
"""
Save entity or list of entities to disk. If a list of entities is supplied
the PDB file will be saved as a multi PDB file. Each of the entities is
wrapped into a MODEL/ENDMDL pair.
If the atom number exceeds 99999, '*****' is used.
:param models: The entity or list of entities (handles or views) to be saved
:param filename: The filename
:type filename: string
:raises: IOException if the restrictions of the PDB format are not satisfied
(with the exception of atom numbers, see above):
* Chain names with more than one character
* Atom positions with coordinates outside range [-999.99, 9999.99]
* Residue names longer than three characters
* Atom names longer than four characters
* Numeric part of :class:`ost.mol.ResNum` outside range [-999, 9999]
* Alternative atom indicators longer than one character
"""
if not getattr(models, '__len__', None):
models=[models]
if isinstance(profile, str):
profile=profiles.Get(profile)
elif isinstance(profile, IOProfile):
profile = profile.Copy()
else:
raise TypeError('profile must be of type string or IOProfile, '+\
'instead of %s'%type(profile))
profile.dialect=_override(profile.dialect, dialect)
writer=PDBWriter(filename, profile)
writer.SetIsPQR(pqr)
if len(models)>1:
writer.write_multi_model=True
for model in models:
writer.Write(model)
try:
from ost import img
LoadMap = LoadImage
SaveMap = SaveImage
except ImportError:
pass
## loads several images and puts them in an ImageList
# \sa \example fft_li.py "View Fourier Transform Example"
def LoadImageList (files):
image_list=img.ImageList()
for file in files:
image=LoadImage(file)
image_list.append(image)
return image_list
LoadMapList=LoadImageList
def LoadCHARMMTraj(crd, dcd_file=None, profile='CHARMM',
lazy_load=False, stride=1,
dialect=None, detect_swap=True,swap_bytes=False):
"""
Load CHARMM trajectory file.
:param crd: EntityHandle or filename of the (PDB) file containing the
structure. The structure must have the same number of atoms as the
trajectory
:param dcd_file: The filename of the DCD file. If not set, and crd is a
string, the filename is set to the <crd>.dcd
:param layz_load: Whether the trajectory should be loaded on demand. Instead
of loading the complete trajectory into memory, the trajectory frames are
loaded from disk when requested.
:param stride: The spacing of the frames to load. When set to 2, for example,
every second frame is loaded from the trajectory. By default, every frame
is loaded.
:param dialect: The dialect for the PDB file to use. See :func:`LoadPDB`. If
set, overrides the value of the profile
:param profile: The IO profile to use for loading the PDB file. See
:doc:`profile`.
:param detect_swap: if True (the default), then automatic detection of endianess
is attempted, otherwise the swap_bytes parameter is used
:param swap_bytes: is detect_swap is False, this flag determines whether bytes
are swapped upon loading or not
"""
if not isinstance(crd, mol.EntityHandle):
if dcd_file==None:
dcd_file='%s.dcd' % os.path.splitext(crd)[0]
crd=LoadPDB(crd, profile=profile, dialect=dialect)
else:
if not dcd_file:
raise ValueError("No DCD filename given")
return LoadCHARMMTraj_(crd, dcd_file, stride, lazy_load, detect_swap, swap_bytes)
def LoadMMCIF(filename, fault_tolerant=None, calpha_only=None,
profile='DEFAULT', remote=False, seqres=False, info=False):
"""
Load a mmCIF file and return one or more entities. Several options allow to
customize the exact behaviour of the mmCIF import. For more information on
these options, see :doc:`profile`.
Residues are flagged as ligand if they are not waters nor covered by an
``entity_poly`` record (ie. they are non-polymer entities in
``pdbx_entity_nonpoly``). Note that all residues except waters will be
flagged as ligands if ``seqres=False`` (the default).
:param filename: File to be loaded
:type filename: :class:`str`
:param fault_tolerant: Enable/disable fault-tolerant import. If set, overrides
the value of :attr:`IOProfile.fault_tolerant`.
:type fault_tolerant: :class:`bool`
:param calpha_only: When set to true, forces the importer to only load atoms
named CA. If set, overrides the value of
:attr:`IOProfile.calpha_only`.
:type calpha_only: :class:`bool`
:param profile: Aggregation of flags and algorithms to control import and
processing of molecular structures. Can either be a
:class:`str` specifying one of the default profiles
['DEFAULT', 'SLOPPY', 'CHARMM', 'STRICT'] or an actual object
of type :class:`ost.io.IOProfile`. If a :class:`str` defines
a default profile, :attr:`IOProfile.processor` is set to
:class:`ost.conop.RuleBasedProcessor` with the currently
set :class:`ost.conop.CompoundLib` available as
:func:`ost.conop.GetDefaultLib()`. If no
:class:`ost.conop.CompoundLib` is available,
:class:`ost.conop.HeuristicProcessor` is used instead. See
:doc:`profile` for more info.
:type profile: :class:`str`/:class:`ost.io.IOProfile`
:param remote: If set to True, the method tries to load the pdb from the
remote pdb repository www.pdb.org. The filename is then
interpreted as the pdb id.
:type remote: :class:`bool`
:param seqres: Whether to read SEQRES records. If True, a
:class:`~ost.seq.SequenceList` object is returned as the second
item. The sequences in the list are named according to the
mmCIF chain name.
This feature requires a default
:class:`compound library <ost.conop.CompoundLib>`
to be defined and accessible via
:func:`~ost.conop.GetDefaultLib` or an empty list is returned.
:type seqres: :class:`bool`
:param info: Whether to return an info container with the other output.
If True, a :class:`MMCifInfo` object is returned as last item.
:type info: :class:`bool`
:rtype: :class:`~ost.mol.EntityHandle` (or tuple if *seqres* or *info* are
True).
:raises: :exc:`~ost.io.IOException` if the import fails due to an erroneous
or non-existent file.
"""
def _override(val1, val2):
if val2!=None:
return val2
else:
return val1
if isinstance(profile, str):
prof = profiles.Get(profile)
else:
prof = profile.Copy()
prof.calpha_only=_override(prof.calpha_only, calpha_only)
prof.fault_tolerant=_override(prof.fault_tolerant, fault_tolerant)
if remote:
from ost.io.remote import RemoteGet
tmp_file = RemoteGet(filename, from_repo='cif')
filename = tmp_file.name
try:
ent = mol.CreateEntity()
reader = MMCifReader(filename, ent, prof)
reader.read_seqres = seqres
# NOTE: to speed up things, we could introduce a restrict_chains parameter
# similar to the one in LoadPDB. Here, it would have to be a list/set
# of chain-name-strings.
#if reader.HasNext():
reader.Parse()
if prof.processor:
prof.processor.Process(ent)
reader.info.ConnectBranchLinks()
#else:
# raise IOError("File doesn't contain any entities")
if seqres and info:
return ent, reader.seqres, reader.info
if seqres:
return ent, reader.seqres
if info:
return ent, reader.info
return ent
except:
raise
# this function uses a dirty trick: should be a member of MMCifInfoBioUnit
# which is totally C++, but we want the method in Python... so we define it
# here (__init__) and add it as a member to the class. With this, the first
# arguement is the usual 'self'.
# documentation for this function was moved to mmcif.rst,
# MMCifInfoBioUnit.PDBize, since this function is not included in SPHINX.
def _PDBize(biounit, asu, seqres=None, min_polymer_size=None,
transformation=False, peptide_min_size=10, nucleicacid_min_size=10,
saccharide_min_size=10):
if min_polymer_size is not None:
pdbizer = mol.alg.PDBize(min_polymer_size=min_polymer_size)
else:
pdbizer = mol.alg.PDBize(peptide_min_size=peptide_min_size,
nucleicacid_min_size=nucleicacid_min_size,
saccharide_min_size=saccharide_min_size)
chains = biounit.GetChainList()
c_intvls = biounit.GetChainIntervalList()
o_intvls = biounit.GetOperationsIntervalList()
ss = seqres
if not ss:
ss = seq.CreateSequenceList()
# create list of operations
# for cartesian products, operations are stored in a list, multiplied with
# the next list of operations and re-stored... until all lists of operations
# are multiplied in an all-against-all manner.
operations = biounit.GetOperations()
for i in range(0,len(c_intvls)):
trans_matrices = geom.Mat4List()
l_operations = operations[o_intvls[i][0]:o_intvls[i][1]]
if len(l_operations) > 0:
for op in l_operations[0]:
rot = geom.Mat4()
rot.PasteRotation(op.rotation)
trans = geom.Mat4()
trans.PasteTranslation(op.translation)
tr = geom.Mat4()
tr = trans * rot
trans_matrices.append(tr)
for op_n in range(1, len(l_operations)):
tmp_ops = geom.Mat4List()
for o in l_operations[op_n]:
rot = geom.Mat4()
rot.PasteRotation(o.rotation)
trans = geom.Mat4()
trans.PasteTranslation(o.translation)
tr = geom.Mat4()
tr = trans * rot
for t_o in trans_matrices:
tp = t_o * tr
tmp_ops.append(tp)
trans_matrices = tmp_ops
# select chains into a view as basis for each transformation
assu = asu.Select('cname='+','.join(mol.QueryQuoteName(name) \
for name in \
chains[c_intvls[i][0]:c_intvls[i][1]]))
pdbizer.Add(assu, trans_matrices, ss)
pdb_bu = pdbizer.Finish(transformation)
if transformation:
return pdb_bu, pdb_bu.GetTransform().GetMatrix()
return pdb_bu
MMCifInfoBioUnit.PDBize = _PDBize