""" PDB parsing class
This module parses PDBs in accordance to PDB Format Description Version 2.2
(1996); it is not very forgiving. Each class in this module corresponds
to a record in the PDB Format Description. Much of the documentation for
the classes is taken directly from the above PDB Format Description.
----------------------------
PDB2PQR -- An automated pipeline for the setup, execution, and analysis of
Poisson-Boltzmann electrostatics calculations
Copyright (c) 2002-2010, Jens Erik Nielsen, University College Dublin;
Nathan A. Baker, Washington University in St. Louis; Paul Czodrowski &
Gerhard Klebe, University of Marburg
All rights reserved.
Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice,
this list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
* Neither the names of University College Dublin, Washington University in
St. Louis, or University of Marburg nor the names of its contributors may
be used to endorse or promote products derived from this software without
specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED
OF THE POSSIBILITY OF SUCH DAMAGE.
----------------------------
"""
__date__ = "4 August 2008"
__author__ = "Todd Dolinsky, Yong Huang"
import string, sys
import copy ### PC
class END:
""" END class
The END records are paired with MODEL records to group individual
structures found in a coordinate entry.
"""
def __init__(self, line):
"""
Initialize by parsing line (nothing to do)
"""
pass
class MASTER:
""" 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.
"""
def __init__(self, line):
"""
Initialize by parsing line
COLUMNS TYPE FIELD DEFINITION
-------------------------------------------------
11-15 int numRemark Number of REMARK records
21-25 int numHet Number of HET records
26-30 int numHelix Number of HELIX records
31-35 int numSheet Number of SHEET records
36-40 int numTurn Number of TURN records
41-45 int numSite Number of SITE records
46-50 int numXform Number of coordinate transformation
records (ORIGX+SCALE+MTRIX)
51-55 int numCoord Number of atomic coordinate records
(ATOM+HETATM)
56-60 int numTer Number of TER records
61-65 int numConect Number of CONECT records
66-70 int numSeq Number of SEQRES records
"""
record = string.strip(line[0:6])
if record == "MASTER":
self.numRemark = int(string.strip(line[10:15]))
self.numHet = int(string.strip(line[20:25]))
self.numHelix = int(string.strip(line[25:30]))
self.numSheet = int(string.strip(line[30:35]))
self.numTurn = int(string.strip(line[35:40]))
self.numSite = int(string.strip(line[40:45]))
self.numXform = int(string.strip(line[45:50]))
self.numCoord = int(string.strip(line[50:55]))
self.numTer = int(string.strip(line[55:60]))
self.numConect = int(string.strip(line[60:65]))
self.numSeq = int(string.strip(line[65:70]))
else: raise ValueError, record
class CONECT:
""" 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.
"""
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
"""
record = string.strip(line[0:6])
if record == "CONECT":
self.serial = int(string.strip(line[6:11]))
try: self.serial1 = int(string.strip(line[11:16]))
except ValueError: self.serial1 = None
try: self.serial2 = int(string.strip(line[16:21]))
except ValueError: self.serial2 = None
try: self.serial3 = int(string.strip(line[21:26]))
except ValueError: self.serial3 = None
try: self.serial4 = int(string.strip(line[26:31]))
except ValueError: self.serial4 = None
try: self.serial5 = int(string.strip(line[31:36]))
except ValueError: self.serial5 = None
try: self.serial6 = int(string.strip(line[36:41]))
except ValueError: self.serial6 = None
try: self.serial7 = int(string.strip(line[41:46]))
except ValueError: self.serial7 = None
try: self.serial8 = int(string.strip(line[46:51]))
except ValueError: self.serial8 = None
try: self.serial9 = int(string.strip(line[51:56]))
except ValueError: self.serial9 = None
try: self.serial10 = int(string.strip(line[56:61]))
except ValueError: self.serial10 = None
else: raise ValueError, record
class ENDMDL:
""" ENDMDL class
The ENDMDL records are paired with MODEL records to group individual
structures found in a coordinate entry.
"""
def __init__(self, line):
"""
Initialize by parsing line (nothing to do)
"""
pass
class TER:
""" TER class
The TER record indicates the end of a list of ATOM/HETATM records for a
chain.
"""
def __init__(self, line):
""" Initialize by parsing line:
COLUMNS TYPE FIELD DEFINITION
-------------------------------------------
7-11 int serial Serial number.
18-20 string resName Residue name.
22 string chainID Chain identifier.
23-26 int resSeq Residue sequence number.
27 string iCode Insertion code.
"""
record = string.strip(line[0:6])
if record == "TER":
try: # Not really needed
self.serial = int(string.strip(line[6:11]))
self.resName = string.strip(line[17:20])
self.chainID = string.strip(line[21])
self.resSeq = int(string.strip(line[22:26]))
self.iCode = string.strip(line[26])
except (IndexError, ValueError):
self.serial = None
self.resName = None
self.chainID = None
self.resSeq = None
self.iCode = None
else: raise ValueError, record
class SIGUIJ:
""" SIGUIJ class
The SIGUIJ records present the anisotropic temperature factors.
"""
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 altLoc Alternate location indicator.
18-20 string resName Residue name.
22 string chainID Chain identifier.
23-26 int resSeq Residue sequence number.
27 string iCode Insertion code.
29-35 int sig11 Sigma U(1,1)
36-42 int sig22 Sigma U(2,2)
43-49 int sig33 Sigma U(3,3)
50-56 int sig12 Sigma U(1,2)
57-63 int sig13 Sigma U(1,3)
64-70 int sig23 Sigma U(2,3)
73-76 string segID Segment identifier, left-justified.
77-78 string element Element symbol, right-justified.
79-80 string charge Charge on the atom.
"""
record = string.strip(line[0:6])
if record == "SIGUIJ":
self.serial = int(string.strip(line[6:11]))
self.name = string.strip(line[12:16])
self.altLoc = string.strip(line[16])
self.resName = string.strip(line[17:20])
self.chainID = string.strip(line[21])
self.resSeq = int(string.strip(line[22:26]))
self.iCode = string.strip(line[26])
self.sig11 = int(string.strip(line[28:35]))
self.sig22 = int(string.strip(line[35:42]))
self.sig33 = int(string.strip(line[42:49]))
self.sig12 = int(string.strip(line[49:56]))
self.sig13 = int(string.strip(line[56:63]))
self.sig23 = int(string.strip(line[63:70]))
self.segID = string.strip(line[72:76])
self.element = string.strip(line[76:78])
self.charge = string.strip(line[78:80])
else: raise ValueError, record
class ANISOU:
""" ANISOU class
The ANISOU records present the anisotropic temperature factors.
"""
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 altLoc Alternate location indicator.
18-20 string resName Residue name.
22 string chainID Chain identifier.
23-26 int resSeq Residue sequence number.
27 string iCode Insertion code.
29-35 int u00 U(1,1)
36-42 int u11 U(2,2)
43-49 int u22 U(3,3)
50-56 int u01 U(1,2)
57-63 int u02 U(1,3)
64-70 int u12 U(2,3)
73-76 string segID Segment identifier, left-justified.
77-78 string element Element symbol, right-justified.
79-80 string charge Charge on the atom.
"""
record = string.strip(line[0:6])
if record == "ANISOU":
self.serial = int(string.strip(line[6:11]))
self.name = string.strip(line[12:16])
self.altLoc = string.strip(line[16])
self.resName = string.strip(line[17:20])
self.chainID = string.strip(line[21])
self.resSeq = int(string.strip(line[22:26]))
self.iCode = string.strip(line[26])
self.u00 = int(string.strip(line[28:35]))
self.u11 = int(string.strip(line[35:42]))
self.u22 = int(string.strip(line[42:49]))
self.u01 = int(string.strip(line[49:56]))
self.u02 = int(string.strip(line[56:63]))
self.u12 = int(string.strip(line[63:70]))
self.segID = string.strip(line[72:76])
self.element = string.strip(line[76:78])
self.charge = string.strip(line[78:80])
else: raise ValueError, record
class SIGATM:
""" SIGATM class
The SIGATM records present the standard deviation of atomic parameters
as they appear in ATOM and HETATM records.
"""
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 altLoc Alternate location indicator.
18-20 string resName Residue name.
22 string chainID Chain identifier.
23-26 int resSeq Residue sequence number.
27 string iCode Code for insertion of residues.
31-38 float sigX Standard devition of orthogonal
coordinates for X in Angstroms.
39-46 float sigY Standard devition of orthogonal
coordinates for Y in Angstroms.
47-54 float sigZ Standard devition of orthogonal
coordinates for Z in Angstroms.
55-60 float sigOcc Standard devition of occupancy.
61-66 float sigTemp Standard devition of temperature factor.
73-76 string segID Segment identifier, left-justified.
77-78 string element Element symbol, right-justified.
79-80 string charge Charge on the atom.
"""
record = string.strip(line[0:6])
if record == "HETATM":
self.serial = int(string.strip(line[6:11]))
self.name = string.strip(line[12:16])
self.altLoc = string.strip(line[16])
self.resName = string.strip(line[17:20])
self.chainID = string.strip(line[21])
self.resSeq = int(string.strip(line[22:26]))
self.iCode = string.strip(line[26])
self.sigX = float(string.strip(line[30:38]))
self.sigY = float(string.strip(line[38:46]))
self.sigZ = float(string.strip(line[46:54]))
self.sigOcc = float(string.strip(line[54:60]))
self.sigTemp = float(string.strip(line[60:66]))
self.segID = string.strip(line[72:76])
self.element = string.strip(line[76:78])
self.charge = string.strip(line[78:80])
else: raise ValueError, record
class HETATM:
""" 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.
"""
def __init__(self,line,sybylType="A.aaa",lBonds=[],lBondedAtoms=[]): ### PC
"""
Initialize by parsing line
COLUMNS TYPE FIELD DEFINITION
---------------------------------------------
7-11 int serial Atom serial number.
13-16 string name Atom name.
17 string altLoc Alternate location indicator.
18-20 string resName Residue name.
22 string chainID Chain identifier.
23-26 int resSeq Residue sequence number.
27 string iCode Code for insertion of residues.
31-38 float x Orthogonal coordinates for X in
Angstroms.
39-46 float y Orthogonal coordinates for Y in
Angstroms.
47-54 float z Orthogonal coordinates for Z in
Angstroms.
55-60 float occupancy Occupancy.
61-66 float tempFactor Temperature factor.
73-76 string segID Segment identifier, left-justified.
77-78 string element Element symbol, right-justified.
79-80 string charge Charge on the atom.
"""
record = string.strip(line[0:6])
if record == "HETATM":
self.serial = int(string.strip(line[6:11]))
self.name = string.strip(line[12:16])
self.altLoc = string.strip(line[16])
try:
self.resName = string.strip(line[17:20])
self.chainID = string.strip(line[21])
self.resSeq = int(string.strip(line[22:26]))
self.iCode = string.strip(line[26])
except:
raise ValueError, 'Residue name must be less than 4 characters!'
self.x = float(string.strip(line[30:38]))
self.y = float(string.strip(line[38:46]))
self.z = float(string.strip(line[46:54]))
### PC
# self.lAtoms = lAtoms
self.sybylType = sybylType
self.lBondedAtoms = lBondedAtoms
self.lBonds = lBonds
self.radius = 1.0
self.isCterm=0
self.isNterm=0
###
try:
self.occupancy = float(string.strip(line[54:60]))
self.tempFactor = float(string.strip(line[60:66]))
self.segID = string.strip(line[72:76])
self.element = string.strip(line[76:78])
self.charge = string.strip(line[78:80])
except ValueError, IndexError:
self.occupancy = 0.00
self.tempFactor = 0.00
self.segID = ""
self.element = ""
self.charge = ""
else: raise ValueError, record
def __str__(self):
"""
Print object as string
COLUMNS TYPE FIELD DEFINITION
---------------------------------------------
7-11 int serial Atom serial number.
13-16 string name Atom name.
17 string altLoc Alternate location indicator.
18-20 string resName Residue name.
22 string chainID Chain identifier.
23-26 int resSeq Residue sequence number.
27 string iCode Code for insertion of residues.
31-38 float x Orthogonal coordinates for X in
Angstroms.
39-46 float y Orthogonal coordinates for Y in
Angstroms.
47-54 float z Orthogonal coordinates for Z in
Angstroms.
55-60 float occupancy Occupancy.
61-66 float tempFactor Temperature factor.
73-76 string segID Segment identifier, left-justified.
77-78 string element Element symbol, right-justified.
79-80 string charge Charge on the atom.
"""
str = ""
tstr = "HETATM"
str = str + string.ljust(tstr, 6)[:6]
tstr = "%d" % self.serial
str = str + string.rjust(tstr, 5)[:5]
str = str + " "
tstr = self.name
if len(tstr) == 4:
str = str + string.ljust(tstr, 4)[:4]
else:
str = str + " " + string.ljust(tstr, 3)[:3]
tstr = self.altLoc
str = str + string.ljust(tstr, 1)[:1]
tstr = self.resName
str = str + string.ljust(tstr, 3)[:3]
str = str + " "
tstr = self.chainID
str = str + string.ljust(tstr, 1)[:1]
tstr = "%d" % self.resSeq
str = str + string.rjust(tstr, 4)[:4]
tstr = self.iCode
str = str + string.ljust(tstr, 1)[:1]
str = str + " "
tstr = "%8.3f" % self.x
str = str + string.ljust(tstr, 8)[:8]
tstr = "%8.3f" % self.y
str = str + string.ljust(tstr, 8)[:8]
tstr = "%8.3f" % self.z
str = str + string.ljust(tstr, 8)[:8]
tstr = "%6.2f" % self.occupancy
str = str + string.ljust(tstr, 6)[:6]
tstr = "%6.2f" % self.tempFactor
str = str + string.rjust(tstr, 6)[:6]
tstr = self.segID
str = str + string.ljust(tstr, 4)[:4]
tstr = self.element
str = str + string.ljust(tstr, 2)[:2]
tstr = self.charge
str = str + string.ljust(tstr, 2)[:2]
return str
### PC
# to do: - parse SUBSTRUCTURE
# - avoid/detect blanks in @<TRIPOS>BOND
# - what happens, if no SUBSTRUCTURE present?
# - different order of SUBSTRUCTURE/MOLECULE
# - readlines instead of read -> blanks are avoided (you get a list)
# - (maybe) flag for parsing each RTI
class MOL2BOND:
"""
Bonding of MOL2 files
"""
def __init__(self, frm, to, type, id=0):
self.to = to # bond to this atom
self.frm = frm # bond from atom
self.type = type # 1=single, 2=double, ar=aromatic
self.id = id # bond_id
class MOL2MOLECULE:
"""
Tripos MOL2 molecule
For further information look at (web page exists: 25 August 2005):
http://www.tripos.com/index.php?family=modules,SimplePage,,,&page=sup_mol2&s=0
"""
def __init__(self):
self.lAtoms = [] # all atoms of class <ATOM>
self.lBonds = [] # all bonds of class <BOND>
self.lPDBAtoms = [] # PDB-like list of all atoms
def read(self,file):
"""
Routines for reading MOL2 file
"""
#self.filename = filename
#data = open(self.filename).read()
data = file.read()
data = data.replace("\r\n", "\n")
data = data.replace("\r", "\n")
# ATOM section
start = data.find("@<TRIPOS>ATOM")
stop = data.find("@<TRIPOS>BOND")
# Do some error checking
if start == -1:
raise Exception, "Unable to find '@<TRIPOS>ATOM' in MOL2 file!"
elif stop == -1:
raise Exception, "Unable to find '@<TRIPOS>BOND' in MOL2 file!"
atoms = data[start+14:stop-2].split("\n")
# BOND section
start = data.find("@<TRIPOS>BOND")
stop = data.find("@<TRIPOS>SUBSTRUCTURE")
# More error checking
if stop == -1:
raise Exception, "Unable to find '@<TRIPOS>SUBSTRUCTURE' in MOL2 file!"
bonds = data[start+14:stop-1].split("\n")
self.parseAtoms(atoms)
self.parseBonds(bonds)
self.createlBondedAtoms()
#self.createPDBlineFromMOL2(atoms)
def parseAtoms(self,AtomList):
"""
for parsing @<TRIPOS>ATOM
"""
for AtomLine in AtomList:
SeparatedAtomLine = AtomLine.split()
# Special handling for blank lines
if len(SeparatedAtomLine) == 0:
continue
# Error checking
if len(SeparatedAtomLine) < 8:
raise Exception, "Bad atom entry in MOL2 file: %s" % AtomLine
fakeRecord = "HETATM"
fakeChain = " L"
try:
mol2pdb = '%s%5i%5s%4s%2s%4i %8.3f%8.3f%8.3f' %\
(fakeRecord,int(SeparatedAtomLine[0]),
SeparatedAtomLine[1],SeparatedAtomLine[7][:4],
fakeChain,int(SeparatedAtomLine[6]),
float(SeparatedAtomLine[2]),float(SeparatedAtomLine[3]),
float(SeparatedAtomLine[4]))
except ValueError:
raise Exception, "Bad atom entry in MOL2 file: %s" % AtomLine
thisAtom = HETATM(mol2pdb, SeparatedAtomLine[5],[],[])
if len(SeparatedAtomLine)>8:
charge=SeparatedAtomLine[8]
try:
thisAtom.mol2charge=float(charge)
except:
print 'Warning. Non-float charge in mol2 file.',charge
thisAtom.mol2charge=None
self.lPDBAtoms.append(mol2pdb)
self.lAtoms.append(thisAtom)
def parseBonds(self,BondList):
"""
for parsing @<TRIPOS>BOND
"""
for BondLine in BondList:
SeparatedBondLine = BondLine.split()
# Special handling for blank lines
if len(SeparatedBondLine) == 0:
continue
if len(SeparatedBondLine) < 4:
raise Exception, "Bad bond entry in MOL2 file: %s" % BondLine
try:
thisBond = MOL2BOND(
int(SeparatedBondLine[1]), # bond frm
int(SeparatedBondLine[2]), # bond to
SeparatedBondLine[3], # bond type
int(SeparatedBondLine[0]) # bond id
)
except ValueError:
raise Exception, "Bad bond entry in MOL2 file: %s" % BondLine
self.lBonds.append(thisBond)
def createlBondedAtoms(self):
"""
Creates for each atom a list of the bonded Atoms
This becomes one attribute of MOL2ATOM!
"""
for bond in self.lBonds:
self.lAtoms[bond.frm-1].lBondedAtoms.append(
self.lAtoms[bond.to-1])
self.lAtoms[bond.to-1].lBondedAtoms.append(
self.lAtoms[bond.frm-1])
atbond = copy.deepcopy(bond)
atbond.other_atom=self.lAtoms[bond.to-1]
self.lAtoms[bond.frm-1].lBonds.append(atbond)
atbond = copy.deepcopy(bond)
atbond.other_atom=self.lAtoms[bond.frm-1]
self.lAtoms[bond.to-1].lBonds.append(atbond)
return
def createPDBlineFromMOL2(self):
FakeType = "HETATM"
return ('%s%5i%5s%4s%2s%5s %8.3f%8.3f%8.3f\n' %
(FakeType, self.serial, self.name,
self.resName, ' L', self.resSeq,
self.x,self.y, self.z))
### PC
class ATOM:
""" 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.
"""
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 altLoc Alternate location indicator.
18-20 string resName Residue name.
22 string chainID Chain identifier.
23-26 int resSeq Residue sequence number.
27 string iCode Code for insertion of residues.
31-38 float x Orthogonal coordinates for X in
Angstroms.
39-46 float y Orthogonal coordinates for Y in
Angstroms.
47-54 float z Orthogonal coordinates for Z in
Angstroms.
55-60 float occupancy Occupancy.
61-66 float tempFactor Temperature factor.
73-76 string segID Segment identifier, left-justified.
77-78 string element Element symbol, right-justified.
79-80 string charge Charge on the atom.
"""
record = string.strip(line[0:6])
if record == "ATOM":
self.serial = int(string.strip(line[6:11]))
self.name = string.strip(line[12:16])
self.altLoc = string.strip(line[16])
self.resName = string.strip(line[17:20])
self.chainID = string.strip(line[21])
self.resSeq = int(string.strip(line[22:26]))
self.iCode = string.strip(line[26])
self.x = float(string.strip(line[30:38]))
self.y = float(string.strip(line[38:46]))
self.z = float(string.strip(line[46:54]))
try:
self.occupancy = float(string.strip(line[54:60]))
self.tempFactor = float(string.strip(line[60:66]))
self.segID = string.strip(line[72:76])
self.element = string.strip(line[76:78])
self.charge = string.strip(line[78:80])
except ValueError, IndexError:
self.occupancy = 0.00
self.tempFactor = 0.00
self.segID = ""
self.element = ""
self.charge = ""
else:
raise ValueError, record
def __str__(self):
"""
Print object as string
COLUMNS TYPE FIELD DEFINITION
---------------------------------------------
7-11 int serial Atom serial number.
13-16 string name Atom name.
17 string altLoc Alternate location indicator.
18-20 string resName Residue name.
22 string chainID Chain identifier.
23-26 int resSeq Residue sequence number.
27 string iCode Code for insertion of residues.
31-38 float x Orthogonal coordinates for X in
Angstroms.
39-46 float y Orthogonal coordinates for Y in
Angstroms.
47-54 float z Orthogonal coordinates for Z in
Angstroms.
55-60 float occupancy Occupancy.
61-66 float tempFactor Temperature factor.
73-76 string segID Segment identifier, left-justified.
77-78 string element Element symbol, right-justified.
79-80 string charge Charge on the atom.
"""
str = ""
tstr = "ATOM"
str = str + string.ljust(tstr, 6)[:6]
tstr = "%d" % self.serial
str = str + string.rjust(tstr, 5)[:5]
str = str + " "
tstr = self.name
if len(tstr) == 4:
str = str + string.ljust(tstr, 4)[:4]
else:
str = str + " " + string.ljust(tstr, 3)[:3]
tstr = self.altLoc
str = str + string.ljust(tstr, 1)[:1]
tstr = self.resName
str = str + string.ljust(tstr, 3)[:3]
str = str + " "
tstr = self.chainID
str = str + string.ljust(tstr, 1)[:1]
tstr = "%d" % self.resSeq
str = str + string.rjust(tstr, 4)[:4]
tstr = self.iCode
str = str + string.ljust(tstr, 1)[:1]
str = str + " "
tstr = "%8.3f" % self.x
str = str + string.ljust(tstr, 8)[:8]
tstr = "%8.3f" % self.y
str = str + string.ljust(tstr, 8)[:8]
tstr = "%8.3f" % self.z
str = str + string.ljust(tstr, 8)[:8]
tstr = "%6.2f" % self.occupancy
str = str + string.ljust(tstr, 6)[:6]
tstr = "%6.2f" % self.tempFactor
str = str + string.ljust(tstr, 6)[:6]
tstr = self.segID
str = str + string.ljust(tstr, 4)[:4]
tstr = self.element
str = str + string.ljust(tstr, 2)[:2]
tstr = self.charge
str = str + string.ljust(tstr, 2)[:2]
return str
class MODEL:
""" 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.
"""
def __init__(self, line):
"""
Initialize by parsing line
COLUMNS TYPE FIELD DEFINITION
-----------------------------------------------------
11-14 int serial Model serial number.
"""
record = string.strip(line[0:6])
if record == "MODEL":
self.serial = int(string.strip(line[10:14]))
else: raise ValueError, record
class TVECT:
""" TVECT class
The TVECT records present the translation vector for infinite
covalently connected structures.
"""
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
"""
record = string.strip(line[0:6])
if record == "TVECT":
self.serial = int(string.strip(line[7:10]))
self.t1 = float(string.strip(line[10:20]))
self.t2 = float(string.strip(line[20:30]))
self.t3 = float(string.strip(line[30:40]))
self.text = string.strip(line[40:70])
else: raise ValueError, record
class MTRIX3:
""" MTRIX3 class
The MTRIX3 (n = 1, 2, or 3) records present transformations expressing
non-crystallographic symmetry.
"""
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 iGiven 1 if coordinates for the representations
which are approximately related by the
transformations of the molecule are contained in
the entry. Otherwise, blank.
"""
record = string.strip(line[0:6])
if record == "MTRIX3":
self.serial = int(string.strip(line[7:10]))
self.mn1 = float(string.strip(line[10:20]))
self.mn2 = float(string.strip(line[20:30]))
self.mn3 = float(string.strip(line[30:40]))
self.vn = float(string.strip(line[45:55]))
self.iGiven = int(string.strip(line[59]))
else: raise ValueError, record
class MTRIX2:
""" MTRIX2 class
The MTRIXn (n = 1, 2, or 3) records present transformations expressing
non-crystallographic symmetry.
"""
def __init__(self, line):
"""
Initialize by parsing line
COLUMNS TYPE FIELD DEFINITION
---------------------------------
8-10 int serial Serial number
11-20 float mn1 M21
21-30 float mn2 M22
31-40 float mn3 M23
46-55 float vn V2
60 int iGiven 1 if coordinates for the representations
which are approximately related by the
transformations of the molecule are contained in
the entry. Otherwise, blank.
"""
record = string.strip(line[0:6])
if record == "MTRIX2":
self.serial = int(string.strip(line[7:10]))
self.mn1 = float(string.strip(line[10:20]))
self.mn2 = float(string.strip(line[20:30]))
self.mn3 = float(string.strip(line[30:40]))
self.vn = float(string.strip(line[45:55]))
self.iGiven = int(string.strip(line[59]))
else: raise ValueError, record
class MTRIX1:
""" MTRIX1 class
The MTRIXn (n = 1, 2, or 3) records present transformations expressing
non-crystallographic symmetry.
"""
def __init__(self, line):
"""
Initialize by parsing line
COLUMNS TYPE FIELD DEFINITION
---------------------------------
8-10 int serial Serial number
11-20 float mn1 M11
21-30 float mn2 M12
31-40 float mn3 M13
46-55 float vn V1
60 int iGiven 1 if coordinates for the representations
which are approximately related by the
transformations of the molecule are contained in
the entry. Otherwise, blank.
"""
record = string.strip(line[0:6])
if record == "MTRIX1":
self.serial = int(string.strip(line[7:10]))
self.mn1 = float(string.strip(line[10:20]))
self.mn2 = float(string.strip(line[20:30]))
self.mn3 = float(string.strip(line[30:40]))
self.vn = float(string.strip(line[45:55]))
try: self.iGiven = int(string.strip(line[45:55]))
except ValueError: self.iGiven = None
except IndexError: self.iGiven = None
else: raise ValueError, record
class SCALE3:
""" SCALE3 class
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.
"""
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
"""
record = string.strip(line[0:6])
if record == "SCALE3":
self.sn1 = float(string.strip(line[10:20]))
self.sn2 = float(string.strip(line[20:30]))
self.sn3 = float(string.strip(line[30:40]))
self.un = float(string.strip(line[45:55]))
else: raise ValueError, record
class SCALE2:
""" SCALE2 class
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.
"""
def __init__(self, line):
"""
Initialize by parsing line
COLUMNS TYPE FIELD DEFINITION
---------------------------------
11-20 float sn1 S21
21-30 float sn2 S22
31-40 float sn3 S23
46-55 float un U2
"""
record = string.strip(line[0:6])
if record == "SCALE2":
self.sn1 = float(string.strip(line[10:20]))
self.sn2 = float(string.strip(line[20:30]))
self.sn3 = float(string.strip(line[30:40]))
self.un = float(string.strip(line[45:55]))
else: raise ValueError, record
class SCALE1:
""" SCALE1 class
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.
"""
def __init__(self, line):
"""
Initialize by parsing line
COLUMNS TYPE FIELD DEFINITION
---------------------------------
11-20 float sn1 S11
21-30 float sn2 S12
31-40 float sn3 S13
46-55 float un U1
"""
record = string.strip(line[0:6])
if record == "SCALE1":
self.sn1 = float(string.strip(line[10:20]))
self.sn2 = float(string.strip(line[20:30]))
self.sn3 = float(string.strip(line[30:40]))
self.un = float(string.strip(line[45:55]))
else: raise ValueError, record
class ORIGX2:
""" ORIGX2 class
The ORIGXn (n = 1, 2, or 3) records present the transformation from the
orthogonal coordinates contained in the entry to the submitted
coordinates.
"""
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
"""
record = string.strip(line[0:6])
if record == "ORIGX2":
self.on1 = float(string.strip(line[10:20]))
self.on2 = float(string.strip(line[20:30]))
self.on3 = float(string.strip(line[30:40]))
self.tn = float(string.strip(line[45:55]))
else: raise ValueError, record
class ORIGX3:
""" ORIGX3 class
The ORIGXn (n = 1, 2, or 3) records present the transformation from the
orthogonal coordinates contained in the entry to the submitted
coordinates.
"""
def __init__(self, line):
"""
Initialize by parsing line
COLUMNS TYPE FIELD DEFINITION
---------------------------------
11-20 float on1 O31
21-30 float on2 O32
31-40 float on3 O33
46-55 float tn T3
"""
record = string.strip(line[0:6])
if record == "ORIGX3":
self.on1 = float(string.strip(line[10:20]))
self.on2 = float(string.strip(line[20:30]))
self.on3 = float(string.strip(line[30:40]))
self.tn = float(string.strip(line[45:55]))
else: raise ValueError, record
class ORIGX1:
""" ORIGX1 class
The ORIGXn (n = 1, 2, or 3) records present the transformation from the
orthogonal coordinates contained in the entry to the submitted
coordinates.
"""
def __init__(self, line):
"""
Initialize by parsing line
COLUMNS TYPE FIELD DEFINITION
---------------------------------
11-20 float on1 O11
21-30 float on2 O12
31-40 float on3 O13
46-55 float tn T1
"""
record = string.strip(line[0:6])
if record == "ORIGX1":
self.on1 = float(string.strip(line[10:20]))
self.on2 = float(string.strip(line[20:30]))
self.on3 = float(string.strip(line[30:40]))
self.tn = float(string.strip(line[45:55]))
else: raise ValueError, record
class CRYST1:
""" 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.
"""
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 sGroup Space group.
67-70 int z Z value.
"""
record = string.strip(line[0:6])
if record == "CRYST1":
self.a = float(string.strip(line[6:15]))
self.b = float(string.strip(line[15:24]))
self.c = float(string.strip(line[24:33]))
self.alpha = float(string.strip(line[33:40]))
self.beta = float(string.strip(line[40:47]))
self.gamma = float(string.strip(line[47:54]))
self.sGroup = string.strip(line[55:65])
self.z = int(string.strip(line[66:70]))
else: raise ValueError, record
class SITE:
""" SITE class
The SITE records supply the identification of groups comprising
important sites in the macromolecule.
"""
def __init__(self, line):
"""
Initialize by parsing the line
COLUMNS TYPE FIELD DEFINITION
--------------------------------------------------------------
8-10 int seqNum Sequence number.
12-14 string siteID Site name.
16-17 int numRes Number of residues comprising site.
19-21 string resName1 Residue name for first residue
comprising site.
23 string chainID1 Chain identifier for first residue
comprising site.
24-27 int seq1 Residue sequence number for first
residue comprising site.
28 string iCode1 Insertion code for first residue
comprising site.
30-32 string resName2 Residue name for second residue
comprising site.
34 string chainID2 Chain identifier for second residue
comprising site.
35-38 int seq2 Residue sequence number for second
residue comprising site.
39 string iCode2 Insertion code for second residue
comprising site.
41-43 string resName3 Residue name for third residue
comprising site.
45 string chainID3 Chain identifier for third residue
comprising site.
46-49 int seq3 Residue sequence number for third
residue comprising site.
50 string iCode3 Insertion code for third residue
comprising site.
52-54 string resName4 Residue name for fourth residue
comprising site.
56 string chainID4 Chain identifier for fourth residue
comprising site.
57-60 int seq4 Residue sequence number for fourth
residue comprising site.
61 string iCode4 Insertion code for fourth residue
comprising site.
"""
record = string.strip(line[0:6])
if record == "SITE":
self.seqNum = int(string.strip(line[7:10]))
self.siteID = string.strip(line[11:14])
self.numRes = int(string.strip(line[15:17]))
self.resName1 = string.strip(line[18:21])
self.chainID1 = string.strip(line[22])
self.seq1 = int(string.strip(line[23:27]))
self.iCode1 = string.strip(line[27])
self.resName2 = string.strip(line[29:32])
self.chainID2 = string.strip(line[33])
self.seq2 = int(string.strip(line[34:38]))
self.iCode2 = string.strip(line[38])
self.resName3 = string.strip(line[40:43])
self.chainID3 = string.strip(line[44])
self.seq3 = int(string.strip(line[45:49]))
self.iCode3 = string.strip(line[49])
self.resName4 = string.strip(line[51:54])
self.chainID4 = string.strip(line[55])
self.seq4 = int(string.strip(line[56:60]))
try: self.iCode4 = string.strip(line[60])
except IndexError: self.iCode4 = None
else: raise ValueError, record
class CISPEP:
""" 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.
"""
def __init__(self, line):
"""
Initialize by parsing line
COLUMNS TYPE FIELD DEFINITION
-----------------------------------------------------------
8-10 int serNum Record serial number.
12-14 string pep1 Residue name.
16 string chainID1 Chain identifier.
18-21 int seqNum1 Residue sequence number.
22 string icode1 Insertion code.
26-28 string pep2 Residue name.
30 string chainID2 Chain identifier.
32-35 int seqNum2 Residue sequence number.
36 string icode2 Insertion code.
44-46 int modNum Identifies the specific model.
54-59 float measure Measure of the angle in degrees.
"""
record = string.strip(line[0:6])
if record == "CISPEP":
self.serNum = int(string.strip(line[7:10]))
self.pep1 = string.strip(line[11:14])
self.chainID1 = string.strip(line[15])
self.seqNum1 = int(string.strip(line[17:21]))
self.icode1 = string.strip(line[21])
self.pep2 = string.strip(line[25:28])
self.chainID2 = string.strip(line[29])
self.seqNum2 = int(string.strip(line[31:35]))
self.icode2 = string.strip(line[35])
self.modNum = int(string.strip(line[43:46]))
self.measure = float(string.strip(line[53:59]))
else: raise ValueError, record
class SLTBRG:
""" SLTBRG field
The SLTBRG records specify salt bridges in the entry.
records and is provided here for convenience in searching.
"""
def __init__(self, line):
"""
Initialize by parsing line
COLUMNS TYPE FIELD DEFINITION
-----------------------------------------------------
13-16 string name1 Atom name.
17 string altLoc1 Alternate location indicator.
18-20 string resName1 Residue name.
22 string chainID1 Chain identifier.
23-26 int resSeq1 Residue sequence number.
27 string iCode1 Insertion code.
43-46 string name2 Atom name.
47 string altLoc2 Alternate location indicator.
48-50 string resName2 Residue name.
52 string chainID2 Chain identifier.
53-56 int resSeq2 Residue sequence number.
57 string iCode2 Insertion code.
60-65 string sym1 Symmetry operator for 1st atom.
67-72 string sym2 Symmetry operator for 2nd atom.
"""
record = string.strip(line[0:6])
if record == "SLTBRG":
self.name1 = string.strip(line[12:16])
self.altLoc1 = string.strip(line[16])
self.resName1 = string.strip(line[17:20])
self.chainID1 = string.strip(line[21])
self.resSeq1 = int(string.strip(line[22:26]))
self.iCode1 = string.strip(line[26])
self.name2 = string.strip(line[42:46])
self.altLoc2 = string.strip(line[46])
self.resName2 = string.strip(line[47:50])
self.chainID2 = string.strip(line[51])
self.resSeq2 = int(string.strip(line[52:56]))
self.iCode2 = string.strip(line[56])
self.sym1 = string.strip(line[59:65])
self.sym2 = string.strip(line[66:72])
else: raise ValueError, record
class HYDBND:
""" HYDBND field
The HYDBND records specify hydrogen bonds in the entry.
"""
def __init__(self, line):
"""
Initialize by parsing line
COLUMNS TYPE FIELD DEFINITION
-----------------------------------------------------------
13-16 string name1 Atom name.
17 string altLoc1 Alternate location indicator.
18-20 string resName1 Residue name.
22 string Chain1 Chain identifier.
23-27 int resSeq1 Residue sequence number.
28 string ICode1 Insertion code.
30-33 string nameH Hydrogen atom name.
34 string altLocH Alternate location indicator.
36 string ChainH Chain identifier.
37-41 int resSeqH Residue sequence number.
42 string iCodeH Insertion code.
44-47 string name2 Atom name.
48 string altLoc2 Alternate location indicator.
49-51 string resName2 Residue name.
53 string chainID2 Chain identifier.
54-58 int resSeq2 Residue sequence number.
59 string iCode2 Insertion code.
60-65 string sym1 Symmetry operator for 1st
non-hydrogen atom.
67-72 string sym2 Symmetry operator for 2nd
non-hydrogen atom.
"""
record = string.strip(line[0:6])
if record == "HYDBND":
self.name1 = string.strip(line[12:16])
self.altLoc1 = string.strip(line[16])
self.resName1 = string.strip(line[17:20])
self.Chain1 = string.strip(line[21])
self.resSeq1 = string.strip(line[22:27])
self.ICode1 = string.strip(line[27])
self.nameH = string.strip(line[29:33])
self.altLocH = string.strip(line[33])
self.ChainH = string.strip(line[35])
self.resSeqH = string.strip(line[36:41])
self.ICodeH = string.strip(line[41])
self.name2 = string.strip(line[43:47])
self.altLoc2 = string.strip(line[47])
self.resName2 = string.strip(line[48:51])
self.Chain2 = string.strip(line[52])
self.resSeq2 = string.strip(line[53:58])
self.ICode2 = string.strip(line[58])
self.sym1 = string.strip(line[59:65])
self.sym2 = string.strip(line[66:72])
else: raise ValueError, record
class LINK:
""" 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.
"""
def __init__(self, line):
"""
Initialize by parsing line
COLUMNS TYPE FIELD DEFINITION
-----------------------------------------------------
13-16 string name1 Atom name.
17 string altLoc1 Alternate location indicator.
18-20 string resName1 Residue name.
22 string chainID1 Chain identifier.
23-26 int resSeq1 Residue sequence number.
27 string iCode1 Insertion code.
43-46 string name2 Atom name.
47 string altLoc2 Alternate location indicator.
48-50 string resName2 Residue name.
52 string chainID2 Chain identifier.
53-56 int resSeq2 Residue sequence number.
57 string iCode2 Insertion code.
60-65 string sym1 Symmetry operator for 1st atom.
67-72 string sym2 Symmetry operator for 2nd atom.
"""
record = string.strip(line[0:6])
if record == "LINK":
self.name1 = string.strip(line[12:16])
self.altLoc1 = string.strip(line[16])
self.resName1 = string.strip(line[17:20])
self.chainID1 = string.strip(line[21])
self.resSeq1 = int(string.strip(line[22:26]))
self.iCode1 = string.strip(line[26])
self.name2 = string.strip(line[42:46])
self.altLoc2 = string.strip(line[46])
self.resName2 = string.strip(line[47:50])
self.chainID2 = string.strip(line[51])
self.resSeq2 = int(string.strip(line[52:56]))
self.iCode2 = string.strip(line[56])
self.sym1 = string.strip(line[59:65])
self.sym2 = string.strip(line[66:72])
else: raise ValueError, record
class SSBOND:
""" SSBOND field
The SSBOND record identifies each disulfide bond in protein and
polypeptide structures by identifying the two residues involved in the
bond.
"""
def __init__(self, line):
"""
Initialize by parsing line
COLUMNS TYPE FIELD DEFINITION
-----------------------------------------------------
8 - 10 int serNum Serial number.
16 string chainID1 Chain identifier.
18 - 21 int seqNum1 Residue sequence number.
22 string icode1 Insertion code.
30 string chainID2 Chain identifier.
32 - 35 int seqNum2 Residue sequence number.
36 string icode2 Insertion code.
60 - 65 string sym1 Symmetry operator for 1st residue.
67 - 72 string sym2 Symmetry operator for 2nd residue.
"""
record = string.strip(line[0:6])
if record == "SSBOND":
self.serNum = int(string.strip(line[7:10]))
self.chainID1 = string.strip(line[15])
self.seqNum1 = int(string.strip(line[17:21]))
self.icode1 = string.strip(line[21])
self.chainID2 = string.strip(line[29])
self.seqNum2 = int(string.strip(line[31:35]))
self.icode2 = string.strip(line[35])
self.sym1 = string.strip(line[59:65])
self.sym2 = string.strip(line[66:72])
else: raise ValueError, record
class TURN:
""" TURN field
The TURN records identify turns and other short loop turns which
normally connect other secondary structure segments.
"""
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 turnId Turn identifier
16-18 string initResName Residue name of initial residue in
turn.
20 string initChainId Chain identifier for the chain
containing this turn.
21-24 int initSeqNum Sequence number of initial residue in
turn.
25 string initICode Insertion code of initial residue in
turn.
27-29 string endResName Residue name of terminal residue of
turn.
31 string endChainId Chain identifier for the chain
containing this turn.
32-35 int endSeqNum Sequence number of terminal residue of
turn.
36 string endICode Insertion code of terminal residue of
turn.
41-70 string comment Associated comment.
"""
record = string.strip(line[0:6])
if record == "TURN":
self.seq = int(string.strip(line[7:10]))
self.turnId = string.strip(line[11:14])
self.initResName = string.strip(line[15:18])
self.initChainId = string.strip(line[19])
self.initSeqNum = int(string.strip(line[20:24]))
self.initICode = string.strip(line[24])
self.endResName = string.strip(line[26:29])
self.endChainId = string.strip(line[30])
self.endSeqNum = int(string.strip(line[31:35]))
self.endICode = string.strip(line[35])
self.comment = string.strip(line[40:70])
else: raise ValueError, record
class SHEET:
""" 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.
"""
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 sheetID Sheet identifier.
15 - 16 int numStrands Number of strands in sheet.
18 - 20 string initResName Residue name of initial residue.
22 string initChainID Chain identifier of initial residue in
strand.
23 - 26 int initSeqNum Sequence number of initial residue in
strand.
27 string initICode Insertion code of initial residue in
strand.
29 - 31 string endResName Residue name of terminal residue.
33 string endChainID Chain identifier of terminal residue.
34 - 37 int endSeqNum Sequence number of terminal residue.
38 string endICode Insertion code of terminal residue.
39 - 40 int sense Sense of strand with respect to
previous strand in the sheet. 0 if
first strand, 1 if parallel, -1 if
anti-parallel.
42 - 45 string curAtom Registration. Atom name in current
strand.
46 - 48 string curResName Registration. Residue name in current
strand.
50 string curChainId Registration. Chain identifier in
current strand.
51 - 54 int curResSeq Registration. Residue sequence number
in current strand.
55 string curICode Registration. Insertion code in current
strand.
57 - 60 string prevAtom Registration. Atom name in previous
strand.
61 - 63 string prevResName Registration. Residue name in previous
strand.
65 string prevChainId Registration. Chain identifier in
previous strand.
66 - 69 int prevResSeq Registration. Residue sequence number
in previous strand.
70 string prevICode Registration. Insertion code in
previous strand.
"""
record = string.strip(line[0:6])
if record == "SHEET":
self.strand = int(string.strip(line[7:10]))
self.sheetID = string.strip(line[11:14])
self.numStrands = int(string.strip(line[14:16]))
self.initResName = string.strip(line[17:20])
self.initChainID = string.strip(line[21])
self.initSeqNum = int(string.strip(line[22:26]))
self.initICode = string.strip(line[26])
self.endResName = string.strip(line[28:31])
self.endChainID = string.strip(line[32])
self.endSeqNum = int(string.strip(line[33:37]))
self.endICode = string.strip(line[37])
self.sense = int(string.strip(line[38:40]))
try:
self.curAtom = string.strip(line[41:45])
self.curResName = string.strip(line[45:48])
self.curChainID = string.strip(line[49])
try: self.curResSeq = int(string.strip(line[50:54]))
except ValueError: self.curResSeq = None
self.curICode = string.strip(line[54])
self.prevAtom = string.strip(line[56:60])
self.prevResName = string.strip(line[60:63])
self.prevChainID = string.strip(line[64])
try: self.prevResSeq = int(string.strip(line[65:69]))
except ValueError: self.prevResSeq = None
self.prevICode = string.strip(line[69])
except IndexError:
self.curAtom = None
self.curResName = None
self.curChainID = None
self.curResSeq = None
self.curICode = None
self.prevAtom = None
self.prevResName = None
self.prevChainID = None
self.prevResSeq = None
self.prevICode = None
else: raise ValueError, record
class HELIX:
""" 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.
"""
def __init__(self, line):
"""
Initialize by parsing line
COLUMNS TYPE FIELD DEFINITION
------------------------------------------------------
8-10 int serNum Serial number of the helix. This
starts at 1 and increases
incrementally.
12-14 string helixID Helix identifier. In addition to a
serial number, each helix is given an
alphanumeric character helix identifier.
16-18 string initResName Name of the initial residue.
20 string initChainID Chain identifier for the chain
containing this helix.
22-25 int initSeqNum Sequence number of the initial residue.
26 string initICode Insertion code of the initial residue.
28-30 string endResName Name of the terminal residue of
the helix.
32 string endChainID Chain identifier for the chain
containing this helix.
34-37 int endSeqNum Sequence number of the terminal residue.
38 string endICode Insertion code of the terminal residue.
39-40 int helixClass Helix class (see below).
41-70 string comment Comment about this helix.
72-76 int length Length of this helix.
"""
record = string.strip(line[0:6])
if record == "HELIX":
self.serNum = int(string.strip(line[7:10]))
self.helixID = string.strip(line[11:14])
self.initResName = string.strip(line[15:18])
self.initChainID = string.strip(line[19])
self.initSeqNum = int(string.strip(line[21:25]))
self.initICode = string.strip(line[25])
self.endResName = string.strip(line[27:30])
self.endChainID = string.strip(line[31])
self.endSeqNum = int(string.strip(line[33:37]))
self.endICode = string.strip(line[37])
try: self.helixClass = int(string.strip(line[38:40]))
except ValueError: self.helixClass = None
self.comment = string.strip(line[40:70])
try: self.length = int(string.strip(line[71:76]))
except ValueError: self.length = None
else: raise ValueError, record
class FORMUL:
""" FORMUL field
The FORMUL record presents the chemical formula and charge of a
non-standard group.
"""
def __init__(self, line):
"""
Initialize by parsing line
COLUMNS TYPE FIELD DEFINITION
-----------------------------------------------------
9-10 int compNum Component number
13-15 string hetID Het identifier
19 string asterisk * for water
20-70 string text Chemical formula
"""
record = string.strip(line[0:6])
if record == "FORMUL":
self.compNum = int(string.strip(line[8:10]))
self.hetID = string.strip(line[12:15])
self.asterisk = string.strip(line[19])
self.text = string.strip(line[19:70])
else: raise ValueError, record
class HETSYN:
""" HETSYN field
This record provides synonyms, if any, for the compound in the
corresponding (i.e., same hetID) HETNAM record. This is to allow
greater flexibility in searching for HET groups.
"""
def __init__(self, line):
"""
Initialize by parsing line
COLUMNS TYPE FIELD DEFINITION
-----------------------------------------------------
12-14 string hetID Het identifier, right-justified.
16-70 string hetSynonyms List of synonyms
"""
record = string.strip(line[0:6])
if record == "HETSYN":
self.hetID = string.strip(line[11:14])
self.hetSynonyms = string.strip(line[15:70])
else: raise ValueError, record
class HETNAM:
""" HETNAM field
This record gives the chemical name of the compound with the given
hetID.
"""
def __init__(self, line):
"""
Initialize by parsing line
COLUMNS TYPE FIELD DEFINITION
-----------------------------------------------------
12-14 string hetID Het identifier, right-justified.
16-70 string text Chemical name.
"""
record = string.strip(line[0:6])
if record == "HETNAM":
self.hetID = string.strip(line[11:14])
self.text = string.strip(line[15:70])
else: raise ValueError, record
class HET:
""" HET field
HET records are used to describe non-standard residues, such as
prosthetic groups, inhibitors, solvent molecules, and ions for which
coordinates are supplied. Groups are considered HET if they are:
- not one of the standard amino acids, and
- not one of the nucleic acids (C, G, A, T, U, and I), and
- not one of the modified versions of nucleic acids (+C, +G, +A, +T,
+U, and +I), and
- not an unknown amino acid or nucleic acid where UNK is used to
indicate the unknown residue name.
Het records also describe heterogens for which the chemical identity is
unknown, in which case the group is assigned the hetID UNK.
"""
def __init__(self, line):
"""
Initialize by parsing line
COLUMNS TYPE FIELD DEFINITION
--------------------------------------------------------
8-10 string hetID Het identifier, right-justified.
13 string ChainID Chain identifier.
14-17 int seqNum Sequence number.
18 string iCode Insertion code.
21-25 int numHetAtoms Number of HETATM records for the
31-70 string text Text describing Het group.
"""
record = string.strip(line[0:6])
if record == "HET":
self.hetID = string.strip(line[7:10])
self.chainID = string.strip(line[12])
try: self.seqNum = int(string.strip(line[13]))
except ValueError: self.seqNum = None
self.iCode = string.strip(line[17])
self.numHetAtoms = int(string.strip(line[20:25]))
self.text = string.strip(line[30:70])
else: raise ValueError, record
class MODRES:
""" 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.
"""
def __init__(self, line):
"""
Initialize by parsing a line
COLUMNS TYPE FIELD DEFINITION
---------------------------------------
8-11 string idCode ID code of this entry.
13-15 string resName Residue name used in this entry.
17 string chainID Chain identifier.
19-22 int seqNum Sequence number.
23 string iCode Insertion code.
25-27 string stdRes Standard residue name.
30-70 string comment Description of the residue modification.
"""
record = string.strip(line[0:6])
if record == "MODRES":
string.idCode = string.strip(line[7:11])
string.resName = string.strip(line[12:15])
string.chainID = string.strip(line[16])
string.seqNum = int(string.strip(line[18:22]))
string.iCode = string.strip(line[22])
string.stdRes = string.strip(line[24:27])
string.comment = string.strip(line[29:70])
else: raise ValueError, record
class SEQRES:
""" SEQRES field
SEQRES records contain the amino acid or nucleic acid sequence of
residues in each chain of the macromolecule that was studied.
"""
def __init__(self, line):
"""
Initialize by parsing a line
COLUMNS TYPE FIELD DEFINITION
-----------------------------------------------------
9-10 int serNum Serial number of the SEQRES record for the
current chain. Starts at 1 and increments
by one each line. Reset to 1 for each
chain.
12 string chainID Chain identifier. This may be any single
legal character, including a blank which is
used if there is only one chain.
14-17 int numRes Number of residues in the chain. This
value is repeated on every record.
20-22 string resName Residue name.
24-26 string resName Residue name.
28-30 string resName Residue name.
32-34 string resName Residue name.
36-38 string resName Residue name.
40-42 string resName Residue name.
44-46 string resName Residue name.
48-50 string resName Residue name.
52-54 string resName Residue name.
56-58 string resName Residue name.
60-62 string resName Residue name.
64-66 string resName Residue name.
68-70 string resName Residue name.
"""
record = string.strip(line[0:6])
if record == "SEQRES":
self.serNum = int(string.strip(line[8:10]))
self.chainID = string.strip(line[11])
self.numRes = int(string.strip(line[13:17]))
self.resName = []
self.resName.append(string.strip(line[19:22]))
self.resName.append(string.strip(line[23:26]))
self.resName.append(string.strip(line[27:30]))
self.resName.append(string.strip(line[31:34]))
self.resName.append(string.strip(line[35:38]))
self.resName.append(string.strip(line[39:42]))
self.resName.append(string.strip(line[43:46]))
self.resName.append(string.strip(line[47:50]))
self.resName.append(string.strip(line[51:54]))
self.resName.append(string.strip(line[55:58]))
self.resName.append(string.strip(line[59:62]))
self.resName.append(string.strip(line[63:66]))
self.resName.append(string.strip(line[67:70]))
else: raise ValueError, record
class SEQADV:
""" 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.
"""
def __init__(self, line):
"""
Initialize by parsing line
COLUMNS TYPE FIELD DEFINITION
-----------------------------------------------------
8-11 string idCode ID code of this entry.
13-15 string resName Name of the PDB residue in conflict.
17 string chainID PDB chain identifier.
19-22 int seqNum PDB sequence number.
23 string iCode PDB insertion code.
25-28 string database Sequence database name.
30-38 string dbIdCode Sequence database accession
number.
40-42 string dbRes Sequence database residue name.
44-48 int dbSeq Sequence database sequence number.
50-70 string conflict Conflict comment.
"""
record = string.strip(line[0:6])
if record == "SEQADV":
self.idCode = string.strip(line[7:11])
self.resName = string.strip(line[12:15])
self.chainID = string.strip(line[16])
try: self.seqNum = int(string.strip(line[19:22]))
except ValueError: self.seqNum = None
self.iCode = string.strip(line[22])
self.database = string.strip(line[24:28])
self.dbIdCode = string.strip(line[29:38])
self.dbRes = string.strip(line[39:42])
self.dbSeq = int(string.strip(line[43:48]))
self.conflict = string.strip(line[49:70])
else: raise ValueError, record
class DBREF:
""" 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.
"""
def __init__(self, line):
"""
Initialize by parsing a line.
COLUMNS TYPE FIELD DEFINITION
------------------------------------------------------
8-11 string idCode ID code of this entry.
13 string chainID Chain identifier.
15-18 int seqBegin Initial sequence number of the PDB
sequence segment.
19 string insertBegin Initial insertion code of the PDB
sequence segment.
21-24 int seqEnd Ending sequence number of the PDB
sequence segment.
25 string insertEnd Ending insertion code of the PDB
sequence segment.
27-32 string database Sequence database name. "PDB" when
a corresponding sequence database
entry has not been identified.
34-41 string dbAccession Sequence database accession code.
For GenBank entries, this is the
NCBI gi number.
43-54 string dbIdCode Sequence database identification
code. For GenBank entries, this is
the accession code.
56-60 int dbseqBegin Initial sequence number of the
database seqment.
61 string dbinsBeg Insertion code of initial residue
of the segment, if PDB is the
reference.
63-67 int dbseqEnd Ending sequence number of the
database segment.
68 string dbinsEnd Insertion code of the ending
residue of the segment, if PDB is
the reference.
"""
record = string.strip(line[0:6])
if record == "DBREF":
self.idCode = string.strip(line[7:11])
self.chainID = string.strip(line[12])
self.seqBegin = int(string.strip(line[14:18]))
self.insertBegin = string.strip(line[18])
self.seqEnd = int(string.strip(line[20:24]))
self.insertEnd = string.strip(line[24])
self.database = string.strip(line[26:32])
self.dbAccession = string.strip(line[33:41])
self.dbIdCode = string.strip(line[42:54])
self.dbseqBegin = int(string.strip(line[55:60]))
self.dbinsBeg = string.strip(line[60])
self.dbseqEnd = int(string.strip(line[62:67]))
try: self.dbinsEnd = string.strip(line[67])
except IndexError: self.dbinsEnd = None
else: raise ValueError, record
class REMARK:
""" REMARK field
REMARK records present experimental details, annotations, comments, and
information not included in other records. In a number of cases,
REMARKs are used to expand the contents of other record types. A new
level of structure is being used for some REMARK records. This is
expected to facilitate searching and will assist in the conversion to a
relational database.
"""
def __init__(self, line):
"""
Initialize by parsing line
"""
record = string.strip(line[0:6])
if record == "REMARK":
self.remarkNum = int(string.strip(line[7:10]))
self.remarkDict = {}
remarkText = line[11:70]
if self.remarkNum == 1:
subfield = string.strip(line[11:20])
if subfield == "REFERENCE":
self.remarkDict["refNum"] = int(string.strip(line[21:70]))
elif subfield == "AUTH":
self.remarkDict["authorList"] = string.strip(line[19:70])
elif subfield == "TITL":
self.remarkDict["title"] = string.strip(line[19:70])
elif subfield == "EDIT":
self.remarkDict["editorList"] = string.strip(line[19:70])
elif subfield == "REF":
self.remarkDict["ref"] = string.strip(line[19:66])
elif subfield == "PUBL":
self.remarkDict["pub"] = string.strip(line[19:70])
elif subfield == "REFN":
self.remarkDict["refn"] = string.strip(line[19:70])
elif self.remarkNum == 2:
restr = string.strip(line[22:27])
try: self.remarkDict["resolution"] = float(restr)
except ValueError:
self.remarkDict["comment"] = string.strip(line[11:70])
else:
self.remarkDict["text"] = string.strip(line[11:70])
class JRNL:
""" 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.
"""
def __init__(self, line):
"""
Initialize by parsing line
COLUMNS TYPE FIELD DEFINITION
-----------------------------------------------
13-70 string text See Details on web.
"""
record = string.strip(line[0:6])
if record == "JRNL":
self.text = string.strip(line[12:70])
else: raise ValueError, record
class SPRSDE:
""" 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.
"""
def __init__(self, line):
"""
Initialize by parsing line
COLUMNS TYPE FIELD DEFINITION
-----------------------------------------------
12-20 string sprsdeDate Date this entry superseded the
listed entries.
22-25 string idCode ID code of this entry.
32-35 string sIdCode ID code of a superseded entry.
37-40 string sIdCode ID code of a superseded entry.
42-45 string sIdCode ID code of a superseded entry.
47-50 string sIdCode ID code of a superseded entry.
52-55 string sIdCode ID code of a superseded entry.
57-60 string sIdCode ID code of a superseded entry.
62-65 string sIdCode ID code of a superseded entry.
67-70 string sIdCode ID code of a superseded entry.
"""
record = string.strip(line[0:6])
if record == "SPRSDE":
self.sprsdeDate = string.strip(line[11:20])
self.idCode = string.strip(line[21:25])
self.sIdCodes = []
self.sIdCodes.append(string.strip(line[31:35]))
self.sIdCodes.append(string.strip(line[36:40]))
self.sIdCodes.append(string.strip(line[41:45]))
self.sIdCodes.append(string.strip(line[46:50]))
self.sIdCodes.append(string.strip(line[51:55]))
self.sIdCodes.append(string.strip(line[56:60]))
self.sIdCodes.append(string.strip(line[61:65]))
self.sIdCodes.append(string.strip(line[66:70]))
else: raise ValueError, record
class REVDAT:
""" REVDAT field
REVDAT records contain a history of the modifications made to an entry
since its release.
"""
def __init__(self, line):
"""
Initialize by parsing a line.
COLUMNS TYPE FIELD DEFINITION
-------------------------------------------------------
8-10 int modNum Modification number.
14-22 string modDate Date of modification (or release for
new entries).
24-28 string modId Identifies this particular modification.
It links to the archive used internally by
PDB.
32 int modType An integer identifying the type of
modification. In case of revisions
with more than one possible modType,
the highest value applicable will be
assigned.
40-45 string record Name of the modified record.
47-52 string record Name of the modified record.
54-59 string record Name of the modified record.
61-66 string record Name of the modified record.
"""
record = string.strip(line[0:6])
if record == "REVDAT":
self.modNum = int(string.strip(line[7:10]))
self.modDate = string.strip(line[13:22])
self.modId = string.strip(line[23:28])
self.modType = int(string.strip(line[31]))
self.records = []
self.records.append(string.strip(line[39:45]))
self.records.append(string.strip(line[46:52]))
self.records.append(string.strip(line[53:59]))
self.records.append(string.strip(line[60:66]))
else: raise ValueError, record
class AUTHOR:
""" AUTHOR field
The AUTHOR record contains the names of the people responsible for the
contents of the entry.
"""
def __init__(self, line):
"""
Initialize by parsing a line
COLUMNS TYPE FIELD DEFINITION
--------------------------------------------------
11-70 string authorList List of the author names, separated by
commas
"""
record = string.strip(line[0:6])
if record == "AUTHOR":
self.authorList = string.strip(line[10:70])
else: raise ValueError, record
class EXPDTA:
""" 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
"""
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
"""
record = string.strip(line[0:6])
if record == "EXPDTA":
self.technique = string.strip(line[10:70])
else: raise ValueError, record
class KEYWDS:
""" 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.
"""
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
"""
record = string.strip(line[0:6])
if record == "KEYWDS":
self.keywds = string.strip(line[10:70])
else: raise ValueError, record
class SOURCE:
""" 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.
"""
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
"""
record = string.strip(line[0:6])
if record == "SOURCE":
self.source = string.strip(line[10:70])
else: raise ValueError, record
class COMPND:
""" 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.
"""
def __init__(self, line):
"""
Initialize by parsing a line
COLUMNS TYPE FIELD DEFINITION
--------------------------------------------------
11-70 string compound Description of the molecular list
components.
"""
record = string.strip(line[0:6])
if record == "COMPND":
self.compound = string.strip(line[10:70])
else: raise ValueError, record
class CAVEAT:
""" CAVEAT field
CAVEAT warns of severe errors in an entry. Use caution when using an
entry containing this record.
"""
def __init__(self, line):
"""
Initialize by parsing line.
COLUMNS TYPE FIELD DEFINITION
----------------------------------------------------
12-15 string idCode PDB ID code of this entry.
20-70 string comment Free text giving the reason for the
CAVEAT.
"""
record = string.strip(line[0:6])
if record == "CAVEAT":
self.idCode = string.strip(line[11:15])
self.comment = string.strip(line[19:70])
else: raise ValueError, record
class TITLE:
""" 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.
"""
def __init__(self, line):
"""
Initialize by parsing a line.
COLUMNS TYPE FIELD DEFINITION
---------------------------------------------
11-70 string title Title of the experiment
"""
record = string.strip(line[0:6])
if record == "TITLE":
self.title = string.strip(line[10:70])
else: raise ValueError, record
class OBSLTE:
""" 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.
"""
def __init__(self, line):
"""
Initialize by parsing a line.
COLUMNS TYPE FIELD DEFINITION
-----------------------------------------------
12-20 string repDate Date that this entry was replaced.
22-25 string idCode ID code of this entry.
32-35 string rIdCode ID code of entry that replaced
this one.
37-40 string rIdCode ID code of entry that replaced
this one.
42-45 string rIdCode ID code of entry that replaced
this one.
47-50 string rIdCode ID code of entry that replaced
this one.
52-55 string rIdCode ID code of entry that replaced
this one.
57-60 string rIdCode ID code of entry that replaced
this one.
62-65 string rIdCode ID code of entry that replaced
this one.
67-70 string rIdCode ID code of entry that replaced
this one.
"""
record = string.strip(line[0:6])
if record == "OBSLTE":
self.repDate = string.strip(line[11:20])
self.idCode = string.strip(line[21:25])
self.rIdCodes = []
self.rIdCodes.append(string.strip(line[31:35]))
self.rIdCodes.append(string.strip(line[36:40]))
self.rIdCodes.append(string.strip(line[41:45]))
self.rIdCodes.append(string.strip(line[46:50]))
self.rIdCodes.append(string.strip(line[51:55]))
self.rIdCodes.append(string.strip(line[56:60]))
self.rIdCodes.append(string.strip(line[61:65]))
self.rIdCodes.append(string.strip(line[67:70]))
else: raise ValueError, record
class HEADER:
""" HEADER field
The HEADER record uniquely identifies a PDB entry through the idCode
field. This record also provides a classification for the entry.
Finally, it contains the date the coordinates were deposited at the
PDB. """
def __init__(self, line):
"""
Initialize by parsing a line.
COLUMNS TYPE FIELD DEFINITION
---------------------------------------------------------
11-50 string classification Classifies the molecule(s)
51-59 string depDate Deposition date. This is the date
the coordinates were received by
the PDB
63-66 string idCode This identifier is unique within PDB
"""
record = string.strip(line[0:6])
if record == "HEADER":
self.classification = string.strip(line[10:50])
self.depDate = string.strip(line[50:59])
self.IDcode = string.strip(line[62:66])
else: raise ValueError, record
def readAtom(line):
"""
If the ATOM/HETATM is not column-formatted, try to get some
information by parsing whitespace from the right. Look for
five floating point numbers followed by the residue number.
Parameters
line: The line to parse(string)
if record == ATOM:
self.serial = int(string.strip(line[6:11]))
self.name = string.strip(line[12:16])
self.altLoc = string.strip(line[16])
self.resName = string.strip(line[17:20])
self.chainID = string.strip(line[21])
self.resSeq = int(string.strip(line[22:26]))
self.iCode = string.strip(line[26])
self.x = float(string.strip(line[30:38]))
self.y = float(string.strip(line[38:46]))
self.z = float(string.strip(line[46:54]))
try:
self.occupancy = float(string.strip(line[54:60]))
self.tempFactor = float(string.strip(line[60:66]))
self.segID = string.strip(line[72:76])
self.element = string.strip(line[76:78])
self.charge = string.strip(line[78:80])
except ValueError, IndexError:
self.occupancy = 0.00
self.tempFactor = 0.00
self.segID = 0
self.element = 0
self.charge = 0
else: raise ValueError, record
"""
# Try to find 5 consecutive floats
words = string.split(line)
size = len(words) - 1
consec = 0
for i in range(size):
entry = words[size - i]
try:
val = float(entry)
consec = consec + 1
if consec == 5:
break
except ValueError:
consec = 0
record = string.strip(line[0:6])
newline = line[0:22]
newline = newline + string.rjust(words[size-i-1],4)
newline = newline + string.rjust("",3)
newline = newline + string.rjust(words[size-i],8)
newline = newline + string.rjust(words[size-i+1],8)
newline = newline + string.rjust(words[size-i+2],8)
newline = newline + string.rjust(words[size-i+3],6)
newline = newline + string.rjust(words[size-i+4],6)
cmdstr = "%s(newline)" % record
obj = eval(cmdstr)
return obj
def readPDB(file):
""" Parse PDB-format data into array of Atom objects.
Parameters
file: open file object
Returns (dict, errlist)
dict: a dictionary indexed by PDB record names
errlist: a list of record names that couldn't be parsed
"""
pdblist = [] # Array of parsed lines (as objects)
errlist = [] # List of records we can't parse
while 1:
line = string.strip(file.readline())
if line == '': break
# We assume we have a method for each PDB record and can therefore
# parse them automatically
try:
record = string.strip(line[0:6])
if record not in errlist:
cmdstr = "%s(line)" % record
obj = eval(cmdstr)
pdblist.append(obj)
except NameError, details:
errlist.append(record)
except StandardError, details:
if record == "ATOM" or record == "HETATM":
try:
obj = readAtom(line)
pdblist.append(obj)
except StandardError, details:
sys.stderr.write("Error parsing line: %s\n" % details)
sys.stderr.write("<%s>\n" % string.strip(line))
elif record == "SITE" or record == "TURN":
pass
elif record == "SSBOND" or record == "LINK":
sys.stderr.write("Warning -- ignoring record: \n")
sys.stderr.write("<%s>\n" % string.strip(line))
else:
sys.stderr.write("Error parsing line: %s\n" % details)
sys.stderr.write("<%s>\n" % string.strip(line))
return pdblist, errlist
def getRandom():
""" Download a random PDB and return the path name.
Returns
path name of downloaded file
"""
import os, random
URL = "ftp://ftp.rcsb.org/pub/pdb/data/structures/all/pdb/"
pdblines = os.popen("ncftpls %s" % URL).readlines()
pdbline = string.join(pdblines)
pdbline = string.replace(pdbline, "\n", "")
pdbline = string.replace(pdbline, "@", "")
pdbline = string.strip(pdbline)
pdblist = string.split(pdbline)
pdbZ = random.choice(pdblist)
os.popen("ncftpget %s/%s" % (URL, pdbZ))
os.popen("uncompress %s" % pdbZ)
return pdbZ[:-2]
def main():
""" Main driver for testing. Parses set number of random PDBs """
npdb = 1
sys.stdout.write("Testing %d PDBs...\n" % npdb)
for i in range(0, npdb):
sys.stdout.write("Getting random PDB...\n")
path = getRandom()
sys.stdout.write("Parsing %s...\n" % path)
pdbdict, errlist = readPDB(open(path, "rU"))
if len(errlist) > 0: sys.stdout.write("\tSkipped records: %s\n" % errlist)
sys.stdout.write("\tNo skipped records.\n")
if __name__ == "__main__": main()
