iddZddlmZmZddlZddlZddlZddlZddlZddl Z ddl Z ddl Z ddl Z ddlmZddlmZddlmZdd lmZdd lmZe jd Ze jd d ZGddejZGddejZGddeZ GddeZ!dS)a^PDB structure files in MDAnalysis --- :mod:`MDAnalysis.coordinates.PDB` ======================================================================== MDAnalysis reads coordinates from PDB files and additional optional data such as B-factors. It is also possible to substitute a PDB file instead of PSF file in order to define the list of atoms (but no connectivity information will be available in this case). PDB files contain both coordinate and atom information. It is also possible to write trajectories as multi-frame (or multi-model) PDB files. This is not very space efficient but is sometimes the lowest common denominator for exchanging trajectories. Single frame and multi-frame PDB files are automatically recognized; the only difference is thath the single-frame PDB is represented as a trajectory with only one frame. In order to write a selection to a PDB file one typically uses the :meth:`MDAnalysis.core.groups.AtomGroup.write` method of the selection:: calphas = universe.select_atoms("name CA") calphas.write("calpha_only.pdb") This uses the coordinates from the current timestep of the trajectory. In order to write a PDB trajectory one needs to first obtain a multi-frame writer (keyword *multiframe* = ``True``) and then iterate through the trajectory, while writing each frame:: calphas = universe.select_atoms("name CA") with MDAnalysis.Writer("calpha_traj.pdb", multiframe=True) as W: for ts in u.trajectory: 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 3.3 standard`_. Using the writer as a context manager ensures that this always happens. Capabilities ------------ 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 3.3 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 them as a trajectory. The :class:`PDBWriter` can write single and multi-frame PDB files as specified by the *multiframe* keyword. By default, it writes single frames. On the other hand, the :class:`MultiPDBWriter` is set up to write a PDB trajectory by default (equivalent to using *multiframe* = ``True``). Examples for working with PDB files ----------------------------------- A **single frame PDB** can be written with the :meth:`~MDAnalysis.core.groups.AtomGroup.write` method of any :class:`~MDAnalysis.core.groups.AtomGroup`:: protein = u.select_atoms("protein") protein.write("protein.pdb") Alternatively, get the single frame writer and supply the :class:`~MDAnalysis.core.groups.AtomGroup`:: protein = u.select_atoms("protein") with MDAnalysis.Writer("protein.pdb") as pdb: pdb.write(protein) In order to write a **multi-frame PDB trajectory** from a universe *u* one can do the following:: with MDAnalysis.Writer("all.pdb", multiframe=True) as pdb: for ts in u.trajectory: pdb.write(u) Similarly, writing only a protein:: protein = u.select_atoms("protein") with MDAnalysis.Writer("protein.pdb", multiframe=True) as pdb: for ts in u.trajectory: pdb.write(protein) Classes ------- .. versionchanged:: 0.16.0 PDB readers and writers based on :class:`Bio.PDB.PDBParser` were retired and removed. .. autoclass:: PDBReader :members: .. autoclass:: PDBWriter :members: .. automethod:: _check_pdb_coordinates .. automethod:: _write_pdb_bonds .. automethod:: _update_frame .. automethod:: _write_timestep .. autoclass:: MultiPDBWriter :members: .. autoclass:: ExtendedPDBReader :members: :inherited-members: .. _`PDB 3.3 standard`: http://www.wwpdb.org/documentation/file-format-content/format33/v3.3.html )StringIOBytesION)util)store_init_arguments)base)Timestep) NoDataErrorzMDAnalysis.coordinates.PBDAtomz resname namecdeZdZdZddgZdddZefdZdZd Z d d Z d Z d Z xZ S) PDBReaderuPDBReader that reads a `PDB-formatted`_ file, no frills. The following *PDB records* are parsed (see `PDB coordinate section`_ for details): - *CRYST1* for unitcell A,B,C, alpha,beta,gamma - *ATOM* or *HETATM* for serial,name,resName,chainID,resSeq,x,y,z,occupancy,tempFactor - *HEADER* (:attr:`header`), *TITLE* (:attr:`title`), *COMPND* (:attr:`compound`), *REMARK* (:attr:`remarks`) - all other lines are ignored Reads multi-`MODEL`_ PDB files as trajectories. The `Timestep.data` dictionary holds the occupancy and tempfactor (bfactor) values for each atom for a given frame. These attributes are commonly appropriated to store other time varying properties and so they are exposed here. Note this does not update the `AtomGroup` attributes, as the topology does not change with trajectory iteration. .. _PDB-formatted: http://www.wwpdb.org/documentation/file-format-content/format33/v3.3.html .. _PDB coordinate section: http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html .. _MODEL: http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#MODEL ============= ============ =========== ============================================= COLUMNS DATA TYPE FIELD DEFINITION ============= ============ =========== ============================================= 1 - 6 Record name "CRYST1" 7 - 15 Real(9.3) a a (Angstroms). 16 - 24 Real(9.3) b b (Angstroms). 25 - 33 Real(9.3) c c (Angstroms). 34 - 40 Real(7.2) alpha alpha (degrees). 41 - 47 Real(7.2) beta beta (degrees). 48 - 54 Real(7.2) gamma gamma (degrees). 1 - 6 Record name "ATOM " 7 - 11 Integer serial Atom serial number. 13 - 16 Atom name Atom name. 17 Character altLoc Alternate location indicator. 18 - 21 Residue name resName Residue name. 22 Character chainID Chain identifier. 23 - 26 Integer resSeq Residue sequence number. 27 AChar iCode Code for insertion of residues. 31 - 38 Real(8.3) x Orthogonal coordinates for X in Angstroms. 39 - 46 Real(8.3) y Orthogonal coordinates for Y in Angstroms. 47 - 54 Real(8.3) z Orthogonal coordinates for Z in Angstroms. 55 - 60 Real(6.2) occupancy Occupancy. 61 - 66 Real(6.2) tempFactor Temperature factor. 67 - 72 (not used in the official PDB format) 73 - 76 String segID (unofficial PDB format*) 77 - 78 LString(2) element Element symbol, right-justified. 79 - 80 LString(2) charge Charge on the atom. ============= ============ =========== ============================================= Notes ----- If a system does not have unit cell parameters (such as in electron microscopy structures), the PDB file format requires the CRYST1_ field to be provided with unitary values (cubic box with sides of 1 Å) and an appropriate REMARK. If unitary values are found within the CRYST1_ field, :code:`PDBReader` will not set unit cell dimensions (which will take the default value :code:`np.zeros(6)`, see Issue #2698) and it will warn the user. .. _CRYST1: http://www.wwpdb.org/documentation/file-format-content/format33/sect8.html#CRYST1 *The columns 73-76 are not part of the official PDB format but are used by some programs to store/operate the segment ID. For instance, Chimera_ assigns it as the attribute `pdbSegment` to allow command-line specification. .. _Chimera: https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html#note6 See Also -------- :class:`PDBWriter` :class:`PDBReader` If you would like to force the use of chainID as the segID when parsing PDB, please use the keyword argument `force_chainids_to_segids=True` (:class:`MDAnalysis.topology.PDBParser.PDBParser`). This will prioritize the chain ID to the segment ID. .. versionchanged:: 0.11.0 * Frames now 0-based instead of 1-based * New :attr:`title` (list with all TITLE lines). .. versionchanged:: 0.19.1 Can now read PDB files with DOS line endings .. versionchanged:: 0.20.0 Strip trajectory header of trailing spaces and newlines .. versionchanged:: 1.0.0 Raise user warning for CRYST1_ record with unitary values (cubic box with sides of 1 Å) and do not set cell dimensions. .. versionchanged:: 2.5.0 Tempfactors (aka bfactors) are now read into the ts.data dictionary each frame. Occupancies are also read into this dictionary. PDBENTNAngstromtimelengthc tt|j|fi| |d|_nh#t$r[ddlm}||j5}|}dddn #1swxYwY|j|_YnwxYw| dd|_ d}g}g}g} |j |jfi|j |_ g} g} t|tjrWt|jt$r=t'|j|_tj|dx} |_d} | r| } | dd d kr)| | ns| dd d kr9| | t7| z n,| dd d kr/| dd}n| dd dkrB|| ddn| dd dkrB|| ddnO| dd dkrA| | d d| | }||_||_||_ | |_!| s| dt7| t7| krdtE| | D}n| }||_#|dd|gz|_$t7||_%|&ddS)a Read coordinates from *filename*. *filename* can be a gzipped or bzip2ed compressed PDB file. If the pdb file contains multiple MODEL records then it is read as a trajectory where the MODEL numbers correspond to frame numbers. n_atomsr) PDBParserN model_offsetrbmagicalsMODELsCRYSTsHEADER BsTITLEPsCOMPNDsREMARKc4g|]\}}t||S)min).0abs d/srv/www/vhosts/g4struct/public_html/venv/lib/python3.11/site-packages/MDAnalysis/coordinates/PDB.py z&PDBReader.__init__..cs$AAATQs1ayyAAAr)'superr__init__rKeyErrorMDAnalysis.topologyrfilenameparsepopr _Timestep _ts_kwargsts isinstancer NamedStreamstreamrrgetvalueencodeanyopen_pdbfilereadlineappendtelllenstripdecodeheadertitlecompoundremarkszip_start_offsets _stop_offsetsn_frames _read_frame)selfr0kwargsrptoprCrDrErFmodelscrystspdbfilelineendoffsets __class__s r)r-zPDBReader.__init__s% (i';;F;;; '!),DLL ' ' ' 6 5 5 5 5 5$$T]33 qggii               ;DLLL '#JJ~q99 $.AAAA h 0 1 1 Kj OX7 7  K&ho&>&>&@&@&G&G&I&IJJHO"&,x">">>$- :##%%DBQBx8## gllnn----bqbX%% gllnns4yy89999bqbY&&be**,,3355bqbX%% T!B$Z--//66889999bqbY&&QrT 0 0 2 2 9 9 ; ;<<<<bqbY&&tABBx~~//6688999) :,llnn       MM!    v;;#f++ % %AAS-@-@AAAGGG%$QRR[C50G   s3 2*BA=1 B=B BB BBc Z|d|jdkt|fi|S)zReturns a PDBWriter for *filename*. Parameters ---------- filename : str filename of the output PDB file Returns ------- :class:`PDBWriter` multiframer) setdefaultrJ PDBWriter)rLr0rMs r)WriterzPDBReader.Writerns7 , (9:::,,V,,,r+c|tj|jd|_d|j_dS)Nr)closerr;r0r<r5framerLs r)_reopenzPDBReader._reopen~s3  T]D99  r+cr||j}ntd|jdz}||S)Nz%PDBReader cannot assign to a timestepr)r5NotImplementedErrorr_rK)rLr5r_s r)_read_next_timestepzPDBReader._read_next_timestepsB :BB&&MNN N Q&&&r+c F |j|}|j|}n#t$r tdwxYwd}t j|j}t j|j}d}|j ||j ||z  }g} | D]} | dddvrv| | dd| dd| dd g | d d ||<n#t$rYnwxYw | d d ||<d }n#t$rYnwxYw|d z }| dddkr t j| dd| dd| dd| dd| dd| dd gtj} t j| t jgdr"t%jdd|j_5| |j_C#t$r7t%jd| d|j_YwxYw||jkr/td|j|||j| |j_|jrR||jj|jj'||jjdd||j_||jjd<|r||jjd<|jS)u Read frame from PDB file. Notes ----- When the CRYST1_ record has unitary values (cubic box with sides of 1 Å), cell dimensions are considered fictitious. An user warning is raised and cell dimensions are set to :code:`np.zeros(6)` (see Issue #2698) .. versionchanged:: 1.0.0 Raise user warning for CRYST1_ record with unitary valuse (cubic box with sides of 1 Å) and do not set cell dimensions. .. versionchanged:: 2.5.0 When seen, `ts.data` is populated with tempfactor information at each frame read. If any atom has a non-parsable (i.e. non float) value in the tempfactor field, the entry is left as `1.0`. NrFr)zATOM HETATM&.6<rTrCRYST1!(/)dtype?rtrtV@ruruz]1 A^3 CRYST1 record, this is usually a placeholder. Unit cell dimensions will be set to None.z@Failed to read CRYST1 record, possibly invalid PDB file, got: {}zInconsistency in file '{}': The number of atoms ({}) in trajectory frame {} differs from the number of atoms ({}) in the corresponding topology. Trajectories with varying numbers of atoms are currently not supported. occupancy tempfactor)rHrI IndexErrorIOErrornpzerosronesr<seekreadrB splitlinesr> ValueErrorarrayfloat32allclosewarningswarnr5 dimensionsformatr0 positions convert_unitsconvert_pos_from_native_posr_data) rLr_startstopposrwrxsaw_tempfactorchunktmp_bufrS cell_dimss r)rKzPDBReader._read_frames( $'.E%e,DD $ $ $t # $HT\** WT\**  5!!! ""4%<007799$$&&1 71 7DBQBx///RU T"R%[$r"u+FGGG%)"R%[IcNN!D*&*2b5kJsO&*NN"DqbqbX%%7 " 2J BK BK BK BK BK !j ! ! !I&{!28,M,M,M#N#N 7! I .2**-6**%"...M!6$<< *.DG&&& .&F $,   6$-eT\BB  $   E  ( ( 6 6 67%-,,TW-?-CDDD $- [!  4)3DGL &ws?0 D D#"D#' D77 EEAH  =I  I c8|jdSN)r<r^r`s r)r^zPDBReader.closes r+r)__name__ __module__ __qualname____doc__runitsrr-r[rardrKr^ __classcell__)rVs@r)rrsbbHU^FZ 0 0E\\\\\|---  ' ' ' 'ooobr+rceZdZdZdddddddd d d d d d ZddgZdddZdddZdZdZ dZ dZ dZ e dde dde d dfZe d!d!e d"d"e d#d#e d$d$e d%d&e d'd(e d'd&e d)d*e d)d+e d,d-e d,d.e d/d/f Z dNd5Zd6Zd7Zd8Zd9Zd:Zd;Zd<Zd=ZdOd>Zejd?Zed@ejdAejfdBZ dPdCZ!dDZ"dEZ#dFZ$dGZ%dQdIZ&dJZ'dKZ(dLZ)dMZ*dS)RrZuPDB 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. The :class:`PDBWriter` can be used to either dump a coordinate set to a PDB file (operating as a "single frame writer", selected with the constructor keyword *multiframe* = ``False``, the default) or by writing a PDB "movie" (multi frame mode, *multiframe* = ``True``), consisting of multiple models (using the MODEL_ and ENDMDL_ records). .. _`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 ---- Writing bonds currently only works when writing a whole :class:`Universe` and if bond information is available in the topology. (For selections smaller than the whole :class:`Universe`, the atom numbering in the CONECT_ records would not match the numbering of the atoms in the new PDB file and therefore a :exc:`NotImplementedError` is raised.) The maximum frame number that can be stored in a PDB file is 9999 and it will wrap around (see :meth:`MODEL` for further details). The CRYST1_ record specifies the unit cell. This record is set to unitary values (cubic box with sides of 1 Å) if unit cell dimensions are not set (:code:`None` or :code:`np.zeros(6)`, see Issue #2698). When the :attr:`record_types` attribute is present (e.g. Universe object was 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. The CONECT_ record is written out, if required, when the output stream is closed. See Also -------- This class is identical to :class:`MultiPDBWriter` with the one exception that it defaults to writing single-frame PDB files as if `multiframe` = ``False`` was selected. .. versionchanged:: 0.7.5 Initial support for multi-frame PDB files. .. versionchanged:: 0.7.6 The *multiframe* keyword was added to select the writing mode. The writing of bond information (CONECT_ records) is now disabled by default but can be enabled with the *bonds* keyword. .. versionchanged:: 0.11.0 Frames now 0-based instead of 1-based .. versionchanged:: 0.14.0 PDB doesn't save charge information .. versionchanged:: 0.20.0 Strip trajectory header of trailing spaces and newlines .. 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) .. versionchanged:: 2.0.0 Add the `redindex` argument. Setting this keyword to ``True`` (the default) preserves the behavior in earlier versions of MDAnalysis. The PDB writer checks for a valid chainID entry instead of using the last character of segid. Should a chainID not be present, or not conform to the PDB standard, the default value of 'X' is used. .. versionchanged:: 2.3.0 Do not write unusable conect records when ag index is larger than 100000. zATOM {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}{charge:2s} zHETATM{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}{charge:2s} zREMARK {0} zCOMPND {0} zHEADER {0} zTITLE {0} zMODEL {0:>4d} zNUMMDL {0:5d} zENDMDL zEND zrCRYST1{box[0]:9.3f}{box[1]:9.3f}{box[2]:9.3f}{ang[0]:7.2f}{ang[1]:7.2f}{ang[2]:7.2f} {spacegroup:<11s}{zvalue:4d} z CONECT{0} ) ATOMrfREMARKCOMPNDHEADERTITLEMODELNUMMDLENDMDLENDrlCONECTrrNrrg"?g-@)r%maxrF)FEASZNMGMNCOBRCUTAMOALBESEPTEUNIIRRHAUGDRU)CMHEMCMBOMMCHGBBE7PMB)0QECPTDCEEAAIMNOCZOMYOMZUN91N12T83933MYBMUCLMCP6DB8DIFEFZLURRDCUCLXMMHLTIRELCPPCIVGHOECCA1PLLPDOEXC14C15F9FOANBLMrBZGrVNLCO1CO2PF5FE1FE2UNLconectrrCreated by PDBWriterTc ||_||_||jn||_||_| |_|dkrt d|x|_|_||_ ||_ tj |jd|_ d|_d|_dS)a8Create a new PDBWriter Parameters ---------- filename: str name of output file start: int (optional) starting timestep (the first frame will have MODEL number `start` + 1 because the PDB standard prescribes MODEL numbers starting at 1) step: int (optional) skip between subsequent timesteps remarks: str (optional) comments to annotate pdb file (added to the *TITLE* record); note that any remarks from the trajectory that serves as input are written to REMARK records with lines longer than :attr:`remark_max_length` (66 characters) being wrapped. convert_units: bool (optional) units are converted to the MDAnalysis base format; [``True``] bonds : {"conect", "all", None} (optional) If set to "conect", then only write those bonds that were already defined in an input PDB file as PDB CONECT_ record. If set to "all", write all bonds (including guessed ones) to the file. ``None`` does not write any bonds. The default is "conect". multiframe: bool (optional) ``False``: write a single frame to the file; ``True``: create a multi frame PDB file in which frames are written as MODEL_ ... ENDMDL_ records. If ``None``, then the class default is chosen. [``None``] reindex: bool (optional) If ``True`` (default), the atom serial is set to be consecutive numbers starting at 1. Else, use the atom id. Nrz 'Start' must be a positive valuewtF)r0rrX _multiframebonds_reindexrrframes_writtensteprFrr;rRhas_ENDfirst_frame_done) rLr0rrrrrFrrXreindexs r)r-zPDBWriter.__init__sd! *)1DOOz   199?@@ @+00 T(  |DM488  %r+ct|drj|jc|js)||nt d|jd|_dS)z Close PDB file and write CONECT and END record .. versionchanged:: 2.0.0 CONECT_ record written just before END_ record rRNzHEND record has already been written before the final closing of the file)hasattrrRr_write_pdb_bondsrloggerwarningr^r`s r)r^zPDBWriter.closes 4 # # ! (@< %%''' < L    r+c|jr;|d|j|j|jdS|d|j|jdS)Nz/MDANALYSIS FRAMES FROM {0:d}, STEP {1:d}: {2!s}zMDANALYSIS FRAME {0:d}: {1!s})rrrrrrFr`s r)_write_pdb_titlezPDBWriter._write_pdb_title.s    JJ6$*di>>      JJ6$*dl33     r+c|jdurdSd|_|jj}||j|||j g}tj|jj D]/}| tj ||j 0|j|n#t$rYnwxYw|jjj|t'jgd|d|d|d|d|d|d t+jd dS|||jjdS) u  Write PDB header. The HEADER_ record is set to :code: `trajectory.header`. The TITLE_ record explicitly mentions MDAnalysis and contains information about trajectory frame(s). The COMPND_ record is set to :code:`trajectory.compound`. The REMARKS_ records are set to :code:`u.trajectory.remarks` The CRYST1_ record specifies the unit cell. This record is set to unitary values (cubic box with sides of 1 Å) if unit cell dimensions are not set. .. 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 sides of 1 Å) are used (PDB standard for CRYST1_). TNrsz6285 UNITARY VALUES FOR THE UNIT CELL AUTOMATICALLY SETz9285 BY MDANALYSIS PDBWRITER BECAUSE UNIT CELL INFORMATIONz285 WAS MISSING.z.285 PROTEIN DATA BANK CONVENTIONS REQUIRE THATz0285 CRYST1 RECORD IS INCLUDED, BUT THE VALUES ONz 285 THIS RECORD ARE MEANINGLESS.zDUnit cell dimensions not found. CRYST1 record set to unitary values.)robjuniverser trajectoryrrr asiterablerFextendtextwrapwrapremark_max_lengthrAttributeErrorr5rrlr{rrrconvert_dimensions_to_unitcell)rLurFrSs r)_write_pdb_headerzPDBWriter._write_pdb_header:s&  D ( ( F $ H  AL!!!  AL!!! G (<== L Lx}T43IJJKKKK DK ! ! !    D  z-PDBWriter._write_pdb_bonds..s$'H'HA'H'H'H'H'H'Hr+indexci|]\}}|| Sr$r$)r&ir#s r) z.PDBWriter._write_pdb_bonds..s.Auqr+r)ridci|]}||Sr$r$)r&id_s r)r&z.PDBWriter._write_pdb_bonds..s>>>CsC>>>r+rc3~K|]7}|j t|dt|dfV8dSrrN) is_guessedgetattrr&bondindex_attributes r)r"z-PDBWriter._write_pdb_bonds..se  DG_55DG_55r+allc3pK|]0}t|dt|dfV1dSr+)r-r.s r)r"z-PDBWriter._write_pdb_bonds..s] DG_55DG_55r+z.bonds has to be either None, 'conect' or 'all'izBAtom with index >=100000 cannot write bonds to PDB CONECT records.c3vK|]3}|v|gtfd|DzV4dS)c g|] }| Sr$r$)r&atmappings r)r*z8PDBWriter._write_pdb_bonds...s"@"@"@272;"@"@"@r+N)sorted)r&r'conr6s r)r"z-PDBWriter._write_pdb_bonds..sa  CxxQZL6"@"@"@"@Q"@"@"@AA Axxx  r+)rrrrset itertoolschainrr enumerateindicesr{sortidsr collections defaultdictlistrrr>r) rLbondsetrra1a2rcr8r0r6s @@@r)rzPDBWriter._write_pdb_bondss :  Fe$$ 8 48,g66  Fio'H'H'H'H'HIJJ = 0%O )$(.*@ J J JGGDHN233EE"O>>48>+=>>>GGDHN.//E : ! ! $ EEZ5  $ EEMNN N%d++  FB'MMbGmmr{f$$ v(=(= 3 GNN2    GNN2               A KKNNNN  r+ct|trtdt|jdkrt d||_|jjj |_ dS)aMethod to initialize important attributes in writer from a AtomGroup or Universe *obj*. Attributes initialized/updated: * :attr:`PDBWriter.obj` (the entity that provides topology information *and* coordinates, either a :class:`~MDAnalysis.core.groups.AtomGroup` or a whole :class:`~MDAnalysis.core.universe.Universe`) * :attr:`PDBWriter.trajectory` (the underlying trajectory :class:`~MDAnalysis.coordinates.base.Reader`) * :attr:`PDBWriter.timestep` (the underlying trajectory :class:`~MDAnalysis.coordinates.timestep.Timestep`) Before calling :meth:`_write_next_frame` this method **must** be called at least once to enable extracting topology information from the current frame. zPDBWriter cannot write Timestep objects directly, since they lack topology information (atom names and types) required in PDB filesrzCannot write empty AtomGroupN) r6r rr@rryrrr r5rLrs r) _update_framezPDBWriter._update_framesm" c8 $ $ >  sy>>Q  ;<< <,),r+c|||||j|jdS)a6Write object *obj* at current trajectory frame to file. *obj* can be a selection (i.e. a :class:`~MDAnalysis.core.groups.AtomGroup`) or a whole :class:`~MDAnalysis.core.universe.Universe`. The last letter of the :attr:`~MDAnalysis.core.groups.Atom.segid` is used as the PDB chainID (but see :meth:`~PDBWriter.ATOM` for details). Parameters ---------- obj The :class:`~MDAnalysis.core.groups.AtomGroup` or :class:`~MDAnalysis.core.universe.Universe` to write. rXN)rIr_write_next_framer5rrHs r)writezPDBWriter.writesP$ 3     tw43CDDDDDr+cv||||j|j}}|jj}|s|jdkr|j}t|t||D]&}||| |j d'| ||dS)aWrite all timesteps associated with *obj* to the PDB file. *obj* can be a :class:`~MDAnalysis.core.groups.AtomGroup` or a :class:`~MDAnalysis.core.universe.Universe`. The method writes the frames from the one specified as *start* until the end, using a step of *step* (*start* and *step* are set in the constructor). Thus, if *u* is a Universe then :: u.trajectory[-2] pdb = PDBWriter("out.pdb", u.atoms.n_atoms) pdb.write_all_timesteps(u) will write a PDB trajectory containing the last 2 frames and :: pdb = PDBWriter("out.pdb", u.atoms.n_atoms, start=12, step=2) pdb.write_all_timesteps(u) will be writing frames 12, 14, 16, ... .. versionchanged:: 0.11.0 Frames now 0-based instead of 1-based .. versionchanged:: 2.0.0 CONECT_ record moved to :meth:`close` rTrKN) rIrrrrr rJr_ranger@rLr5r^)rLrrrtraj framenumbers r)write_all_timestepszPDBWriter.write_all_timesteps2s: 3    j$)t|&  **JE D 488 = =K     " "47t " < < < <  U r+c |) |j}n #t$rd}t|dwxYw||j|fi|dS)awrite a new timestep to the PDB file :Keywords: *ts* :class:`timestep.Timestep` object containing coordinates to be written to trajectory file; if ``None`` then :attr:`PDBWriter.ts`` is tried. *multiframe* ``False``: write a single frame (default); ``True`` behave as a trajectory writer .. Note:: Before using this method with another :class:`timestep.Timestep` in the *ts* argument, :meth:`PDBWriter._update_frame` *must* be called with the :class:`~MDAnalysis.core.groups.AtomGroup.Universe` as its argument so that topology information can be gathered. .. versionchanged:: 1.0.0 Renamed from `write_next_timestep` to `_write_next_frame`. Nz9PBDWriter: no coordinate data to write to trajectory file)r5rr r_write_timestep)rLr5rMerrmsgs r)rLzPDBWriter._write_next_framees* : 4W! 4 4 4&"&))t3  4 ##%%%R**6*****s )c|dkrdSt|dkr |ddSt|dkrd|S||ks\|dd|jvsK|dksE||jvr|dddks.||jvr|ddd kst |||jvr,t |||jvrd |Sd |S) aDeduce how the atom name should be aligned. Atom name format can be deduced from the atom type, yet atom type is not always available. This function uses the atom name and residue name to deduce how the atom name should be formatted. The rules in use got inferred from an analysis of the PDB. See gist at for more details. rNrz {} rUNKHGCLz{:<4}z {:<3})r@rions special_hg special_clPair include_pairs exclude_pairs)rLatomnameresnames r)_deduce_PDB_atom_namezPDBWriter._deduce_PDB_atom_names r>>2 x==A  BQB<  ]]a  >>(++ + x  |ty((5  4?**x|t/C/C4?**x|t/C/CGX&&$*<<<7H%%T-???>>(++ +x(((r+chargesreturnctj|jtjst d|t }d||dk<tj|dkdD]:}||dkrd}t |t||d||<;tj|dkdD]-}||dkrd}t |||d ||<.|S) aFormat formal charges to match PDB requirements. Formal charge entry is set to empty if charge is 0, otherwise the charge is set to a two character ````` entry, e.g. ``1+`` or ``2-``. This method also verifies that formal charges can adhere to the PDB format (i.e. charge cannot be > 9 or < -9). Parameters ---------- charges: np.ndarray NumPy array of integers representing the formal charges of the atoms being written. Returns ------- np.ndarray NumPy array of dtype object with strings representing the formal charges of the atoms being written. z,formal charges array should be of `int` typerriz3formal charge < -9 is not supported by PDB standard- z2formal charge > 9 is not supported by PDB standard+) r{ issubdtyperrintegerrastypeobjectwhereabs)rd outchargesr%rUs r)_format_PDB_chargeszPDBWriter._format_PDB_chargess .}W]BJ77 MKLL L^^F++ &( :?#'A+&&q) 2 2AqzBN ((("71:111JqMM'A+&&q) - -AqzA~~M (((&qz,,,JqMMr+c"jjj}jr|d}|rjdzfd}|dd}|dd}|d d}|d d}|d d } |d d} |dd} |dd} |dd} |dd}|dd}|dd}d}|| d} js& j }nA#t$rtdwxYwtj tdz}ttD]o}i}t!j||d|d<| ||||d<||dd|d<||dd |d!<t!j| |d |d"<||dd|d#<|||d$<| ||d%<| ||d&<||dd |d'<| ||d(<||dd)|d*<|||d+< jj||jd.i|G#t0$rd,||d-}t3|dwxYw|rxjdz c_dS)/a Write a new timestep *ts* to file Does unit conversion if necessary. By setting *multiframe* = ``True``, MODEL_ ... ENDMDL_ records are written to represent trajectory frames in a multi-model PDB file. (At the moment we do *not* write the NUMMDL_ record.) The *multiframe* = ``False`` keyword signals that the :class:`PDBWriter` is in single frame mode and no MODEL_ records are written. .. 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.) .. 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) .. versionchanged:: 2.0.0 When only :attr:`record_types` attribute is present, instead of using ATOM_ for both ATOM_ and HETATM_, HETATM_ record types are properly written out (Issue #1753). Writing now only uses the contents of the elements attribute instead of guessing by default. If the elements are missing, empty records are written out (Issue #2423). Atoms are now checked for a valid chainID instead of being overwritten by the last letter of the `segid` (Issue #3144). F)inplacerc t|S#t$r[jdkr(tjd||t j|gtzcYSwxYw)zTry and pull info off atoms, else fake it attrname - the field to pull of AtomGroup (plural!) default - default value in case attrname not found rz?Found no information for attr: '{}' Using default value of '{}') r-rrrrrr{rr@)attrnamedefaultrrLs r)get_attrz+PDBWriter._write_timestep..get_attrs 8uh///! 8 8 8&!++M!6(G44 x CJJ 677777 8sA"A87A8altLocs resnamesrXicodessegidschainIDsrresids occupanciesrt tempfactorsgnamesXelements record_typesr formalchargesrcd}d}d}t|D]I\}}|dkrd}|||<t|dkrd}|||<.|sd}|||<J|r'tjd||r'tjd||r'tjd||S)zValidate each atom's chainID chainids - np array of chainIDs default - default value in case chainID is considered invalid FrTrzNFound chainIDs with invalid length. Corresponding atoms will use value of '{}'zVFound chainIDs using unnaccepted character. Corresponding atoms will use value of '{}'zBFound missing chainIDs. Corresponding atoms will use value of '{}')r<r@isalnumrrr)chainidsrvinvalid_length_idsinvalid_char_ids missing_idsr%chainids r)validate_chainidsz4PDBWriter._write_timestep..validate_chainidss "' $ K'11 * * 7b=="&K")HQKK\\A%%)-&")HQKK ***'+$")HQK!  vg    vg   vg Or+zUThe "id" topology attribute is not set. Either set the attribute or use reindex=True.rserialnameNaltLocrWresNameresSeqiCoderrw tempFactorsegIDchainIDrelementchargezFound z? for the record type, but only allowed types are ATOM or HETATMr$)rrrrconvert_pos_to_nativerrrqrr?rr r{aranger@rOr ltruncate_intrcupperrRrMfmtrr.rr)rLr5rXrrwaltlocsrzr{r|rr~rr atomnamesrrformal_chargesratom_idsr%valsrUrs` @r)rTzPDBWriter._write_timestepsFo   A,,S%,@@C  0 JJt*Q. / / / 8 8 8 8 8 8"(9c**8J..(C(((C((8J++(A&&h}c22 h}c22 HWc** 8J,,x77 11((?A2N2NOO' ' ' R%$Xs33} 1  9!   !D  yU,,q0Hs5zz"" 3 3AD!/ QDN 55! hqkDL%QZ^DN&qk"1"oDO!/q 1==DN"1IbqbMDMa&DK +AD !,QD "1IbqbMDM&qkDO&qk"1"o3355DO+A.DN 3 ""#C48LO#<#C#K#Kd#K#KLLLL 3 3 3=\!_===!((d2  3   KKMMM q sDD56J??'K&ct|dsdS|j}|j|jd|dS)zWrite HEADER_ record. .. versionchanged:: 0.20.0 Strip `trajectory.header` since it can be modified by the user and should be sanitized (Issue #2324) rCNr)rrCrArRrMrr)rLr rCs r)rzPDBWriter.HEADERps`z8,,  F"((** 48H-44V<<=====r+cd|}|j|jd|dS)zWrite TITLE_ record.ryrNjoinrRrMrr)rLrDrSs r)rzPDBWriter.TITLE|sBxx 48G,33D99:::::r+c|D]:}|j|jd|;dS)zWrite generic REMARKS_ record (without number). Each string provided in *remarks* is written as a separate REMARKS_ record. rNrRrMrr)rLrFremarks r)rzPDBWriter.REMARKsO B BF L  tx188@@ A A A A B Br+ct|dsdS|j}|D]:}|j|jd|;dS)NrEr)rrErRrMrr)rLr rErFs r)rzPDBWriter.COMPNDshz:..  F& = =A L  tx188;; < < < < = =r+P 1c|j|jd|dd|dd||dS)zWrite CRYST1_ record.rlNrv)boxang spacegroupzvaluer)rLrrrs r)rlzPDBWriter.CRYST1sa  HX  % %rrNqrrN% &       r+c |j|jdt t |dddS)aWWrite the MODEL_ record. .. note:: The maximum MODEL number is limited to 9999 in the PDB standard (i.e., 4 digits). If frame numbers are larger than 9999, they will wrap around, i.e., 9998, 9999, 0, 1, 2, ... .. versionchanged:: 0.19.0 Maximum model number is enforced. rN)rRrMrrintstr)rL modelnumbers r)rzPDBWriter.MODELsY  HW  $ $S[)9)9"##)>%?%? @ @     r+cl|js%|j|jdd|_dS)a%Write END_ record. Only a single END record is written. Calling END multiple times has no effect. Because :meth:`~PDBWriter.close` also calls this method right before closing the file it is recommended to *not* call :meth:`~PDBWriter.END` explicitly. rTN)rrRrMrr`s r)rz PDBWriter.ENDs5| 0 L  tx / / / r+cP|j|jddS)zWrite the ENDMDL_ record.rN)rRrMrr`s r)rzPDBWriter.ENDMDLs% 48H-.....r+cd|D}d|}|j|jd|dS)zWrite CONECT_ record.c8g|]}d|S)z{0:5d})r)r&entrys r)r*z$PDBWriter.CONECT..s$===U(//%((===r+rrNr)rLrs r)rzPDBWriter.CONECTsU==f=== 48H-44V<<=====r+)rNrrrTNTr)F)rr)+rrrrrrrrrrXr[r\r]r^r_r`r-r^rrrrrIrMrRrL functoolscacherc staticmethodr{ndarrayrqrTrrrrrlrrrrr$r+r)rZrZs]WWv K  K %##"&& - 5  C8U^FZ 0 0E' ::OJ D4CJJ@T%''eT):):DDEEE4111f++++B_))_)6&RZ&BJ&&&\&Pc!c!c!c!J > > >;;; BBB===        "   ///>>>>>r+rZceZdZdZdZdS)ExtendedPDBReadera.PDBReader that reads a PDB-formatted file with five-digit residue numbers. 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 by popular programs such as VMD_. See Also -------- :class:`PDBReader` .. _VMD: http://www.ks.uiuc.edu/Research/vmd/ .. versionadded:: 0.8 XPDBN)rrrrrr$r+r)rrs$FFFr+rc"eZdZdZddgZdZdZdS)MultiPDBWriteraYPDB 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. By default, :class:`MultiPDBWriter` writes a PDB "movie" (multi frame mode, *multiframe* = ``True``), consisting of multiple models (using the MODEL_ and ENDMDL_ records). .. _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 -------- This class is identical to :class:`PDBWriter` with the one exception that it defaults to writing multi-frame PDB files instead of single frames. .. versionadded:: 0.7.6 rrTFN)rrrrrrX singleframer$r+r)rrs-4U^FJKKKr+r)"riorrrrr:r rloggingr@numpyr{rlibrlib.utilrrr timestepr exceptionsr getLoggerr namedtupler^ ReaderBaser WriterBaserZrrr$r+r)rs2uul! ++++++$$$$$$  7 8 8{fn55\\\\\\\\~ ~>~>~>~>~>~>~>~>B ,Yr+