"""
Utilities for PDB2PQR Suite
This module provides various utilities for the PDB2PQR suite to be
imported into other Python scripts.
----------------------------
PDB2PQR -- An automated pipeline for the setup, execution, and analysis of
Poisson-Boltzmann electrostatics calculations
Copyright (c) 2002-2010, Jens Erik Nielsen, University College Dublin;
Nathan A. Baker, Washington University in St. Louis; Paul Czodrowski &
Gerhard Klebe, University of Marburg
All rights reserved.
Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice,
this list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
* Neither the names of University College Dublin, Washington University in
St. Louis, or University of Marburg nor the names of its contributors may
be used to endorse or promote products derived from this software without
specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED
OF THE POSSIBILITY OF SUCH DAMAGE.
----------------------------
"""
__date__ = "6 November 2007"
__author__ = "Todd Dolinsky, Yong Huang"
SMALL = 1.0e-7
DIHEDRAL = 57.2958
import string
import math
import os
import sys
def sortDictByValue(dict):
"""
Sort a dictionary by its values
Parameters
dict: The dictionary to sort (dict)
Returns
items: The dictionary sorted by value (list)
"""
items = [(v, k) for k, v in dict.items()]
items.sort()
items.reverse()
items = [ k for v, k in items]
return items
def shortestPath(graph, start, end, path=[]):
"""
Uses recursion to find the shortest path from one node to
another in an unweighted graph. Adapted from
http://www.python.org/doc/essays/graphs.html .
Parameters:
graph: A mapping of the graph to analyze, of the form
{0: [1,2], 1:[3,4], ...} . Each key has a list
of edges.
start: The ID of the key to start the analysis from
end: The ID of the key to end the analysis
path: Optional argument used during the recursive step
to keep the current path up to that point
Returns:
(variable): Returns a list of the shortest path (list)
Returns None if start and end are not
connected
"""
path = path + [start]
if start == end:
return path
if not graph.has_key(start):
return None
shortest = None
for node in graph[start]:
if node not in path:
newpath = shortestPath(graph, node, end, path)
if newpath:
if not shortest or len(newpath) < len(shortest):
shortest = newpath
return shortest
def analyzeConnectivity(map, key):
"""
Analyze the connectivity of a given map using the key value.
Parameters
map: The map to analyze (dict)
key: The key value (variable)
Returns
list: A list of connected values to the key (list)
"""
list = []
keys = [key]
while len(keys) > 0:
key = keys[0]
if key not in list:
list.append(key)
# The following 4 lines are modified by Greg Cipriano as a bug fix
if key in map:
for value in map[key]:
if value not in list:
keys.append(value)
keys.pop(keys.index(key))
return list
def getAngle(coords1, coords2, coords3):
"""
Get the angle between three coordinates
Parameters
coords1: The first coordinate set (atom)
coords2: The second (vertex) coordinate set (atom)
coords3: The third coordinate set (atom)
Returns
angle: The angle between the atoms (float)
"""
angle = 0.0
c1 = subtract(coords3, coords2)
c2 = subtract(coords1, coords2)
norm1 = normalize(c1)
norm2 = normalize(c2)
dotted = dot(norm1, norm2)
if dotted > 1.0: # If normalized, this is due to rounding error
dotted = 1.0
rad = abs(math.acos(dotted))
angle = rad*180.0/math.pi
if angle > 180.0:
angle = 360.0 - angle
return angle
def getFFfile(name):
"""
Grab the forcefield file. May or may not residue in the dat/
directory.
"""
path = ""
dirs = sys.path + ["dat"]
if name in ["amber", "charmm", "parse", "tyl06", "peoepb", "swanson"]: name = name.upper()
names = ["dat/%s.DAT" % name]
names.append("%s.DAT" % name)
names.append("%s.dat" % name)
names.append("dat/%s" % name)
names.append(name)
for guess in names:
if os.path.isfile(guess):
return guess
for p in dirs:
testpath = "%s/%s" % (p, guess)
if os.path.isfile(testpath):
return testpath
# If we get here return empty string
return ""
def getNamesFile(name):
"""
Grab the *.names file that contains the XML mapping.
Parameters
name: The name of the forcefield (string)
Returns
path: The path to the file (string)
"""
path = ""
dirs = sys.path + ["dat"]
if name in ["amber", "charmm", "parse", "tyl06", "peoepb", "swanson"]: name = name.upper()
names = ["dat/%s.names" % name]
names.append("%s.names" % name)
for guess in names:
if os.path.isfile(guess):
return guess
for p in dirs:
testpath = "%s/%s" % (p, guess)
if os.path.isfile(testpath):
return testpath
# If we get here return empty string
return ""
def getDatFile(name):
"""
Grab a data file. If the file cannot be found in the
given directory, try the current system path.
Parameters
name: The name of the file to get (string)
Returns
path: The path to the file (string)
"""
path = ""
if os.path.isfile(name):
path = name
for p in sys.path:
testpath = "%s/%s" % (p, name)
if os.path.isfile(testpath):
path = testpath
return path
def getPDBFile(path):
"""
Obtain a PDB file. First check the path given on the command
line - if that file is not available, obtain the file from the
PDB webserver at http://www.rcsb.org/pdb/ .
Parameters
path: Name of PDB file to obtain (string)
Returns
file: File object containing PDB file (file object)
"""
import os, urllib
file = None
if not os.path.isfile(path):
URLpath = "http://www.rcsb.org/pdb/cgi/export.cgi/" + path + \
".pdb?format=PDB&pdbId=" + path + "&compression=None"
file = urllib.urlopen(URLpath)
else:
file = open(path, 'rU')
return file
def distance(coords1, coords2):
"""
Calculate the distance between two coordinates, as denoted by
dist = sqrt((x2- x1)^2 + (y2 - y1)^2 + (z2 - z1)^2))
Parameters
coords1: Coordinates of form [x,y,z]
coords2: Coordinates of form [x,y,z]
Returns
dist: Distance between the two coordinates (float)
"""
dist = 0.0
list = []
p = coords2[0] - coords1[0]
q = coords2[1] - coords1[1]
r = coords2[2] - coords1[2]
dist = math.sqrt(p*p + q*q + r*r)
return dist
def add(coords1, coords2):
"""
Add one 3-dimensional point to another
Parameters
coords1: coordinates of form [x,y,z]
coords2: coordinates of form [x,y,z]
Returns
list: List of coordinates equal to coords2 + coords1 (list)
"""
x = coords1[0] + coords2[0]
y = coords1[1] + coords2[1]
z = coords1[2] + coords2[2]
return [x,y,z]
def subtract(coords1, coords2):
"""
Subtract one 3-dimensional point from another
Parameters
coords1: coordinates of form [x,y,z]
coords2: coordinates of form [x,y,z]
Returns
list: List of coordinates equal to coords1 - coords2 (list)
"""
x = coords1[0] - coords2[0]
y = coords1[1] - coords2[1]
z = coords1[2] - coords2[2]
return [x,y,z]
def cross(coords1, coords2):
"""
Find the cross product of two 3-dimensional points
Parameters
coords1: coordinates of form [x,y,z]
coords2: coordinates of form [x,y,z]
Returns
list: Cross product coords2 and coords1 (list)
"""
list = []
x = coords1[1]*coords2[2] - coords1[2]*coords2[1]
y = coords1[2]*coords2[0] - coords1[0]*coords2[2]
z = coords1[0]*coords2[1] - coords1[1]*coords2[0]
list = [x,y,z]
return list
def dot(coords1, coords2):
"""
Find the dot product of two 3-dimensional points
Parameters
coords1: coordinates of form [x,y,z]
coords2: coordinates of form [x,y,z]
Returns
value: Dot product coords2 and coords1 (float)
"""
value = 0.0
for i in range(3):
value += coords1[i]*coords2[i]
return value
def normalize(coords):
"""
Normalize a set of coordinates
Parameters
coords: coordinates of form [x,y,z]
Returns
list: normalized coordinates (list)
"""
list = []
dist = math.sqrt(pow(coords[0],2) + pow(coords[1],2) + pow(coords[2],2))
if dist > SMALL:
a = coords[0]/dist
b = coords[1]/dist
c = coords[2]/dist
list = [a,b,c]
else:
list = coords
return list
def factorial(n):
"""
Returns the factorial of the given number n
"""
if n <= 1 : return 1
return n*factorial(n-1)
def getDihedral(coords1, coords2, coords3, coords4):
"""
Calculate the angle using the four atoms
Parameters
coords1: First of four coordinates of form [x,y,z]
coords2: Second of four
coords3: Third of four
coords4: Fourth of four
Returns
value: Size of the angle (float)
"""
value = 0.0
list43 = subtract(coords4, coords3)
list32 = subtract(coords3, coords2)
list12 = subtract(coords1, coords2)
A = cross(list12, list32)
Anorm = normalize(A)
B = cross(list43, list32)
Bnorm = normalize(B)
scal = dot(Anorm, Bnorm)
if abs(scal + 1.0) < SMALL:
value = 180.0
elif abs(scal - 1.0) < SMALL:
value = 0.0
else:
value = DIHEDRAL * math.acos(scal)
chiral = dot(cross(Anorm, Bnorm),list32)
if chiral < 0:
value = value * -1.0
return value
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