Pyadmin: 1 revision

2014-03-28T01:49:16Z

1 revision

MartinChristen: New script to get statistics on b-factors ~~~~

2013-02-14T11:30:54Z

New script to get statistics on b-factors ~~~~

New page

= Overview =
This script calculates statistics on the B-values for all atoms in the selected object, prints the information on screen and appends it to a file called "cluster_count.txt".

= Usage =
<source lang="python">
cluster_count object
</source>

= Example =
<source lang="python">
cluster_count 1ubq

#output on screen:

Number of atoms in ' 1ubq ': 602
Minimum and Maximum B-values: 2.0 42.75
Average B-value: 13.4131063029
Standard deviation of the B-values: 8.70767140923
This data will be appended to cluster_count.txt

#output in file cluster_count.txt; the format is:
#objectname N minB maxB aveB stdevB
1ubq 602 2.000 42.750 13.413 8.708
</source>

= The Code =
<source lang="python">

# Script: cluster_count.py
# Copyleft 2010 Martin Christen

from pymol import cmd,stored
def cluster_count(selection):

"""
AUTHOR

Martin Christen

DESCRIPTION

This script calculates statistics on the B-values for all atoms in
the selected object, prints the information on screen and appends
it to the file "cluster_count.txt".

Output format on screen:
------------------------
Number of atoms in 'selection': 0
Minimum and Maximum B-values: 0.0
Average B-value : 0.0
Standard deviation of the B-values (best): 0.0 (0.0)
This data will be appended to cluster_count.txt

Output format in cluster_count.txt:
-----------------------------------
selection N minB maxB aveB stdevB

EXAMPLE

cluster_count 1ubq

Number of atoms in ' 1ubq ': 602
Minimum and Maximum B-values: 2.0 42.75
Average B-value: 13.4131063029
Standard deviation of the B-values: 8.70767140923
This data will be appended to cluster_count.txt

(in cluster_count.txt:)
1ubq 602 2.000 42.750 13.413 8.708

USAGE

cluster_count selection

"""

# get list of B-factors from selection
m = cmd.get_model(selection)
sel = []
b_list = []
dummy = []
for i in range(len(m.atom)):
b_list.append(m.atom[i].b)

#determine min and max
try: max_b = max(b_list)
except ValueError: max_b=0
try: min_b = min(b_list)
except ValueError: min_b=0

#determine average
try: average_b= float(sum(b_list)) / len(b_list)
except ZeroDivisionError: average_b=0

#determine standard deviation
for i in range(len(m.atom)):
if m.atom[i]>average_b:
dummy.append((m.atom[i].b-average_b)**2)
if m.atom[i]<average_b:
dummy.append((average_b-m.atom[i].b)**2)
try: stdev_b= (sum(dummy) / (len(m.atom)-1))**(1/2.0)
except ZeroDivisionError: stdev_b=0

#print values on screen
print "Number of atoms in '", selection,"': ", len(b_list)
print "Minimum and Maximum B-values: ", min_b, max_b
print "Average B-value: ", average_b
print "Standard deviation of the B-values: ", stdev_b
print "This data will be appended to cluster_count.txt"

#write information to cluster_count.txt
f=open('cluster_count.txt','a')
print >>f, '%-10s %8d %8.3f %8.3f %8.3f %8.3f' % (selection, len(m.atom), min_b, max_b, average_b, stdev_b)
f.close()
cmd.extend("cluster_count",cluster_count)
</source>

[[Category:Script_Library]]
[[Category:ObjSel_Scripts]]

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Cluster Count - Revision history

Pyadmin: 1 revision

MartinChristen: New script to get statistics on b-factors ~~~~