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HETATM record type written out #2880

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Aug 14, 2020
Merged

HETATM record type written out #2880

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e708aa7
added HETATM fmt and conditional
mieczyslaw Jul 30, 2020
884d613
fix no attribute case
mieczyslaw Jul 30, 2020
46115ce
address reviewer's comments
mieczyslaw Aug 2, 2020
9e646ec
changes as suggested by the reviewer
mieczyslaw Aug 5, 2020
0705ae8
additional comments addressed
mieczyslaw Aug 6, 2020
09278fc
use outfile fixture
mieczyslaw Aug 6, 2020
44f63c3
links sorted out
mieczyslaw Aug 6, 2020
96fbfbc
remove duplicated _CRYST1
mieczyslaw Aug 6, 2020
9c30e0f
merge current develop, solve merge conflicts in AUTHORS
mieczyslaw Aug 12, 2020
31e58bb
address reviewer comments
mieczyslaw Aug 12, 2020
908746f
match exception message
mieczyslaw Aug 12, 2020
d806658
line lenght fix
mieczyslaw Aug 12, 2020
88802f9
change PDB version to 3.3
mieczyslaw Aug 13, 2020
de923b2
resolve conflicts
mieczyslaw Aug 13, 2020
4b44ecb
Issue 2906
IAlibay Aug 14, 2020
eff5759
Merge branch 'develop' into feature/write_hetatm_record_type_issue_1753
IAlibay Aug 14, 2020
6890a31
reviewer's request
mieczyslaw Aug 14, 2020
d344006
reviewer's request
mieczyslaw Aug 14, 2020
e82974c
reviewer's request
mieczyslaw Aug 14, 2020
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1 change: 1 addition & 0 deletions package/AUTHORS
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Original file line number Diff line number Diff line change
Expand Up @@ -149,6 +149,7 @@ Chronological list of authors
- Marcello Sega
- Edis Jakupovic
- Nicholas Craven
- Mieczyslaw Torchala

External code
-------------
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5 changes: 4 additions & 1 deletion package/CHANGELOG
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Expand Up @@ -15,11 +15,14 @@ The rules for this file:
------------------------------------------------------------------------------
??/??/?? tylerjereddy, richardjgowers, IAlibay, hmacdope, orbeckst, cbouy,
lilyminium, daveminh, jbarnoud, yuxuanzhuang, VOD555, ianmkenney,
calcraven， xiki-tempula
calcraven, xiki-tempula, mieczyslaw

* 2.0.0

Fixes
* Instead of using ATOM for both ATOM and HETATM, HETATM record type
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keyword is properly written out by PDB writer (Issue #1753, PR #2880).
* Change referenced PDB standard version to 3.3 (Issue #2906).
* Fixed reading in masses and charges from a hoomdxml file
(Issue #2888, PR #2889)
* Bond attribute is no longer set if PDB file contains no CONECT records
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116 changes: 58 additions & 58 deletions package/MDAnalysis/coordinates/PDB.py
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Expand Up @@ -55,7 +55,7 @@
W.write(calphas)

It is important to *always close the trajectory* when done because only at this
step is the final END_ record written, which is required by the `PDB 3.2
step is the final END_ record written, which is required by the `PDB 3.3
standard`_. Using the writer as a context manager ensures that this always
happens.

Expand All @@ -65,7 +65,7 @@

A pure-Python implementation for PDB files commonly encountered in MD
simulations comes under the names :class:`PDBReader` and :class:`PDBWriter`. It
only implements a subset of the `PDB 3.2 standard`_ and also allows some
only implements a subset of the `PDB 3.3 standard`_ and also allows some
typical enhancements such as 4-letter resids (introduced by CHARMM/NAMD).

The :class:`PDBReader` can read multi-frame PDB files and represents
Expand Down Expand Up @@ -136,8 +136,8 @@
:inherited-members:


.. _`PDB 3.2 standard`:
http://www.wwpdb.org/documentation/file-format-content/format32/v3.2.html
.. _`PDB 3.3 standard`:
http://www.wwpdb.org/documentation/file-format-content/format33/v3.3.html

"""
from io import StringIO, BytesIO
Expand Down Expand Up @@ -177,11 +177,11 @@ class PDBReader(base.ReaderBase):
Reads multi-`MODEL`_ PDB files as trajectories.

.. _PDB-formatted:
http://www.wwpdb.org/documentation/file-format-content/format32/v3.2.html
http://www.wwpdb.org/documentation/file-format-content/format33/v3.3.html
.. _PDB coordinate section:
http://www.wwpdb.org/documentation/file-format-content/format32/sect9.html
http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html
.. _MODEL:
http://www.wwpdb.org/documentation/file-format-content/format32/sect9.html#MODEL
http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#MODEL

============= ============ =========== =============================================
COLUMNS DATA TYPE FIELD DEFINITION
Expand Down Expand Up @@ -459,7 +459,7 @@ def close(self):


class PDBWriter(base.WriterBase):
"""PDB writer that implements a subset of the `PDB 3.2 standard`_ .
"""PDB writer that implements a subset of the `PDB 3.3 standard`_ .

PDB format as used by NAMD/CHARMM: 4-letter resnames and segID are allowed,
altLoc is written.
Expand All @@ -470,12 +470,19 @@ class PDBWriter(base.WriterBase):
PDB "movie" (multi frame mode, *multiframe* = ``True``), consisting of
multiple models (using the MODEL_ and ENDMDL_ records).

.. _`PDB 3.2 standard`:
http://www.wwpdb.org/documentation/file-format-content/format32/v3.2.html
.. _MODEL: http://www.wwpdb.org/documentation/file-format-content/format32/sect9.html#MODEL
.. _ENDMDL: http://www.wwpdb.org/documentation/file-format-content/format32/sect9.html#ENDMDL
.. _CONECT: http://www.wwpdb.org/documentation/file-format-content/format32/sect10.html#CONECT

.. _`PDB 3.3 standard`:
http://www.wwpdb.org/documentation/file-format-content/format33/v3.3.html
.. _ATOM: http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM
.. _COMPND: http://www.wwpdb.org/documentation/file-format-content/format33/sect2.html#COMPND
.. _CONECT: http://www.wwpdb.org/documentation/file-format-content/format33/sect10.html#CONECT
.. _END: http://www.wwpdb.org/documentation/file-format-content/format33/sect11.html#END
.. _ENDMDL: http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ENDMDL
.. _HEADER: http://www.wwpdb.org/documentation/file-format-content/format33/sect2.html#HEADER
.. _HETATM: http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#HETATM
.. _MODEL: http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#MODEL
.. _NUMMDL: http://www.wwpdb.org/documentation/file-format-content/format33/sect2.html#NUMMDL
.. _REMARKS: http://www.wwpdb.org/documentation/file-format-content/format33/remarks.html
.. _TITLE: http://www.wwpdb.org/documentation/file-format-content/format33/sect2.html#TITLE

Note
----
Expand All @@ -493,6 +500,11 @@ class PDBWriter(base.WriterBase):
are not set (:code:`None` or :code:`np.zeros(6)`,
see Issue #2698).

When the record_types attribute is present (e.g. Universe object was
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created by loading a PDB file), ATOM_ and HETATM_ record type keywords
are written out accordingly. Otherwise, the ATOM_ record type is the
default output.

See Also
--------
This class is identical to :class:`MultiPDBWriter` with the one
Expand Down Expand Up @@ -528,6 +540,11 @@ class PDBWriter(base.WriterBase):
"{chainID:1s}{resSeq:4d}{iCode:1s}"
" {pos[0]:8.3f}{pos[1]:8.3f}{pos[2]:8.3f}{occupancy:6.2f}"
"{tempFactor:6.2f} {segID:<4s}{element:>2s}\n"),
'HETATM': (
"HETATM{serial:5d} {name:<4s}{altLoc:<1s}{resName:<4s}"
"{chainID:1s}{resSeq:4d}{iCode:1s}"
" {pos[0]:8.3f}{pos[1]:8.3f}{pos[2]:8.3f}{occupancy:6.2f}"
"{tempFactor:6.2f} {segID:<4s}{element:>2s}\n"),
'REMARK': "REMARK {0}\n",
'COMPND': "COMPND {0}\n",
'HEADER': "HEADER {0}\n",
Expand Down Expand Up @@ -608,10 +625,6 @@ def __init__(self, filename, bonds="conect", n_atoms=None, start=0, step=1,
multi frame PDB file in which frames are written as MODEL_ ... ENDMDL_
records. If ``None``, then the class default is chosen. [``None``]

.. _CONECT: http://www.wwpdb.org/documentation/file-format-content/format32/sect10.html#CONECT
.. _MODEL: http://www.wwpdb.org/documentation/file-format-content/format32/sect9.html#MODEL
.. _ENDMDL: http://www.wwpdb.org/documentation/file-format-content/format32/sect9.html#ENDMDL

"""
# n_atoms = None : dummy keyword argument
# (not used, but Writer() always provides n_atoms as the second argument)
Expand Down Expand Up @@ -668,9 +681,6 @@ def _write_pdb_header(self):
unitary values (cubic box with sides of 1 Å) if unit cell dimensions
are not set.

.. _COMPND: http://www.wwpdb.org/documentation/file-format-content/format33/sect2.html#COMPND
.. _REMARKS: http://www.wwpdb.org/documentation/file-format-content/format33/remarks.html

.. versionchanged: 1.0.0
Fix writing of PDB file without unit cell dimensions (Issue #2679).
If cell dimensions are not found, unitary values (cubic box with
Expand Down Expand Up @@ -981,19 +991,21 @@ def _write_timestep(self, ts, multiframe=False):
:class:`PDBWriter` is in single frame mode and no MODEL_
records are written.

.. _MODEL: http://www.wwpdb.org/documentation/file-format-content/format32/sect9.html#MODEL
.. _ENDMDL: http://www.wwpdb.org/documentation/file-format-content/format32/sect9.html#ENDMDL
.. _NUMMDL: http://www.wwpdb.org/documentation/file-format-content/format32/sect2.html#NUMMDL

.. versionchanged:: 0.7.6
The *multiframe* keyword was added, which completely determines if
MODEL records are written. (Previously, this was decided based on the
underlying trajectory and only if ``len(traj) > 1`` would MODEL records
have been written.)
MODEL_ records are written. (Previously, this was decided based on
the underlying trajectory and only if ``len(traj) > 1`` would
MODEL records have been written.)

.. versionchanged:: 1.0.0
ChainID now comes from the last character of segid, as stated in the documentation.
An indexing issue meant it previously used the first charater (Issue #2224)
ChainID now comes from the last character of segid, as stated in
the documentation. An indexing issue meant it previously used the
first charater (Issue #2224)

.. versionchanged:: 2.0.0
When only record_type attribute is present, instead of
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using ATOM_ for both ATOM_ and HETATM_, HETATM_ record
types are properly written out (Issue #1753).

"""
atoms = self.obj.atoms
Expand Down Expand Up @@ -1028,6 +1040,7 @@ def get_attr(attrname, default):
occupancies = get_attr('occupancies', 1.0)
tempfactors = get_attr('tempfactors', 0.0)
atomnames = get_attr('names', 'X')
record_types = get_attr('record_types', 'ATOM')

for i, atom in enumerate(atoms):
vals = {}
Expand All @@ -1044,17 +1057,21 @@ def get_attr(attrname, default):
vals['segID'] = segids[i][:4]
vals['element'] = guess_atom_element(atomnames[i].strip())[:2]

# .. _ATOM: http://www.wwpdb.org/documentation/file-format-content/format32/sect9.html#ATOM
self.pdbfile.write(self.fmt['ATOM'].format(**vals))
# record_type attribute, if exists, can be ATOM or HETATM
try:
self.pdbfile.write(self.fmt[record_types[i]].format(**vals))
except KeyError:
errmsg = (f"Found {record_types[i]} for the record type, but "
f"only allowed types are ATOM or HETATM")
raise ValueError(errmsg) from None

if multiframe:
self.ENDMDL()
self.frames_written += 1

def HEADER(self, trajectory):
"""Write HEADER_ record.

.. _HEADER: http://www.wwpdb.org/documentation/file-format-content/format32/sect2.html#HEADER

.. versionchanged:: 0.20.0
Strip `trajectory.header` since it can be modified by the user and should be
sanitized (Issue #2324)
Expand All @@ -1067,23 +1084,16 @@ def HEADER(self, trajectory):
def TITLE(self, *title):
"""Write TITLE_ record.

.. _TITLE: http://www.wwpdb.org/documentation/file-format-content/format32/sect2.html

"""
line = " ".join(title) # TODO: should do continuation automatically
self.pdbfile.write(self.fmt['TITLE'].format(line))

def REMARK(self, *remarks):
"""Write generic REMARK_ record (without number).
"""Write generic REMARKS_ record (without number).

Each string provided in *remarks* is written as a separate REMARK_
Each string provided in *remarks* is written as a separate REMARKS_
record.

See also `REMARK (update)`_.

.. _REMARK: http://www.wwpdb.org/documentation/file-format-content/format32/remarks1.html
.. _REMARK (update): http://www.wwpdb.org/documentation/file-format-content/format32/remarks2.html

"""
for remark in remarks:
self.pdbfile.write(self.fmt['REMARK'].format(remark))
Expand Down Expand Up @@ -1113,10 +1123,6 @@ def MODEL(self, modelnumber):
standard (i.e., 4 digits). If frame numbers are larger than
9999, they will wrap around, i.e., 9998, 9999, 0, 1, 2, ...


.. _MODEL: http://www.wwpdb.org/documentation/file-format-content/format32/sect9.html#MODEL


.. versionchanged:: 0.19.0
Maximum model number is enforced.

Expand All @@ -1131,8 +1137,6 @@ def END(self):
method right before closing the file it is recommended to *not* call
:meth:`~PDBWriter.END` explicitly.

.. _END: http://www.wwpdb.org/documentation/file-format-content/format32/sect11.html#END

"""
if not self.has_END:
# only write a single END record
Expand All @@ -1142,16 +1146,12 @@ def END(self):
def ENDMDL(self):
"""Write the ENDMDL_ record.

.. _ENDMDL: http://www.wwpdb.org/documentation/file-format-content/format32/sect9.html#ENDMDL

"""
self.pdbfile.write(self.fmt['ENDMDL'])

def CONECT(self, conect):
"""Write CONECT_ record.

.. _CONECT: http://www.wwpdb.org/documentation/file-format-content/format32/sect10.html#CONECT

"""
conect = ["{0:5d}".format(entry + 1) for entry in conect]
conect = "".join(conect)
Expand All @@ -1161,7 +1161,7 @@ def CONECT(self, conect):
class ExtendedPDBReader(PDBReader):
"""PDBReader that reads a PDB-formatted file with five-digit residue numbers.

This reader does not conform to the `PDB 3.2 standard`_ because it allows
This reader does not conform to the `PDB 3.3 standard`_ because it allows
five-digit residue numbers that may take up columns 23 to 27 (inclusive)
instead of being confined to 23-26 (with column 27 being reserved for the
insertion code in the PDB standard). PDB files in this format are written
Expand All @@ -1180,7 +1180,7 @@ class ExtendedPDBReader(PDBReader):


class MultiPDBWriter(PDBWriter):
"""PDB writer that implements a subset of the `PDB 3.2 standard`_ .
"""PDB writer that implements a subset of the `PDB 3.3 standard`_ .

PDB format as used by NAMD/CHARMM: 4-letter resnames and segID, altLoc
is written.
Expand All @@ -1190,9 +1190,9 @@ class MultiPDBWriter(PDBWriter):
and ENDMDL_ records).


.. _MODEL: http://www.wwpdb.org/documentation/file-format-content/format32/sect9.html#MODEL
.. _ENDMDL: http://www.wwpdb.org/documentation/file-format-content/format32/sect9.html#ENDMDL
.. _CONECT: http://www.wwpdb.org/documentation/file-format-content/format32/sect10.html#CONECT
.. _MODEL: http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#MODEL
.. _ENDMDL: http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ENDMDL
.. _CONECT: http://www.wwpdb.org/documentation/file-format-content/format33/sect10.html#CONECT


See Also
Expand Down
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