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<!doctype html PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<html><head><title>Python: module pross</title>
</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>pross</strong></big></big></font></td
><td align=right valign=bottom
><font color="#ffffff" face="helvetica, arial"><a href=".">index</a><br><a href="file:/home/ijstokes/github/pross/pross.py">/home/ijstokes/github/pross/pross.py</a></font></td></tr></table>
<p><tt>Calulate all torsion angles and assign secondary structure and mesostate code.<br>
<br>
This module uses much of the code from the original BIOMOL collection of<br>
utilities written by Raj Srinivasani with enhancements by Nick Fitzkee.<br>
<br>
The script was put together by Pat Fleming so that a user would not need<br>
to have the BIOMOL distribution installed to run PROSS.<br>
<br>
Note that since Raj's time the definitions of mesostates has been superceded<br>
by the fine grained 30 deg x 30 deg grid for most purposes. Either mesostate<br>
grid will work for PROSS. Give your choice as an argument (see USAGE below).<br>
<br>
Date: September 2004<br>
Author: Pat Fleming, pat.fleming@jhu.edu</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="#fffff" 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="gzip.html">gzip</a><br>
</td><td width="25%" valign=top><a href="math.html">math</a><br>
<a href="re.html">re</a><br>
</td><td width="25%" valign=top><a href="string.html">string</a><br>
<a href="sys.html">sys</a><br>
</td><td width="25%" valign=top><a href="types.html">types</a><br>
</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="pross.html#Atom3d">Atom3d</a>
</font></dt><dt><font face="helvetica, arial"><a href="pross.html#PDBFile">PDBFile</a>
</font></dt><dt><font face="helvetica, arial"><a href="pross.html#TypedList">TypedList</a>
</font></dt><dd>
<dl>
<dt><font face="helvetica, arial"><a href="pross.html#molChain">molChain</a>
</font></dt><dd>
<dl>
<dt><font face="helvetica, arial"><a href="pross.html#Protein">Protein</a>
</font></dt></dl>
</dd>
<dt><font face="helvetica, arial"><a href="pross.html#molMol">molMol</a>
</font></dt><dt><font face="helvetica, arial"><a href="pross.html#molResidue">molResidue</a>
</font></dt><dd>
<dl>
<dt><font face="helvetica, arial"><a href="pross.html#AminoAcid">AminoAcid</a>
</font></dt></dl>
</dd>
</dl>
</dd>
</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="AminoAcid">class <strong>AminoAcid</strong></a>(<a href="pross.html#molResidue">molResidue</a>)</font></td></tr>
<tr><td bgcolor="#ffc8d8"><tt> </tt></td><td> </td>
<td width="100%"><dl><dt>Method resolution order:</dt>
<dd><a href="pross.html#AminoAcid">AminoAcid</a></dd>
<dd><a href="pross.html#molResidue">molResidue</a></dd>
<dd><a href="pross.html#TypedList">TypedList</a></dd>
</dl>
<hr>
Methods defined here:<br>
<dl><dt><a name="AminoAcid-assign_radii"><strong>assign_radii</strong></a>(self)</dt></dl>
<dl><dt><a name="AminoAcid-chi1"><strong>chi1</strong></a>(self)</dt></dl>
<dl><dt><a name="AminoAcid-chi2"><strong>chi2</strong></a>(self)</dt></dl>
<dl><dt><a name="AminoAcid-chi3"><strong>chi3</strong></a>(self)</dt></dl>
<dl><dt><a name="AminoAcid-chi4"><strong>chi4</strong></a>(self)</dt></dl>
<hr>
Methods inherited from <a href="pross.html#molResidue">molResidue</a>:<br>
<dl><dt><a name="AminoAcid-__init__"><strong>__init__</strong></a>(self, name<font color="#909090">=''</font>, atoms<font color="#909090">=None</font>, **kw)</dt></dl>
<dl><dt><a name="AminoAcid-atom_coordinates"><strong>atom_coordinates</strong></a>(self, *names)</dt><dd><tt>returns coordinates of named atoms.<br>
If names is omitted all atom coordinates are returned.</tt></dd></dl>
<dl><dt><a name="AminoAcid-atoms"><strong>atoms</strong></a>(self)</dt><dd><tt>Returns a list of atoms within the <a href="#molResidue">molResidue</a> list.</tt></dd></dl>
<dl><dt><a name="AminoAcid-atoms_not_with_name"><strong>atoms_not_with_name</strong></a>(self, *names)</dt><dd><tt>returns atoms in residue excluding specified names</tt></dd></dl>
<dl><dt><a name="AminoAcid-atoms_with_name"><strong>atoms_with_name</strong></a>(self, *names)</dt><dd><tt>returns atoms in residue with specified names</tt></dd></dl>
<dl><dt><a name="AminoAcid-delete_atoms_with_name"><strong>delete_atoms_with_name</strong></a>(self, *names)</dt><dd><tt>delete atoms in residue with specified names</tt></dd></dl>
<dl><dt><a name="AminoAcid-has_atom"><strong>has_atom</strong></a>(self, name)</dt><dd><tt>returns true if residue has an atom named 'name'</tt></dd></dl>
<dl><dt><a name="AminoAcid-num_atoms"><strong>num_atoms</strong></a>(self)</dt><dd><tt>returns the number of atoms in residue</tt></dd></dl>
<dl><dt><a name="AminoAcid-type"><strong>type</strong></a>(self)</dt></dl>
<hr>
Methods inherited from <a href="pross.html#TypedList">TypedList</a>:<br>
<dl><dt><a name="AminoAcid-__add__"><strong>__add__</strong></a>(self, other)</dt><dd><tt>Adds a list to a <a href="#TypedList">TypedList</a>, as long as it's of the same type.</tt></dd></dl>
<dl><dt><a name="AminoAcid-__copy__"><strong>__copy__</strong></a>(self)</dt><dd><tt>Returns a copy of a <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="AminoAcid-__deepcopy__"><strong>__deepcopy__</strong></a> = __copy__(self)</dt><dd><tt>Returns a copy of a <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="AminoAcid-__delitem__"><strong>__delitem__</strong></a>(self, i)</dt><dd><tt>Removes an item from the <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="AminoAcid-__delslice__"><strong>__delslice__</strong></a>(self, i, j)</dt><dd><tt>Deleted a slice of items located between indices i and j.</tt></dd></dl>
<dl><dt><a name="AminoAcid-__getitem__"><strong>__getitem__</strong></a>(self, i)</dt><dd><tt>Returns an item from the <a href="#TypedList">TypedList</a> located at index i.</tt></dd></dl>
<dl><dt><a name="AminoAcid-__getslice__"><strong>__getslice__</strong></a>(self, i, j)</dt><dd><tt>Returns a slice of the typed list between indexes i and j.</tt></dd></dl>
<dl><dt><a name="AminoAcid-__len__"><strong>__len__</strong></a>(self)</dt><dd><tt>Returns the length of the <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="AminoAcid-__mul__"><strong>__mul__</strong></a>(self, other)</dt><dd><tt>Multiply set of elements and another, and store in new.elements.</tt></dd></dl>
<dl><dt><a name="AminoAcid-__repr__"><strong>__repr__</strong></a>(self)</dt><dd><tt>Returns a printable representation of the <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="AminoAcid-__rmul__"><strong>__rmul__</strong></a> = __mul__(self, other)</dt><dd><tt>Multiply set of elements and another, and store in new.elements.</tt></dd></dl>
<dl><dt><a name="AminoAcid-__setitem__"><strong>__setitem__</strong></a>(self, i, v)</dt><dd><tt>Sets item at index i to the value of v.</tt></dd></dl>
<dl><dt><a name="AminoAcid-__setslice__"><strong>__setslice__</strong></a>(self, i, j, v)</dt><dd><tt>Sets the value of a slice of items between i and j to v.</tt></dd></dl>
<dl><dt><a name="AminoAcid-__str__"><strong>__str__</strong></a>(self)</dt><dd><tt>Returns all elements of the <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="AminoAcid-append"><strong>append</strong></a>(self, el)</dt><dd><tt>Add an element to the <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="AminoAcid-clone"><strong>clone</strong></a> = __copy__(self)</dt><dd><tt>Returns a copy of a <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="AminoAcid-count"><strong>count</strong></a>(self, el)</dt><dd><tt>Returns the number of elements in a <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="AminoAcid-extend"><strong>extend</strong></a>(self, els)</dt><dd><tt>Add an attribute to an element in a <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="AminoAcid-index"><strong>index</strong></a>(self, el)</dt><dd><tt>Return an index if the items in a <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="AminoAcid-indices"><strong>indices</strong></a>(self, len<font color="#909090">=<built-in function len></font>)</dt><dd><tt>Returns the length of a range of indices.</tt></dd></dl>
<dl><dt><a name="AminoAcid-insert"><strong>insert</strong></a>(self, pos, el)</dt><dd><tt>Insert an element in a <a href="#TypedList">TypedList</a> at position pos.</tt></dd></dl>
<dl><dt><a name="AminoAcid-pop"><strong>pop</strong></a>(self)</dt><dd><tt>Remove the last element in a <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="AminoAcid-remove"><strong>remove</strong></a>(self, el)</dt><dd><tt>Remove an element from a <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="AminoAcid-reverse"><strong>reverse</strong></a>(self)</dt><dd><tt>Reverse the order of elements in a <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="AminoAcid-reverse_indices"><strong>reverse_indices</strong></a>(self, len<font color="#909090">=<built-in function len></font>)</dt><dd><tt>Reverses indices of elements in a <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="AminoAcid-sort"><strong>sort</strong></a>(self)</dt><dd><tt>Sort the elements in a <a href="#TypedList">TypedList</a>.</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="Atom3d">class <strong>Atom3d</strong></a></font></td></tr>
<tr bgcolor="#ffc8d8"><td rowspan=2><tt> </tt></td>
<td colspan=2><tt>A <a href="#TypedList">TypedList</a> class for atoms with 3-D coordinates.<br> </tt></td></tr>
<tr><td> </td>
<td width="100%">Methods defined here:<br>
<dl><dt><a name="Atom3d-__copy__"><strong>__copy__</strong></a> = <a href="#Atom3d-clone">clone</a>(self)</dt></dl>
<dl><dt><a name="Atom3d-__init__"><strong>__init__</strong></a>(self, x, y, z, cnf<font color="#909090">={}</font>)</dt></dl>
<dl><dt><a name="Atom3d-__repr__"><strong>__repr__</strong></a>(self)</dt><dd><tt>Formats atom coordinates into a printable format.</tt></dd></dl>
<dl><dt><a name="Atom3d-__str__"><strong>__str__</strong></a> = <a href="#Atom3d-__repr__">__repr__</a>(self)</dt></dl>
<dl><dt><a name="Atom3d-angle"><strong>angle</strong></a>(self, a, b, sqrt<font color="#909090">=<built-in function sqrt></font>, acos<font color="#909090">=<built-in function acos></font>)</dt></dl>
<dl><dt><a name="Atom3d-clone"><strong>clone</strong></a>(self)</dt><dd><tt>Creates a copy of the <a href="#Atom3d">Atom3d</a> list.</tt></dd></dl>
<dl><dt><a name="Atom3d-coords"><strong>coords</strong></a>(self)</dt><dd><tt>Returns the 3-D coordinates of an atom.</tt></dd></dl>
<dl><dt><a name="Atom3d-distance"><strong>distance</strong></a>(self, other, sqrt<font color="#909090">=<built-in function sqrt></font>)</dt><dd><tt>Calculate the distance between an atom and a specified other.</tt></dd></dl>
<dl><dt><a name="Atom3d-set_coords"><strong>set_coords</strong></a>(self, x, y<font color="#909090">=None</font>, z<font color="#909090">=None</font>)</dt><dd><tt>Sets the 3-D coordinates of an atom.</tt></dd></dl>
<dl><dt><a name="Atom3d-sqr_distance"><strong>sqr_distance</strong></a>(self, other)</dt></dl>
<dl><dt><a name="Atom3d-torsion"><strong>torsion</strong></a>(self, a, b, c, sqrt<font color="#909090">=<built-in function sqrt></font>, acos<font color="#909090">=<built-in function acos></font>)</dt></dl>
<dl><dt><a name="Atom3d-xcoord"><strong>xcoord</strong></a>(self, v<font color="#909090">=None</font>)</dt><dd><tt>Returns the x-coordinate of an atom.</tt></dd></dl>
<dl><dt><a name="Atom3d-ycoord"><strong>ycoord</strong></a>(self, v<font color="#909090">=None</font>)</dt><dd><tt>Returns the y-coordinate of an atom.</tt></dd></dl>
<dl><dt><a name="Atom3d-zcoord"><strong>zcoord</strong></a>(self, v<font color="#909090">=None</font>)</dt><dd><tt>Returns the z-coordinate of an atom.</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="PDBFile">class <strong>PDBFile</strong></a></font></td></tr>
<tr bgcolor="#ffc8d8"><td rowspan=2><tt> </tt></td>
<td colspan=2><tt>Contains methods for reading chains from a PDB File.<br> </tt></td></tr>
<tr><td> </td>
<td width="100%">Methods defined here:<br>
<dl><dt><a name="PDBFile-__init__"><strong>__init__</strong></a>(self, filename)</dt></dl>
<dl><dt><a name="PDBFile-read"><strong>read</strong></a>(self, as_protein<font color="#909090">=0</font>, as_rna<font color="#909090">=0</font>, as_dna<font color="#909090">=0</font>)</dt></dl>
<dl><dt><a name="PDBFile-read_chain"><strong>read_chain</strong></a>(self, as_protein<font color="#909090">=0</font>, as_rna<font color="#909090">=0</font>, as_dna<font color="#909090">=0</font>)</dt></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="Protein">class <strong>Protein</strong></a>(<a href="pross.html#molChain">molChain</a>)</font></td></tr>
<tr bgcolor="#ffc8d8"><td rowspan=2><tt> </tt></td>
<td colspan=2><tt>A <a href="#TypedList">TypedList</a> containing Proteins, set by `_is_a_protein`.<br> </tt></td></tr>
<tr><td> </td>
<td width="100%"><dl><dt>Method resolution order:</dt>
<dd><a href="pross.html#Protein">Protein</a></dd>
<dd><a href="pross.html#molChain">molChain</a></dd>
<dd><a href="pross.html#TypedList">TypedList</a></dd>
</dl>
<hr>
Methods defined here:<br>
<dl><dt><a name="Protein-backbone_atoms"><strong>backbone_atoms</strong></a>(self, *ids)</dt><dd><tt>If the atom name matches any in bb_atoms, make a new residue and add to a chain.</tt></dd></dl>
<dl><dt><a name="Protein-chi1"><strong>chi1</strong></a>(self, i)</dt></dl>
<dl><dt><a name="Protein-chi2"><strong>chi2</strong></a>(self, i)</dt></dl>
<dl><dt><a name="Protein-chi3"><strong>chi3</strong></a>(self, i)</dt></dl>
<dl><dt><a name="Protein-chi4"><strong>chi4</strong></a>(self, i)</dt></dl>
<dl><dt><a name="Protein-clean"><strong>clean</strong></a>(self)</dt><dd><tt><a href="#Protein-clean">clean</a>() - remove residues if they lack N, CA, or C atoms</tt></dd></dl>
<dl><dt><a name="Protein-codes"><strong>codes</strong></a>(self, phi<font color="#909090">=None</font>, psi<font color="#909090">=None</font>, ome<font color="#909090">=None</font>, mcodes<font color="#909090">=None</font>)</dt><dd><tt>Executes the rc_codes method on a protein.</tt></dd></dl>
<dl><dt><a name="Protein-gaps"><strong>gaps</strong></a>(self)</dt><dd><tt><a href="#Protein-gaps">gaps</a>() - identify gaps in the chain<br>
<br>
This function does a simple check to determine whether CA atoms are<br>
contiguous in the peptide chain. First it, checks that CA atoms<br>
exist for all residues. If that's okay, it checks to see if the<br>
distance is less than 18**0.5 A. If either of these checks fail,<br>
residues involved in a gap have their .gap attribute set to true.</tt></dd></dl>
<dl><dt><a name="Protein-omega"><strong>omega</strong></a>(self, i)</dt><dd><tt><a href="#Protein-omega">omega</a>(i) - calculate omega torsion for index i<br>
<br>
This function calcualtes the value of the omega torsion for<br>
index i. Note: this value is widely calculated using atoms<br>
CA(i-1), C(i-1), N(i), and CA(i). These atoms are used for<br>
this calculation. However, other LINUS programs use the fllowing<br>
atoms: CA(i), C(i), N(i+1), CA(i+1). Forewarned is forearmed.</tt></dd></dl>
<dl><dt><a name="Protein-phi"><strong>phi</strong></a>(self, i)</dt></dl>
<dl><dt><a name="Protein-pross"><strong>pross</strong></a>(self, phi<font color="#909090">=None</font>, psi<font color="#909090">=None</font>, ome<font color="#909090">=None</font>, mcodes<font color="#909090">=None</font>)</dt><dd><tt>Executes the rc_ss method on a protein.</tt></dd></dl>
<dl><dt><a name="Protein-psi"><strong>psi</strong></a>(self, i)</dt></dl>
<dl><dt><a name="Protein-sequence"><strong>sequence</strong></a>(self, one<font color="#909090">=0</font>)</dt><dd><tt>Returns a protein sequence.</tt></dd></dl>
<dl><dt><a name="Protein-torsions"><strong>torsions</strong></a>(self, i<font color="#909090">=None</font>, map<font color="#909090">=<built-in function map></font>)</dt></dl>
<dl><dt><a name="Protein-type"><strong>type</strong></a>(self)</dt></dl>
<hr>
Methods inherited from <a href="pross.html#molChain">molChain</a>:<br>
<dl><dt><a name="Protein-__init__"><strong>__init__</strong></a>(self, name<font color="#909090">=''</font>, residues<font color="#909090">=None</font>, **kw)</dt></dl>
<dl><dt><a name="Protein-assign_radii"><strong>assign_radii</strong></a>(self)</dt><dd><tt>Assigns the radius of residues in a <a href="#molChain">molChain</a></tt></dd></dl>
<dl><dt><a name="Protein-atom_coordinates"><strong>atom_coordinates</strong></a>(self, *names)</dt><dd><tt>returns coordinates of named atoms. if names is None<br>
all atom coordinates are returned.</tt></dd></dl>
<dl><dt><a name="Protein-atoms"><strong>atoms</strong></a>(self)</dt><dd><tt>returns a python list of atoms in a residue.</tt></dd></dl>
<dl><dt><a name="Protein-atoms_not_with_name"><strong>atoms_not_with_name</strong></a>(self, *names)</dt><dd><tt>returns atoms in residue excluding specified names</tt></dd></dl>
<dl><dt><a name="Protein-atoms_with_name"><strong>atoms_with_name</strong></a>(self, *names)</dt><dd><tt>Returns a list of atoms that match the specified names.</tt></dd></dl>
<dl><dt><a name="Protein-delete_alt_locs"><strong>delete_alt_locs</strong></a>(self)</dt><dd><tt>delete_alt_locs - remove secondary conformations in the chain<br>
<br>
In a chain with multiple occupancy and alternate location identifiers,<br>
it is often desirable to eliminate the secondary conformations for<br>
use in simulation, etc. This function (abitrarily) finds and selects<br>
the first given conformation and deletes all other conformations.</tt></dd></dl>
<dl><dt><a name="Protein-delete_atoms_with_name"><strong>delete_atoms_with_name</strong></a>(self, *names)</dt><dd><tt>delete atoms in residue with specified names</tt></dd></dl>
<dl><dt><a name="Protein-delete_hetero"><strong>delete_hetero</strong></a>(self)</dt><dd><tt>delete all hetero atoms from a protein<br>
<br>
This function removes all HETATM records from the molecular<br>
structure. This include waters, heme groups, as well as residues<br>
with nonstandard structures</tt></dd></dl>
<dl><dt><a name="Protein-delete_residues_with_name"><strong>delete_residues_with_name</strong></a>(self, *names)</dt><dd><tt>delete specified residues from Chain</tt></dd></dl>
<dl><dt><a name="Protein-delete_waters"><strong>delete_waters</strong></a>(self)</dt><dd><tt>Delete water molecules from residues in the <a href="#molChain">molChain</a>.</tt></dd></dl>
<dl><dt><a name="Protein-num_atoms"><strong>num_atoms</strong></a>(self)</dt><dd><tt>Returns the number of atoms in each residue within a chain.</tt></dd></dl>
<dl><dt><a name="Protein-num_residues"><strong>num_residues</strong></a>(self)</dt><dd><tt>Returns the number of residues within a chain.</tt></dd></dl>
<dl><dt><a name="Protein-preserve_chain_hetero"><strong>preserve_chain_hetero</strong></a>(self)</dt><dd><tt>prevent hetero residues from being deleted as hetero atoms<br>
<br>
Normally, delete_hetero will delete all hetero atoms from a<br>
molecule. This includes waters and heterogroups (hemes, etc.),<br>
but it also includes hetero residues--nonstandard residues<br>
that have backbone connectivity but perhaps extra atoms (e.g.<br>
S-hydroxy-cysteine). Deleting these residues may disrupt an<br>
otherwise continuous chain and may be undesirable.<br>
<br>
Given that a chain has a valid SEQRES entry, this function will<br>
'unset' the hetero flag for heterogroups that are involved in<br>
the sequence itself. When delete_hetero is run, these atoms<br>
will be preserved.</tt></dd></dl>
<dl><dt><a name="Protein-residues_not_with_name"><strong>residues_not_with_name</strong></a>(self, *names)</dt><dd><tt>returns residues excluding specified names as a python list</tt></dd></dl>
<dl><dt><a name="Protein-residues_with_name"><strong>residues_with_name</strong></a>(self, *names)</dt><dd><tt>returns specified residues as a python list</tt></dd></dl>
<dl><dt><a name="Protein-rotatex"><strong>rotatex</strong></a>(self, theta)</dt><dd><tt>Rotates residues in the <a href="#molChain">molChain</a> by the X-axis.</tt></dd></dl>
<dl><dt><a name="Protein-rotatey"><strong>rotatey</strong></a>(self, theta)</dt><dd><tt>Rotates residues in the <a href="#molChain">molChain</a> by the Y-axis.</tt></dd></dl>
<dl><dt><a name="Protein-rotatez"><strong>rotatez</strong></a>(self, theta)</dt><dd><tt>Rotates residues in the <a href="#molChain">molChain</a> by the Z-axis.</tt></dd></dl>
<dl><dt><a name="Protein-translate"><strong>translate</strong></a>(self, dx, dy<font color="#909090">=None</font>, dz<font color="#909090">=None</font>)</dt></dl>
<hr>
Methods inherited from <a href="pross.html#TypedList">TypedList</a>:<br>
<dl><dt><a name="Protein-__add__"><strong>__add__</strong></a>(self, other)</dt><dd><tt>Adds a list to a <a href="#TypedList">TypedList</a>, as long as it's of the same type.</tt></dd></dl>
<dl><dt><a name="Protein-__copy__"><strong>__copy__</strong></a>(self)</dt><dd><tt>Returns a copy of a <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="Protein-__deepcopy__"><strong>__deepcopy__</strong></a> = __copy__(self)</dt><dd><tt>Returns a copy of a <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="Protein-__delitem__"><strong>__delitem__</strong></a>(self, i)</dt><dd><tt>Removes an item from the <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="Protein-__delslice__"><strong>__delslice__</strong></a>(self, i, j)</dt><dd><tt>Deleted a slice of items located between indices i and j.</tt></dd></dl>
<dl><dt><a name="Protein-__getitem__"><strong>__getitem__</strong></a>(self, i)</dt><dd><tt>Returns an item from the <a href="#TypedList">TypedList</a> located at index i.</tt></dd></dl>
<dl><dt><a name="Protein-__getslice__"><strong>__getslice__</strong></a>(self, i, j)</dt><dd><tt>Returns a slice of the typed list between indexes i and j.</tt></dd></dl>
<dl><dt><a name="Protein-__len__"><strong>__len__</strong></a>(self)</dt><dd><tt>Returns the length of the <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="Protein-__mul__"><strong>__mul__</strong></a>(self, other)</dt><dd><tt>Multiply set of elements and another, and store in new.elements.</tt></dd></dl>
<dl><dt><a name="Protein-__repr__"><strong>__repr__</strong></a>(self)</dt><dd><tt>Returns a printable representation of the <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="Protein-__rmul__"><strong>__rmul__</strong></a> = __mul__(self, other)</dt><dd><tt>Multiply set of elements and another, and store in new.elements.</tt></dd></dl>
<dl><dt><a name="Protein-__setitem__"><strong>__setitem__</strong></a>(self, i, v)</dt><dd><tt>Sets item at index i to the value of v.</tt></dd></dl>
<dl><dt><a name="Protein-__setslice__"><strong>__setslice__</strong></a>(self, i, j, v)</dt><dd><tt>Sets the value of a slice of items between i and j to v.</tt></dd></dl>
<dl><dt><a name="Protein-__str__"><strong>__str__</strong></a>(self)</dt><dd><tt>Returns all elements of the <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="Protein-append"><strong>append</strong></a>(self, el)</dt><dd><tt>Add an element to the <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="Protein-clone"><strong>clone</strong></a> = __copy__(self)</dt><dd><tt>Returns a copy of a <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="Protein-count"><strong>count</strong></a>(self, el)</dt><dd><tt>Returns the number of elements in a <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="Protein-extend"><strong>extend</strong></a>(self, els)</dt><dd><tt>Add an attribute to an element in a <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="Protein-index"><strong>index</strong></a>(self, el)</dt><dd><tt>Return an index if the items in a <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="Protein-indices"><strong>indices</strong></a>(self, len<font color="#909090">=<built-in function len></font>)</dt><dd><tt>Returns the length of a range of indices.</tt></dd></dl>
<dl><dt><a name="Protein-insert"><strong>insert</strong></a>(self, pos, el)</dt><dd><tt>Insert an element in a <a href="#TypedList">TypedList</a> at position pos.</tt></dd></dl>
<dl><dt><a name="Protein-pop"><strong>pop</strong></a>(self)</dt><dd><tt>Remove the last element in a <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="Protein-remove"><strong>remove</strong></a>(self, el)</dt><dd><tt>Remove an element from a <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="Protein-reverse"><strong>reverse</strong></a>(self)</dt><dd><tt>Reverse the order of elements in a <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="Protein-reverse_indices"><strong>reverse_indices</strong></a>(self, len<font color="#909090">=<built-in function len></font>)</dt><dd><tt>Reverses indices of elements in a <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="Protein-sort"><strong>sort</strong></a>(self)</dt><dd><tt>Sort the elements in a <a href="#TypedList">TypedList</a>.</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="TypedList">class <strong>TypedList</strong></a></font></td></tr>
<tr bgcolor="#ffc8d8"><td rowspan=2><tt> </tt></td>
<td colspan=2><tt>A Python list restricted to having objects of the same type.<br>
An instance of a <a href="#TypedList">TypedList</a> is created as follows:<br>
<br>
mylist = <a href="#TypedList">TypedList</a>(function, [elements])<br>
<br>
where function is a python function which takes an argument<br>
and returns 1 or 0 indicating whether the object represented<br>
by the argument is of the correct type, and elements is an optional<br>
list of elements to be added into the instance. Here is a<br>
full blown example.<br>
<br>
def is_int(o):<br>
return type(o) == type(0)<br>
<br>
mylist = <a href="#TypedList">TypedList</a>(is_int, [0, 1, 2, 3])<br>
<br>
New elements are added to the list as follows:<br>
mylist.<a href="#TypedList-append">append</a>(25)<br>
<br>
Instances of <a href="#TypedList">TypedList</a> support all operations available for<br>
Python Lists (as of Python version 1.5.2a2)<br> </tt></td></tr>
<tr><td> </td>
<td width="100%">Methods defined here:<br>
<dl><dt><a name="TypedList-__add__"><strong>__add__</strong></a>(self, other)</dt><dd><tt>Adds a list to a <a href="#TypedList">TypedList</a>, as long as it's of the same type.</tt></dd></dl>
<dl><dt><a name="TypedList-__copy__"><strong>__copy__</strong></a>(self)</dt><dd><tt>Returns a copy of a <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="TypedList-__deepcopy__"><strong>__deepcopy__</strong></a> = <a href="#TypedList-__copy__">__copy__</a>(self)</dt></dl>
<dl><dt><a name="TypedList-__delitem__"><strong>__delitem__</strong></a>(self, i)</dt><dd><tt>Removes an item from the <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="TypedList-__delslice__"><strong>__delslice__</strong></a>(self, i, j)</dt><dd><tt>Deleted a slice of items located between indices i and j.</tt></dd></dl>
<dl><dt><a name="TypedList-__getitem__"><strong>__getitem__</strong></a>(self, i)</dt><dd><tt>Returns an item from the <a href="#TypedList">TypedList</a> located at index i.</tt></dd></dl>
<dl><dt><a name="TypedList-__getslice__"><strong>__getslice__</strong></a>(self, i, j)</dt><dd><tt>Returns a slice of the typed list between indexes i and j.</tt></dd></dl>
<dl><dt><a name="TypedList-__init__"><strong>__init__</strong></a>(self, function, elements<font color="#909090">=None</font>)</dt></dl>
<dl><dt><a name="TypedList-__len__"><strong>__len__</strong></a>(self)</dt><dd><tt>Returns the length of the <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="TypedList-__mul__"><strong>__mul__</strong></a>(self, other)</dt><dd><tt>Multiply set of elements and another, and store in new.elements.</tt></dd></dl>
<dl><dt><a name="TypedList-__repr__"><strong>__repr__</strong></a>(self)</dt><dd><tt>Returns a printable representation of the <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="TypedList-__rmul__"><strong>__rmul__</strong></a> = <a href="#TypedList-__mul__">__mul__</a>(self, other)</dt></dl>
<dl><dt><a name="TypedList-__setitem__"><strong>__setitem__</strong></a>(self, i, v)</dt><dd><tt>Sets item at index i to the value of v.</tt></dd></dl>
<dl><dt><a name="TypedList-__setslice__"><strong>__setslice__</strong></a>(self, i, j, v)</dt><dd><tt>Sets the value of a slice of items between i and j to v.</tt></dd></dl>
<dl><dt><a name="TypedList-__str__"><strong>__str__</strong></a>(self)</dt><dd><tt>Returns all elements of the <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="TypedList-append"><strong>append</strong></a>(self, el)</dt><dd><tt>Add an element to the <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="TypedList-clone"><strong>clone</strong></a> = <a href="#TypedList-__copy__">__copy__</a>(self)</dt></dl>
<dl><dt><a name="TypedList-count"><strong>count</strong></a>(self, el)</dt><dd><tt>Returns the number of elements in a <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="TypedList-extend"><strong>extend</strong></a>(self, els)</dt><dd><tt>Add an attribute to an element in a <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="TypedList-index"><strong>index</strong></a>(self, el)</dt><dd><tt>Return an index if the items in a <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="TypedList-indices"><strong>indices</strong></a>(self, len<font color="#909090">=<built-in function len></font>)</dt><dd><tt>Returns the length of a range of indices.</tt></dd></dl>
<dl><dt><a name="TypedList-insert"><strong>insert</strong></a>(self, pos, el)</dt><dd><tt>Insert an element in a <a href="#TypedList">TypedList</a> at position pos.</tt></dd></dl>
<dl><dt><a name="TypedList-pop"><strong>pop</strong></a>(self)</dt><dd><tt>Remove the last element in a <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="TypedList-remove"><strong>remove</strong></a>(self, el)</dt><dd><tt>Remove an element from a <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="TypedList-reverse"><strong>reverse</strong></a>(self)</dt><dd><tt>Reverse the order of elements in a <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="TypedList-reverse_indices"><strong>reverse_indices</strong></a>(self, len<font color="#909090">=<built-in function len></font>)</dt><dd><tt>Reverses indices of elements in a <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="TypedList-sort"><strong>sort</strong></a>(self)</dt><dd><tt>Sort the elements in a <a href="#TypedList">TypedList</a>.</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="molChain">class <strong>molChain</strong></a>(<a href="pross.html#TypedList">TypedList</a>)</font></td></tr>
<tr bgcolor="#ffc8d8"><td rowspan=2><tt> </tt></td>
<td colspan=2><tt>A <a href="#TypedList">TypedList</a> containing only items of the chain<br>
type, set with `is_a_chain`<br> </tt></td></tr>
<tr><td> </td>
<td width="100%">Methods defined here:<br>
<dl><dt><a name="molChain-__init__"><strong>__init__</strong></a>(self, name<font color="#909090">=''</font>, residues<font color="#909090">=None</font>, **kw)</dt></dl>
<dl><dt><a name="molChain-assign_radii"><strong>assign_radii</strong></a>(self)</dt><dd><tt>Assigns the radius of residues in a <a href="#molChain">molChain</a></tt></dd></dl>
<dl><dt><a name="molChain-atom_coordinates"><strong>atom_coordinates</strong></a>(self, *names)</dt><dd><tt>returns coordinates of named atoms. if names is None<br>
all atom coordinates are returned.</tt></dd></dl>
<dl><dt><a name="molChain-atoms"><strong>atoms</strong></a>(self)</dt><dd><tt>returns a python list of atoms in a residue.</tt></dd></dl>
<dl><dt><a name="molChain-atoms_not_with_name"><strong>atoms_not_with_name</strong></a>(self, *names)</dt><dd><tt>returns atoms in residue excluding specified names</tt></dd></dl>
<dl><dt><a name="molChain-atoms_with_name"><strong>atoms_with_name</strong></a>(self, *names)</dt><dd><tt>Returns a list of atoms that match the specified names.</tt></dd></dl>
<dl><dt><a name="molChain-delete_alt_locs"><strong>delete_alt_locs</strong></a>(self)</dt><dd><tt>delete_alt_locs - remove secondary conformations in the chain<br>
<br>
In a chain with multiple occupancy and alternate location identifiers,<br>
it is often desirable to eliminate the secondary conformations for<br>
use in simulation, etc. This function (abitrarily) finds and selects<br>
the first given conformation and deletes all other conformations.</tt></dd></dl>
<dl><dt><a name="molChain-delete_atoms_with_name"><strong>delete_atoms_with_name</strong></a>(self, *names)</dt><dd><tt>delete atoms in residue with specified names</tt></dd></dl>
<dl><dt><a name="molChain-delete_hetero"><strong>delete_hetero</strong></a>(self)</dt><dd><tt>delete all hetero atoms from a protein<br>
<br>
This function removes all HETATM records from the molecular<br>
structure. This include waters, heme groups, as well as residues<br>
with nonstandard structures</tt></dd></dl>
<dl><dt><a name="molChain-delete_residues_with_name"><strong>delete_residues_with_name</strong></a>(self, *names)</dt><dd><tt>delete specified residues from Chain</tt></dd></dl>
<dl><dt><a name="molChain-delete_waters"><strong>delete_waters</strong></a>(self)</dt><dd><tt>Delete water molecules from residues in the <a href="#molChain">molChain</a>.</tt></dd></dl>
<dl><dt><a name="molChain-num_atoms"><strong>num_atoms</strong></a>(self)</dt><dd><tt>Returns the number of atoms in each residue within a chain.</tt></dd></dl>
<dl><dt><a name="molChain-num_residues"><strong>num_residues</strong></a>(self)</dt><dd><tt>Returns the number of residues within a chain.</tt></dd></dl>
<dl><dt><a name="molChain-preserve_chain_hetero"><strong>preserve_chain_hetero</strong></a>(self)</dt><dd><tt>prevent hetero residues from being deleted as hetero atoms<br>
<br>
Normally, delete_hetero will delete all hetero atoms from a<br>
molecule. This includes waters and heterogroups (hemes, etc.),<br>
but it also includes hetero residues--nonstandard residues<br>
that have backbone connectivity but perhaps extra atoms (e.g.<br>
S-hydroxy-cysteine). Deleting these residues may disrupt an<br>
otherwise continuous chain and may be undesirable.<br>
<br>
Given that a chain has a valid SEQRES entry, this function will<br>
'unset' the hetero flag for heterogroups that are involved in<br>
the sequence itself. When delete_hetero is run, these atoms<br>
will be preserved.</tt></dd></dl>
<dl><dt><a name="molChain-residues_not_with_name"><strong>residues_not_with_name</strong></a>(self, *names)</dt><dd><tt>returns residues excluding specified names as a python list</tt></dd></dl>
<dl><dt><a name="molChain-residues_with_name"><strong>residues_with_name</strong></a>(self, *names)</dt><dd><tt>returns specified residues as a python list</tt></dd></dl>
<dl><dt><a name="molChain-rotatex"><strong>rotatex</strong></a>(self, theta)</dt><dd><tt>Rotates residues in the <a href="#molChain">molChain</a> by the X-axis.</tt></dd></dl>
<dl><dt><a name="molChain-rotatey"><strong>rotatey</strong></a>(self, theta)</dt><dd><tt>Rotates residues in the <a href="#molChain">molChain</a> by the Y-axis.</tt></dd></dl>
<dl><dt><a name="molChain-rotatez"><strong>rotatez</strong></a>(self, theta)</dt><dd><tt>Rotates residues in the <a href="#molChain">molChain</a> by the Z-axis.</tt></dd></dl>
<dl><dt><a name="molChain-translate"><strong>translate</strong></a>(self, dx, dy<font color="#909090">=None</font>, dz<font color="#909090">=None</font>)</dt></dl>
<dl><dt><a name="molChain-type"><strong>type</strong></a>(self)</dt><dd><tt>Returns the type of the <a href="#molChain">molChain</a>. Should always be `Chain`</tt></dd></dl>
<hr>
Methods inherited from <a href="pross.html#TypedList">TypedList</a>:<br>
<dl><dt><a name="molChain-__add__"><strong>__add__</strong></a>(self, other)</dt><dd><tt>Adds a list to a <a href="#TypedList">TypedList</a>, as long as it's of the same type.</tt></dd></dl>
<dl><dt><a name="molChain-__copy__"><strong>__copy__</strong></a>(self)</dt><dd><tt>Returns a copy of a <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="molChain-__deepcopy__"><strong>__deepcopy__</strong></a> = __copy__(self)</dt><dd><tt>Returns a copy of a <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="molChain-__delitem__"><strong>__delitem__</strong></a>(self, i)</dt><dd><tt>Removes an item from the <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="molChain-__delslice__"><strong>__delslice__</strong></a>(self, i, j)</dt><dd><tt>Deleted a slice of items located between indices i and j.</tt></dd></dl>
<dl><dt><a name="molChain-__getitem__"><strong>__getitem__</strong></a>(self, i)</dt><dd><tt>Returns an item from the <a href="#TypedList">TypedList</a> located at index i.</tt></dd></dl>
<dl><dt><a name="molChain-__getslice__"><strong>__getslice__</strong></a>(self, i, j)</dt><dd><tt>Returns a slice of the typed list between indexes i and j.</tt></dd></dl>
<dl><dt><a name="molChain-__len__"><strong>__len__</strong></a>(self)</dt><dd><tt>Returns the length of the <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="molChain-__mul__"><strong>__mul__</strong></a>(self, other)</dt><dd><tt>Multiply set of elements and another, and store in new.elements.</tt></dd></dl>
<dl><dt><a name="molChain-__repr__"><strong>__repr__</strong></a>(self)</dt><dd><tt>Returns a printable representation of the <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="molChain-__rmul__"><strong>__rmul__</strong></a> = __mul__(self, other)</dt><dd><tt>Multiply set of elements and another, and store in new.elements.</tt></dd></dl>
<dl><dt><a name="molChain-__setitem__"><strong>__setitem__</strong></a>(self, i, v)</dt><dd><tt>Sets item at index i to the value of v.</tt></dd></dl>
<dl><dt><a name="molChain-__setslice__"><strong>__setslice__</strong></a>(self, i, j, v)</dt><dd><tt>Sets the value of a slice of items between i and j to v.</tt></dd></dl>
<dl><dt><a name="molChain-__str__"><strong>__str__</strong></a>(self)</dt><dd><tt>Returns all elements of the <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="molChain-append"><strong>append</strong></a>(self, el)</dt><dd><tt>Add an element to the <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="molChain-clone"><strong>clone</strong></a> = __copy__(self)</dt><dd><tt>Returns a copy of a <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="molChain-count"><strong>count</strong></a>(self, el)</dt><dd><tt>Returns the number of elements in a <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="molChain-extend"><strong>extend</strong></a>(self, els)</dt><dd><tt>Add an attribute to an element in a <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="molChain-index"><strong>index</strong></a>(self, el)</dt><dd><tt>Return an index if the items in a <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="molChain-indices"><strong>indices</strong></a>(self, len<font color="#909090">=<built-in function len></font>)</dt><dd><tt>Returns the length of a range of indices.</tt></dd></dl>
<dl><dt><a name="molChain-insert"><strong>insert</strong></a>(self, pos, el)</dt><dd><tt>Insert an element in a <a href="#TypedList">TypedList</a> at position pos.</tt></dd></dl>
<dl><dt><a name="molChain-pop"><strong>pop</strong></a>(self)</dt><dd><tt>Remove the last element in a <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="molChain-remove"><strong>remove</strong></a>(self, el)</dt><dd><tt>Remove an element from a <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="molChain-reverse"><strong>reverse</strong></a>(self)</dt><dd><tt>Reverse the order of elements in a <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="molChain-reverse_indices"><strong>reverse_indices</strong></a>(self, len<font color="#909090">=<built-in function len></font>)</dt><dd><tt>Reverses indices of elements in a <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="molChain-sort"><strong>sort</strong></a>(self)</dt><dd><tt>Sort the elements in a <a href="#TypedList">TypedList</a>.</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="molMol">class <strong>molMol</strong></a>(<a href="pross.html#TypedList">TypedList</a>)</font></td></tr>
<tr bgcolor="#ffc8d8"><td rowspan=2><tt> </tt></td>
<td colspan=2><tt>A typed list containing only molecule objects,<br>
as set by `is_a_mol<br> </tt></td></tr>
<tr><td> </td>
<td width="100%">Methods defined here:<br>
<dl><dt><a name="molMol-__init__"><strong>__init__</strong></a>(self, name<font color="#909090">=''</font>, chains<font color="#909090">=None</font>)</dt></dl>
<dl><dt><a name="molMol-assign_radii"><strong>assign_radii</strong></a>(self)</dt><dd><tt>Assign the radius of each of the chains in the <a href="#molMol">molMol</a> <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="molMol-atom_coordinates"><strong>atom_coordinates</strong></a>(self, *names)</dt><dd><tt>Returns a python list with the coordinates of specified atoms.</tt></dd></dl>
<dl><dt><a name="molMol-atoms"><strong>atoms</strong></a>(self)</dt><dd><tt>Returns a list of the atoms in the <a href="#molMol">molMol</a> list.</tt></dd></dl>
<dl><dt><a name="molMol-atoms_not_with_name"><strong>atoms_not_with_name</strong></a>(self, *names)</dt><dd><tt>returns atoms in assembly excluding specified names</tt></dd></dl>
<dl><dt><a name="molMol-atoms_with_name"><strong>atoms_with_name</strong></a>(self, *names)</dt><dd><tt>Returns a list of atoms named with specified names.</tt></dd></dl>
<dl><dt><a name="molMol-chains_with_name"><strong>chains_with_name</strong></a>(self, *names)</dt><dd><tt>Returns each of the chains named with specified names.</tt></dd></dl>
<dl><dt><a name="molMol-delete_alt_locs"><strong>delete_alt_locs</strong></a>(self)</dt><dd><tt>delete_alt_locs - remove all secondary conformations</tt></dd></dl>
<dl><dt><a name="molMol-delete_atoms_with_name"><strong>delete_atoms_with_name</strong></a>(self, *names)</dt><dd><tt>delete atoms in assembly with specified names</tt></dd></dl>
<dl><dt><a name="molMol-delete_hetero"><strong>delete_hetero</strong></a>(self)</dt><dd><tt>Executes the delete_hetero method on chains in the <a href="#molMol">molMol</a> <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="molMol-delete_water"><strong>delete_water</strong></a>(self)</dt><dd><tt>Delete the water molecules from chains in the <a href="#molMol">molMol</a> <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="molMol-num_atoms"><strong>num_atoms</strong></a>(self)</dt><dd><tt>Returns the number of atoms in each of the chains in the <a href="#molMol">molMol</a> list.</tt></dd></dl>
<dl><dt><a name="molMol-num_chain"><strong>num_chain</strong></a>(self)</dt><dd><tt>Returns the number of chains in the <a href="#molMol">molMol</a> list.</tt></dd></dl>
<dl><dt><a name="molMol-num_res"><strong>num_res</strong></a>(self)</dt><dd><tt>Returns the number of residues in each of the chains in the <a href="#molMol">molMol</a> list.</tt></dd></dl>
<dl><dt><a name="molMol-pdb"><strong>pdb</strong></a>(self, file, renum<font color="#909090">=0</font>, seq<font color="#909090">=1</font>)</dt><dd><tt><a href="#molMol-pdb">pdb</a>(file, renum=0, seq=1) - write a PDB file<br>
<br>
Given a file name/open file handle (with .gz option), this function<br>
will write the PDB coordinate file corresponding to the current<br>
molecular object. If renum is true, then residue indices will be<br>
renumbered starting from 1, if seq is true, then SEQRES records<br>
will be written in the PDB file.<br>
<br>
This function is a wrapper for pdbout.write_pdb.</tt></dd></dl>
<dl><dt><a name="molMol-preserve_chain_hetero"><strong>preserve_chain_hetero</strong></a>(self)</dt><dd><tt>Executes the preserve_chain_hetero method on chains in the <a href="#molMol">molMol</a> <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="molMol-residues_with_name"><strong>residues_with_name</strong></a>(self, *names)</dt><dd><tt>Returns each of the residues named with specified names.</tt></dd></dl>
<hr>
Methods inherited from <a href="pross.html#TypedList">TypedList</a>:<br>
<dl><dt><a name="molMol-__add__"><strong>__add__</strong></a>(self, other)</dt><dd><tt>Adds a list to a <a href="#TypedList">TypedList</a>, as long as it's of the same type.</tt></dd></dl>
<dl><dt><a name="molMol-__copy__"><strong>__copy__</strong></a>(self)</dt><dd><tt>Returns a copy of a <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="molMol-__deepcopy__"><strong>__deepcopy__</strong></a> = __copy__(self)</dt><dd><tt>Returns a copy of a <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="molMol-__delitem__"><strong>__delitem__</strong></a>(self, i)</dt><dd><tt>Removes an item from the <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="molMol-__delslice__"><strong>__delslice__</strong></a>(self, i, j)</dt><dd><tt>Deleted a slice of items located between indices i and j.</tt></dd></dl>
<dl><dt><a name="molMol-__getitem__"><strong>__getitem__</strong></a>(self, i)</dt><dd><tt>Returns an item from the <a href="#TypedList">TypedList</a> located at index i.</tt></dd></dl>
<dl><dt><a name="molMol-__getslice__"><strong>__getslice__</strong></a>(self, i, j)</dt><dd><tt>Returns a slice of the typed list between indexes i and j.</tt></dd></dl>
<dl><dt><a name="molMol-__len__"><strong>__len__</strong></a>(self)</dt><dd><tt>Returns the length of the <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="molMol-__mul__"><strong>__mul__</strong></a>(self, other)</dt><dd><tt>Multiply set of elements and another, and store in new.elements.</tt></dd></dl>
<dl><dt><a name="molMol-__repr__"><strong>__repr__</strong></a>(self)</dt><dd><tt>Returns a printable representation of the <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="molMol-__rmul__"><strong>__rmul__</strong></a> = __mul__(self, other)</dt><dd><tt>Multiply set of elements and another, and store in new.elements.</tt></dd></dl>
<dl><dt><a name="molMol-__setitem__"><strong>__setitem__</strong></a>(self, i, v)</dt><dd><tt>Sets item at index i to the value of v.</tt></dd></dl>
<dl><dt><a name="molMol-__setslice__"><strong>__setslice__</strong></a>(self, i, j, v)</dt><dd><tt>Sets the value of a slice of items between i and j to v.</tt></dd></dl>
<dl><dt><a name="molMol-__str__"><strong>__str__</strong></a>(self)</dt><dd><tt>Returns all elements of the <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="molMol-append"><strong>append</strong></a>(self, el)</dt><dd><tt>Add an element to the <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="molMol-clone"><strong>clone</strong></a> = __copy__(self)</dt><dd><tt>Returns a copy of a <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="molMol-count"><strong>count</strong></a>(self, el)</dt><dd><tt>Returns the number of elements in a <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="molMol-extend"><strong>extend</strong></a>(self, els)</dt><dd><tt>Add an attribute to an element in a <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="molMol-index"><strong>index</strong></a>(self, el)</dt><dd><tt>Return an index if the items in a <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="molMol-indices"><strong>indices</strong></a>(self, len<font color="#909090">=<built-in function len></font>)</dt><dd><tt>Returns the length of a range of indices.</tt></dd></dl>
<dl><dt><a name="molMol-insert"><strong>insert</strong></a>(self, pos, el)</dt><dd><tt>Insert an element in a <a href="#TypedList">TypedList</a> at position pos.</tt></dd></dl>
<dl><dt><a name="molMol-pop"><strong>pop</strong></a>(self)</dt><dd><tt>Remove the last element in a <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="molMol-remove"><strong>remove</strong></a>(self, el)</dt><dd><tt>Remove an element from a <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="molMol-reverse"><strong>reverse</strong></a>(self)</dt><dd><tt>Reverse the order of elements in a <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="molMol-reverse_indices"><strong>reverse_indices</strong></a>(self, len<font color="#909090">=<built-in function len></font>)</dt><dd><tt>Reverses indices of elements in a <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="molMol-sort"><strong>sort</strong></a>(self)</dt><dd><tt>Sort the elements in a <a href="#TypedList">TypedList</a>.</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="molResidue">class <strong>molResidue</strong></a>(<a href="pross.html#TypedList">TypedList</a>)</font></td></tr>
<tr bgcolor="#ffc8d8"><td rowspan=2><tt> </tt></td>
<td colspan=2><tt>A <a href="#TypedList">TypedList</a> containing only objects of the residue<br>
type, set with `is_a_residue`<br> </tt></td></tr>
<tr><td> </td>
<td width="100%">Methods defined here:<br>
<dl><dt><a name="molResidue-__init__"><strong>__init__</strong></a>(self, name<font color="#909090">=''</font>, atoms<font color="#909090">=None</font>, **kw)</dt></dl>
<dl><dt><a name="molResidue-assign_radii"><strong>assign_radii</strong></a>(self)</dt></dl>
<dl><dt><a name="molResidue-atom_coordinates"><strong>atom_coordinates</strong></a>(self, *names)</dt><dd><tt>returns coordinates of named atoms.<br>
If names is omitted all atom coordinates are returned.</tt></dd></dl>
<dl><dt><a name="molResidue-atoms"><strong>atoms</strong></a>(self)</dt><dd><tt>Returns a list of atoms within the <a href="#molResidue">molResidue</a> list.</tt></dd></dl>
<dl><dt><a name="molResidue-atoms_not_with_name"><strong>atoms_not_with_name</strong></a>(self, *names)</dt><dd><tt>returns atoms in residue excluding specified names</tt></dd></dl>
<dl><dt><a name="molResidue-atoms_with_name"><strong>atoms_with_name</strong></a>(self, *names)</dt><dd><tt>returns atoms in residue with specified names</tt></dd></dl>
<dl><dt><a name="molResidue-delete_atoms_with_name"><strong>delete_atoms_with_name</strong></a>(self, *names)</dt><dd><tt>delete atoms in residue with specified names</tt></dd></dl>
<dl><dt><a name="molResidue-has_atom"><strong>has_atom</strong></a>(self, name)</dt><dd><tt>returns true if residue has an atom named 'name'</tt></dd></dl>
<dl><dt><a name="molResidue-num_atoms"><strong>num_atoms</strong></a>(self)</dt><dd><tt>returns the number of atoms in residue</tt></dd></dl>
<dl><dt><a name="molResidue-type"><strong>type</strong></a>(self)</dt></dl>
<hr>
Methods inherited from <a href="pross.html#TypedList">TypedList</a>:<br>
<dl><dt><a name="molResidue-__add__"><strong>__add__</strong></a>(self, other)</dt><dd><tt>Adds a list to a <a href="#TypedList">TypedList</a>, as long as it's of the same type.</tt></dd></dl>
<dl><dt><a name="molResidue-__copy__"><strong>__copy__</strong></a>(self)</dt><dd><tt>Returns a copy of a <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="molResidue-__deepcopy__"><strong>__deepcopy__</strong></a> = __copy__(self)</dt><dd><tt>Returns a copy of a <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="molResidue-__delitem__"><strong>__delitem__</strong></a>(self, i)</dt><dd><tt>Removes an item from the <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="molResidue-__delslice__"><strong>__delslice__</strong></a>(self, i, j)</dt><dd><tt>Deleted a slice of items located between indices i and j.</tt></dd></dl>
<dl><dt><a name="molResidue-__getitem__"><strong>__getitem__</strong></a>(self, i)</dt><dd><tt>Returns an item from the <a href="#TypedList">TypedList</a> located at index i.</tt></dd></dl>
<dl><dt><a name="molResidue-__getslice__"><strong>__getslice__</strong></a>(self, i, j)</dt><dd><tt>Returns a slice of the typed list between indexes i and j.</tt></dd></dl>
<dl><dt><a name="molResidue-__len__"><strong>__len__</strong></a>(self)</dt><dd><tt>Returns the length of the <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="molResidue-__mul__"><strong>__mul__</strong></a>(self, other)</dt><dd><tt>Multiply set of elements and another, and store in new.elements.</tt></dd></dl>
<dl><dt><a name="molResidue-__repr__"><strong>__repr__</strong></a>(self)</dt><dd><tt>Returns a printable representation of the <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="molResidue-__rmul__"><strong>__rmul__</strong></a> = __mul__(self, other)</dt><dd><tt>Multiply set of elements and another, and store in new.elements.</tt></dd></dl>
<dl><dt><a name="molResidue-__setitem__"><strong>__setitem__</strong></a>(self, i, v)</dt><dd><tt>Sets item at index i to the value of v.</tt></dd></dl>
<dl><dt><a name="molResidue-__setslice__"><strong>__setslice__</strong></a>(self, i, j, v)</dt><dd><tt>Sets the value of a slice of items between i and j to v.</tt></dd></dl>
<dl><dt><a name="molResidue-__str__"><strong>__str__</strong></a>(self)</dt><dd><tt>Returns all elements of the <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="molResidue-append"><strong>append</strong></a>(self, el)</dt><dd><tt>Add an element to the <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="molResidue-clone"><strong>clone</strong></a> = __copy__(self)</dt><dd><tt>Returns a copy of a <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="molResidue-count"><strong>count</strong></a>(self, el)</dt><dd><tt>Returns the number of elements in a <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="molResidue-extend"><strong>extend</strong></a>(self, els)</dt><dd><tt>Add an attribute to an element in a <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="molResidue-index"><strong>index</strong></a>(self, el)</dt><dd><tt>Return an index if the items in a <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="molResidue-indices"><strong>indices</strong></a>(self, len<font color="#909090">=<built-in function len></font>)</dt><dd><tt>Returns the length of a range of indices.</tt></dd></dl>
<dl><dt><a name="molResidue-insert"><strong>insert</strong></a>(self, pos, el)</dt><dd><tt>Insert an element in a <a href="#TypedList">TypedList</a> at position pos.</tt></dd></dl>
<dl><dt><a name="molResidue-pop"><strong>pop</strong></a>(self)</dt><dd><tt>Remove the last element in a <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="molResidue-remove"><strong>remove</strong></a>(self, el)</dt><dd><tt>Remove an element from a <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="molResidue-reverse"><strong>reverse</strong></a>(self)</dt><dd><tt>Reverse the order of elements in a <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="molResidue-reverse_indices"><strong>reverse_indices</strong></a>(self, len<font color="#909090">=<built-in function len></font>)</dt><dd><tt>Reverses indices of elements in a <a href="#TypedList">TypedList</a>.</tt></dd></dl>
<dl><dt><a name="molResidue-sort"><strong>sort</strong></a>(self)</dt><dd><tt>Sort the elements in a <a href="#TypedList">TypedList</a>.</tt></dd></dl>
</td></tr></table></td></tr></table><p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#eeaa77">
<td colspan=3 valign=bottom> <br>
<font color="#ffffff" face="helvetica, arial"><big><strong>Functions</strong></big></font></td></tr>
<tr><td bgcolor="#eeaa77"><tt> </tt></td><td> </td>
<td width="100%"><dl><dt><a name="-atom_build"><strong>atom_build</strong></a>(t, atom<font color="#909090">=<class pross.Atom3d></font>)</dt><dd><tt>Returns an Atom3b object.</tt></dd></dl>
<dl><dt><a name="-fromint"><strong>fromint</strong></a>(v1, dis, v2, a, v3, t, sqrt<font color="#909090">=<built-in function sqrt></font>, sin<font color="#909090">=<built-in function sin></font>, cos<font color="#909090">=<built-in function cos></font>)</dt></dl>
<dl><dt><a name="-get_sequences"><strong>get_sequences</strong></a>(file)</dt><dd><tt>Find the residue sequences and return them in a dictionary.</tt></dd></dl>
<dl><dt><a name="-is_atom"><strong>is_atom</strong></a>(o)</dt><dd><tt>Determine if an object in a <a href="#TypedList">TypedList</a> is an atom.</tt></dd></dl>
<dl><dt><a name="-is_chain"><strong>is_chain</strong></a>(o)</dt><dd><tt>Determine if an object in a <a href="#TypedList">TypedList</a> is a chain.</tt></dd></dl>
<dl><dt><a name="-is_mol"><strong>is_mol</strong></a>(o)</dt><dd><tt>Determine if an object in a <a href="#TypedList">TypedList</a> is a molecule.</tt></dd></dl>
<dl><dt><a name="-is_protein"><strong>is_protein</strong></a>(chain)</dt><dd><tt>Determines if residues in a chain are proteins.</tt></dd></dl>
<dl><dt><a name="-is_residue"><strong>is_residue</strong></a>(o)</dt><dd><tt>Determine if an object in a <a href="#TypedList">TypedList</a> is a residue.</tt></dd></dl>
<dl><dt><a name="-pack_pdb_line"><strong>pack_pdb_line</strong></a>(atom, idx, aan, aanum, ic, cn, f, fmt)</dt><dd><tt>pack_pdb_line - construct an ATOM record for a PDB file<br>
<br>
pack_pdb_line takes the following arguments:<br>
<br>
o atom An atom3d object, used for extracting coordinates, occupancy<br>
atom name, alternate location, and B-factor. If these<br>
attributes aren't contained in the object, reasonable defaults<br>
are used.<br>
<br>
o idx The atom serial number<br>
<br>
o aan The name of the containing amino residue (DNA base)<br>
<br>
o aanum The number of the containing residue (DNA base)<br>
<br>
o ic The insertion code for homologous residue numbering<br>
<br>
o cn The name of the chain<br>
<br>
o f An open file handle where the format will be written.<br>
<br>
o fmt A format to be used. Generally this is either for ATOM or<br>
HETATM records.</tt></dd></dl>
<dl><dt><a name="-pad"><strong>pad</strong></a>(nm)</dt><dd><tt><a href="#-pad">pad</a>(nm) - a function to pad an atom name with appropraiate spaces</tt></dd></dl>
<dl><dt><a name="-rc_codes"><strong>rc_codes</strong></a>(chain, phi<font color="#909090">=None</font>, psi<font color="#909090">=None</font>, ome<font color="#909090">=None</font>, mcodes<font color="#909090">=None</font>)</dt><dd><tt><a href="#-rc_codes">rc_codes</a>(chain, phi, psi, ome) - return rotamer codes<br>
<br>
Given a protein chain (and optionally phi, psi, omega), this<br>
function will return a list of mesostate codes that<br>
applies to the chain, as determined by res_rc.</tt></dd></dl>
<dl><dt><a name="-rc_ss"><strong>rc_ss</strong></a>(chain, phi<font color="#909090">=None</font>, psi<font color="#909090">=None</font>, ome<font color="#909090">=None</font>, mcodes<font color="#909090">=None</font>)</dt><dd><tt><a href="#-rc_ss">rc_ss</a>(chain, phi, psi, ome) - calculate secondary structure<br>
<br>
This function calculates the secondary structure using the PROSS method<br>
with rotamer codes. Given a chain, and optionally a list of phi,<br>
psi, and omega, it calculates the backbone secondary structure of<br>
the chain. The return value is (phi, psi, ome, sst), where<br>
phi, psi, and ome are calculated if not specified, and sst is the<br>
secondary structure codes: H = helix, E = strand, P = PII, C = coil.</tt></dd></dl>
<dl><dt><a name="-read_pdb"><strong>read_pdb</strong></a>(f, as_protein<font color="#909090">=0</font>, as_rna<font color="#909090">=0</font>, as_dna<font color="#909090">=0</font>, all_models<font color="#909090">=0</font>, unpack<font color="#909090">=<function unpack_pdb_line></font>, atom_build<font color="#909090">=<function atom_build></font>)</dt><dd><tt>read_pdb - read the entire contents of a PDB file as a molcule object<br>
<br>
This function parses a PDB file and returns a heirarchic data structure<br>
that can be used to browse atomic contents. The heirarchic data elements<br>
are built on 'typed' lists. The first level is a list of 'chains',<br>
where a chain can be non-specific or a protein, DNA, or RNA chain. A<br>
chain (of any type) is a list of residues, and a residue is a list of<br>
atoms. Atoms are defined as a full-blown Python object, with its own<br>
member functions and data (including x, y, z). Residues and chains are<br>
derived from the <a href="#TypedList">TypedList</a> object, but can have their own member data<br>
and functions--for example, the *pross* function is only available for<br>
<a href="#Protein">Protein</a> chains, and chains in general have a public variable *name*<br>
the described the SegID for that chain.<br>
<br>
read_pdb takes the following arguments:<br>
<br>
o f A file containing PDB data. If *f* is a string, it will<br>
be checked for a '.gz' extension. Given that it contains<br>
GZipped data, the file will be opened as a GZipFile and<br>
parsed accordingly. If no '.gz' extension is present,<br>
the file will be opened as a regular text file.<br>
Alternatively, f can be an open file object with the<br>
'readline' member function. If this is the case, the file<br>
will not be closed upon exiting, and read_pdb will read<br>
until the 'END' token is reached.<br>
<br>
o as_protein Read the PDB as a protein. It will have the protein<br>
specific member functions that allow calculation of torsion<br>
angles, etc. By default this is false, and the type is<br>
determined automatically from the residue types.<br>
<br>
o as_rna Read the PDB as RNA. As above, this is false by default<br>
and determined automatically.<br>
<br>
o as_dna Read the PDB as DNA. As above, this is false by default<br>
and determined automatically.<br>
<br>
o all_models A boolean. The default is false. If true, all NMR models<br>
will be read in as differing chains rather than just the<br>
first one.</tt></dd></dl>
<dl><dt><a name="-res_rc"><strong>res_rc</strong></a>(r1, r2, r3<font color="#909090">=180</font>, mcodes<font color="#909090">=None</font>)</dt><dd><tt><a href="#-res_rc">res_rc</a>(r1, r2, r3) - get mesostate code for a residue<br>
<br>
Given a phi (r1), psi (r2), and omega (r3) torsion angle, calculate<br>
the mesostate code that describes that residue. <br>
A mesostate will be returned in<br>
all but two cases: if omega deviates from planarity by more than 90<br>
degrees, '*' is returned. Also, if any torsions are greater than<br>
180.0 (biomol assignes 999.0 degrees to angles that that are<br>
indeterminate), prosst.INVALID is returned. Here, r3 defaults to<br>
180.0.</tt></dd></dl>
<dl><dt><a name="-run"><strong>run</strong></a>(file, mcode)</dt><dd><tt>Reads a pdb file and iterates through each chain, and groups residues<br>
Together, and then finally, writes the residues to angfile.</tt></dd></dl>
<dl><dt><a name="-terminate"><strong>terminate</strong></a>(snum, rn, cn, rnum, icode, f)</dt><dd><tt>terminate - write a TER record to a PDB file</tt></dd></dl>
<dl><dt><a name="-unpack_pdb_line"><strong>unpack_pdb_line</strong></a>(line, ATOF<font color="#909090">=<function _atof></font>, ATOI<font color="#909090">=<function _atoi></font>, STRIP<font color="#909090">=<function strip></font>)</dt><dd><tt>Gather atom information from the pdb lines, convert them to a usable format.</tt></dd></dl>
<dl><dt><a name="-write_pdb"><strong>write_pdb</strong></a>(myMol, f, renum<font color="#909090">=0</font>, seq<font color="#909090">=None</font>, pack<font color="#909090">=<function pack_pdb_line></font>)</dt><dd><tt>write_pdb - write a PDB file from a molecular object<br>
<br>
write_pdb takes a biomol.Mol object and creates a PDB file<br>
based on the definitions given. It can support all atomic<br>
properties as well as insertion codes and alternate locations.<br>
Essentially, biomol is designed such that if the original molecule<br>
has all that stuff it will be retained in the final PDB file. If<br>
that is not desired, you must make the modifications to the Mol<br>
object yourself (or use one of the utilities).<br>
<br>
write_pdb takes the following arguments:<br>
<br>
o myMol The **mol.Mol** object to be written.<br>
<br>
o f A file instruction. This can be a string, in which<br>
case f will be interpreted as a filename. If the<br>
string f ends with .gz, the resulting file will be<br>
compressed using gzip. Alternatively, f can be an<br>
open file object (it must have the write attribute).<br>
If f is an object, the PDB will be written to the<br>
object. When f is a file object, SEQRES and END<br>
records will not be written by default.<br>
<br>
o seq A boolean that determines whether SEQRES records<br>
will be written. By default this is true (except in<br>
the case where f is an object).</tt></dd></dl>
<dl><dt><a name="-write_sequences"><strong>write_sequences</strong></a>(chain, f)</dt><dd><tt>write_sequences - write SEQRES records to a PDB file<br>
<br>
write_sequences takes the following arguments:<br>
<br>
o chain A mol.Chain type whose residues/bases will be displayed<br>
<br>
o f An open file handle where information will be written.</tt></dd></dl>
</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>CHI1_ATOMS</strong> = {'ARG': ('N', 'CA', 'CB', 'CG'), 'ASN': ('N', 'CA', 'CB', 'CG'), 'ASP': ('N', 'CA', 'CB', 'CG'), 'ASX': ('N', 'CA', 'CB', 'CG'), 'CYS': ('N', 'CA', 'CB', 'SG'), 'CYX': ('N', 'CA', 'CB', 'CG'), 'GLN': ('N', 'CA', 'CB', 'CG'), 'GLU': ('N', 'CA', 'CB', 'CG'), 'GLX': ('N', 'CA', 'CB', 'CG'), 'HIS': ('N', 'CA', 'CB', 'CG'), ...}<br>
<strong>CHI2_ATOMS</strong> = {'ARG': ('CA', 'CB', 'CG', 'CD'), 'ASN': ('CA', 'CB', 'CG', 'OD1'), 'ASP': ('CA', 'CB', 'CG', 'OD1'), 'ASX': ('CA', 'CB', 'CG', 'OD1'), 'GLN': ('CA', 'CB', 'CG', 'CD'), 'GLU': ('CA', 'CB', 'CG', 'CD'), 'GLX': ('CA', 'CB', 'CG', 'CD'), 'HIS': ('CA', 'CB', 'CG', 'ND1'), 'ILE': ('CA', 'CB', 'CG1', 'CD1'), 'LEU': ('CA', 'CB', 'CG', 'CD1'), ...}<br>
<strong>CHI3_ATOMS</strong> = {'ARG': ('CB', 'CG', 'CD', 'NE'), 'GLN': ('CB', 'CG', 'CD', 'OE1'), 'GLU': ('CB', 'CG', 'CD', 'OE1'), 'GLX': ('CB', 'CG', 'CD', 'OE1'), 'LYS': ('CB', 'CG', 'CD', 'CE'), 'MET': ('CB', 'CG', 'SD', 'CE')}<br>
<strong>CHI4_ATOMS</strong> = {'ARG': ('CG', 'CD', 'NE', 'CZ'), 'LYS': ('CG', 'CD', 'CE', 'NZ')}<br>
<strong>HAVE_EXTEND</strong> = True<br>
<strong>HAVE_NUMPY</strong> = 0<br>
<strong>HAVE_POP</strong> = True<br>
<strong>MSDEFS</strong> = {'fgmeso': {'CODE_LENGTH': 2, 'DELTA': 30.0, 'HELIX': <_sre.SRE_Pattern object>, 'INVALID': '??', 'OMEGA': '**', 'PHI_OFF': 0.0, 'PII': {'Dk': 1, 'Dl': 1, 'Ek': 1, 'El': 1}, 'PSI_OFF': 15.0, 'RC_DICT': {(-150, -165): 'Ba', (-150, -135): 'Bb', (-150, -105): 'Bc', (-150, -75): 'Bd', (-150, -45): 'Be', (-150, -15): 'Bf', (-150, 15): 'Bg', (-150, 45): 'Bh', (-150, 75): 'Bi', (-150, 105): 'Bj', ...}, 'STRAND': <_sre.SRE_Pattern object>, ...}, 'oldmeso': {'CODE_LENGTH': 1, 'DELTA': 60.0, 'HELIX': <_sre.SRE_Pattern object>, 'INVALID': '?', 'OMEGA': '*', 'PHI_OFF': 0.0, 'PII': {'M': 1, 'R': 1}, 'PSI_OFF': 0.0, 'RC_DICT': {(-120, -120): 'H', (-120, -60): 'I', (-120, 0): 'J', (-120, 60): 'K', (-120, 120): 'L', (-120, 180): 'G', (-60, -120): 'N', (-60, -60): 'O', (-60, 0): 'P', (-60, 60): 'Q', ...}, 'STRAND': <_sre.SRE_Pattern object>, ...}}<br>
<strong>ONE_LETTER_CODES</strong> = {'ALA': 'A', 'ARG': 'R', 'ASN': 'N', 'ASP': 'D', 'CYS': 'C', 'GLN': 'Q', 'GLU': 'E', 'GLY': 'G', 'HIS': 'H', 'ILE': 'I', ...}<br>
<strong>RESIDUES</strong> = ['ALA', 'ARG', 'ASN', 'ASP', 'CYS', 'CYX', 'GLN', 'GLU', 'GLX', 'GLY', 'HIS', 'HIP', 'ILE', 'LEU', 'LYS', 'MET', 'PHE', 'PRO', 'SER', 'THR', ...]<br>
<strong>UP_ALTLOC</strong> = 2<br>
<strong>UP_CHAINID</strong> = 4<br>
<strong>UP_ICODE</strong> = 6<br>
<strong>UP_NAME</strong> = 1<br>
<strong>UP_OCCUPANCY</strong> = 10<br>
<strong>UP_RESNAME</strong> = 3<br>
<strong>UP_RESSEQ</strong> = 5<br>
<strong>UP_SERIAL</strong> = 0<br>
<strong>UP_TEMPFACTOR</strong> = 11<br>
<strong>UP_X</strong> = 7<br>
<strong>UP_Y</strong> = 8<br>
<strong>UP_Z</strong> = 9<br>
<strong>USAGE</strong> = '<font color="#c040c0">\n</font>python PROSS.py pdbfile [oldmeso | fgmeso]<font color="#c040c0">\n</font>Choo...d mesostate definitions.<font color="#c040c0">\n</font>Default is finegrained.<font color="#c040c0">\n</font>'<br>
<strong>default</strong> = 'fgmeso'<br>
<strong>helix</strong> = ('O', 'P')<br>
<strong>mydefs</strong> = {'CODE_LENGTH': 1, 'DELTA': 60.0, 'HELIX': <_sre.SRE_Pattern object>, 'INVALID': '?', 'OMEGA': '*', 'PHI_OFF': 0.0, 'PII': {'M': 1, 'R': 1}, 'PSI_OFF': 0.0, 'RC_DICT': {(-120, -120): 'H', (-120, -60): 'I', (-120, 0): 'J', (-120, 60): 'K', (-120, 120): 'L', (-120, 180): 'G', (-60, -120): 'N', (-60, -60): 'O', (-60, 0): 'P', (-60, 60): 'Q', ...}, 'STRAND': <_sre.SRE_Pattern object>, ...}<br>
<strong>pat_helix</strong> = '((O)|(P)){5,}'<br>
<strong>pat_strand</strong> = '((L)|(G)|(F)|(A)){3,}'<br>
<strong>strand</strong> = ('L', 'G', 'F', 'A')</td></tr></table>
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