Difference between revisions of "Path2pdb.py"
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import>Em427 |
import>Em427 |
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(9 intermediate revisions by the same user not shown) | |||
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− | ''path. |
+ | ''path.info'' file can be easy converted to the PDB format using Python program presented below. PDB file can be loaded to VMD and you can visualize your path. Because of simplicity all residues have the same name ALA therefore better is to load topology file and as next the PDB file. |
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+ | To do this save the code in ''path2pdb.py'' file, change privileges of this file: |
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chmod 755 path2pdb.py |
chmod 755 path2pdb.py |
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./path2pdb.py |
./path2pdb.py |
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---- |
---- |
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for i in range(len(ff)/(2+2*atomNumber)): |
for i in range(len(ff)/(2+2*atomNumber)): |
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− | m = atomNumber*2+2 |
+ | m = atomNumber*2+2 # number of lines for each stationary points |
+ | l = atomNumber+2 # number of lines before coordinates |
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− | mm = 1 |
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+ | mm = 1 # number of residue |
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for j in range(atomNumber): |
for j in range(atomNumber): |
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− | x = float(string.split(ff[m*i+ |
+ | x = float(string.split(ff[m*i+l+j])[0]) |
− | y = float(string.split(ff[m*i+ |
+ | y = float(string.split(ff[m*i+l+j])[1]) |
− | z = float(string.split(ff[m*i+ |
+ | z = float(string.split(ff[m*i+l+j])[2]) |
if (atomName[j]=='N' and atomName[j+1]=='H'): |
if (atomName[j]=='N' and atomName[j+1]=='H'): |
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mm = mm+1 |
mm = mm+1 |
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Line 83: | Line 85: | ||
xyz.write("\n") |
xyz.write("\n") |
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xyz.close() |
xyz.close() |
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+ | |||
+ | |||
+ | '''Note''': this script works when ''path.info'' file was obtain without NOFRQS keyword. If NOFRQS was used, please, change values of two variables: |
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+ | |||
+ | m = atomNumber+2 # number of lines for each stationary points |
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+ | l = 2 # number of lines before coordinates |
Latest revision as of 20:01, 1 July 2008
Script useful for AMBER9 and NAB users
path.info file can be easy converted to the PDB format using Python program presented below. PDB file can be loaded to VMD and you can visualize your path. Because of simplicity all residues have the same name ALA therefore better is to load topology file and as next the PDB file.
To do this save the code in path2pdb.py file, change privileges of this file:
chmod 755 path2pdb.py
and type:
./path2pdb.py
#!/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.pdb ## ./path2pdb.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][j*4:(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][j*4:4*(j+1)])) info = open("path.info").read() ff = string.split(info, "\n") xyz = open('path_all.pdb','w') for i in range(len(ff)/(2+2*atomNumber)): m = atomNumber*2+2 # number of lines for each stationary points l = atomNumber+2 # number of lines before coordinates mm = 1 # number of residue for j in range(atomNumber): x = float(string.split(ff[m*i+l+j])[0]) y = float(string.split(ff[m*i+l+j])[1]) z = float(string.split(ff[m*i+l+j])[2]) if (atomName[j]=='N' and atomName[j+1]=='H'): mm = mm+1 else: xyz.write("%4s%7d %-4s %4s%5d%12.3f%8.3f%8.3f\n" % ('ATOM', j+1, atomName[j], 'ALA', mm, x, y, z)) xyz.write("END\n") xyz.write("\n") 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