""" 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.
.. codeauthor:: Todd Dolinsky
.. codeauthor:: Yong Huang
.. codeauthor:: Nathan Baker
"""
import logging
_LOGGER = logging.getLogger(__name__)
LINE_PARSERS = {}
[docs]
def register_line_parser(klass):
"""Register a line parser in the global dictionary.
:param klass: class for line parser
"""
LINE_PARSERS[klass.__name__] = klass
return klass
[docs]
class BaseRecord:
"""Base class for all records.
Verifies the received record type.
"""
[docs]
def __init__(self, line):
record = line[0:6].strip()
if record != self.__class__.__name__:
raise ValueError(record)
self.original_text = line.rstrip("\r\n")
def __str__(self):
return self.original_text
[docs]
def record_type(self):
"""Return PDB record type as string.
:return: record type
:rtype: str
"""
return self.original_text.split()[0]
[docs]
@register_line_parser
class END(BaseRecord):
"""END class
The END records are paired with MODEL records to group individual
structures found in a coordinate entry.
"""
[docs]
def __init__(self, line):
"""Initialize with line.
:param line: line with PDB class
:type line: str
"""
super().__init__(line)
[docs]
@register_line_parser
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.
"""
[docs]
def __init__(self, line):
"""Initialize by parsing line
+---------+------+------------+-------------------------------------+
| COLUMNS | TYPE | FIELD | DEFINITION |
+=========+======+============+=====================================+
| 11-15 | int | num_remark | Number of REMARK records |
+---------+------+------------+-------------------------------------+
| 21-25 | int | num_het | 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 |
+---------+------+------------+-------------------------------------+
:param line: line with PDB class
:type line: str
"""
super().__init__(line)
self.num_remark = int(line[10:15].strip())
self.num_het = int(line[20:25].strip())
self.num_helix = int(line[25:30].strip())
self.num_sheet = int(line[30:35].strip())
self.num_turn = int(line[35:40].strip())
self.num_site = int(line[40:45].strip())
self.num_xform = int(line[45:50].strip())
self.num_coord = int(line[50:55].strip())
self.num_ter = int(line[55:60].strip())
self.num_conect = int(line[60:65].strip())
self.num_seq = int(line[65:70].strip())
[docs]
@register_line_parser
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.
"""
[docs]
def __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 |
+---------+------+----------+---------------------------------------+
:param line: line with PDB class
:type line: str
"""
super().__init__(line)
self.serial = int(line[6:11].strip())
try:
self.serial1 = int(line[11:16].strip())
except ValueError:
self.serial1 = None
try:
self.serial2 = int(line[16:21].strip())
except ValueError:
self.serial2 = None
try:
self.serial3 = int(line[21:26].strip())
except ValueError:
self.serial3 = None
try:
self.serial4 = int(line[26:31].strip())
except ValueError:
self.serial4 = None
try:
self.serial5 = int(line[31:36].strip())
except ValueError:
self.serial5 = None
try:
self.serial6 = int(line[36:41].strip())
except ValueError:
self.serial6 = None
try:
self.serial7 = int(line[41:46].strip())
except ValueError:
self.serial7 = None
try:
self.serial8 = int(line[46:51].strip())
except ValueError:
self.serial8 = None
try:
self.serial9 = int(line[51:56].strip())
except ValueError:
self.serial9 = None
try:
self.serial10 = int(line[56:61].strip())
except ValueError:
self.serial10 = None
[docs]
@register_line_parser
class NUMMDL(BaseRecord):
"""NUMMDL class
The NUMMDL record indicates total number of models in a PDB entry.
"""
[docs]
def __init__(self, line):
"""Initialize by parsing line
+---------+------+-------------+-------------------+
| COLUMNS | TYPE | FIELD | DEFINITION |
+=========+======+=============+===================+
| 11-14 | int | modelNumber | Number of models. |
+---------+------+-------------+-------------------+
:param line: line with PDB class
:type line: str
"""
super().__init__(line)
try:
self.model_number = int(line[10:14].strip())
except ValueError:
self.model_number = None
[docs]
@register_line_parser
class ENDMDL(BaseRecord):
"""ENDMDL class
The ENDMDL records are paired with MODEL records to group individual
structures found in a coordinate entry.
"""
[docs]
def __init__(self, line):
super().__init__(line)
[docs]
@register_line_parser
class TER(BaseRecord):
"""TER class
The TER record indicates the end of a list of ATOM/HETATM records for a
chain.
"""
[docs]
def __init__(self, line):
"""Initialize by parsing line:
+---------+--------+----------+--------------------------+
| COLUMNS | TYPE | FIELD | DEFINITION |
+=========+========+==========+==========================+
| 7-11 | int | serial | Serial number. |
+---------+--------+----------+--------------------------+
| 18-20 | string | res_name | Residue name. |
+---------+--------+----------+--------------------------+
| 22 | string | chain_id | Chain identifier. |
+---------+--------+----------+--------------------------+
| 23-26 | int | res_seq | Residue sequence number. |
+---------+--------+----------+--------------------------+
| 27 | string | ins_code | Insertion code. |
+---------+--------+----------+--------------------------+
:param line: line with PDB class
:type line: str
"""
super().__init__(line)
try: # Not really needed
self.serial = int(line[6:11].strip())
self.res_name = line[17:20].strip()
self.chain_id = line[21].strip()
self.res_seq = int(line[22:26].strip())
self.ins_code = line[26].strip()
except (IndexError, ValueError):
self.serial = None
self.res_name = None
self.chain_id = None
self.res_seq = None
self.ins_code = None
[docs]
@register_line_parser
class SIGUIJ(BaseRecord):
"""SIGUIJ class
The SIGUIJ records present the anisotropic temperature factors.
"""
[docs]
def __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 | alt_loc | Alternate location indicator. |
+---------+--------+----------+-------------------------------------+
| 18-20 | string | res_name | Residue name. |
+---------+--------+----------+-------------------------------------+
| 22 | string | chain_id | Chain identifier. |
+---------+--------+----------+-------------------------------------+
| 23-26 | int | res_seq | Residue sequence number. |
+---------+--------+----------+-------------------------------------+
| 27 | string | ins_code | 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 | seg_id | Segment identifier, left-justified. |
+---------+--------+----------+-------------------------------------+
| 77-78 | string | el.ment | Element symbol, right-justified. |
+---------+--------+----------+-------------------------------------+
| 79-80 | string | charge | Charge on the atom. |
+---------+--------+----------+-------------------------------------+
:param line: line with PDB class
:type line: str
"""
super().__init__(line)
self.serial = int(line[6:11].strip())
self.name = line[12:16].strip()
self.alt_loc = line[16].strip()
self.res_name = line[17:20].strip()
self.chain_id = line[21].strip()
self.res_seq = int(line[22:26].strip())
self.ins_code = line[26].strip()
self.sig11 = int(line[28:35].strip())
self.sig22 = int(line[35:42].strip())
self.sig33 = int(line[42:49].strip())
self.sig12 = int(line[49:56].strip())
self.sig13 = int(line[56:63].strip())
self.sig23 = int(line[63:70].strip())
self.seg_id = line[72:76].strip()
self.element = line[76:78].strip()
self.charge = line[78:80].strip()
[docs]
@register_line_parser
class ANISOU(BaseRecord):
"""ANISOU class
The ANISOU records present the anisotropic temperature factors.
"""
[docs]
def __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 | alt_loc | Alternate location indicator. |
+---------+--------+----------+-------------------------------------+
| 18-20 | string | res_name | Residue name. |
+---------+--------+----------+-------------------------------------+
| 22 | string | chain_id | Chain identifier. |
+---------+--------+----------+-------------------------------------+
| 23-26 | int | res_seq | Residue sequence number. |
+---------+--------+----------+-------------------------------------+
| 27 | string | ins_code | 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 | seg_id | Segment identifier, left-justified. |
+---------+--------+----------+-------------------------------------+
| 77-78 | string | element | Element symbol, right-justified. |
+---------+--------+----------+-------------------------------------+
| 79-80 | string | charge | Charge on the atom. |
+---------+--------+----------+-------------------------------------+
:param line: line with PDB class
:type line: str
"""
super().__init__(line)
self.serial = int(line[6:11].strip())
self.name = line[12:16].strip()
self.alt_loc = line[16].strip()
self.res_name = line[17:20].strip()
self.chain_id = line[21].strip()
self.res_seq = int(line[22:26].strip())
self.ins_code = line[26].strip()
self.u00 = int(line[28:35].strip())
self.u11 = int(line[35:42].strip())
self.u22 = int(line[42:49].strip())
self.u01 = int(line[49:56].strip())
self.u02 = int(line[56:63].strip())
self.u12 = int(line[63:70].strip())
self.seg_id = line[72:76].strip()
self.element = line[76:78].strip()
self.charge = line[78:80].strip()
[docs]
@register_line_parser
class SIGATM(BaseRecord):
"""SIGATM class
The SIGATM records present the standard deviation of atomic parameters
as they appear in ATOM and HETATM records.
"""
[docs]
def __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 | alt_loc | Alternate location indicator. |
+---------+--------+----------+-------------------------------------+
| 18-20 | string | res_name | Residue name. |
+---------+--------+----------+-------------------------------------+
| 22 | string | chain_id | Chain identifier. |
+---------+--------+----------+-------------------------------------+
| 23-26 | int | res_seq | Residue sequence number. |
+---------+--------+----------+-------------------------------------+
| 27 | string | ins_code | Code for insertion of residues. |
+---------+--------+----------+-------------------------------------+
| 31-38 | float | sig_x | Standard deviation of orthogonal |
| | | | coordinates for X in Angstroms. |
+---------+--------+----------+-------------------------------------+
| 39-46 | float | sig_y | Standard deviation of orthogonal |
| | | | coordinates for Y in Angstroms. |
+---------+--------+----------+-------------------------------------+
| 47-54 | float | sig_z | Standard deviation of orthogonal |
| | | | coordinates for Z in Angstroms. |
+---------+--------+----------+-------------------------------------+
| 55-60 | float | sig_occ | Standard deviation of occupancy. |
+---------+--------+----------+-------------------------------------+
| 61-66 | float | sig_temp | Standard deviation of temperature |
| | | | factor. |
+---------+--------+----------+-------------------------------------+
| 73-76 | string | seg_id | Segment identifier, left-justified. |
+---------+--------+----------+-------------------------------------+
| 77-78 | string | element | Element symbol, right-justified. |
+---------+--------+----------+-------------------------------------+
| 79-80 | string | charge | Charge on the atom. |
+---------+--------+----------+-------------------------------------+
:param line: line with PDB class
:type line: str
"""
super().__init__(line)
self.serial = int(line[6:11].strip())
self.name = line[12:16].strip()
self.alt_loc = line[16].strip()
self.res_name = line[17:20].strip()
self.chain_id = line[21].strip()
self.res_seq = int(line[22:26].strip())
self.ins_code = line[26].strip()
self.sig_x = float(line[30:38].strip())
self.sig_y = float(line[38:46].strip())
self.sig_z = float(line[46:54].strip())
self.sig_occ = float(line[54:60].strip())
self.sig_temp = float(line[60:66].strip())
self.seg_id = line[72:76].strip()
self.element = line[76:78].strip()
self.charge = line[78:80].strip()
[docs]
@register_line_parser
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.
"""
[docs]
def __init__(
self, line, sybyl_type="A.aaa", l_bonds=[], l_bonded_atoms=[]
):
"""Initialize by parsing line
+---------+--------+-------------+-----------------------------------+
| COLUMNS | TYPE | FIELD | DEFINITION |
+=========+========+=============+===================================+
| 7-11 | int | serial | Atom serial number. |
+---------+--------+-------------+-----------------------------------+
| 13-16 | string | name | Atom name. |
+---------+--------+-------------+-----------------------------------+
| 17 | string | alt_loc | Alternate location indicator. |
+---------+--------+-------------+-----------------------------------+
| 18-20 | string | res_name | Residue name. |
+---------+--------+-------------+-----------------------------------+
| 22 | string | chain_id | Chain identifier. |
+---------+--------+-------------+-----------------------------------+
| 23-26 | int | res_seq | Residue sequence number. |
+---------+--------+-------------+-----------------------------------+
| 27 | string | ins_code | 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 | temp_factor | Temperature factor. |
+---------+--------+-------------+-----------------------------------+
| 73-76 | string | seg_id | Segment identifier, left- |
| | | | justified. |
+---------+--------+-------------+-----------------------------------+
| 77-78 | string | element | Element symbol, right-justified. |
+---------+--------+-------------+-----------------------------------+
| 79-80 | string | charge | Charge on the atom. |
+---------+--------+-------------+-----------------------------------+
:param line: line with PDB class
:type line: str
"""
super().__init__(line)
self.serial = int(line[6:11].strip())
self.name = line[12:16].strip()
self.alt_loc = line[16].strip()
try:
self.res_name = line[17:20].strip()
self.chain_id = line[21].strip()
self.res_seq = int(line[22:26].strip())
self.ins_code = line[26].strip()
except IndexError:
raise ValueError("Residue name must be less than 4 characters!")
self.x = float(line[30:38].strip())
self.y = float(line[38:46].strip())
self.z = float(line[46:54].strip())
self.sybyl_type = sybyl_type
self.l_bonded_atoms = l_bonded_atoms
self.l_bonds = l_bonds
self.radius = 1.0
self.is_c_term = 0
self.is_n_term = 0
self.mol2charge = None
try:
self.occupancy = float(line[54:60].strip())
self.temp_factor = float(line[60:66].strip())
self.seg_id = line[72:76].strip()
self.element = line[76:78].strip()
self.charge = line[78:80].strip()
except (ValueError, IndexError):
self.occupancy = 0.00
self.temp_factor = 0.00
self.seg_id = ""
self.element = ""
self.charge = ""
[docs]
@register_line_parser
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.
"""
[docs]
def __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 | alt_loc | Alternate location indicator. |
+---------+--------+-------------+-----------------------------------+
| 18-20 | string | res_name | Residue name. |
+---------+--------+-------------+-----------------------------------+
| 22 | string | chain_id | Chain identifier. |
+---------+--------+-------------+-----------------------------------+
| 23-26 | int | res_seq | Residue sequence number. |
+---------+--------+-------------+-----------------------------------+
| 27 | string | ins_code | 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 | temp_factor | Temperature factor. |
+---------+--------+-------------+-----------------------------------+
| 73-76 | string | seg_id | Segment identifier, |
| | | | left-justified. |
+---------+--------+-------------+-----------------------------------+
| 77-78 | string | element | Element symbol, right-justified. |
+---------+--------+-------------+-----------------------------------+
| 79-80 | string | charge | Charge on the atom. |
+---------+--------+-------------+-----------------------------------+
:param line: line with PDB class
:type line: str
"""
super().__init__(line)
self.serial = int(line[6:11].strip())
self.name = line[12:16].strip()
self.alt_loc = line[16].strip()
self.res_name = line[17:20].strip()
self.chain_id = line[21].strip()
self.res_seq = int(line[22:26].strip())
self.ins_code = line[26].strip()
self.x = float(line[30:38].strip())
self.y = float(line[38:46].strip())
self.z = float(line[46:54].strip())
try:
self.occupancy = float(line[54:60].strip())
self.temp_factor = float(line[60:66].strip())
self.seg_id = line[72:76].strip()
self.element = line[76:78].strip()
self.charge = line[78:80].strip()
except (ValueError, IndexError):
self.occupancy = 0.00
self.temp_factor = 0.00
self.seg_id = ""
self.element = ""
self.charge = ""
[docs]
@register_line_parser
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.
"""
[docs]
def __init__(self, line):
"""Initialize by parsing line
+---------+------+--------+----------------------+
| COLUMNS | TYPE | FIELD | DEFINITION |
+=========+======+========+======================+
| 11-14 | int | serial | Model serial number. |
+---------+------+--------+----------------------+
:param line: line with PDB class
:type line: str
"""
super().__init__(line)
self.serial = int(line[10:14].strip())
[docs]
@register_line_parser
class TVECT(BaseRecord):
"""TVECT class
The TVECT records present the translation vector for infinite
covalently connected structures.
"""
[docs]
def __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 |
+---------+--------+--------+----------------------------------+
:param line: line with PDB class
:type line: str
"""
super().__init__(line)
self.serial = int(line[7:10].strip())
self.trans1 = float(line[10:20].strip())
self.trans2 = float(line[20:30].strip())
self.trans3 = float(line[30:40].strip())
self.text = line[40:70].strip()
[docs]
class MTRIXn(BaseRecord):
"""MTRIXn baseclass
The MTRIXn (n = 1, 2, or 3) records present transformations expressing
non-crystallographic symmetry.
"""
[docs]
def __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 | i_given | 1 if coordinates for the |
| | | | representations which are approximately|
| | | | related by the transformations of the |
| | | | molecule are contained in the entry. |
| | | | Otherwise, blank. |
+---------+-------+---------+----------------------------------------+
:param line: line with PDB class
:type line: str
"""
super().__init__(line)
self.serial = int(line[7:10].strip())
self.mn1 = float(line[10:20].strip())
self.mn2 = float(line[20:30].strip())
self.mn3 = float(line[30:40].strip())
self.vecn = float(line[45:55].strip())
try:
self.i_given = int(line[59].strip())
except (ValueError, IndexError):
self.i_given = None
[docs]
@register_line_parser
class MTRIX3(MTRIXn):
"""MATRIX3 PDB entry"""
[docs]
@register_line_parser
class MTRIX2(MTRIXn):
"""MATRIX2 PDB entry"""
[docs]
@register_line_parser
class MTRIX1(MTRIXn):
"""MATRIX1 PDB entry"""
[docs]
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.
"""
[docs]
def __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 |
+---------+-------+-------+------------+
:param line: line with PDB class
:type line: str
"""
super().__init__(line)
self.sn1 = float(line[10:20].strip())
self.sn2 = float(line[20:30].strip())
self.sn3 = float(line[30:40].strip())
self.unif = float(line[45:55].strip())
[docs]
@register_line_parser
class SCALE3(SCALEn):
"""SCALE3 PDB entry"""
[docs]
@register_line_parser
class SCALE2(SCALEn):
"""SCALE2 PDB entry"""
[docs]
@register_line_parser
class SCALE1(SCALEn):
"""SCALE2 PDB entry"""
[docs]
class ORIGXn(BaseRecord):
"""ORIGXn class
The ORIGXn (n = 1, 2, or 3) records present the transformation from the
orthogonal coordinates contained in the entry to the submitted
coordinates.
"""
[docs]
def __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 |
+---------+-------+-------+------------+
:param line: line with PDB class
:type line: str
"""
super().__init__(line)
self.on1 = float(line[10:20].strip())
self.on2 = float(line[20:30].strip())
self.on3 = float(line[30:40].strip())
self.tn = float(line[45:55].strip())
[docs]
@register_line_parser
class ORIGX2(ORIGXn):
"""ORIGX2 PDB entry"""
[docs]
@register_line_parser
class ORIGX3(ORIGXn):
"""ORIGX3 PDB entry"""
[docs]
@register_line_parser
class ORIGX1(ORIGXn):
"""ORIGX3 PDB entry"""
[docs]
@register_line_parser
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.
"""
[docs]
def __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 | space_group | Space group. |
+---------+--------+-------------+------------------+
| 67-70 | int | z | Z value. |
+---------+--------+-------------+------------------+
:param line: line with PDB class
:type line: str
"""
super().__init__(line)
self.a = float(line[6:15].strip())
self.b = float(line[15:24].strip())
self.c = float(line[24:33].strip())
self.alpha = float(line[33:40].strip())
self.beta = float(line[40:47].strip())
self.gamma = float(line[47:54].strip())
self.space_group = line[55:65].strip()
self.z = int(line[66:70].strip())
[docs]
@register_line_parser
class SITE(BaseRecord):
"""SITE class
The SITE records supply the identification of groups comprising
important sites in the macromolecule.
"""
[docs]
def __init__(self, line):
"""Initialize by parsing the line
+---------+--------+-----------+-------------------------------------+
| COLUMNS | TYPE | FIELD | DEFINITION |
| 8-10 | int | seq_num | Sequence number. |
+---------+--------+-----------+-------------------------------------+
| 12-14 | string | site_id | Site name. |
+---------+--------+-----------+-------------------------------------+
| 16-17 | int | num_res | Number of residues comprising site. |
+---------+--------+-----------+-------------------------------------+
| 19-21 | string | res_name1 | Residue name for first residue |
| | | | comprising site. |
+---------+--------+-----------+-------------------------------------+
| 23 | string | chain_id1 | Chain identifier for first residue |
| | | | comprising site. |
+---------+--------+-----------+-------------------------------------+
| 24-27 | int | seq1 | Residue sequence number for first |
| | | | residue comprising site. |
+---------+--------+-----------+-------------------------------------+
| 28 | string | ins_code1 | Insertion code for first residue |
| | | | comprising site. |
+---------+--------+-----------+-------------------------------------+
| 30-32 | string | res_name2 | Residue name for second residue |
| | | | comprising site. |
+---------+--------+-----------+-------------------------------------+
| 34 | string | chain_id2 | Chain identifier for second residue |
| | | | comprising site. |
+---------+--------+-----------+-------------------------------------+
| 35-38 | int | seq2 | Residue sequence number for second |
| | | | residue comprising site. |
+---------+--------+-----------+-------------------------------------+
| 39 | string | ins_code2 | Insertion code for second residue |
| | | | comprising site. |
+---------+--------+-----------+-------------------------------------+
| 41-43 | string | res_name3 | Residue name for third residue |
| | | | comprising site. |
+---------+--------+-----------+-------------------------------------+
| 45 | string | chain_id3 | Chain identifier for third residue |
| | | | comprising site. |
+---------+--------+-----------+-------------------------------------+
| 46-49 | int | seq3 | Residue sequence number for third |
| | | | residue comprising site. |
+---------+--------+-----------+-------------------------------------+
| 50 | string | ins_code3 | Insertion code for third residue |
| | | | comprising site. |
+---------+--------+-----------+-------------------------------------+
| 52-54 | string | res_name4 | Residue name for fourth residue |
| | | | comprising site. |
+---------+--------+-----------+-------------------------------------+
| 56 | string | chain_id4 | Chain identifier for fourth residue |
| | | | comprising site. |
+---------+--------+-----------+-------------------------------------+
| 57-60 | int | seq4 | Residue sequence number for fourth |
| | | | residue comprising site. |
+---------+--------+-----------+-------------------------------------+
| 61 | string | ins_code4 | Insertion code for fourth residue |
| | | | comprising site. |
+---------+--------+-----------+-------------------------------------+
:param line: line with PDB class
:type line: str
"""
super().__init__(line)
self.seq_num = int(line[7:10].strip())
self.site_id = line[11:14].strip()
self.num_res = int(line[15:17].strip())
self.res_name1 = line[18:21].strip()
self.chain_id1 = line[22].strip()
self.seq1 = int(line[23:27].strip())
self.ins_code1 = line[27].strip()
self.res_name2 = line[29:32].strip()
self.chain_id2 = line[33].strip()
self.seq2 = int(line[34:38].strip())
self.ins_code2 = line[38].strip()
self.res_name3 = line[40:43].strip()
self.chain_id3 = line[44].strip()
self.seq3 = int(line[45:49].strip())
self.ins_code3 = line[49].strip()
self.res_name4 = line[51:54].strip()
self.chain_id4 = line[55].strip()
self.seq4 = int(line[56:60].strip())
try:
self.ins_code4 = line[60].strip()
except IndexError:
self.ins_code4 = None
[docs]
@register_line_parser
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.
"""
[docs]
def __init__(self, line):
"""Initialize by parsing line
+---------+--------+-----------+----------------------------------+
| COLUMNS | TYPE | FIELD | DEFINITION |
+=========+========+===========+==================================+
| 8-10 | int | ser_num | Record serial number. |
+---------+--------+-----------+----------------------------------+
| 12-14 | string | pep1 | Residue name. |
+---------+--------+-----------+----------------------------------+
| 16 | string | chain_id1 | Chain identifier. |
+---------+--------+-----------+----------------------------------+
| 18-21 | int | seq_num1 | Residue sequence number. |
+---------+--------+-----------+----------------------------------+
| 22 | string | icode1 | Insertion code. |
+---------+--------+-----------+----------------------------------+
| 26-28 | string | pep2 | Residue name. |
+---------+--------+-----------+----------------------------------+
| 30 | string | chain_id2 | Chain identifier. |
+---------+--------+-----------+----------------------------------+
| 32-35 | int | seq_num2 | Residue sequence number. |
+---------+--------+-----------+----------------------------------+
| 36 | string | icode2 | Insertion code. |
+---------+--------+-----------+----------------------------------+
| 44-46 | int | mod_num | Identifies the specific model. |
+---------+--------+-----------+----------------------------------+
| 54-59 | float | measure | Measure of the angle in degrees. |
+---------+--------+-----------+----------------------------------+
:param line: line with PDB class
:type line: str
"""
super().__init__(line)
self.ser_num = int(line[7:10].strip())
self.pep1 = line[11:14].strip()
self.chain_id1 = line[15].strip()
self.seq_num1 = int(line[17:21].strip())
self.icode1 = line[21].strip()
self.pep2 = line[25:28].strip()
self.chain_id2 = line[29].strip()
self.seq_num2 = int(line[31:35].strip())
self.icode2 = line[35].strip()
self.mod_num = int(line[43:46].strip())
self.measure = float(line[53:59].strip())
[docs]
@register_line_parser
class SLTBRG(BaseRecord):
"""SLTBRG field
The SLTBRG records specify salt bridges in the entry.
records and is provided here for convenience in searching.
"""
[docs]
def __init__(self, line):
"""Initialize by parsing line
+---------+--------+-----------+---------------------------------+
| COLUMNS | TYPE | FIELD | DEFINITION |
+=========+========+===========+=================================+
| 13-16 | string | name1 | Atom name. |
+---------+--------+-----------+---------------------------------+
| 17 | string | alt_loc1 | Alternate location indicator. |
+---------+--------+-----------+---------------------------------+
| 18-20 | string | res_name1 | Residue name. |
+---------+--------+-----------+---------------------------------+
| 22 | string | chain_id1 | Chain identifier. |
+---------+--------+-----------+---------------------------------+
| 23-26 | int | res_seq1 | Residue sequence number. |
+---------+--------+-----------+---------------------------------+
| 27 | string | ins_code1 | Insertion code. |
+---------+--------+-----------+---------------------------------+
| 43-46 | string | name2 | Atom name. |
+---------+--------+-----------+---------------------------------+
| 47 | string | alt_loc2 | Alternate location indicator. |
+---------+--------+-----------+---------------------------------+
| 48-50 | string | res_name2 | Residue name. |
+---------+--------+-----------+---------------------------------+
| 52 | string | chain_id2 | Chain identifier. |
+---------+--------+-----------+---------------------------------+
| 53-56 | int | res_seq2 | Residue sequence number. |
+---------+--------+-----------+---------------------------------+
| 57 | string | ins_code2 | Insertion code. |
+---------+--------+-----------+---------------------------------+
| 60-65 | string | sym1 | Symmetry operator for 1st atom. |
+---------+--------+-----------+---------------------------------+
| 67-72 | string | sym2 | Symmetry operator for 2nd atom. |
+---------+--------+-----------+---------------------------------+
:param line: line with PDB class
:type line: str
"""
super().__init__(line)
self.name1 = line[12:16].strip()
self.alt_loc1 = line[16].strip()
self.res_name1 = line[17:20].strip()
self.chain_id1 = line[21].strip()
self.res_seq1 = int(line[22:26].strip())
self.ins_code1 = line[26].strip()
self.name2 = line[42:46].strip()
self.alt_loc2 = line[46].strip()
self.res_name2 = line[47:50].strip()
self.chain_id2 = line[51].strip()
self.res_seq2 = int(line[52:56].strip())
self.ins_code2 = line[56].strip()
self.sym1 = line[59:65].strip()
self.sym2 = line[66:72].strip()
[docs]
@register_line_parser
class HYDBND(BaseRecord):
"""HYDBND field
The HYDBND records specify hydrogen bonds in the entry.
"""
[docs]
def __init__(self, line):
"""Initialize by parsing line
+---------+--------+-----------+-------------------------------------+
| COLUMNS | TYPE | FIELD | DEFINITION |
+=========+========+===========+=====================================+
| 13-16 | string | name1 | Atom name. |
+---------+--------+-----------+-------------------------------------+
| 17 | string | alt_loc1 | Alternate location indicator. |
+---------+--------+-----------+-------------------------------------+
| 18-20 | string | res_name1 | Residue name. |
+---------+--------+-----------+-------------------------------------+
| 22 | string | chain1 | Chain identifier. |
+---------+--------+-----------+-------------------------------------+
| 23-27 | int | res_seq1 | Residue sequence number. |
+---------+--------+-----------+-------------------------------------+
| 28 | string | i_code1 | Insertion code. |
+---------+--------+-----------+-------------------------------------+
| 30-33 | string | name_h | Hydrogen atom name. |
+---------+--------+-----------+-------------------------------------+
| 34 | string | alt_loc_h | Alternate location indicator. |
+---------+--------+-----------+-------------------------------------+
| 36 | string | chain_h | Chain identifier. |
+---------+--------+-----------+-------------------------------------+
| 37-41 | int | res_seq_h | Residue sequence number. |
+---------+--------+-----------+-------------------------------------+
| 42 | string | ins_codeH | Insertion code. |
+---------+--------+-----------+-------------------------------------+
| 44-47 | string | name2 | Atom name. |
+---------+--------+-----------+-------------------------------------+
| 48 | string | alt_loc2 | Alternate location indicator. |
+---------+--------+-----------+-------------------------------------+
| 49-51 | string | res_name2 | Residue name. |
+---------+--------+-----------+-------------------------------------+
| 53 | string | chain_id2 | Chain identifier. |
+---------+--------+-----------+-------------------------------------+
| 54-58 | int | res_seq2 | Residue sequence number. |
+---------+--------+-----------+-------------------------------------+
| 59 | string | ins_code2 | Insertion code. |
+---------+--------+-----------+-------------------------------------+
| 60-65 | string | sym1 | Symmetry operator for 1st |
| | | | non-hydrogen atom. |
+---------+--------+-----------+-------------------------------------+
| 67-72 | string | sym2 | Symmetry operator for 2nd |
| | | | non-hydrogen atom. |
+---------+--------+-----------+-------------------------------------+
:param line: line with PDB class
:type line: str
"""
super().__init__(line)
self.name1 = line[12:16].strip()
self.alt_loc1 = line[16].strip()
self.res_name1 = line[17:20].strip()
self.chain1 = line[21].strip()
self.res_seq1 = line[22:27].strip()
self.i_code1 = line[27].strip()
self.name_h = line[29:33].strip()
self.alt_loc_h = line[33].strip()
self.chain_h = line[35].strip()
self.res_seq_h = line[36:41].strip()
self.i_code_h = line[41].strip()
self.name2 = line[43:47].strip()
self.alt_loc2 = line[47].strip()
self.res_name2 = line[48:51].strip()
self.chain2 = line[52].strip()
self.res_seq2 = line[53:58].strip()
self.i_code2 = line[58].strip()
self.sym1 = line[59:65].strip()
self.sym2 = line[66:72].strip()
[docs]
@register_line_parser
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.
"""
[docs]
def __init__(self, line):
"""Initialize by parsing line
+---------+--------+-----------+---------------------------------+
| COLUMNS | TYPE | FIELD | DEFINITION |
+=========+========+===========+=================================+
| 13-16 | string | name1 | Atom name. |
+---------+--------+-----------+---------------------------------+
| 17 | string | alt_loc1 | Alternate location indicator. |
+---------+--------+-----------+---------------------------------+
| 18-20 | string | res_name1 | Residue name. |
+---------+--------+-----------+---------------------------------+
| 22 | string | chain_id1 | Chain identifier. |
+---------+--------+-----------+---------------------------------+
| 23-26 | int | res_seq1 | Residue sequence number. |
+---------+--------+-----------+---------------------------------+
| 27 | string | ins_code1 | Insertion code. |
+---------+--------+-----------+---------------------------------+
| 43-46 | string | name2 | Atom name. |
+---------+--------+-----------+---------------------------------+
| 47 | string | alt_loc2 | Alternate location indicator. |
+---------+--------+-----------+---------------------------------+
| 48-50 | string | res_name2 | Residue name. |
+---------+--------+-----------+---------------------------------+
| 52 | string | chain_id2 | Chain identifier. |
+---------+--------+-----------+---------------------------------+
| 53-56 | int | res_seq2 | Residue sequence number. |
+---------+--------+-----------+---------------------------------+
| 57 | string | ins_code2 | Insertion code. |
+---------+--------+-----------+---------------------------------+
| 60-65 | string | sym1 | Symmetry operator for 1st atom. |
+---------+--------+-----------+---------------------------------+
| 67-72 | string | sym2 | Symmetry operator for 2nd atom. |
+---------+--------+-----------+---------------------------------+
:param line: line with PDB class
:type line: str
"""
super().__init__(line)
self.name1 = line[12:16].strip()
self.alt_loc1 = line[16].strip()
self.res_name1 = line[17:20].strip()
self.chain_id1 = line[21].strip()
self.res_seq1 = int(line[22:26].strip())
self.ins_code1 = line[26].strip()
self.name2 = line[42:46].strip()
self.alt_loc2 = line[46].strip()
self.res_name2 = line[47:50].strip()
self.chain_id2 = line[51].strip()
self.res_seq2 = int(line[52:56].strip())
self.ins_code2 = line[56].strip()
self.sym1 = line[59:65].strip()
self.sym2 = line[66:72].strip()
[docs]
@register_line_parser
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.
"""
[docs]
def __init__(self, line):
"""Initialize by parsing line
+---------+--------+-----------+------------------------------------+
| COLUMNS | TYPE | FIELD | DEFINITION |
+=========+========+===========+====================================+
| 8-10 | int | ser_num | Serial number. |
+---------+--------+-----------+------------------------------------+
| 16 | string | chain_id1 | Chain identifier. |
+---------+--------+-----------+------------------------------------+
| 18-21 | int | seq_num1 | Residue sequence number. |
+---------+--------+-----------+------------------------------------+
| 22 | string | icode1 | Insertion code. |
+---------+--------+-----------+------------------------------------+
| 30 | string | chain_id2 | Chain identifier. |
+---------+--------+-----------+------------------------------------+
| 32-35 | int | seq_num2 | 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. |
+---------+--------+-----------+------------------------------------+
:param line: line with PDB class
:type line: str
"""
super().__init__(line)
self.ser_num = int(line[7:10].strip())
self.chain_id1 = line[15].strip()
self.seq_num1 = int(line[17:21].strip())
self.icode1 = line[21].strip()
self.chain_id2 = line[29].strip()
self.seq_num2 = int(line[31:35].strip())
self.icode2 = line[35].strip()
self.sym1 = line[59:65].strip()
self.sym2 = line[66:72].strip()
[docs]
@register_line_parser
class TURN(BaseRecord):
"""TURN field
The TURN records identify turns and other short loop turns which normally
connect other secondary structure segments.
"""
[docs]
def __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 | turn_id | Turn identifier. |
+---------+--------+---------------+---------------------------------+
| 16-18 | string | init_res_name | Residue name of initial residue |
| | | | in turn. |
+---------+--------+---------------+---------------------------------+
| 20 | string | init_chain_id | Chain identifier for the chain |
| | | | containing this turn. |
+---------+--------+---------------+---------------------------------+
| 21-24 | int | init_seq_num | Sequence number of initial |
| | | | residue in turn. |
+---------+--------+---------------+---------------------------------+
| 25 | string | init_i_code | Insertion code of initial |
| | | | residue in turn. |
+---------+--------+---------------+---------------------------------+
| 27-29 | string | end_res_name | Residue name of terminal residue|
| | | | of turn. |
+---------+--------+---------------+---------------------------------+
| 31 | string | end_chain_id | Chain identifier for the chain |
| | | | containing this turn. |
+---------+--------+---------------+---------------------------------+
| 32-35 | int | end_seq_num | Sequence number of terminal |
| | | | residue of turn. |
+---------+--------+---------------+---------------------------------+
| 36 | string | end_i_code | Insertion code of terminal |
| | | | residue of turn. |
+---------+--------+---------------+---------------------------------+
| 41-70 | string | comment | Associated comment. |
+---------+--------+---------------+---------------------------------+
:param line: line with PDB class
:type line: str
"""
super().__init__(line)
self.seq = int(line[7:10].strip())
self.turn_id = line[11:14].strip()
self.init_res_name = line[15:18].strip()
self.init_chain_id = line[19].strip()
self.init_seq_num = int(line[20:24].strip())
self.init_i_code = line[24].strip()
self.end_res_name = line[26:29].strip()
self.end_chain_id = line[30].strip()
self.end_seq_num = int(line[31:35].strip())
self.end_i_code = line[35].strip()
self.comment = line[40:70].strip()
[docs]
@register_line_parser
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.
"""
[docs]
def __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 | sheet_id | Sheet identifier. |
+---------+--------+---------------+---------------------------------+
| 15-16 | int | num_strands | Number of strands in sheet. |
+---------+--------+---------------+---------------------------------+
| 18-20 | string | init_res_name | Residue name of initial residue.|
+---------+--------+---------------+---------------------------------+
| 22 | string | init_chain_id | Chain identifier of initial |
| | | | residue in strand. |
+---------+--------+---------------+---------------------------------+
| 23-26 | int | init_seq_num | Sequence number of initial |
| | | | residue in strand. |
+---------+--------+---------------+---------------------------------+
| 27 | string | init_i_code | Insertion code of initial |
| | | | residue in strand. |
+---------+--------+---------------+---------------------------------+
| 29-31 | string | end_res_name | Residue name of terminal |
| | | | residue. |
+---------+--------+---------------+---------------------------------+
| 33 | string | end_chain_id | Chain identifier of terminal |
| | | | residue. |
+---------+--------+---------------+---------------------------------+
| 34-37 | int | end_seq_num | Sequence number of terminal |
| | | | residue. |
+---------+--------+---------------+---------------------------------+
| 38 | string | end_i_code | 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 | cur_atom | Registration. Atom name in |
| | | | current strand. |
+---------+--------+---------------+---------------------------------+
| 46-48 | string | curr_res_name | Registration. Residue name in |
| | | | current strand. |
+---------+--------+---------------+---------------------------------+
| 50 | string | curChainId | Registration. Chain identifier |
| | | | in current strand. |
+---------+--------+---------------+---------------------------------+
| 51-54 | int | curr_res_seq | Registration. Residue sequence |
| | | | number in current strand. |
+---------+--------+---------------+---------------------------------+
| 55 | string | curr_ins_code | Registration. Insertion code in |
| | | | current strand. |
+---------+--------+---------------+---------------------------------+
| 57-60 | string | prev_atom | Registration. Atom name in |
| | | | previous strand. |
+---------+--------+---------------+---------------------------------+
| 61-63 | string | prev_res_name | Registration. Residue name in |
| | | | previous strand. |
+---------+--------+---------------+---------------------------------+
| 65 | string | prevChainId | Registration. Chain identifier |
| | | | in previous strand. |
+---------+--------+---------------+---------------------------------+
| 66-69 | int | prev_res_seq | Registration. Residue sequence |
| | | | number in previous strand. |
+---------+--------+---------------+---------------------------------+
| 70 | string | prev_ins_code | Registration. Insertion code in |
| | | | previous strand. |
+---------+--------+---------------+---------------------------------+
:param line: line with PDB class
:type line: str
"""
super().__init__(line)
self.strand = int(line[7:10].strip())
self.sheet_id = line[11:14].strip()
self.num_strands = int(line[14:16].strip())
self.init_res_name = line[17:20].strip()
self.init_chain_id = line[21].strip()
self.init_seq_num = int(line[22:26].strip())
self.init_i_code = line[26].strip()
self.end_res_name = line[28:31].strip()
self.end_chain_id = line[32].strip()
self.end_seq_num = int(line[33:37].strip())
self.end_i_code = line[37].strip()
self.sense = int(line[38:40].strip())
try:
self.cur_atom = line[41:45].strip()
self.curr_res_name = line[45:48].strip()
self.curr_chain_id = line[49].strip()
try:
self.curr_res_seq = int(line[50:54].strip())
except ValueError:
self.curr_res_seq = None
self.curr_ins_code = line[54].strip()
self.prev_atom = line[56:60].strip()
self.prev_res_name = line[60:63].strip()
self.prev_chain_id = line[64].strip()
try:
self.prev_res_seq = int(line[65:69].strip())
except ValueError:
self.prev_res_seq = None
self.prev_ins_code = line[69].strip()
except IndexError:
self.cur_atom = None
self.curr_res_name = None
self.curr_chain_id = None
self.curr_res_seq = None
self.curr_ins_code = None
self.prev_atom = None
self.prev_res_name = None
self.prev_chain_id = None
self.prev_res_seq = None
self.prev_ins_code = None
[docs]
@register_line_parser
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.
"""
[docs]
def __init__(self, line):
"""Initialize by parsing line
+---------+--------+---------------+---------------------------------+
| COLUMNS | TYPE | FIELD | DEFINITION |
+=========+========+===============+=================================+
| 8-10 | int | ser_num | Serial number of the helix. This|
| | | | starts at 1 and increases |
| | | | incrementally. |
+---------+--------+---------------+---------------------------------+
| 12-14 | string | helix_id | Helix identifier. In addition |
| | | | to a serial number, each helix |
| | | | is given an alphanumeric |
| | | | character helix identifier. |
+---------+--------+---------------+---------------------------------+
| 16-18 | string | init_res_name | Name of the initial residue. |
+---------+--------+---------------+---------------------------------+
| 20 | string | init_chain_id | Chain identifier for the chain |
| | | | containing this helix. |
+---------+--------+---------------+---------------------------------+
| 22-25 | int | init_seq_num | Sequence number of the initial |
| | | | residue. |
+---------+--------+---------------+---------------------------------+
| 26 | string | init_i_code | Insertion code of the initial |
| | | | residue. |
+---------+--------+---------------+---------------------------------+
| 28-30 | string | end_res_name | Name of the terminal residue of |
| | | | the helix. |
+---------+--------+---------------+---------------------------------+
| 32 | string | end_chain_id | Chain identifier for the chain |
| | | | containing this helix. |
+---------+--------+---------------+---------------------------------+
| 34-37 | int | end_seq_num | Sequence number of the terminal |
| | | | residue. |
+---------+--------+---------------+---------------------------------+
| 38 | string | end_i_code | Insertion code of the terminal |
| | | | residue. |
+---------+--------+---------------+---------------------------------+
| 39-40 | int | helix_class | Helix class (see below). |
+---------+--------+---------------+---------------------------------+
| 41-70 | string | comment | Comment about this helix. |
+---------+--------+---------------+---------------------------------+
| 72-76 | int | length | Length of this helix. |
+---------+--------+---------------+---------------------------------+
:param line: line with PDB class
:type line: str
"""
super().__init__(line)
self.ser_num = int(line[7:10].strip())
self.helix_id = line[11:14].strip()
self.init_res_name = line[15:18].strip()
self.init_chain_id = line[19].strip()
self.init_seq_num = int(line[21:25].strip())
self.init_i_code = line[25].strip()
self.end_res_name = line[27:30].strip()
self.end_chain_id = line[31].strip()
self.end_seq_num = int(line[33:37].strip())
self.end_i_code = line[37].strip()
try:
self.helix_class = int(line[38:40].strip())
except ValueError:
self.helix_class = None
self.comment = line[40:70].strip()
try:
self.length = int(line[71:76].strip())
except ValueError:
self.length = None
[docs]
@register_line_parser
class HETSYN(BaseRecord):
"""HETSYN field
This record provides synonyms, if any, for the compound in the
corresponding (i.e., same hetatm_id) HETNAM record. This is to allow
greater flexibility in searching for HET groups.
"""
[docs]
def __init__(self, line):
"""Initialize by parsing line
+---------+--------+-----------------+-------------------+
| COLUMNS | TYPE | FIELD | DEFINITION |
+=========+========+=================+===================+
| 12-14 | string | hetatm_id | Het identifier, |
| | | | right-justified. |
+---------+--------+-----------------+-------------------+
| 16-70 | string | hetatm_synonyms | List of synonyms |
+---------+--------+-----------------+-------------------+
:param line: line with PDB class
:type line: str
"""
super().__init__(line)
self.hetatm_id = line[11:14].strip()
self.hetatm_synonyms = line[15:70].strip()
[docs]
@register_line_parser
class HETNAM(BaseRecord):
"""HETNAM field
This record gives the chemical name of the compound with the
given hetatm_id."""
[docs]
def __init__(self, line):
"""Initialize by parsing line
+---------+--------+-----------+----------------------------------+
| COLUMNS | TYPE | FIELD | DEFINITION |
+=========+========+===========+==================================+
| 12-14 | string | hetatm_id | Het identifier, right-justified. |
+---------+--------+-----------+----------------------------------+
| 16-70 | string | text | Chemical name. |
+---------+--------+-----------+----------------------------------+
:param line: line with PDB class
:type line: str
"""
super().__init__(line)
self.hetatm_id = line[11:14].strip()
self.text = line[15:70].strip()
[docs]
@register_line_parser
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 hetatm_id UNK.
"""
[docs]
def __init__(self, line):
"""Initialize by parsing line
+---------+--------+---------------+---------------------------------+
| COLUMNS | TYPE | FIELD | DEFINITION |
+=========+========+===============+=================================+
| 8-10 | string | hetatm_id | Het identifier, right-justified.|
+---------+--------+---------------+---------------------------------+
| 13 | string | ChainID | Chain identifier. |
+---------+--------+---------------+---------------------------------+
| 14-17 | int | seq_num | Sequence number. |
+---------+--------+---------------+---------------------------------+
| 18 | string | ins_code | Insertion code. |
+---------+--------+---------------+---------------------------------+
| 21-25 | int | num_het_atoms | Number of HETATM records. |
+---------+--------+---------------+---------------------------------+
| 31-70 | string | text | Text describing Het group. |
+---------+--------+---------------+---------------------------------+
:param line: line with PDB class
:type line: str
"""
super().__init__(line)
self.hetatm_id = line[7:10].strip()
self.chain_id = line[12].strip()
try:
self.seq_num = int(line[13].strip())
except ValueError:
self.seq_num = None
self.ins_code = line[17].strip()
self.num_het_atoms = int(line[20:25].strip())
self.text = line[30:70].strip()
[docs]
@register_line_parser
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.
"""
[docs]
def __init__(self, line):
"""Initialize by parsing a line
+---------+--------+----------+--------------------------------------+
| COLUMNS | TYPE | FIELD | DEFINITION |
+=========+========+==========+======================================+
| 8-11 | string | id_code | ID code of this entry. |
+---------+--------+----------+--------------------------------------+
| 13-15 | string | res_name | Residue name used in this entry. |
+---------+--------+----------+--------------------------------------+
| 17 | string | chain_id | Chain identifier. |
+---------+--------+----------+--------------------------------------+
| 19-22 | int | seq_num | Sequence number. |
+---------+--------+----------+--------------------------------------+
| 23 | string | ins_code | Insertion code. |
+---------+--------+----------+--------------------------------------+
| 25-27 | string | stdRes | Standard residue name. |
+---------+--------+----------+--------------------------------------+
| 30-70 | string | comment | Description of the residue |
| | | | modification. |
+---------+--------+----------+--------------------------------------+
:param line: line with PDB class
:type line: str
"""
super().__init__(line)
self.id_code = line[7:11].strip()
self.res_name = line[12:15].strip()
self.chain_id = line[16].strip()
self.seq_num = int(line[18:22].strip())
self.ins_code = line[22].strip()
self.stdRes = line[24:27].strip()
self.comment = line[29:70].strip()
[docs]
@register_line_parser
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.
"""
[docs]
def __init__(self, line):
"""Initialize by parsing a line
+---------+--------+----------+--------------------------------------+
| COLUMNS | TYPE | FIELD | DEFINITION |
+=========+========+==========+======================================+
| 9-10 | int | ser_num | 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 | chain_id | Chain identifier. This may be any |
| | | | single legal character, including a |
| | | | blank which is used if there is only |
| | | | one chain. |
+---------+--------+----------+--------------------------------------+
| 14-17 | int | num_res | Number of residues in the chain. This|
| | | | value is repeated on every record. |
+---------+--------+----------+--------------------------------------+
| 20-22 | string | res_name | Residue name. |
+---------+--------+----------+--------------------------------------+
| 24-26 | string | res_name | Residue name. |
+---------+--------+----------+--------------------------------------+
| 28-30 | string | res_name | Residue name. |
+---------+--------+----------+--------------------------------------+
| 32-34 | string | res_name | Residue name. |
+---------+--------+----------+--------------------------------------+
| 36-38 | string | res_name | Residue name. |
+---------+--------+----------+--------------------------------------+
| 40-42 | string | res_name | Residue name. |
+---------+--------+----------+--------------------------------------+
| 44-46 | string | res_name | Residue name. |
+---------+--------+----------+--------------------------------------+
| 48-50 | string | res_name | Residue name. |
+---------+--------+----------+--------------------------------------+
| 52-54 | string | res_name | Residue name. |
+---------+--------+----------+--------------------------------------+
| 56-58 | string | res_name | Residue name. |
+---------+--------+----------+--------------------------------------+
| 60-62 | string | res_name | Residue name. |
+---------+--------+----------+--------------------------------------+
| 64-66 | string | res_name | Residue name. |
+---------+--------+----------+--------------------------------------+
| 68-70 | string | res_name | Residue name. |
+---------+--------+----------+--------------------------------------+
:param line: line with PDB class
:type line: str
"""
super().__init__(line)
self.ser_num = int(line[8:10].strip())
self.chain_id = line[11].strip()
self.num_res = int(line[13:17].strip())
self.res_name = [line[19:22].strip()]
self.res_name.append(line[23:26].strip())
self.res_name.append(line[27:30].strip())
self.res_name.append(line[31:34].strip())
self.res_name.append(line[35:38].strip())
self.res_name.append(line[39:42].strip())
self.res_name.append(line[43:46].strip())
self.res_name.append(line[47:50].strip())
self.res_name.append(line[51:54].strip())
self.res_name.append(line[55:58].strip())
self.res_name.append(line[59:62].strip())
self.res_name.append(line[63:66].strip())
self.res_name.append(line[67:70].strip())
[docs]
@register_line_parser
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.
"""
[docs]
def __init__(self, line):
"""Initialize by parsing line
+---------+--------+------------+------------------------------------+
| COLUMNS | TYPE | FIELD | DEFINITION |
+=========+========+============+====================================+
| 8-11 | string | id_code | ID code of this entry. |
+---------+--------+------------+------------------------------------+
| 13-15 | string | res_name | Name of the PDB residue in |
| | | | conflict. |
+---------+--------+------------+------------------------------------+
| 17 | string | chain_id | PDB chain identifier. |
+---------+--------+------------+------------------------------------+
| 19-22 | int | seq_num | PDB sequence number. |
+---------+--------+------------+------------------------------------+
| 23 | string | ins_code | PDB insertion code. |
+---------+--------+------------+------------------------------------+
| 25-28 | string | database | Sequence database name. |
+---------+--------+------------+------------------------------------+
| 30-38 | string | db_id_code | Sequence database accession number.|
+---------+--------+------------+------------------------------------+
| 40-42 | string | db_res | Sequence database residue name. |
+---------+--------+------------+------------------------------------+
| 44-48 | int | db_seq | Sequence database sequence number. |
+---------+--------+------------+------------------------------------+
| 50-70 | string | conflict | Conflict comment. |
+---------+--------+------------+------------------------------------+
:param line: line with PDB class
:type line: str
"""
super().__init__(line)
self.id_code = line[7:11].strip()
self.res_name = line[12:15].strip()
self.chain_id = line[16].strip()
try:
self.seq_num = int(line[19:22].strip())
except ValueError:
self.seq_num = None
self.ins_code = line[22].strip()
self.database = line[24:28].strip()
self.db_id_code = line[29:38].strip()
self.db_res = line[39:42].strip()
try:
self.db_seq = int(line[43:48].strip())
except ValueError:
self.db_seq = None
self.conflict = line[49:70].strip()
[docs]
@register_line_parser
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.
"""
[docs]
def __init__(self, line):
"""Initialize by parsing a line.
+---------+--------+--------------+----------------------------------+
| COLUMNS | TYPE | FIELD | DEFINITION |
+=========+========+==============+==================================+
| 8-11 | string | id_code | ID code of this entry. |
+---------+--------+--------------+----------------------------------+
| 13 | string | chain_id | Chain identifier. |
+---------+--------+--------------+----------------------------------+
| 15-18 | int | seq_begin | Initial sequence number of the |
| | | | PDB sequence segment. |
+---------+--------+--------------+----------------------------------+
| 19 | string | insert_begin | Initial insertion code of the |
| | | | PDB sequence segment. |
+---------+--------+--------------+----------------------------------+
| 21-24 | int | seq_end | Ending sequence number of the |
| | | | PDB sequence segment. |
+---------+--------+--------------+----------------------------------+
| 25 | string | insert_end | 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 | db_accession | Sequence database accession code.|
| | | | For GenBank entries, this is the |
| | | | NCBI gi number. |
+---------+--------+--------------+----------------------------------+
| 43-54 | string | db_id_code | Sequence database identification |
| | | | code. For GenBank entries, this |
| | | | is the accession code. |
+---------+--------+--------------+----------------------------------+
| 56-60 | int | db_seq_begin | Initial sequence number of the |
| | | | database seqment. |
+---------+--------+--------------+----------------------------------+
| 61 | string | db_ins_begin | Insertion code of initial residue|
| | | | of the segment, if PDB is the |
| | | | reference. |
+---------+--------+--------------+----------------------------------+
| 63-67 | int | dbseq_end | Ending sequence number of the |
| | | | database segment. |
+---------+--------+--------------+----------------------------------+
| 68 | string | db_ins_end | Insertion code of the ending |
| | | | residue of the |
| | | | segment, if PDB is the reference.|
+---------+--------+--------------+----------------------------------+
:param line: line with PDB class
:type line: str
"""
super().__init__(line)
self.id_code = line[7:11].strip()
self.chain_id = line[12].strip()
self.seq_begin = int(line[14:18].strip())
self.insert_begin = line[18].strip()
self.seq_end = int(line[20:24].strip())
self.insert_end = line[24].strip()
self.database = line[26:32].strip()
self.db_accession = line[33:41].strip()
self.db_id_code = line[42:54].strip()
self.db_seq_begin = int(line[55:60].strip())
self.db_ins_begin = line[60].strip()
self.dbseq_end = int(line[62:67].strip())
try:
self.db_ins_end = line[67].strip()
except IndexError:
self.db_ins_end = None
[docs]
@register_line_parser
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.
"""
[docs]
def __init__(self, line):
"""Initialize by parsing line
+---------+--------+-------+---------------------+
| COLUMNS | TYPE | FIELD | DEFINITION |
+=========+========+=======+=====================+
| 13-70 | string | text | See details on web. |
+---------+--------+-------+---------------------+
:param line: line with PDB class
:type line: str
"""
super().__init__(line)
self.text = line[12:70].strip()
[docs]
@register_line_parser
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.
"""
[docs]
def __init__(self, line):
"""Initialize by parsing line
+---------+--------+------------+------------------------------------+
| COLUMNS | TYPE | FIELD | DEFINITION |
+=========+========+============+====================================+
| 12-20 | string | super_date | Date this entry superseded the |
| | | | listed entries. |
+---------+--------+------------+------------------------------------+
| 22-25 | string | id_code | ID code of this entry. |
+---------+--------+------------+------------------------------------+
| 32-35 | string | sid_code | ID code of a superseded entry. |
+---------+--------+------------+------------------------------------+
| 37-40 | string | sid_code | ID code of a superseded entry. |
+---------+--------+------------+------------------------------------+
| 42-45 | string | sid_code | ID code of a superseded entry. |
+---------+--------+------------+------------------------------------+
| 47-50 | string | sid_code | ID code of a superseded entry. |
+---------+--------+------------+------------------------------------+
| 52-55 | string | sid_code | ID code of a superseded entry. |
+---------+--------+------------+------------------------------------+
| 57-60 | string | sid_code | ID code of a superseded entry. |
+---------+--------+------------+------------------------------------+
| 62-65 | string | sid_code | ID code of a superseded entry. |
+---------+--------+------------+------------------------------------+
| 67-70 | string | sid_code | ID code of a superseded entry. |
+---------+--------+------------+------------------------------------+
:param line: line with PDB class
:type line: str
"""
super().__init__(line)
self.super_date = line[11:20].strip()
self.id_code = line[21:25].strip()
self.super_id_codes = [line[31:35].strip()]
self.super_id_codes.append(line[36:40].strip())
self.super_id_codes.append(line[41:45].strip())
self.super_id_codes.append(line[46:50].strip())
self.super_id_codes.append(line[51:55].strip())
self.super_id_codes.append(line[56:60].strip())
self.super_id_codes.append(line[61:65].strip())
self.super_id_codes.append(line[66:70].strip())
[docs]
@register_line_parser
class REVDAT(BaseRecord):
"""REVDAT field
REVDAT records contain a history of the modifications made to an entry
since its release.
"""
[docs]
def __init__(self, line):
"""Initialize by parsing a line.
.. todo::
If multiple modifications are present, only the last one in the
file is preserved.
+---------+--------+----------+--------------------------------------+
| COLUMNS | TYPE | FIELD | DEFINITION |
+=========+========+==========+======================================+
| 8-10 | int | mod_num | Modification number. |
+---------+--------+----------+--------------------------------------+
| 14-22 | string | mod_date | Date of modification (or release for |
| | | | new entries). |
+---------+--------+----------+--------------------------------------+
| 24-28 | string | mod_id | Identifies this particular |
| | | | modification. It links to the archive|
| | | | used internally by PDB. |
+---------+--------+----------+--------------------------------------+
| 32 | int | mod_type | An integer identifying the type of |
| | | | modification. In case of revisions |
| | | | with more than one possible mod_type,|
| | | | 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. |
+---------+--------+----------+--------------------------------------+
:param line: line with PDB class
:type line: str
"""
super().__init__(line)
self.mod_num = int(line[7:10].strip())
self.mod_date = line[13:22].strip()
self.mod_id = line[23:28].strip()
mod_type = line[31].strip()
if mod_type:
self.mod_type = int(mod_type)
self.records = [line[39:45].strip()]
self.records.append(line[46:52].strip())
self.records.append(line[53:59].strip())
self.records.append(line[60:66].strip())
[docs]
@register_line_parser
class AUTHOR(BaseRecord):
"""AUTHOR field
The AUTHOR record contains the names of the people responsible for the
contents of the entry.
"""
[docs]
def __init__(self, line):
"""Initialize by parsing a line
+---------+--------+-------------+-----------------------------------+
| COLUMNS | TYPE | FIELD | DEFINITION |
+=========+========+=============+===================================+
| 11-70 | string | author_list | List of the author names, |
| | | | separated by commas |
+---------+--------+-------------+-----------------------------------+
:param line: line with PDB class
:type line: str
"""
super().__init__(line)
self.author_list = line[10:70].strip()
[docs]
@register_line_parser
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
"""
[docs]
def __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 |
+---------+--------+-----------+-------------------------------------+
:param line: line with PDB class
:type line: str
"""
super().__init__(line)
self.technique = line[10:70].strip()
[docs]
@register_line_parser
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.
"""
[docs]
def __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 |
+---------+--------+--------+----------------------------------------+
:param line: line with PDB class
:type line: str
"""
super().__init__(line)
self.keywds = line[10:70].strip()
[docs]
@register_line_parser
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.
"""
[docs]
def __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 |
+---------+--------+--------+----------------------------------------+
:param line: line with PDB class
:type line: str
"""
super().__init__(line)
self.source = line[10:70].strip()
[docs]
@register_line_parser
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.
"""
[docs]
def __init__(self, line):
"""Initialize by parsing a line
+---------+--------+----------+--------------------------------------+
| COLUMNS | TYPE | FIELD | DEFINITION |
+=========+========+==========+======================================+
| 11-70 | string | compound | Description of the molecular list |
| | | | components. |
+---------+--------+----------+--------------------------------------+
:param line: line with PDB class
:type line: str
"""
super().__init__(line)
self.compound = line[10:70].strip()
[docs]
@register_line_parser
class CAVEAT(BaseRecord):
"""CAVEAT field
CAVEAT warns of severe errors in an entry. Use caution when using an entry
containing this record.
"""
[docs]
def __init__(self, line):
"""Initialize by parsing line.
+---------+--------+---------+---------------------------------------+
| COLUMNS | TYPE | FIELD | DEFINITION |
+=========+========+=========+=======================================+
| 12-15 | string | id_code | PDB ID code of this entry. |
+---------+--------+---------+---------------------------------------+
| 20-70 | string | comment | Free text giving the reason for the |
| | | | CAVEAT. |
+---------+--------+---------+---------------------------------------+
:param line: line with PDB class
:type line: str
"""
super().__init__(line)
self.id_code = line[11:15].strip()
self.comment = line[19:70].strip()
[docs]
@register_line_parser
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.
"""
[docs]
def __init__(self, line):
"""Initialize by parsing a line.
+---------+--------+-------+--------------------------+
| COLUMNS | TYPE | FIELD | DEFINITION |
+=========+========+=======+==========================+
| 11-70 | string | title | Title of the experiment |
+---------+--------+-------+--------------------------+
:param line: line with PDB class
:type line: str
"""
super().__init__(line)
self.title = line[10:70].strip()
[docs]
@register_line_parser
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.
"""
[docs]
def __init__(self, line):
"""Initialize by parsing a line.
+---------+--------+--------------+----------------------------------+
| COLUMNS | TYPE | FIELD | DEFINITION |
+=========+========+==============+==================================+
| 12-20 | string | replace_date | Date that this entry was |
| | | | replaced. |
+---------+--------+--------------+----------------------------------+
| 22-25 | string | id_code | ID code of this entry. |
+---------+--------+--------------+----------------------------------+
| 32-35 | string | rid_code | ID code of entry that replaced |
| | | | this one. |
+---------+--------+--------------+----------------------------------+
| 37-40 | string | rid_code | ID code of entry that replaced |
| | | | this one. |
+---------+--------+--------------+----------------------------------+
| 42-45 | string | rid_code | ID code of entry that replaced |
| | | | this one. |
+---------+--------+--------------+----------------------------------+
| 47-50 | string | rid_code | ID code of entry that replaced |
| | | | this one. |
+---------+--------+--------------+----------------------------------+
| 52-55 | string | rid_code | ID code of entry that replaced |
| | | | this one. |
+---------+--------+--------------+----------------------------------+
| 57-60 | string | rid_code | ID code of entry that replaced |
| | | | this one. |
+---------+--------+--------------+----------------------------------+
| 62-65 | string | rid_code | ID code of entry that replaced |
| | | | this one. |
+---------+--------+--------------+----------------------------------+
| 67-70 | string | rid_code | ID code of entry that replaced |
| | | | this one. |
+---------+--------+--------------+----------------------------------+
:param line: line with PDB class
:type line: str
"""
super().__init__(line)
self.replace_date = line[11:20].strip()
self.id_code = line[21:25].strip()
self.replace_id_codes = [line[31:35].strip()]
self.replace_id_codes.append(line[36:40].strip())
self.replace_id_codes.append(line[41:45].strip())
self.replace_id_codes.append(line[46:50].strip())
self.replace_id_codes.append(line[51:55].strip())
self.replace_id_codes.append(line[56:60].strip())
self.replace_id_codes.append(line[61:65].strip())
self.replace_id_codes.append(line[67:70].strip())
[docs]
def read_atom(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.
:param line: the line to parse
:type line: str
"""
# Try to find 5 consecutive floats
words = str.split(line)
size = len(words) - 1
consec = 0
iword = 0
for i in range(size):
entry = words[size - i]
try:
_ = float(entry)
consec += 1
if consec == 5:
iword = i
break
except ValueError:
consec = 0
record = line[0:6].strip()
newline = line[0:22]
newline = newline + str.rjust(words[size - iword - 1], 4)
newline = newline + str.rjust("", 3)
newline = newline + str.rjust(words[size - iword], 8)
newline = newline + str.rjust(words[size - iword + 1], 8)
newline = newline + str.rjust(words[size - iword + 2], 8)
newline = newline + str.rjust(words[size - iword + 3], 6)
newline = newline + str.rjust(words[size - iword + 4], 6)
klass = LINE_PARSERS[record]
return klass(newline)
[docs]
def read_pdb(file_):
"""Parse PDB-format data into array of Atom objects.
:param file_: open File-like object
:type file_: file
:return: (a list of objects from this module, a list of record names that
couldn't be parsed)
:rtype: (list, list)
"""
pdblist = [] # Array of parsed lines (as objects)
errlist = [] # List of records we can't parse
# We can come up with nothing if can't get our file off the web.
if file_ is None:
return pdblist, errlist
while True:
line = file_.readline().strip()
if line == "":
break
# We assume we have a method for each PDB record and can therefore
# parse them automatically
record = ""
try:
record = line[0:6].strip()
if record not in errlist:
klass = LINE_PARSERS[record]
obj = klass(line)
pdblist.append(obj)
except (KeyError, ValueError) as details:
if record not in ["HETATM", "ATOM"]:
errlist.append(record)
_LOGGER.error(f"Error parsing line: {details}")
_LOGGER.error(f"<{line.strip()}>")
_LOGGER.error(
f"Truncating remaining errors for record type:{record}"
)
else:
raise details
except IndexError as details:
if record in ["ATOM", "HETATM"]:
try:
obj = read_atom(line)
pdblist.append(obj)
except IndexError as details:
_LOGGER.error(f"Error parsing line: {details},")
_LOGGER.error(f"<{line.strip()}>")
elif record in ["SITE", "TURN"]:
pass
elif record in ["SSBOND", "LINK"]:
_LOGGER.error("Warning -- ignoring record:")
_LOGGER.error(f"<{line.strip()}>")
else:
_LOGGER.error(f"Error parsing line: {details},")
_LOGGER.error(f"<{line.strip()}>")
return pdblist, errlist