Path2xyz.py - Revision history

import>Em427 at 16:20, 30 June 2008

2008-06-30T16:20:55Z

← Older revision		Revision as of 16:20, 30 June 2008
Line 78:		Line 78:
	xyz.write("\n")		xyz.write("\n")
	xyz.close()		xyz.close()


			'''Note''': this script works when ''path.info'' file was obtain without NOFRQS keyword. If NOFRQS was used, please, change values of two variables:

			m = atomNumber+2 # number of lines for each stationary points
			l = 2 # number of lines before coordinates

import>Em427 at 17:49, 2 May 2008

2008-05-02T17:49:24Z

← Older revision		Revision as of 17:49, 2 May 2008
Line 69:		Line 69:

	for i in range(len(ff)/(2+2*atomNumber)):		for i in range(len(ff)/(2+2*atomNumber)):
	m = atomNumber*2+2		m = atomNumber*2+2 # number of lines for each stationary points
	l = atomNumber+2 # number of lines before coordinates		l = atomNumber+2 # number of lines before coordinates
	# xyz.write("%d\n%s %s\n" % (atomNumber, ff[mi], ff[mi+1])) # energy and symmetry		# xyz.write("%d\n%s %s\n" % (atomNumber, ff[mi], ff[mi+1])) # energy and symmetry

import>Em427 at 17:48, 2 May 2008

2008-05-02T17:48:31Z

← Older revision		Revision as of 17:48, 2 May 2008
Line 70:		Line 70:
	for i in range(len(ff)/(2+2*atomNumber)):		for i in range(len(ff)/(2+2*atomNumber)):
	m = atomNumber*2+2		m = atomNumber*2+2
			l = atomNumber+2 # number of lines before coordinates
	# xyz.write("%d\n%s %s\n" % (atomNumber, ff[mi], ff[mi+1])) # energy and symmetry		# xyz.write("%d\n%s %s\n" % (atomNumber, ff[mi], ff[mi+1])) # energy and symmetry
	xyz.write("%d\n%s\n" % (atomNumber, ff[m*i])) # energy		xyz.write("%d\n%s\n" % (atomNumber, ff[m*i])) # energy
	for j in range(atomNumber):		for j in range(atomNumber):
	xyz.write("%-4s %s\n" % (atomName[j], ff[m*i+85+j]))		xyz.write("%-4s %s\n" % (atomName[j], ff[m*i+l+j]))

	xyz.write("\n")		xyz.write("\n")

import>Em427 at 15:30, 30 April 2008

2008-04-30T15:30:57Z

← Older revision		Revision as of 15:30, 30 April 2008
Line 2:		Line 2:


	''path.info'' file can be ~~easy~~ converted ~~also~~ to xyz format using Python program presented below. To do this save the code in ''path2xyz.py'' file, ~~next~~ change privileges of ~~this~~ file:		''path.info'' file can be converted to xyz format using Python program presented below. To do this save the code in ''path2xyz.py'' file, change privileges of the file:

	chmod 755 path2xyz.py		chmod 755 path2xyz.py

import>Em427 at 15:27, 30 April 2008

2008-04-30T15:27:55Z

← Older revision		Revision as of 15:27, 30 April 2008
Line 1:		Line 1:
			Script useful for AMBER9 and NAB users


	''path.info'' file can be easy converted also to xyz format using Python program presented below. To do this save the code in ''path2xyz.py'' file, next change privileges of this file:		''path.info'' file can be easy converted also to xyz format using Python program presented below. To do this save the code in ''path2xyz.py'' file, next change privileges of this file:

Line 6:		Line 9:

	./path2xyz.py		./path2xyz.py


	----		----
	----		----


	#!/usr/bin/env python		#!/usr/bin/env python

import>Em427 at 15:18, 30 April 2008

2008-04-30T15:18:54Z

← Older revision		Revision as of 15:18, 30 April 2008
Line 1:		Line 1:
	path.info file can be easy converted also to xyz format using Python program presented below. To do this save the code in path2xyz.py file, next change privileges of this file:		''path.info'' file can be easy converted also to xyz format using Python program presented below. To do this save the code in ''path2xyz.py'' file, next change privileges of this file:

	chmod 755 path2xyz.py		chmod 755 path2xyz.py

import>Em427 at 15:18, 30 April 2008

2008-04-30T15:18:36Z

← Older revision		Revision as of 15:18, 30 April 2008
Line 9:		Line 9:
	----		----
	----		----

			#!/usr/bin/env python

			import sys
			import string

			###############################################################
			## #
			## Edyta Malolepsza #
			## David Wales' group, University of Cambridge #
			## in case of problems please send email: em427@cam.ac.uk #
			## #
			###############################################################
			##
			## transform path.info into path_all.xyz
			## ./path2xyz.py
			##
			###############################################################

			prmtop = open("coords.prmtop").read()
			f = string.split(prmtop, "\n")

			q0 = f.index("%FLAG POINTERS ")
			q1 = f.index("%FLAG ATOM_NAME ")
			q2 = f.index("%FLAG RESIDUE_LABEL ")
			q3 = f.index("%FLAG RESIDUE_POINTER ")

			## names of tables are related to names in prmtop file

			atomNumber = int(string.split(f[q0+2])[0])

			atomName = []
			residueLabel = []

			an = 0
			line = 0
			while (an<atomNumber):
			for j in range(20):
			if (an<atomNumber):
			an = an+1
			atomName.append(f[q1+2+line][j4:(j+1)4].strip())
			else:
			break
			line = line+1

			for i in range(q3-q2-2):
			for j in range((len(f[q2+2+i])+1)/4):
			residueLabel.append(string.strip(f[q2+2+i][j4:4(j+1)]))

			info = open("path.info").read()
			ff = string.split(info, "\n")

			xyz = open('path_all.xyz','w')

			for i in range(len(ff)/(2+2*atomNumber)):
			m = atomNumber*2+2
			# xyz.write("%d\n%s %s\n" % (atomNumber, ff[mi], ff[mi+1])) # energy and symmetry
			xyz.write("%d\n%s\n" % (atomNumber, ff[m*i])) # energy
			for j in range(atomNumber):
			xyz.write("%-4s %s\n" % (atomName[j], ff[m*i+85+j]))

			xyz.write("\n")
			xyz.close()

import>Em427 at 15:17, 30 April 2008

2008-04-30T15:17:39Z

New page

path.info file can be easy converted also to xyz format using Python program presented below. To do this save the code in path2xyz.py file, next change privileges of this file:

chmod 755 path2xyz.py

and type:

./path2xyz.py

----
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