src.pdb (4 August 2008) | index /Users/d3y382/workspaces/apbs-pdb2pqr/pdb2pqr/src/pdb.py

`PDB parsing class
This module parses PDBs in accordance to PDB Format Description Version 2.2
(1996); it is not very forgiving. Each class in this module corresponds
to a record in the PDB Format Description. Much of the documentation for
the classes is taken directly from the above PDB Format Description.
----------------------------
PDB2PQR -- An automated pipeline for the setup, execution, and analysis of
Poisson-Boltzmann electrostatics calculations
Copyright (c) 2002-2011, Jens Erik Nielsen, University College Dublin;
Nathan A. Baker, Battelle Memorial Institute, Developed at the Pacific
Northwest National Laboratory, operated by Battelle Memorial Institute,
Pacific Northwest Division for the U.S. Department Energy.;
Paul Czodrowski & Gerhard Klebe, University of Marburg.
All rights reserved.
Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice,
this list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
* Neither the names of University College Dublin, Battelle Memorial Institute,
Pacific Northwest National Laboratory, US Department of Energy, or University
of Marburg nor the names of its contributors may be used to endorse or promote
products derived from this software without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED
OF THE POSSIBILITY OF SUCH DAMAGE.
----------------------------`

Modules

``

copy | string | sys |

Classes

``

__builtin__.object
  BaseRecord
    ANISOU
    ATOM
    AUTHOR
    CAVEAT
    CISPEP
    COMPND
    CONECT
    CRYST1
    DBREF
    END
    ENDMDL
    EXPDTA
    FORMUL
    HEADER
    HELIX
    HET
    HETATM
    HETNAM
    HETSYN
    HYDBND
    JRNL
    KEYWDS
    LINK
    MASTER
    MODEL
    MODRES
    MTRIXn
      MTRIX1
      MTRIX2
      MTRIX3
    NUMMDL
    OBSLTE
    ORIGXn
      ORIGX1
      ORIGX2
      ORIGX3
    REMARK
    REVDAT
    SCALEn
      SCALE1
      SCALE2
      SCALE3
    SEQADV
    SEQRES
    SHEET
    SIGATM
    SIGUIJ
    SITE
    SLTBRG
    SOURCE
    SPRSDE
    SSBOND
    TER
    TITLE
    TURN
    TVECT
MOL2BOND
MOL2MOLECULE

class ANISOU(BaseRecord)
`` | `ANISOU class The ANISOU records present the anisotropic temperature factors.`

Method resolution order:
  ANISOU
  BaseRecord
  __builtin__.object

Methods defined here:

__init__(self, line)
  `Initialize by parsing line:
  COLUMNS TYPE FIELD DEFINITION
  ------------------------------------------------------
  7-11 int serial Atom serial number.
  13-16 string name Atom name.
  17 string altLoc Alternate location indicator.
  18-20 string resName Residue name.
  22 string chainID Chain identifier.
  23-26 int resSeq Residue sequence number.
  27 string iCode Insertion code.
  29-35 int u00 U(1,1)
  36-42 int u11 U(2,2)
  43-49 int u22 U(3,3)
  50-56 int u01 U(1,2)
  57-63 int u02 U(1,3)
  64-70 int u12 U(2,3)
  73-76 string segID Segment identifier, left-justified.
  77-78 string element Element symbol, right-justified.
  79-80 string charge Charge on the atom.`

Methods inherited from BaseRecord:

__str__(self)

Data descriptors inherited from BaseRecord:

__dict__
  `dictionary for instance variables (if defined)`

__weakref__
  `list of weak references to the object (if defined)`

class ATOM(BaseRecord)
`` | `ATOM class The ATOM records present the atomic coordinates for standard residues. They also present the occupancy and temperature factor for each atom. Heterogen coordinates use the HETATM record type. The element symbol is always present on each ATOM record; segment identifier and charge are optional.`

Method resolution order:
  ATOM
  BaseRecord
  __builtin__.object

Methods defined here:

__init__(self, line)
  `Initialize by parsing line
  COLUMNS TYPE FIELD DEFINITION
  ---------------------------------------------
  7-11 int serial Atom serial number.
  13-16 string name Atom name.
  17 string altLoc Alternate location indicator.
  18-20 string resName Residue name.
  22 string chainID Chain identifier.
  23-26 int resSeq Residue sequence number.
  27 string iCode Code for insertion of residues.
  31-38 float x Orthogonal coordinates for X in
  Angstroms.
  39-46 float y Orthogonal coordinates for Y in
  Angstroms.
  47-54 float z Orthogonal coordinates for Z in
  Angstroms.
  55-60 float occupancy Occupancy.
  61-66 float tempFactor Temperature factor.
  73-76 string segID Segment identifier, left-justified.
  77-78 string element Element symbol, right-justified.
  79-80 string charge Charge on the atom.`

Methods inherited from BaseRecord:

__str__(self)

Data descriptors inherited from BaseRecord:

__dict__
  `dictionary for instance variables (if defined)`

__weakref__
  `list of weak references to the object (if defined)`

class AUTHOR(BaseRecord)
`` | `AUTHOR field The AUTHOR record contains the names of the people responsible for the contents of the entry.`

Method resolution order:
  AUTHOR
  BaseRecord
  __builtin__.object

Methods defined here:

__init__(self, line)
  `Initialize by parsing a line
  COLUMNS TYPE FIELD DEFINITION
  --------------------------------------------------
  11-70 string authorList List of the author names, separated by
  commas`

Methods inherited from BaseRecord:

__str__(self)

Data descriptors inherited from BaseRecord:

__dict__
  `dictionary for instance variables (if defined)`

__weakref__
  `list of weak references to the object (if defined)`

class BaseRecord(__builtin__.object)
`` | `Base class for all records. Verifies the received record type`

Methods defined here:

__init__(self, line)

__str__(self)

Data descriptors defined here:

__dict__
  `dictionary for instance variables (if defined)`

__weakref__
  `list of weak references to the object (if defined)`

class CAVEAT(BaseRecord)
`` | `CAVEAT field CAVEAT warns of severe errors in an entry. Use caution when using an entry containing this record.`

Method resolution order:
  CAVEAT
  BaseRecord
  __builtin__.object

Methods defined here:

__init__(self, line)
  `Initialize by parsing line.
  COLUMNS TYPE FIELD DEFINITION
  ----------------------------------------------------
  12-15 string idCode PDB ID code of this entry.
  20-70 string comment Free text giving the reason for the
  CAVEAT.`

Methods inherited from BaseRecord:

__str__(self)

Data descriptors inherited from BaseRecord:

__dict__
  `dictionary for instance variables (if defined)`

__weakref__
  `list of weak references to the object (if defined)`

class CISPEP(BaseRecord)
`` | `CISPEP field CISPEP records specify the prolines and other peptides found to be in the cis conformation. This record replaces the use of footnote records to list cis peptides.`

Method resolution order:
  CISPEP
  BaseRecord
  __builtin__.object

Methods defined here:

__init__(self, line)
  `Initialize by parsing line
  COLUMNS TYPE FIELD DEFINITION
  -----------------------------------------------------------
  8-10 int serNum Record serial number.
  12-14 string pep1 Residue name.
  16 string chainID1 Chain identifier.
  18-21 int seqNum1 Residue sequence number.
  22 string icode1 Insertion code.
  26-28 string pep2 Residue name.
  30 string chainID2 Chain identifier.
  32-35 int seqNum2 Residue sequence number.
  36 string icode2 Insertion code.
  44-46 int modNum Identifies the specific model.
  54-59 float measure Measure of the angle in degrees.`

Methods inherited from BaseRecord:

__str__(self)

Data descriptors inherited from BaseRecord:

__dict__
  `dictionary for instance variables (if defined)`

__weakref__
  `list of weak references to the object (if defined)`

class COMPND(BaseRecord)

``

`COMPND field
The COMPND record describes the macromolecular contents of an entry.
Each macromolecule found in the entry is described by a set of token:
value pairs, and is referred to as a COMPND record component. Since the
concept of a molecule is difficult to specify exactly, PDB staff may
exercise editorial judgment in consultation with depositors in
assigning these names.
For each macromolecular component, the molecule name, synonyms, number
assigned by the Enzyme Commission (EC), and other relevant details are
specified.
`

Method resolution order:
  COMPND
  BaseRecord
  __builtin__.object

Methods defined here:

__init__(self, line)
  `Initialize by parsing a line
  COLUMNS TYPE FIELD DEFINITION
  --------------------------------------------------
  11-70 string compound Description of the molecular list
  components.`

Methods inherited from BaseRecord:

__str__(self)

Data descriptors inherited from BaseRecord:

__dict__
  `dictionary for instance variables (if defined)`

__weakref__
  `list of weak references to the object (if defined)`

class CONECT(BaseRecord)

``

`CONECT class
The CONECT records specify connectivity between atoms for which
coordinates are supplied. The connectivity is described using the atom
serial number as found in the entry. CONECT records are mandatory for
HET groups (excluding water) and for other bonds not specified in the
standard residue connectivity table which involve atoms in standard
residues (see Appendix 4 for the list of standard residues). These
records are generated by the PDB.
`

Method resolution order:
  CONECT
  BaseRecord
  __builtin__.object

Methods defined here:

__init__(self, line)
  `Initialize by parsing line
  COLUMNS TYPE FIELD DEFINITION
  --------------------------------------------
  7-11 int serial Atom serial number
  12-16 int serial1 Serial number of bonded atom
  17-21 int serial2 Serial number of bonded atom
  22-26 int serial3 Serial number of bonded atom
  27-31 int serial4 Serial number of bonded atom
  32-36 int serial5 Serial number of hydrogen bonded atom
  37-41 int serial6 Serial number of hydrogen bonded atom
  42-46 int serial7 Serial number of salt bridged atom
  47-51 int serial8 Serial number of hydrogen bonded atom
  52-56 int serial9 Serial number of hydrogen bonded atom
  57-61 int serial10 Serial number of salt bridged atom`

Methods inherited from BaseRecord:

__str__(self)

Data descriptors inherited from BaseRecord:

__dict__
  `dictionary for instance variables (if defined)`

__weakref__
  `list of weak references to the object (if defined)`

class CRYST1(BaseRecord)
`` | `CRYST1 class The CRYST1 record presents the unit cell parameters, space group, and Z value. If the structure was not determined by crystallographic means, CRYST1 simply defines a unit cube.`

Method resolution order:
  CRYST1
  BaseRecord
  __builtin__.object

Methods defined here:

__init__(self, line)
  `Initialize by parsing line
  COLUMNS TYPE FIELD DEFINITION
  ---------------------------------------
  7-15 float a a (Angstroms).
  16-24 float b b (Angstroms).
  25-33 float c c (Angstroms).
  34-40 float alpha alpha (degrees).
  41-47 float beta beta (degrees).
  48-54 float gamma gamma (degrees).
  56-66 string sGroup Space group.
  67-70 int z Z value.`

Methods inherited from BaseRecord:

__str__(self)

Data descriptors inherited from BaseRecord:

__dict__
  `dictionary for instance variables (if defined)`

__weakref__
  `list of weak references to the object (if defined)`

class DBREF(BaseRecord)

``

`DBREF field
The DBREF record provides cross-reference links between PDB sequences
and the corresponding database entry or entries. A cross reference to
the sequence database is mandatory for each peptide chain with a length
greater than ten (10) residues. For nucleic acid entries a DBREF record
pointing to the Nucleic Acid Database (NDB) is mandatory when the
corresponding entry exists in NDB.
`

Method resolution order:
  DBREF
  BaseRecord
  __builtin__.object

Methods defined here:

__init__(self, line)
  `Initialize by parsing a line.
  COLUMNS TYPE FIELD DEFINITION
  ------------------------------------------------------
  8-11 string idCode ID code of this entry.
  13 string chainID Chain identifier.
  15-18 int seqBegin Initial sequence number of the PDB
  sequence segment.
  19 string insertBegin Initial insertion code of the PDB
  sequence segment.
  21-24 int seqEnd Ending sequence number of the PDB
  sequence segment.
  25 string insertEnd Ending insertion code of the PDB
  sequence segment.
  27-32 string database Sequence database name. "PDB" when
  a corresponding sequence database
  entry has not been identified.
  34-41 string dbAccession Sequence database accession code.
  For GenBank entries, this is the
  NCBI gi number.
  43-54 string dbIdCode Sequence database identification
  code. For GenBank entries, this is
  the accession code.
  56-60 int dbseqBegin Initial sequence number of the
  database seqment.
  61 string dbinsBeg Insertion code of initial residue
  of the segment, if PDB is the
  reference.
  63-67 int dbseqEnd Ending sequence number of the
  database segment.
  68 string dbinsEnd Insertion code of the ending
  residue of the segment, if PDB is
  the reference.`

Methods inherited from BaseRecord:

__str__(self)

Data descriptors inherited from BaseRecord:

__dict__
  `dictionary for instance variables (if defined)`

__weakref__
  `list of weak references to the object (if defined)`

class END(BaseRecord)
`` | `END class The END records are paired with MODEL records to group individual structures found in a coordinate entry.`

Method resolution order:
  END
  BaseRecord
  __builtin__.object

Methods defined here:

__init__(self, line)
  `Initialize by parsing line (nothing to do)`

Methods inherited from BaseRecord:

__str__(self)

Data descriptors inherited from BaseRecord:

__dict__
  `dictionary for instance variables (if defined)`

__weakref__
  `list of weak references to the object (if defined)`

class ENDMDL(BaseRecord)
`` | `ENDMDL class The ENDMDL records are paired with MODEL records to group individual structures found in a coordinate entry.`

Method resolution order:
  ENDMDL
  BaseRecord
  __builtin__.object

Methods defined here:

__init__(self, line)
  `Initialize by parsing line (nothing to do)`

Methods inherited from BaseRecord:

__str__(self)

Data descriptors inherited from BaseRecord:

__dict__
  `dictionary for instance variables (if defined)`

__weakref__
  `list of weak references to the object (if defined)`

class EXPDTA(BaseRecord)
`` | `EXPDTA field The EXPDTA record identifies the experimental technique used. This may refer to the type of radiation and sample, or include the spectroscopic or modeling technique. Permitted values include: ELECTRON DIFFRACTION FIBER DIFFRACTION FLUORESCENCE TRANSFER NEUTRON DIFFRACTION NMR THEORETICAL MODEL X-RAY DIFFRACTION`

Method resolution order:
  EXPDTA
  BaseRecord
  __builtin__.object

Methods defined here:

__init__(self, line)
  `Initialize by parsing a line
  COLUMNS TYPE FIELD DEFINITION
  --------------------------------------------------
  11-70 string technique The experimental technique(s) with
  optional comment describing the sample
  or experiment`

Methods inherited from BaseRecord:

__str__(self)

Data descriptors inherited from BaseRecord:

__dict__
  `dictionary for instance variables (if defined)`

__weakref__
  `list of weak references to the object (if defined)`

class FORMUL(BaseRecord)
`` | `FORMUL field The FORMUL record presents the chemical formula and charge of a non-standard group.`

Method resolution order:
  FORMUL
  BaseRecord
  __builtin__.object

Methods defined here:

__init__(self, line)
  `Initialize by parsing line
  COLUMNS TYPE FIELD DEFINITION
  -----------------------------------------------------
  9-10 int compNum Component number
  13-15 string hetID Het identifier
  19 string asterisk * for water
  20-70 string text Chemical formula`

Methods inherited from BaseRecord:

__str__(self)

Data descriptors inherited from BaseRecord:

__dict__
  `dictionary for instance variables (if defined)`

__weakref__
  `list of weak references to the object (if defined)`

class HEADER(BaseRecord)
`` | `HEADER field The HEADER record uniquely identifies a PDB entry through the idCode field. This record also provides a classification for the entry. Finally, it contains the date the coordinates were deposited at the PDB.`

Method resolution order:
  HEADER
  BaseRecord
  __builtin__.object

Methods defined here:

__init__(self, line)
  `Initialize by parsing a line.
  COLUMNS TYPE FIELD DEFINITION
  ---------------------------------------------------------
  11-50 string classification Classifies the molecule(s)
  51-59 string depDate Deposition date. This is the date
  the coordinates were received by
  the PDB
  63-66 string idCode This identifier is unique within PDB`

Methods inherited from BaseRecord:

__str__(self)

Data descriptors inherited from BaseRecord:

__dict__
  `dictionary for instance variables (if defined)`

__weakref__
  `list of weak references to the object (if defined)`

class HELIX(BaseRecord)
`` | `HELIX field HELIX records are used to identify the position of helices in the molecule. Helices are both named and numbered. The residues where the helix begins and ends are noted, as well as the total length.`

Method resolution order:
  HELIX
  BaseRecord
  __builtin__.object

Methods defined here:

__init__(self, line)
  `Initialize by parsing line
  COLUMNS TYPE FIELD DEFINITION
  ------------------------------------------------------
  8-10 int serNum Serial number of the helix. This
  starts at 1 and increases
  incrementally.
  12-14 string helixID Helix identifier. In addition to a
  serial number, each helix is given an
  alphanumeric character helix identifier.
  16-18 string initResName Name of the initial residue.
  20 string initChainID Chain identifier for the chain
  containing this helix.
  22-25 int initSeqNum Sequence number of the initial residue.
  26 string initICode Insertion code of the initial residue.
  28-30 string endResName Name of the terminal residue of
  the helix.
  32 string endChainID Chain identifier for the chain
  containing this helix.
  34-37 int endSeqNum Sequence number of the terminal residue.
  38 string endICode Insertion code of the terminal residue.
  39-40 int helixClass Helix class (see below).
  41-70 string comment Comment about this helix.
  72-76 int length Length of this helix.`

Methods inherited from BaseRecord:

__str__(self)

Data descriptors inherited from BaseRecord:

__dict__
  `dictionary for instance variables (if defined)`

__weakref__
  `list of weak references to the object (if defined)`

class HET(BaseRecord)

``

`HET field
HET records are used to describe non-standard residues, such as
prosthetic groups, inhibitors, solvent molecules, and ions for which
coordinates are supplied. Groups are considered HET if they are:
- not one of the standard amino acids, and
- not one of the nucleic acids (C, G, A, T, U, and I), and
- not one of the modified versions of nucleic acids (+C, +G, +A, +T,
+U, and +I), and
- not an unknown amino acid or nucleic acid where UNK is used to
indicate the unknown residue name.
Het records also describe heterogens for which the chemical identity is
unknown, in which case the group is assigned the hetID UNK.
`

Method resolution order:
  HET
  BaseRecord
  __builtin__.object

Methods defined here:

__init__(self, line)
  `Initialize by parsing line
  COLUMNS TYPE FIELD DEFINITION
  --------------------------------------------------------
  8-10 string hetID Het identifier, right-justified.
  13 string ChainID Chain identifier.
  14-17 int seqNum Sequence number.
  18 string iCode Insertion code.
  21-25 int numHetAtoms Number of HETATM records for the
  31-70 string text Text describing Het group.`

Methods inherited from BaseRecord:

__str__(self)

Data descriptors inherited from BaseRecord:

__dict__
  `dictionary for instance variables (if defined)`

__weakref__
  `list of weak references to the object (if defined)`

class HETATM(BaseRecord)
`` | `HETATM class The HETATM records present the atomic coordinate records for atoms within "non-standard" groups. These records are used for water molecules and atoms presented in HET groups.`

Method resolution order:
  HETATM
  BaseRecord
  __builtin__.object

Methods defined here:

__init__(self, line, sybylType='A.aaa', lBonds=[], lBondedAtoms=[])
  `Initialize by parsing line
  COLUMNS TYPE FIELD DEFINITION
  ---------------------------------------------
  7-11 int serial Atom serial number.
  13-16 string name Atom name.
  17 string altLoc Alternate location indicator.
  18-20 string resName Residue name.
  22 string chainID Chain identifier.
  23-26 int resSeq Residue sequence number.
  27 string iCode Code for insertion of residues.
  31-38 float x Orthogonal coordinates for X in
  Angstroms.
  39-46 float y Orthogonal coordinates for Y in
  Angstroms.
  47-54 float z Orthogonal coordinates for Z in
  Angstroms.
  55-60 float occupancy Occupancy.
  61-66 float tempFactor Temperature factor.
  73-76 string segID Segment identifier, left-justified.
  77-78 string element Element symbol, right-justified.
  79-80 string charge Charge on the atom.`

Methods inherited from BaseRecord:

__str__(self)

Data descriptors inherited from BaseRecord:

__dict__
  `dictionary for instance variables (if defined)`

__weakref__
  `list of weak references to the object (if defined)`

class HETNAM(BaseRecord)
`` | `HETNAM field This record gives the chemical name of the compound with the given hetID.`

Method resolution order:
  HETNAM
  BaseRecord
  __builtin__.object

Methods defined here:

__init__(self, line)
  `Initialize by parsing line
  COLUMNS TYPE FIELD DEFINITION
  -----------------------------------------------------
  12-14 string hetID Het identifier, right-justified.
  16-70 string text Chemical name.`

Methods inherited from BaseRecord:

__str__(self)

Data descriptors inherited from BaseRecord:

__dict__
  `dictionary for instance variables (if defined)`

__weakref__
  `list of weak references to the object (if defined)`

class HETSYN(BaseRecord)
`` | `HETSYN field This record provides synonyms, if any, for the compound in the corresponding (i.e., same hetID) HETNAM record. This is to allow greater flexibility in searching for HET groups.`

Method resolution order:
  HETSYN
  BaseRecord
  __builtin__.object

Methods defined here:

__init__(self, line)
  `Initialize by parsing line
  COLUMNS TYPE FIELD DEFINITION
  -----------------------------------------------------
  12-14 string hetID Het identifier, right-justified.
  16-70 string hetSynonyms List of synonyms`

Methods inherited from BaseRecord:

__str__(self)

Data descriptors inherited from BaseRecord:

__dict__
  `dictionary for instance variables (if defined)`

__weakref__
  `list of weak references to the object (if defined)`

class HYDBND(BaseRecord)
`` | `HYDBND field The HYDBND records specify hydrogen bonds in the entry.`

Method resolution order:
  HYDBND
  BaseRecord
  __builtin__.object

Methods defined here:

__init__(self, line)
  `Initialize by parsing line
  COLUMNS TYPE FIELD DEFINITION
  -----------------------------------------------------------
  13-16 string name1 Atom name.
  17 string altLoc1 Alternate location indicator.
  18-20 string resName1 Residue name.
  22 string Chain1 Chain identifier.
  23-27 int resSeq1 Residue sequence number.
  28 string ICode1 Insertion code.
  30-33 string nameH Hydrogen atom name.
  34 string altLocH Alternate location indicator.
  36 string ChainH Chain identifier.
  37-41 int resSeqH Residue sequence number.
  42 string iCodeH Insertion code.
  44-47 string name2 Atom name.
  48 string altLoc2 Alternate location indicator.
  49-51 string resName2 Residue name.
  53 string chainID2 Chain identifier.
  54-58 int resSeq2 Residue sequence number.
  59 string iCode2 Insertion code.
  60-65 string sym1 Symmetry operator for 1st
  non-hydrogen atom.
  67-72 string sym2 Symmetry operator for 2nd
  non-hydrogen atom.`

Methods inherited from BaseRecord:

__str__(self)

Data descriptors inherited from BaseRecord:

__dict__
  `dictionary for instance variables (if defined)`

__weakref__
  `list of weak references to the object (if defined)`

class JRNL(BaseRecord)
`` | `JRNL field The JRNL record contains the primary literature citation that describes the experiment which resulted in the deposited coordinate set. There is at most one JRNL reference per entry. If there is no primary reference, then there is no JRNL reference. Other references are given in REMARK 1.`

Method resolution order:
  JRNL
  BaseRecord
  __builtin__.object

Methods defined here:

__init__(self, line)
  `Initialize by parsing line
  COLUMNS TYPE FIELD DEFINITION
  -----------------------------------------------
  13-70 string text See Details on web.`

Methods inherited from BaseRecord:

__str__(self)

Data descriptors inherited from BaseRecord:

__dict__
  `dictionary for instance variables (if defined)`

__weakref__
  `list of weak references to the object (if defined)`

class KEYWDS(BaseRecord)

``

`KEYWDS field
The KEYWDS record contains a set of terms relevant to the entry. Terms
in the KEYWDS record provide a simple means of categorizing entries and
may be used to generate index files. This record addresses some of the
limitations found in the classification field of the HEADER record. It
provides the opportunity to add further annotation to the entry in a
concise and computer-searchable fashion.
`

Method resolution order:
  KEYWDS
  BaseRecord
  __builtin__.object

Methods defined here:

__init__(self, line)
  `Initialize by parsing a line
  COLUMNS TYPE FIELD DEFINITION
  --------------------------------------------------
  11-70 string keywds Comma-separated list of keywords relevant
  to the entry`

Methods inherited from BaseRecord:

__str__(self)

Data descriptors inherited from BaseRecord:

__dict__
  `dictionary for instance variables (if defined)`

__weakref__
  `list of weak references to the object (if defined)`

class LINK(BaseRecord)
`` | `LINK field The LINK records specify connectivity between residues that is not implied by the primary structure. Connectivity is expressed in terms of the atom names. This record supplements information given in CONECT records and is provided here for convenience in searching.`

Method resolution order:
  LINK
  BaseRecord
  __builtin__.object

Methods defined here:

__init__(self, line)
  `Initialize by parsing line
  COLUMNS TYPE FIELD DEFINITION
  -----------------------------------------------------
  13-16 string name1 Atom name.
  17 string altLoc1 Alternate location indicator.
  18-20 string resName1 Residue name.
  22 string chainID1 Chain identifier.
  23-26 int resSeq1 Residue sequence number.
  27 string iCode1 Insertion code.
  43-46 string name2 Atom name.
  47 string altLoc2 Alternate location indicator.
  48-50 string resName2 Residue name.
  52 string chainID2 Chain identifier.
  53-56 int resSeq2 Residue sequence number.
  57 string iCode2 Insertion code.
  60-65 string sym1 Symmetry operator for 1st atom.
  67-72 string sym2 Symmetry operator for 2nd atom.`

Methods inherited from BaseRecord:

__str__(self)

Data descriptors inherited from BaseRecord:

__dict__
  `dictionary for instance variables (if defined)`

__weakref__
  `list of weak references to the object (if defined)`

class MASTER(BaseRecord)
`` | `MASTER class The MASTER record is a control record for bookkeeping. It lists the number of lines in the coordinate entry or file for selected record types.`

Method resolution order:
  MASTER
  BaseRecord
  __builtin__.object

Methods defined here:

__init__(self, line)
  `Initialize by parsing line
  COLUMNS TYPE FIELD DEFINITION
  -------------------------------------------------
  11-15 int numRemark Number of REMARK records
  21-25 int numHet Number of HET records
  26-30 int numHelix Number of HELIX records
  31-35 int numSheet Number of SHEET records
  36-40 int numTurn Number of TURN records
  41-45 int numSite Number of SITE records
  46-50 int numXform Number of coordinate transformation
  records (ORIGX+SCALE+MTRIX)
  51-55 int numCoord Number of atomic coordinate records
  (ATOM+HETATM)
  56-60 int numTer Number of TER records
  61-65 int numConect Number of CONECT records
  66-70 int numSeq Number of SEQRES records`

Methods inherited from BaseRecord:

__str__(self)

Data descriptors inherited from BaseRecord:

__dict__
  `dictionary for instance variables (if defined)`

__weakref__
  `list of weak references to the object (if defined)`

class MODEL(BaseRecord)
`` | `MODEL class The MODEL record specifies the model serial number when multiple structures are presented in a single coordinate entry, as is often the case with structures determined by NMR.`

Method resolution order:
  MODEL
  BaseRecord
  __builtin__.object

Methods defined here:

__init__(self, line)
  `Initialize by parsing line
  COLUMNS TYPE FIELD DEFINITION
  -----------------------------------------------------
  11-14 int serial Model serial number.`

Methods inherited from BaseRecord:

__str__(self)

Data descriptors inherited from BaseRecord:

__dict__
  `dictionary for instance variables (if defined)`

__weakref__
  `list of weak references to the object (if defined)`

class MODRES(BaseRecord)
`` | `MODRES field The MODRES record provides descriptions of modifications (e.g., chemical or post-translational) to protein and nucleic acid residues. Included are a mapping between residue names given in a PDB entry and standard residues.`

Method resolution order:
  MODRES
  BaseRecord
  __builtin__.object

Methods defined here:

__init__(self, line)
  `Initialize by parsing a line
  COLUMNS TYPE FIELD DEFINITION
  ---------------------------------------
  8-11 string idCode ID code of this entry.
  13-15 string resName Residue name used in this entry.
  17 string chainID Chain identifier.
  19-22 int seqNum Sequence number.
  23 string iCode Insertion code.
  25-27 string stdRes Standard residue name.
  30-70 string comment Description of the residue modification.`

Methods inherited from BaseRecord:

__str__(self)

Data descriptors inherited from BaseRecord:

__dict__
  `dictionary for instance variables (if defined)`

__weakref__
  `list of weak references to the object (if defined)`

class MOL2BOND
`` | `Bonding of MOL2 files`

Methods defined here:

__init__(self, frm, to, type, id=0)

class MOL2MOLECULE
`` | `Tripos MOL2 molecule For further information look at (web page exists: 25 August 2005): http://www.tripos.com/index.php?family=modules,SimplePage,,,&page=sup_mol2&s=0`

Methods defined here:

__init__(self)

createPDBlineFromMOL2(self)

createlBondedAtoms(self)
  `Creates for each atom a list of the bonded Atoms
  This becomes one attribute of MOL2ATOM!`

parseAtoms(self, AtomList)
  `for parsing @<TRIPOS>ATOM`

parseBonds(self, BondList)
  `for parsing @<TRIPOS>BOND`

read(self, file)
  `Routines for reading MOL2 file`

class MTRIX1(MTRIXn)

``

Method resolution order:
  MTRIX1
  MTRIXn
  BaseRecord
  __builtin__.object

Methods inherited from MTRIXn:

__init__(self, line)
  `Initialize by parsing line
  COLUMNS TYPE FIELD DEFINITION
  ---------------------------------
  8-10 int serial Serial number
  11-20 float mn1 M31
  21-30 float mn2 M32
  31-40 float mn3 M33
  46-55 float vn V3
  60 int iGiven 1 if coordinates for the representations
  which are approximately related by the
  transformations of the molecule are contained in
  the entry. Otherwise, blank.`

Methods inherited from BaseRecord:

__str__(self)

Data descriptors inherited from BaseRecord:

__dict__
  `dictionary for instance variables (if defined)`

__weakref__
  `list of weak references to the object (if defined)`

class MTRIX2(MTRIXn)

``

Method resolution order:
  MTRIX2
  MTRIXn
  BaseRecord
  __builtin__.object

Methods inherited from MTRIXn:

__init__(self, line)
  `Initialize by parsing line
  COLUMNS TYPE FIELD DEFINITION
  ---------------------------------
  8-10 int serial Serial number
  11-20 float mn1 M31
  21-30 float mn2 M32
  31-40 float mn3 M33
  46-55 float vn V3
  60 int iGiven 1 if coordinates for the representations
  which are approximately related by the
  transformations of the molecule are contained in
  the entry. Otherwise, blank.`

Methods inherited from BaseRecord:

__str__(self)

Data descriptors inherited from BaseRecord:

__dict__
  `dictionary for instance variables (if defined)`

__weakref__
  `list of weak references to the object (if defined)`

class MTRIX3(MTRIXn)

``

Method resolution order:
  MTRIX3
  MTRIXn
  BaseRecord
  __builtin__.object

Methods inherited from MTRIXn:

__init__(self, line)
  `Initialize by parsing line
  COLUMNS TYPE FIELD DEFINITION
  ---------------------------------
  8-10 int serial Serial number
  11-20 float mn1 M31
  21-30 float mn2 M32
  31-40 float mn3 M33
  46-55 float vn V3
  60 int iGiven 1 if coordinates for the representations
  which are approximately related by the
  transformations of the molecule are contained in
  the entry. Otherwise, blank.`

Methods inherited from BaseRecord:

__str__(self)

Data descriptors inherited from BaseRecord:

__dict__
  `dictionary for instance variables (if defined)`

__weakref__
  `list of weak references to the object (if defined)`

class MTRIXn(BaseRecord)
`` | `MTRIXn baseclass The MTRIXn (n = 1, 2, or 3) records present transformations expressing non-crystallographic symmetry.`

Method resolution order:
  MTRIXn
  BaseRecord
  __builtin__.object

Methods defined here:

__init__(self, line)
  `Initialize by parsing line
  COLUMNS TYPE FIELD DEFINITION
  ---------------------------------
  8-10 int serial Serial number
  11-20 float mn1 M31
  21-30 float mn2 M32
  31-40 float mn3 M33
  46-55 float vn V3
  60 int iGiven 1 if coordinates for the representations
  which are approximately related by the
  transformations of the molecule are contained in
  the entry. Otherwise, blank.`

Methods inherited from BaseRecord:

__str__(self)

Data descriptors inherited from BaseRecord:

__dict__
  `dictionary for instance variables (if defined)`

__weakref__
  `list of weak references to the object (if defined)`

class NUMMDL(BaseRecord)
`` | `NUMMDL class The NUMMDL record indicates total number of models in a PDB entry.`

Method resolution order:
  NUMMDL
  BaseRecord
  __builtin__.object

Methods defined here:

__init__(self, line)
  `Initialize by parsing line
  COLUMNS TYPE FIELD DEFINITION
  -----------------------------------------------------------
  11-14 int modelNumber Number of models.`

Methods inherited from BaseRecord:

__str__(self)

Data descriptors inherited from BaseRecord:

__dict__
  `dictionary for instance variables (if defined)`

__weakref__
  `list of weak references to the object (if defined)`

class OBSLTE(BaseRecord)
`` | `OBSLTE field This record acts as a flag in an entry which has been withdrawn from the PDB's full release. It indicates which, if any, new entries have replaced the withdrawn entry. The format allows for the case of multiple new entries replacing one existing entry.`

Method resolution order:
  OBSLTE
  BaseRecord
  __builtin__.object

Methods defined here:

__init__(self, line)
  `Initialize by parsing a line.
  COLUMNS TYPE FIELD DEFINITION
  -----------------------------------------------
  12-20 string repDate Date that this entry was replaced.
  22-25 string idCode ID code of this entry.
  32-35 string rIdCode ID code of entry that replaced
  this one.
  37-40 string rIdCode ID code of entry that replaced
  this one.
  42-45 string rIdCode ID code of entry that replaced
  this one.
  47-50 string rIdCode ID code of entry that replaced
  this one.
  52-55 string rIdCode ID code of entry that replaced
  this one.
  57-60 string rIdCode ID code of entry that replaced
  this one.
  62-65 string rIdCode ID code of entry that replaced
  this one.
  67-70 string rIdCode ID code of entry that replaced
  this one.`

Methods inherited from BaseRecord:

__str__(self)

Data descriptors inherited from BaseRecord:

__dict__
  `dictionary for instance variables (if defined)`

__weakref__
  `list of weak references to the object (if defined)`

class ORIGX1(ORIGXn)

``

Method resolution order:
  ORIGX1
  ORIGXn
  BaseRecord
  __builtin__.object

Methods inherited from ORIGXn:

__init__(self, line)
  `Initialize by parsing line
  COLUMNS TYPE FIELD DEFINITION
  ---------------------------------
  11-20 float on1 O21
  21-30 float on2 O22
  31-40 float on3 O23
  46-55 float tn T2`

Methods inherited from BaseRecord:

__str__(self)

Data descriptors inherited from BaseRecord:

__dict__
  `dictionary for instance variables (if defined)`

__weakref__
  `list of weak references to the object (if defined)`

class ORIGX2(ORIGXn)

``

Method resolution order:
  ORIGX2
  ORIGXn
  BaseRecord
  __builtin__.object

Methods inherited from ORIGXn:

__init__(self, line)
  `Initialize by parsing line
  COLUMNS TYPE FIELD DEFINITION
  ---------------------------------
  11-20 float on1 O21
  21-30 float on2 O22
  31-40 float on3 O23
  46-55 float tn T2`

Methods inherited from BaseRecord:

__str__(self)

Data descriptors inherited from BaseRecord:

__dict__
  `dictionary for instance variables (if defined)`

__weakref__
  `list of weak references to the object (if defined)`

class ORIGX3(ORIGXn)

``

Method resolution order:
  ORIGX3
  ORIGXn
  BaseRecord
  __builtin__.object

Methods inherited from ORIGXn:

__init__(self, line)
  `Initialize by parsing line
  COLUMNS TYPE FIELD DEFINITION
  ---------------------------------
  11-20 float on1 O21
  21-30 float on2 O22
  31-40 float on3 O23
  46-55 float tn T2`

Methods inherited from BaseRecord:

__str__(self)

Data descriptors inherited from BaseRecord:

__dict__
  `dictionary for instance variables (if defined)`

__weakref__
  `list of weak references to the object (if defined)`

class ORIGXn(BaseRecord)
`` | `ORIGX2 class The ORIGXn (n = 1, 2, or 3) records present the transformation from the orthogonal coordinates contained in the entry to the submitted coordinates.`

Method resolution order:
  ORIGXn
  BaseRecord
  __builtin__.object

Methods defined here:

__init__(self, line)
  `Initialize by parsing line
  COLUMNS TYPE FIELD DEFINITION
  ---------------------------------
  11-20 float on1 O21
  21-30 float on2 O22
  31-40 float on3 O23
  46-55 float tn T2`

Methods inherited from BaseRecord:

__str__(self)

Data descriptors inherited from BaseRecord:

__dict__
  `dictionary for instance variables (if defined)`

__weakref__
  `list of weak references to the object (if defined)`

class REMARK(BaseRecord)
`` | `REMARK field REMARK records present experimental details, annotations, comments, and information not included in other records. In a number of cases, REMARKs are used to expand the contents of other record types. A new level of structure is being used for some REMARK records. This is expected to facilitate searching and will assist in the conversion to a relational database.`

Method resolution order:
  REMARK
  BaseRecord
  __builtin__.object

Methods defined here:

__init__(self, line)
  `Initialize by parsing line`

Methods inherited from BaseRecord:

__str__(self)

Data descriptors inherited from BaseRecord:

__dict__
  `dictionary for instance variables (if defined)`

__weakref__
  `list of weak references to the object (if defined)`

class REVDAT(BaseRecord)
`` | `REVDAT field REVDAT records contain a history of the modifications made to an entry since its release.`

Method resolution order:
  REVDAT
  BaseRecord
  __builtin__.object

Methods defined here:

__init__(self, line)
  `Initialize by parsing a line.
  COLUMNS TYPE FIELD DEFINITION
  -------------------------------------------------------
  8-10 int modNum Modification number.
  14-22 string modDate Date of modification (or release for
  new entries).
  24-28 string modId Identifies this particular modification.
  It links to the archive used internally by
  PDB.
  32 int modType An integer identifying the type of
  modification. In case of revisions
  with more than one possible modType,
  the highest value applicable will be
  assigned.
  40-45 string record Name of the modified record.
  47-52 string record Name of the modified record.
  54-59 string record Name of the modified record.
  61-66 string record Name of the modified record.`

Methods inherited from BaseRecord:

__str__(self)

Data descriptors inherited from BaseRecord:

__dict__
  `dictionary for instance variables (if defined)`

__weakref__
  `list of weak references to the object (if defined)`

class SCALE1(SCALEn)

``

Method resolution order:
  SCALE1
  SCALEn
  BaseRecord
  __builtin__.object

Methods inherited from SCALEn:

__init__(self, line)
  `Initialize by parsing line
  COLUMNS TYPE FIELD DEFINITION
  ---------------------------------
  11-20 float sn1 S31
  21-30 float sn2 S32
  31-40 float sn3 S33
  46-55 float un U3`

Methods inherited from BaseRecord:

__str__(self)

Data descriptors inherited from BaseRecord:

__dict__
  `dictionary for instance variables (if defined)`

__weakref__
  `list of weak references to the object (if defined)`

class SCALE2(SCALEn)

``

Method resolution order:
  SCALE2
  SCALEn
  BaseRecord
  __builtin__.object

Methods inherited from SCALEn:

__init__(self, line)
  `Initialize by parsing line
  COLUMNS TYPE FIELD DEFINITION
  ---------------------------------
  11-20 float sn1 S31
  21-30 float sn2 S32
  31-40 float sn3 S33
  46-55 float un U3`

Methods inherited from BaseRecord:

__str__(self)

Data descriptors inherited from BaseRecord:

__dict__
  `dictionary for instance variables (if defined)`

__weakref__
  `list of weak references to the object (if defined)`

class SCALE3(SCALEn)

``

Method resolution order:
  SCALE3
  SCALEn
  BaseRecord
  __builtin__.object

Methods inherited from SCALEn:

__init__(self, line)
  `Initialize by parsing line
  COLUMNS TYPE FIELD DEFINITION
  ---------------------------------
  11-20 float sn1 S31
  21-30 float sn2 S32
  31-40 float sn3 S33
  46-55 float un U3`

Methods inherited from BaseRecord:

__str__(self)

Data descriptors inherited from BaseRecord:

__dict__
  `dictionary for instance variables (if defined)`

__weakref__
  `list of weak references to the object (if defined)`

class SCALEn(BaseRecord)
`` | `SCALEn baseclass The SCALEn (n = 1, 2, or 3) records present the transformation from the orthogonal coordinates as contained in the entry to fractional crystallographic coordinates. Non-standard coordinate systems should be explained in the remarks.`

Method resolution order:
  SCALEn
  BaseRecord
  __builtin__.object

Methods defined here:

__init__(self, line)
  `Initialize by parsing line
  COLUMNS TYPE FIELD DEFINITION
  ---------------------------------
  11-20 float sn1 S31
  21-30 float sn2 S32
  31-40 float sn3 S33
  46-55 float un U3`

Methods inherited from BaseRecord:

__str__(self)

Data descriptors inherited from BaseRecord:

__dict__
  `dictionary for instance variables (if defined)`

__weakref__
  `list of weak references to the object (if defined)`

class SEQADV(BaseRecord)

``

`SEQADV field
The SEQADV record identifies conflicts between sequence information in
the ATOM records of the PDB entry and the sequence database entry given
on DBREF. Please note that these records were designed to identify
differences and not errors. No assumption is made as to which database
contains the correct data. PDB may include REMARK records in the entry
that reflect the depositor's view of which database has the correct
sequence.
`

Method resolution order:
  SEQADV
  BaseRecord
  __builtin__.object

Methods defined here:

__init__(self, line)
  `Initialize by parsing line
  COLUMNS TYPE FIELD DEFINITION
  -----------------------------------------------------
  8-11 string idCode ID code of this entry.
  13-15 string resName Name of the PDB residue in conflict.
  17 string chainID PDB chain identifier.
  19-22 int seqNum PDB sequence number.
  23 string iCode PDB insertion code.
  25-28 string database Sequence database name.
  30-38 string dbIdCode Sequence database accession
  number.
  40-42 string dbRes Sequence database residue name.
  44-48 int dbSeq Sequence database sequence number.
  50-70 string conflict Conflict comment.`

Methods inherited from BaseRecord:

__str__(self)

Data descriptors inherited from BaseRecord:

__dict__
  `dictionary for instance variables (if defined)`

__weakref__
  `list of weak references to the object (if defined)`

class SEQRES(BaseRecord)
`` | `SEQRES field SEQRES records contain the amino acid or nucleic acid sequence of residues in each chain of the macromolecule that was studied.`

Method resolution order:
  SEQRES
  BaseRecord
  __builtin__.object

Methods defined here:

__init__(self, line)
  `Initialize by parsing a line
  COLUMNS TYPE FIELD DEFINITION
  -----------------------------------------------------
  9-10 int serNum Serial number of the SEQRES record for the
  current chain. Starts at 1 and increments
  by one each line. Reset to 1 for each
  chain.
  12 string chainID Chain identifier. This may be any single
  legal character, including a blank which is
  used if there is only one chain.
  14-17 int numRes Number of residues in the chain. This
  value is repeated on every record.
  20-22 string resName Residue name.
  24-26 string resName Residue name.
  28-30 string resName Residue name.
  32-34 string resName Residue name.
  36-38 string resName Residue name.
  40-42 string resName Residue name.
  44-46 string resName Residue name.
  48-50 string resName Residue name.
  52-54 string resName Residue name.
  56-58 string resName Residue name.
  60-62 string resName Residue name.
  64-66 string resName Residue name.
  68-70 string resName Residue name.`

Methods inherited from BaseRecord:

__str__(self)

Data descriptors inherited from BaseRecord:

__dict__
  `dictionary for instance variables (if defined)`

__weakref__
  `list of weak references to the object (if defined)`

class SHEET(BaseRecord)
`` | `SHEET field SHEET records are used to identify the position of sheets in the molecule. Sheets are both named and numbered. The residues where the sheet begins and ends are noted.`

Method resolution order:
  SHEET
  BaseRecord
  __builtin__.object

Methods defined here:

__init__(self, line)
  `Initialize by parsing line
  COLUMNS TYPE FIELD DEFINITION
  -------------------------------------------------
  8 - 10 int strand Strand number which starts at 1 for
  each strand within a sheet and
  increases by one.
  12 - 14 string sheetID Sheet identifier.
  15 - 16 int numStrands Number of strands in sheet.
  18 - 20 string initResName Residue name of initial residue.
  22 string initChainID Chain identifier of initial residue in
  strand.
  23 - 26 int initSeqNum Sequence number of initial residue in
  strand.
  27 string initICode Insertion code of initial residue in
  strand.
  29 - 31 string endResName Residue name of terminal residue.
  33 string endChainID Chain identifier of terminal residue.
  34 - 37 int endSeqNum Sequence number of terminal residue.
  38 string endICode Insertion code of terminal residue.
  39 - 40 int sense Sense of strand with respect to
  previous strand in the sheet. 0 if
  first strand, 1 if parallel, -1 if
  anti-parallel.
  42 - 45 string curAtom Registration. Atom name in current
  strand.
  46 - 48 string curResName Registration. Residue name in current
  strand.
  50 string curChainId Registration. Chain identifier in
  current strand.
  51 - 54 int curResSeq Registration. Residue sequence number
  in current strand.
  55 string curICode Registration. Insertion code in current
  strand.
  57 - 60 string prevAtom Registration. Atom name in previous
  strand.
  61 - 63 string prevResName Registration. Residue name in previous
  strand.
  65 string prevChainId Registration. Chain identifier in
  previous strand.
  66 - 69 int prevResSeq Registration. Residue sequence number
  in previous strand.
  70 string prevICode Registration. Insertion code in
  previous strand.`

Methods inherited from BaseRecord:

__str__(self)

Data descriptors inherited from BaseRecord:

__dict__
  `dictionary for instance variables (if defined)`

__weakref__
  `list of weak references to the object (if defined)`

class SIGATM(BaseRecord)
`` | `SIGATM class The SIGATM records present the standard deviation of atomic parameters as they appear in ATOM and HETATM records.`

Method resolution order:
  SIGATM
  BaseRecord
  __builtin__.object

Methods defined here:

__init__(self, line)
  `Initialize by parsing line
  COLUMNS TYPE FIELD DEFINITION
  ---------------------------------------------
  7-11 int serial Atom serial number.
  13-16 string name Atom name.
  17 string altLoc Alternate location indicator.
  18-20 string resName Residue name.
  22 string chainID Chain identifier.
  23-26 int resSeq Residue sequence number.
  27 string iCode Code for insertion of residues.
  31-38 float sigX Standard devition of orthogonal
  coordinates for X in Angstroms.
  39-46 float sigY Standard devition of orthogonal
  coordinates for Y in Angstroms.
  47-54 float sigZ Standard devition of orthogonal
  coordinates for Z in Angstroms.
  55-60 float sigOcc Standard devition of occupancy.
  61-66 float sigTemp Standard devition of temperature factor.
  73-76 string segID Segment identifier, left-justified.
  77-78 string element Element symbol, right-justified.
  79-80 string charge Charge on the atom.`

Methods inherited from BaseRecord:

__str__(self)

Data descriptors inherited from BaseRecord:

__dict__
  `dictionary for instance variables (if defined)`

__weakref__
  `list of weak references to the object (if defined)`

class SIGUIJ(BaseRecord)
`` | `SIGUIJ class The SIGUIJ records present the anisotropic temperature factors.`

Method resolution order:
  SIGUIJ
  BaseRecord
  __builtin__.object

Methods defined here:

__init__(self, line)
  `Initialize by parsing line:
  COLUMNS TYPE FIELD DEFINITION
  ------------------------------------------------------
  7-11 int serial Atom serial number.
  13-16 string name Atom name.
  17 string altLoc Alternate location indicator.
  18-20 string resName Residue name.
  22 string chainID Chain identifier.
  23-26 int resSeq Residue sequence number.
  27 string iCode Insertion code.
  29-35 int sig11 Sigma U(1,1)
  36-42 int sig22 Sigma U(2,2)
  43-49 int sig33 Sigma U(3,3)
  50-56 int sig12 Sigma U(1,2)
  57-63 int sig13 Sigma U(1,3)
  64-70 int sig23 Sigma U(2,3)
  73-76 string segID Segment identifier, left-justified.
  77-78 string element Element symbol, right-justified.
  79-80 string charge Charge on the atom.`

Methods inherited from BaseRecord:

__str__(self)

Data descriptors inherited from BaseRecord:

__dict__
  `dictionary for instance variables (if defined)`

__weakref__
  `list of weak references to the object (if defined)`

class SITE(BaseRecord)
`` | `SITE class The SITE records supply the identification of groups comprising important sites in the macromolecule.`

Method resolution order:
  SITE
  BaseRecord
  __builtin__.object

Methods defined here:

__init__(self, line)
  `Initialize by parsing the line
  COLUMNS TYPE FIELD DEFINITION
  --------------------------------------------------------------
  8-10 int seqNum Sequence number.
  12-14 string siteID Site name.
  16-17 int numRes Number of residues comprising site.
  19-21 string resName1 Residue name for first residue
  comprising site.
  23 string chainID1 Chain identifier for first residue
  comprising site.
  24-27 int seq1 Residue sequence number for first
  residue comprising site.
  28 string iCode1 Insertion code for first residue
  comprising site.
  30-32 string resName2 Residue name for second residue
  comprising site.
  34 string chainID2 Chain identifier for second residue
  comprising site.
  35-38 int seq2 Residue sequence number for second
  residue comprising site.
  39 string iCode2 Insertion code for second residue
  comprising site.
  41-43 string resName3 Residue name for third residue
  comprising site.
  45 string chainID3 Chain identifier for third residue
  comprising site.
  46-49 int seq3 Residue sequence number for third
  residue comprising site.
  50 string iCode3 Insertion code for third residue
  comprising site.
  52-54 string resName4 Residue name for fourth residue
  comprising site.
  56 string chainID4 Chain identifier for fourth residue
  comprising site.
  57-60 int seq4 Residue sequence number for fourth
  residue comprising site.
  61 string iCode4 Insertion code for fourth residue
  comprising site.`

Methods inherited from BaseRecord:

__str__(self)

Data descriptors inherited from BaseRecord:

__dict__
  `dictionary for instance variables (if defined)`

__weakref__
  `list of weak references to the object (if defined)`

class SLTBRG(BaseRecord)
`` | `SLTBRG field The SLTBRG records specify salt bridges in the entry. records and is provided here for convenience in searching.`

Method resolution order:
  SLTBRG
  BaseRecord
  __builtin__.object

Methods defined here:

__init__(self, line)
  `Initialize by parsing line
  COLUMNS TYPE FIELD DEFINITION
  -----------------------------------------------------
  13-16 string name1 Atom name.
  17 string altLoc1 Alternate location indicator.
  18-20 string resName1 Residue name.
  22 string chainID1 Chain identifier.
  23-26 int resSeq1 Residue sequence number.
  27 string iCode1 Insertion code.
  43-46 string name2 Atom name.
  47 string altLoc2 Alternate location indicator.
  48-50 string resName2 Residue name.
  52 string chainID2 Chain identifier.
  53-56 int resSeq2 Residue sequence number.
  57 string iCode2 Insertion code.
  60-65 string sym1 Symmetry operator for 1st atom.
  67-72 string sym2 Symmetry operator for 2nd atom.`

Methods inherited from BaseRecord:

__str__(self)

Data descriptors inherited from BaseRecord:

__dict__
  `dictionary for instance variables (if defined)`

__weakref__
  `list of weak references to the object (if defined)`

class SOURCE(BaseRecord)
`` | `SOURCE field The SOURCE record specifies the biological and/or chemical source of each biological molecule in the entry. Sources are described by both the common name and the scientific name, e.g., genus and species. Strain and/or cell-line for immortalized cells are given when they help to uniquely identify the biological entity studied.`

Method resolution order:
  SOURCE
  BaseRecord
  __builtin__.object

Methods defined here:

__init__(self, line)
  `Initialize by parsing a line
  COLUMNS TYPE FIELD DEFINITION
  --------------------------------------------------
  11-70 string source Identifies the source of the macromolecule
  in a token: value format`

Methods inherited from BaseRecord:

__str__(self)

Data descriptors inherited from BaseRecord:

__dict__
  `dictionary for instance variables (if defined)`

__weakref__
  `list of weak references to the object (if defined)`

class SPRSDE(BaseRecord)
`` | `SPRSDE field The SPRSDE records contain a list of the ID codes of entries that were made obsolete by the given coordinate entry and withdrawn from the PDB release set. One entry may replace many. It is PDB policy that only the principal investigator of a structure has the authority to withdraw it.`

Method resolution order:
  SPRSDE
  BaseRecord
  __builtin__.object

Methods defined here:

__init__(self, line)
  `Initialize by parsing line
  COLUMNS TYPE FIELD DEFINITION
  -----------------------------------------------
  12-20 string sprsdeDate Date this entry superseded the
  listed entries.
  22-25 string idCode ID code of this entry.
  32-35 string sIdCode ID code of a superseded entry.
  37-40 string sIdCode ID code of a superseded entry.
  42-45 string sIdCode ID code of a superseded entry.
  47-50 string sIdCode ID code of a superseded entry.
  52-55 string sIdCode ID code of a superseded entry.
  57-60 string sIdCode ID code of a superseded entry.
  62-65 string sIdCode ID code of a superseded entry.
  67-70 string sIdCode ID code of a superseded entry.`

Methods inherited from BaseRecord:

__str__(self)

Data descriptors inherited from BaseRecord:

__dict__
  `dictionary for instance variables (if defined)`

__weakref__
  `list of weak references to the object (if defined)`

class SSBOND(BaseRecord)
`` | `SSBOND field The SSBOND record identifies each disulfide bond in protein and polypeptide structures by identifying the two residues involved in the bond.`

Method resolution order:
  SSBOND
  BaseRecord
  __builtin__.object

Methods defined here:

__init__(self, line)
  `Initialize by parsing line
  COLUMNS TYPE FIELD DEFINITION
  -----------------------------------------------------
  8 - 10 int serNum Serial number.
  16 string chainID1 Chain identifier.
  18 - 21 int seqNum1 Residue sequence number.
  22 string icode1 Insertion code.
  30 string chainID2 Chain identifier.
  32 - 35 int seqNum2 Residue sequence number.
  36 string icode2 Insertion code.
  60 - 65 string sym1 Symmetry operator for 1st residue.
  67 - 72 string sym2 Symmetry operator for 2nd residue.`

Methods inherited from BaseRecord:

__str__(self)

Data descriptors inherited from BaseRecord:

__dict__
  `dictionary for instance variables (if defined)`

__weakref__
  `list of weak references to the object (if defined)`

class TER(BaseRecord)
`` | `TER class The TER record indicates the end of a list of ATOM/HETATM records for a chain.`

Method resolution order:
  TER
  BaseRecord
  __builtin__.object

Methods defined here:

__init__(self, line)
  `Initialize by parsing line:
  COLUMNS TYPE FIELD DEFINITION
  -------------------------------------------
  7-11 int serial Serial number.
  18-20 string resName Residue name.
  22 string chainID Chain identifier.
  23-26 int resSeq Residue sequence number.
  27 string iCode Insertion code.`

Methods inherited from BaseRecord:

__str__(self)

Data descriptors inherited from BaseRecord:

__dict__
  `dictionary for instance variables (if defined)`

__weakref__
  `list of weak references to the object (if defined)`

class TITLE(BaseRecord)
`` | `TITLE field The TITLE record contains a title for the experiment or analysis that is represented in the entry. It should identify an entry in the PDB in the same way that a title identifies a paper.`

Method resolution order:
  TITLE
  BaseRecord
  __builtin__.object

Methods defined here:

__init__(self, line)
  `Initialize by parsing a line.
  COLUMNS TYPE FIELD DEFINITION
  ---------------------------------------------
  11-70 string title Title of the experiment`

Methods inherited from BaseRecord:

__str__(self)

Data descriptors inherited from BaseRecord:

__dict__
  `dictionary for instance variables (if defined)`

__weakref__
  `list of weak references to the object (if defined)`

class TURN(BaseRecord)
`` | `TURN field The TURN records identify turns and other short loop turns which normally connect other secondary structure segments.`

Method resolution order:
  TURN
  BaseRecord
  __builtin__.object

Methods defined here:

__init__(self, line)
  `Initialize by parsing line
  COLUMNS TYPE FIELD DEFINITION
  ---------------------------------------------------------
  8-10 int seq Turn number; starts with 1 and
  increments by one.
  12-14 string turnId Turn identifier
  16-18 string initResName Residue name of initial residue in
  turn.
  20 string initChainId Chain identifier for the chain
  containing this turn.
  21-24 int initSeqNum Sequence number of initial residue in
  turn.
  25 string initICode Insertion code of initial residue in
  turn.
  27-29 string endResName Residue name of terminal residue of
  turn.
  31 string endChainId Chain identifier for the chain
  containing this turn.
  32-35 int endSeqNum Sequence number of terminal residue of
  turn.
  36 string endICode Insertion code of terminal residue of
  turn.
  41-70 string comment Associated comment.`

Methods inherited from BaseRecord:

__str__(self)

Data descriptors inherited from BaseRecord:

__dict__
  `dictionary for instance variables (if defined)`

__weakref__
  `list of weak references to the object (if defined)`

class TVECT(BaseRecord)
`` | `TVECT class The TVECT records present the translation vector for infinite covalently connected structures.`

Method resolution order:
  TVECT
  BaseRecord
  __builtin__.object

Methods defined here:

__init__(self, line)
  `Initialize by parsing line
  COLUMNS TYPE FIELD DEFINITION
  ---------------------------------
  8-10 int serial Serial number
  11-20 float t1 Components of translation vector
  21-30 float t2 Components of translation vector
  31-40 float t2 Components of translation vector
  41-70 string text Comments`

Methods inherited from BaseRecord:

__str__(self)

Data descriptors inherited from BaseRecord:

__dict__
  `dictionary for instance variables (if defined)`

__weakref__
  `list of weak references to the object (if defined)`

Functions

``

RegisterLineParser(klass)

getRandom()
  `Download a random PDB and return the path name.
  Returns
  path name of downloaded file`

main()
  `Main driver for testing. Parses set number of random PDBs`

readAtom(line)
  `If the ATOM/HETATM is not column-formatted, try to get some
  information by parsing whitespace from the right. Look for
  five floating point numbers followed by the residue number.
  Parameters
  line: The line to parse(string)
  if record == ATOM:
  self.serial = int(string.strip(line[6:11]))
  self.name = string.strip(line[12:16])
  self.altLoc = string.strip(line[16])
  self.resName = string.strip(line[17:20])
  self.chainID = string.strip(line[21])
  self.resSeq = int(string.strip(line[22:26]))
  self.iCode = string.strip(line[26])
  self.x = float(string.strip(line[30:38]))
  self.y = float(string.strip(line[38:46]))
  self.z = float(string.strip(line[46:54]))
  try:
  self.occupancy = float(string.strip(line[54:60]))
  self.tempFactor = float(string.strip(line[60:66]))
  self.segID = string.strip(line[72:76])
  self.element = string.strip(line[76:78])
  self.charge = string.strip(line[78:80])
  except ValueError, IndexError:
  self.occupancy = 0.00
  self.tempFactor = 0.00
  self.segID = 0
  self.element = 0
  self.charge = 0
  else: raise ValueError, record`

readPDB(file)
  `Parse PDB-format data into array of Atom objects.
  Parameters
  file: open file object
  Returns (dict, errlist)
  dict: a dictionary indexed by PDB record names
  errlist: a list of record names that couldn't be parsed`

Data

``

__author__ = 'Todd Dolinsky, Yong Huang'
__date__ = '4 August 2008'
lineParsers = {'ANISOU': <class 'src.pdb.ANISOU'>, 'ATOM': <class 'src.pdb.ATOM'>, 'AUTHOR': <class 'src.pdb.AUTHOR'>, 'CAVEAT': <class 'src.pdb.CAVEAT'>, 'CISPEP': <class 'src.pdb.CISPEP'>, 'COMPND': <class 'src.pdb.COMPND'>, 'CONECT': <class 'src.pdb.CONECT'>, 'CRYST1': <class 'src.pdb.CRYST1'>, 'DBREF': <class 'src.pdb.DBREF'>, 'END': <class 'src.pdb.END'>, ...}

Author
`` |  | Todd Dolinsky, Yong Huang