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<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<html><head><title>Python: module src.structures</title>
<meta charset="utf-8">
</head><body bgcolor="#f0f0f8">
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="heading">
<tr bgcolor="#7799ee">
<td valign=bottom> <br>
<font color="#ffffff" face="helvetica, arial"> <br><big><big><strong><a href="src.html"><font color="#ffffff">src</font></a>.structures</strong></big></big> (28 February 2006)</font></td
><td align=right valign=bottom
><font color="#ffffff" face="helvetica, arial"><a href=".">index</a><br><a href="file:/Users/d3y382/workspaces/apbs-pdb2pqr/pdb2pqr/src/structures.py">/Users/d3y382/workspaces/apbs-pdb2pqr/pdb2pqr/src/structures.py</a></font></td></tr></table>
<p><tt>Structures for PDB2PQR<br>
<br>
This module contains the structure objects used in PDB2PQR and their<br>
associated methods.<br>
<br>
----------------------------<br>
<br>
PDB2PQR -- An automated pipeline for the setup, execution, and analysis of<br>
Poisson-Boltzmann electrostatics calculations<br>
<br>
Copyright (c) 2002-2011, Jens Erik Nielsen, University College Dublin; <br>
Nathan A. Baker, Battelle Memorial Institute, Developed at the Pacific <br>
Northwest National Laboratory, operated by Battelle Memorial Institute, <br>
Pacific Northwest Division for the U.S. Department Energy.; <br>
Paul Czodrowski & Gerhard Klebe, University of Marburg.<br>
<br>
All rights reserved.<br>
<br>
Redistribution and use in source and binary forms, with or without modification, <br>
are permitted provided that the following conditions are met:<br>
<br>
* Redistributions of source code must retain the above copyright notice, <br>
this list of conditions and the following disclaimer.<br>
* Redistributions in binary form must reproduce the above copyright notice, <br>
this list of conditions and the following disclaimer in the documentation <br>
and/or other materials provided with the distribution.<br>
* Neither the names of University College Dublin, Battelle Memorial Institute,<br>
Pacific Northwest National Laboratory, US Department of Energy, or University<br>
of Marburg nor the names of its contributors may be used to endorse or promote<br>
products derived from this software without specific prior written permission.<br>
<br>
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND <br>
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED <br>
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. <br>
IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, <br>
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, <br>
BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, <br>
DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF <br>
LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE <br>
OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED <br>
OF THE POSSIBILITY OF SUCH DAMAGE.<br>
<br>
----------------------------</tt></p>
<p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#aa55cc">
<td colspan=3 valign=bottom> <br>
<font color="#ffffff" face="helvetica, arial"><big><strong>Modules</strong></big></font></td></tr>
<tr><td bgcolor="#aa55cc"><tt> </tt></td><td> </td>
<td width="100%"><table width="100%" summary="list"><tr><td width="25%" valign=top><a href="copy.html">copy</a><br>
<a href="math.html">math</a><br>
</td><td width="25%" valign=top><a href="os.html">os</a><br>
<a href="string.html">string</a><br>
</td><td width="25%" valign=top><a href="sys.html">sys</a><br>
</td><td width="25%" valign=top></td></tr></table></td></tr></table><p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#ee77aa">
<td colspan=3 valign=bottom> <br>
<font color="#ffffff" face="helvetica, arial"><big><strong>Classes</strong></big></font></td></tr>
<tr><td bgcolor="#ee77aa"><tt> </tt></td><td> </td>
<td width="100%"><dl>
<dt><font face="helvetica, arial"><a href="src.pdb.html#ATOM">src.pdb.ATOM</a>(<a href="src.pdb.html#BaseRecord">src.pdb.BaseRecord</a>)
</font></dt><dd>
<dl>
<dt><font face="helvetica, arial"><a href="src.structures.html#Atom">Atom</a>
</font></dt></dl>
</dd>
<dt><font face="helvetica, arial"><a href="src.structures.html#Chain">Chain</a>
</font></dt><dt><font face="helvetica, arial"><a href="src.structures.html#Residue">Residue</a>
</font></dt></dl>
<p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#ffc8d8">
<td colspan=3 valign=bottom> <br>
<font color="#000000" face="helvetica, arial"><a name="Atom">class <strong>Atom</strong></a>(<a href="src.pdb.html#ATOM">src.pdb.ATOM</a>)</font></td></tr>
<tr bgcolor="#ffc8d8"><td rowspan=2><tt> </tt></td>
<td colspan=2><tt>Class <a href="#Atom">Atom</a><br>
<br>
The <a href="#Atom">Atom</a> class inherits off the <a href="src.pdb.html#ATOM">ATOM</a> object in pdb.py. It is used<br>
for adding fields not found in the pdb that may be useful for analysis.<br>
Also simplifies code by combining <a href="src.pdb.html#ATOM">ATOM</a> and HETATM objects into a<br>
single class.<br> </tt></td></tr>
<tr><td> </td>
<td width="100%"><dl><dt>Method resolution order:</dt>
<dd><a href="src.structures.html#Atom">Atom</a></dd>
<dd><a href="src.pdb.html#ATOM">src.pdb.ATOM</a></dd>
<dd><a href="src.pdb.html#BaseRecord">src.pdb.BaseRecord</a></dd>
<dd><a href="__builtin__.html#object">__builtin__.object</a></dd>
</dl>
<hr>
Methods defined here:<br>
<dl><dt><a name="Atom-__init__"><strong>__init__</strong></a>(self, atom, type, residue)</dt><dd><tt>Initialize the new <a href="#Atom">Atom</a> object by using the old object.<br>
<br>
Parameters<br>
atom: The original <a href="src.pdb.html#ATOM">ATOM</a> object (<a href="src.pdb.html#ATOM">ATOM</a>)<br>
type: Either <a href="src.pdb.html#ATOM">ATOM</a> or HETATM (string)<br>
residue: A pointer back to the parent residue object (<a href="#Residue">Residue</a>)</tt></dd></dl>
<dl><dt><a name="Atom-__str__"><strong>__str__</strong></a>(self)</dt><dd><tt>Returns a string of the new atom type. Uses the <a href="src.pdb.html#ATOM">ATOM</a> string<br>
output but changes the first field to either by <a href="src.pdb.html#ATOM">ATOM</a> or<br>
HETATM as necessary.<br>
<br>
This is used to create the output for pqr files! No touchy!<br>
<br>
Returns<br>
str: String with <a href="src.pdb.html#ATOM">ATOM</a>/HETATM field set appropriately</tt></dd></dl>
<dl><dt><a name="Atom-addBond"><strong>addBond</strong></a>(self, bondedatom)</dt><dd><tt>Add a bond to the list of bonds<br>
<br>
Parameters:<br>
bondedatom: The atom to bond to (<a href="#Atom">Atom</a>)</tt></dd></dl>
<dl><dt><a name="Atom-get"><strong>get</strong></a>(self, name)</dt><dd><tt>Get a member of the <a href="#Atom">Atom</a> class<br>
<br>
Parameters<br>
name: The name of the member (string)<br>
Possible Values<br>
type: The type of <a href="#Atom">Atom</a> (either <a href="src.pdb.html#ATOM">ATOM</a> or HETATM)<br>
serial: <a href="#Atom">Atom</a> serial number<br>
name: <a href="#Atom">Atom</a> name<br>
altLoc: Alternate location<br>
resName: <a href="#Residue">Residue</a> name<br>
chainID: <a href="#Chain">Chain</a> identifier<br>
resSeq: <a href="#Residue">Residue</a> sequence number<br>
iCode: Code for insertion of residues<br>
x: Orthogonal coordinates for X in Angstroms.<br>
y: Orthogonal coordinates for Y in Angstroms.<br>
z: Orthogonal coordinates for Z in Angstroms.<br>
occupancy: Occupancy<br>
tempFactor: Temperature Factor<br>
segID: Segment identifier<br>
element: Element symbol<br>
charge: Charge on the atom<br>
bonds: The bonds associated with the atom<br>
interbonds: The intrabonds associated with the atom<br>
extrabonds: The extrabonds assocaited with the atom<br>
residue: The parent residue of the atom<br>
radius: The radius of the atom<br>
ffcharge: The forcefield charge on the atom<br>
hdonor: Whether the atom is a hydrogen donor<br>
hacceptor: Whether the atom is a hydrogen acceptor<br>
Returns<br>
item: The value of the member</tt></dd></dl>
<dl><dt><a name="Atom-getCommonStringRep"><strong>getCommonStringRep</strong></a>(self, chainflag<font color="#909090">=False</font>)</dt><dd><tt>Returns a string of the common column of the new atom type. <br>
Uses the <a href="src.pdb.html#ATOM">ATOM</a> string output but changes the first field <br>
to either by <a href="src.pdb.html#ATOM">ATOM</a> or HETATM as necessary.<br>
<br>
This is used to create the output for pqr and pdb files! No touchy!<br>
<br>
Returns<br>
outstr: String with <a href="src.pdb.html#ATOM">ATOM</a>/HETATM field set appropriately</tt></dd></dl>
<dl><dt><a name="Atom-getCoords"><strong>getCoords</strong></a>(self)</dt><dd><tt>Return the x,y,z coordinates of the atom in list form<br>
<br>
Returns<br>
List of the coordinates (list)</tt></dd></dl>
<dl><dt><a name="Atom-getPDBString"><strong>getPDBString</strong></a>(self)</dt><dd><tt>Returns a string of the new atom type. Uses the <a href="src.pdb.html#ATOM">ATOM</a> string<br>
output but changes the first field to either by <a href="src.pdb.html#ATOM">ATOM</a> or<br>
HETATM as necessary.<br>
<br>
This is for the pdb representation of the atom. The propka30 module <br>
depends on this being correct. No touchy!<br>
<br>
Returns<br>
str: String with <a href="src.pdb.html#ATOM">ATOM</a>/HETATM field set appropriately</tt></dd></dl>
<dl><dt><a name="Atom-getPQRString"><strong>getPQRString</strong></a>(self, chainflag<font color="#909090">=False</font>)</dt><dd><tt>Returns a string of the new atom type. Uses the <a href="src.pdb.html#ATOM">ATOM</a> string<br>
output but changes the first field to either by <a href="src.pdb.html#ATOM">ATOM</a> or<br>
HETATM as necessary.<br>
<br>
This is used to create the output for pqr files! No touchy!<br>
<br>
Returns<br>
str: String with <a href="src.pdb.html#ATOM">ATOM</a>/HETATM field set appropriately</tt></dd></dl>
<dl><dt><a name="Atom-hasReference"><strong>hasReference</strong></a>(self)</dt><dd><tt>Determine if the atom object has a reference object or not.<br>
All known atoms should have reference objects.<br>
<br>
Returns<br>
True if atom has a reference object, False otherwise.</tt></dd></dl>
<dl><dt><a name="Atom-isBackbone"><strong>isBackbone</strong></a>(self)</dt><dd><tt>Return true if atom name is in backbone, otherwise false<br>
<br>
Returns<br>
state: 1 if true, 0 if false</tt></dd></dl>
<dl><dt><a name="Atom-isHydrogen"><strong>isHydrogen</strong></a>(self)</dt><dd><tt>Is this atom a Hydrogen atom?<br>
<br>
Returns<br>
value: 1 if <a href="#Atom">Atom</a> is a Hydrogen, 0 otherwise</tt></dd></dl>
<dl><dt><a name="Atom-set"><strong>set</strong></a>(self, name, value)</dt><dd><tt>Set a member of the <a href="#Atom">Atom</a> class<br>
<br>
Parameters<br>
name: The name of the member (string)<br>
value: The value to set the member to<br>
Possible Values<br>
type: The type of <a href="#Atom">Atom</a> (either <a href="src.pdb.html#ATOM">ATOM</a> or HETATM)<br>
serial: <a href="#Atom">Atom</a> serial number<br>
name: <a href="#Atom">Atom</a> name<br>
altLoc: Alternate location<br>
resName: <a href="#Residue">Residue</a> name<br>
chainID: <a href="#Chain">Chain</a> identifier<br>
resSeq: <a href="#Residue">Residue</a> sequence number<br>
iCode: Code for insertion of residues<br>
x: Orthogonal coordinates for X in Angstroms.<br>
y: Orthogonal coordinates for Y in Angstroms.<br>
z: Orthogonal coordinates for Z in Angstroms.<br>
occupancy: Occupancy<br>
tempFactor: Temperature Factor<br>
segID: Segment identifier<br>
element: Element symbol<br>
charge: Charge on the atom<br>
residue: The parent residue of the atom<br>
radius: The radius of the atom<br>
ffcharge: The forcefield charge on the atom<br>
hdonor: Whether the atom is a hydrogen donor<br>
hacceptor: Whether the atom is a hydrogen acceptor</tt></dd></dl>
<hr>
Data descriptors inherited from <a href="src.pdb.html#BaseRecord">src.pdb.BaseRecord</a>:<br>
<dl><dt><strong>__dict__</strong></dt>
<dd><tt>dictionary for instance variables (if defined)</tt></dd>
</dl>
<dl><dt><strong>__weakref__</strong></dt>
<dd><tt>list of weak references to the object (if defined)</tt></dd>
</dl>
</td></tr></table> <p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#ffc8d8">
<td colspan=3 valign=bottom> <br>
<font color="#000000" face="helvetica, arial"><a name="Chain">class <strong>Chain</strong></a></font></td></tr>
<tr bgcolor="#ffc8d8"><td rowspan=2><tt> </tt></td>
<td colspan=2><tt><a href="#Chain">Chain</a> class<br>
<br>
The chain class contains information about each chain within a given<br>
Protein object.<br> </tt></td></tr>
<tr><td> </td>
<td width="100%">Methods defined here:<br>
<dl><dt><a name="Chain-__init__"><strong>__init__</strong></a>(self, chainID)</dt><dd><tt>Initialize the class<br>
<br>
Parameters<br>
chainID: The chainID for this chain as denoted in<br>
the PDB file (string)</tt></dd></dl>
<dl><dt><a name="Chain-addResidue"><strong>addResidue</strong></a>(self, residue)</dt><dd><tt>Add a residue to the chain<br>
<br>
Parameters<br>
residue: The residue to be added (<a href="#Residue">Residue</a>)</tt></dd></dl>
<dl><dt><a name="Chain-get"><strong>get</strong></a>(self, name)</dt><dd><tt>Get a member of the <a href="#Chain">Chain</a> class<br>
<br>
Parameters<br>
name: The name of the member<br>
Possible Values<br>
ID: The ID of the chain<br>
Residues: The list of residues within the <a href="#Chain">Chain</a><br>
Returns<br>
item: The value of the member</tt></dd></dl>
<dl><dt><a name="Chain-getAtoms"><strong>getAtoms</strong></a>(self)</dt><dd><tt>Return a list of <a href="#Atom">Atom</a> objects contained in this chain<br>
<br>
Returns<br>
atomlist: List of <a href="#Atom">Atom</a> objects (list)</tt></dd></dl>
<dl><dt><a name="Chain-getResidues"><strong>getResidues</strong></a>(self)</dt><dd><tt>Return a list of <a href="#Residue">Residue</a> objects in this chain</tt></dd></dl>
<dl><dt><a name="Chain-getSummary"><strong>getSummary</strong></a>(self)</dt></dl>
<dl><dt><a name="Chain-numAtoms"><strong>numAtoms</strong></a>(self)</dt><dd><tt>Get the number of atoms for the chain<br>
<br>
Returns<br>
count: Number of atoms in the chain (int)</tt></dd></dl>
<dl><dt><a name="Chain-numResidues"><strong>numResidues</strong></a>(self)</dt><dd><tt>Get the number of residues for the chain<br>
<br>
Returns<br>
count: Number of residues in the chain (int)</tt></dd></dl>
<dl><dt><a name="Chain-renumberResidues"><strong>renumberResidues</strong></a>(self)</dt><dd><tt>Renumber Atoms based on actual <a href="#Residue">Residue</a> number and not PDB resSeq</tt></dd></dl>
</td></tr></table> <p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#ffc8d8">
<td colspan=3 valign=bottom> <br>
<font color="#000000" face="helvetica, arial"><a name="Residue">class <strong>Residue</strong></a></font></td></tr>
<tr bgcolor="#ffc8d8"><td rowspan=2><tt> </tt></td>
<td colspan=2><tt><a href="#Residue">Residue</a> class<br>
<br>
The residue class contains a list of <a href="#Atom">Atom</a> objects associated with that<br>
residue and other helper functions.<br> </tt></td></tr>
<tr><td> </td>
<td width="100%">Methods defined here:<br>
<dl><dt><a name="Residue-__init__"><strong>__init__</strong></a>(self, atoms)</dt><dd><tt>Initialize the class<br>
<br>
Parameters<br>
atoms: A list of <a href="#Atom">Atom</a> objects to be stored in this class<br>
(list)</tt></dd></dl>
<dl><dt><a name="Residue-__str__"><strong>__str__</strong></a>(self)</dt><dd><tt>Basic string representation</tt></dd></dl>
<dl><dt><a name="Residue-addAtom"><strong>addAtom</strong></a>(self, atom)</dt><dd><tt>Add the atom object to the residue.<br>
<br>
Parameters<br>
atom: The object to be added (<a href="src.pdb.html#ATOM">ATOM</a>)</tt></dd></dl>
<dl><dt><a name="Residue-addMissing"><strong>addMissing</strong></a>(self, value)</dt><dd><tt>Add the value to the list of missing atoms<br>
<br>
Parameters<br>
value: The name of the missing atom (string)</tt></dd></dl>
<dl><dt><a name="Residue-createAtom"><strong>createAtom</strong></a>(self, name, newcoords, type)</dt><dd><tt>Add a new atom object to the residue. Uses an atom<br>
currently in the residue to seed the new atom<br>
object, then replaces the coordinates and name accordingly.<br>
<br>
Parameters<br>
name: The name of the new atom (string)<br>
newcoords: The x,y,z coordinates of the new atom (list)<br>
type: The type of atom, <a href="src.pdb.html#ATOM">ATOM</a> or HETATM</tt></dd></dl>
<dl><dt><a name="Residue-get"><strong>get</strong></a>(self, name)</dt><dd><tt>Get a member of the <a href="#Residue">Residue</a> class<br>
<br>
Parameters<br>
name: The name of the member (string)<br>
Possible Values<br>
atoms: The atoms in the residue<br>
name: The name of the residue<br>
chainID: The chainID associated with the residue<br>
resSeq: The sequence number of the residue<br>
icode: The iCode of the residue<br>
SSbonded: 1 if the residue has a SS bond, 0 otherwise<br>
SSbondpartner: The residue of the bond partner<br>
type: The type associated with this residue<br>
isNterm: # of hydrogens if the residue is the N-Terminus, 0 otherwise<br>
isCterm: 1 if the residue is the C-Terminus, 0 otherwise<br>
missing: List of missing atoms of the residue<br>
Returns<br>
item: The value of the member</tt></dd></dl>
<dl><dt><a name="Residue-getAtom"><strong>getAtom</strong></a>(self, name)</dt><dd><tt>Retrieve an atom from the mapping<br>
<br>
Parameters<br>
resname: The name of the residue to retrieve (string)</tt></dd></dl>
<dl><dt><a name="Residue-getAtoms"><strong>getAtoms</strong></a>(self)</dt></dl>
<dl><dt><a name="Residue-getCharge"><strong>getCharge</strong></a>(self)</dt><dd><tt>Get the total charge of the residue. In order to get rid<br>
of floating point rounding error, do the string<br>
transformation.<br>
<br>
Returns:<br>
charge: The charge of the residue (float)</tt></dd></dl>
<dl><dt><a name="Residue-hasAtom"><strong>hasAtom</strong></a>(self, name)</dt></dl>
<dl><dt><a name="Residue-letterCode"><strong>letterCode</strong></a>(self)</dt></dl>
<dl><dt><a name="Residue-numAtoms"><strong>numAtoms</strong></a>(self)</dt><dd><tt>Get the number of atoms for the residue<br>
<br>
Returns<br>
Number of atoms in the residue (int)</tt></dd></dl>
<dl><dt><a name="Residue-removeAtom"><strong>removeAtom</strong></a>(self, atomname)</dt><dd><tt>Remove an atom from the residue object.<br>
<br>
Parameters<br>
atomname: The name of the atom to be removed (string)</tt></dd></dl>
<dl><dt><a name="Residue-renameAtom"><strong>renameAtom</strong></a>(self, oldname, newname)</dt><dd><tt>Rename an atom to a new name<br>
<br>
Parameters<br>
oldname: The old atom name (string)<br>
newname: The new atom name (string)</tt></dd></dl>
<dl><dt><a name="Residue-renameResidue"><strong>renameResidue</strong></a>(self, name)</dt><dd><tt>Rename a given residue<br>
<br>
Parameters<br>
name: The new name of the residue</tt></dd></dl>
<dl><dt><a name="Residue-reorder"><strong>reorder</strong></a>(self)</dt><dd><tt>Reorder the atoms to start with N, CA, C, O if they exist</tt></dd></dl>
<dl><dt><a name="Residue-rotateTetrahedral"><strong>rotateTetrahedral</strong></a>(self, atom1, atom2, angle)</dt><dd><tt>Rotate about the atom1-atom2 bond by a given angle<br>
All atoms connected to atom2 will rotate.<br>
<br>
Parameters:<br>
atom1: The first atom of the bond to rotate about (atom)<br>
atom2: The second atom of the bond to rotate about (atom)<br>
angle: The number of degrees to rotate (float)</tt></dd></dl>
<dl><dt><a name="Residue-set"><strong>set</strong></a>(self, name, value)</dt><dd><tt>Set a member of the <a href="#Residue">Residue</a> class to a specific value <br>
<br>
Parameters<br>
name: The name of the object to set (string)<br>
value: The object to append<br>
Possible Values<br>
atoms: The atoms in the residue<br>
name: The name of the residue<br>
chain: The chainID associated with the residue<br>
resSeq: The sequence number of the residue<br>
icode: The iCode of the residue<br>
SSbonded: 1 if the residue has a SS bond, 0 otherwise<br>
SSbondpartner: The residue of the bond partner<br>
type: The type associated with this residue<br>
isNterm: # of hydrogens if the residue is the N-Terminus, 0 otherwise<br>
isCterm: 1 if the residue is the C-Terminus, 0 otherwise<br>
isDirty: 1 if the residue is not missing atoms,<br>
0 otherwise<br>
Notes<br>
resSeq points to the residue.setResSeq function<br>
Returns<br>
item: The value of the member</tt></dd></dl>
<dl><dt><a name="Residue-setChainID"><strong>setChainID</strong></a>(self, value)</dt><dd><tt>Set the chainID field to a certain value</tt></dd></dl>
<dl><dt><a name="Residue-setDonorsAndAcceptors"><strong>setDonorsAndAcceptors</strong></a>(self)</dt><dd><tt>Set the donors and acceptors within the residue</tt></dd></dl>
<dl><dt><a name="Residue-setResSeq"><strong>setResSeq</strong></a>(self, value)</dt><dd><tt>Set the atom field resSeq to a certain value and<br>
change the residue's information. The icode field is no longer<br>
useful.<br>
<br>
Parameters<br>
value: The new value of resSeq (int)</tt></dd></dl>
<dl><dt><a name="Residue-update_terminus_status"><strong>update_terminus_status</strong></a>(self)</dt><dd><tt>Update the isNterms and isCterm flags</tt></dd></dl>
</td></tr></table></td></tr></table><p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#55aa55">
<td colspan=3 valign=bottom> <br>
<font color="#ffffff" face="helvetica, arial"><big><strong>Data</strong></big></font></td></tr>
<tr><td bgcolor="#55aa55"><tt> </tt></td><td> </td>
<td width="100%"><strong>BACKBONE</strong> = ['N', 'CA', 'C', 'O', 'O2', 'HA', 'HN', 'H', 'tN']<br>
<strong>DIHEDRAL</strong> = 57.2958<br>
<strong>INSTALLDIR</strong> = '/Users/d3y382/pdb2pqr/'<br>
<strong>SMALL</strong> = 1e-07<br>
<strong>TMPDIR</strong> = 'tmp/'<br>
<strong>__author__</strong> = 'Todd Dolinsky'<br>
<strong>__date__</strong> = '28 February 2006'<br>
<strong>lineParsers</strong> = {'ANISOU': <class 'src.pdb.ANISOU'>, 'ATOM': <class 'src.pdb.ATOM'>, 'AUTHOR': <class 'src.pdb.AUTHOR'>, 'CAVEAT': <class 'src.pdb.CAVEAT'>, 'CISPEP': <class 'src.pdb.CISPEP'>, 'COMPND': <class 'src.pdb.COMPND'>, 'CONECT': <class 'src.pdb.CONECT'>, 'CRYST1': <class 'src.pdb.CRYST1'>, 'DBREF': <class 'src.pdb.DBREF'>, 'END': <class 'src.pdb.END'>, ...}</td></tr></table><p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#7799ee">
<td colspan=3 valign=bottom> <br>
<font color="#ffffff" face="helvetica, arial"><big><strong>Author</strong></big></font></td></tr>
<tr><td bgcolor="#7799ee"><tt> </tt></td><td> </td>
<td width="100%">Todd Dolinsky</td></tr></table>
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