Useful Python Scripts - Revision history

import>Jss43 at 13:11, 7 October 2008

2008-10-07T13:11:54Z

@@ Line 5: / Line 5: @@
 This [[Media:pdb2xleap.txt|script]] takes a filename as command line argument reads the respective .pdb file and converts it to an xleap
 readable format. The initial file is overwritten, but the original file is retained in filename.orig.
 <pre>
 #!/usr/bin/env python
@@ Line 99: / Line 98: @@
 </pre>
 This addition doesn't cause any breakage if run using a later version of python.

import>Jss43: /* Fortran module dependencies */

2008-09-30T16:04:05Z

Fortran module dependencies

← Older revision		Revision as of 16:04, 30 September 2008
Line 90:		Line 90:
	to produce all the graphs in one shot. (Note ~/local/bin is on my path.)		to produce all the graphs in one shot. (Note ~/local/bin is on my path.)

	If you are using python 2.4, James suggests adding the following lines to the get_dependencies.py script:		If you are using python 2.4, James suggests adding the following lines to the get_dependencies.py script, after the ''import re,sys'' line:
	<pre>		<pre>
	import re,sys
	# 2.4 compatibility:		# 2.4 compatibility:
	try:		try:
Line 99:		Line 98:
	from sets import Set as set		from sets import Set as set
	</pre>		</pre>
			This addition doesn't cause any breakage if run using a later version of python.

import>Am592: /* Fortran module dependencies */

2008-09-30T15:52:58Z

Fortran module dependencies

← Older revision		Revision as of 15:52, 30 September 2008
Line 91:		Line 91:

	If you are using python 2.4, James suggests adding the following lines to the get_dependencies.py script:		If you are using python 2.4, James suggests adding the following lines to the get_dependencies.py script:
			<pre>

	import re,sys		import re,sys
	# 2.4 compatibility:		# 2.4 compatibility:
Line 98:		Line 98:
	except NameError:		except NameError:
	from sets import Set as set		from sets import Set as set
			</pre>

import>Am592: /* Fortran module dependencies */

2008-09-30T15:51:54Z

Fortran module dependencies

← Older revision		Revision as of 15:51, 30 September 2008
Line 89:		Line 89:
	~/src/dependencies $ for f in *.dot; do dot -Tps $f -o `basename $f .dot`.ps; done		~/src/dependencies $ for f in *.dot; do dot -Tps $f -o `basename $f .dot`.ps; done
	to produce all the graphs in one shot. (Note ~/local/bin is on my path.)		to produce all the graphs in one shot. (Note ~/local/bin is on my path.)

			If you are using python 2.4, James suggests adding the following lines to the get_dependencies.py script:

			import re,sys
			# 2.4 compatibility:
			try:
			set(['abc'])
			except NameError:
			from sets import Set as set

import>Jss43 at 22:05, 29 September 2008

2008-09-29T22:05:06Z

← Older revision		Revision as of 22:05, 29 September 2008
Line 64:		Line 64:
	== Fortran module dependencies ==		== Fortran module dependencies ==

			[[Image:Modules_use_main.png\|thumb\|Module dependency graph\|500px]]

	It is useful to be able to view the dependencies on modules in a fortran code graphically. This is especially helpful when trying to reorder code for a cleaner flow, trying to remove issues leading to circular dependencies, or for becoming familiar with the structure of a new code.		It is useful to be able to view the dependencies on modules in a fortran code graphically. This is especially helpful when trying to reorder code for a cleaner flow, trying to remove issues leading to circular dependencies, or for becoming familiar with the structure of a new code.

Line 84:		Line 86:
	Producing graphs from the output requires [http://www.graphviz.org graphviz]. This is not installed in the sector, but is easy to [[Useful_Makefiles#Graphviz\|compile]].		Producing graphs from the output requires [http://www.graphviz.org graphviz]. This is not installed in the sector, but is easy to [[Useful_Makefiles#Graphviz\|compile]].

	Run the desired parser (e.g. one of those provided by graphviz) on the resultant dot files. I find dot works best. I run:		Run the desired parser (e.g. one of those provided by graphviz) on the resultant dot files. I find dot works best for our graphs. I run:
	~/src/dependencies $ for f in *.dot; do dot -Tps $f -o `basename $f .dot`.ps; done		~/src/dependencies $ for f in *.dot; do dot -Tps $f -o `basename $f .dot`.ps; done
	to produce all the graphs in one shot. (Note ~/local/bin is on my path.)		to produce all the graphs in one shot. (Note ~/local/bin is on my path.)

import>Jss43: /* Converting .pdb files from vmd to xleap readable format */

2008-09-29T21:56:28Z

Converting .pdb files from vmd to xleap readable format

@@ Line 3: / Line 3: @@
 == Converting .pdb files from vmd to xleap readable format ==
-This script takes a filename as command line argument reads the respective .pdb file and converts it to an xleap
+This [[Media:pdb2xleap.txt|script]] takes a filename as command line argument reads the respective .pdb file and converts it to an xleap
 readable format. The initial file is overwritten, but the original file is retained in filename.orig.
 <pre>
 #!/usr/bin/env python
@@ Line 60: / Line 61: @@
 </pre>

import>Ho246 at 13:41, 19 August 2008

2008-08-19T13:41:36Z

← Older revision		Revision as of 13:41, 19 August 2008
Line 1:		Line 1:
	On this script you will find (and can add!) Python scripts, that may be useful in any work-related way.		On this script you will find (and can add!) Python scripts, that may be useful in any work-related way.

			== Converting .pdb files from vmd to xleap readable format ==

			This script takes a filename as command line argument reads the respective .pdb file and converts it to an xleap
			readable format. The initial file is overwritten, but the original file is retained in filename.orig.
			<pre>
			#!/usr/bin/env python
			# -- coding: latin1 --

			import sys

			def main():
			fname = sys.argv[1]

			fin = open( fname, "r")
			lines = fin.readlines()
			fin.close()

			lin2=[]

			foumod=open( fname+".orig","w")
			fomod=open( fname,"w")


			counter=1
			first=True
			oldnum=""
			for l in lines:
			if l.find( "CRYST")==-1:
			l2=l.replace( " X ", " ")
			if len( l2)>16:
			if l2[13].isdigit():
			subs=l2[12:16]
			subs2=l2[13:17]
			l2=l2.replace( subs, subs2)

			if (not first) and len( l2)>25:
			if oldnum!=l2[25]:
			oldnum=l2[25]
			print oldnum
			lin2.append( "TER\n")
			counter+=1
			first=False
			lin2.append( l2)
			else:
			counter-=1
			lin2.insert(-1,"TER\n")

			for i in range( counter):
			lines.append( "")

			for l,l2 in zip( lines, lin2):
			foumod.write( l)
			fomod.write( l2)


			if __name__ == "__main__":
			main()

			</pre>

import>Ho246 at 13:31, 19 August 2008

2008-08-19T13:31:34Z

New page

On this script you will find (and can add!) Python scripts, that may be useful in any work-related way.