I am new to python. I wrote my own text script and the programm from somebody else.
This is my script followed by the incomplete putput( i need help in this)
filepath = ./phd/top500H
filenames = [ ]
motifDescription = Chain
chainID = 'betabulgeloop5'
torsion-bound = (2.C 3.N 3.CA 3.C) -80 +/- 60
torsion-bound = (3.N 3.CA 3.C 4.N) -25 +/- 65
torsion-bound = (3.C 4.N 4.CA 4.C) -80 +/- 60
torsion-bound = (4.N 4.CA 4.C 5.N) -25 +/- 65
torsion-bound = (4.C 5.N 5.CA 5.C) 80 +/- 60
torsion-bound = (5.N 5.CA 5.C 6.N) 25 +/- 65
torsion-bound = (2.C 2.CA 2.CB 2.CG) -80 +/- 60
torsion-bound = (3.N 2.C 2.CA 2.CB) -25 +/- 65
hydrogen-bond = (2.CG 2.OD1 6.H 6.N) 3.0 90.0 90.0
hydrogen-bond = (2.C 2.O 5.H 5.N) 3.0 90.0 90.0
Residue position = 1
Residue position = 2
Residue position = 3
Residue position = 4
Residue position = 5
Residue position = 6
Residue position = 7
measures = Distance (2.OD1 4.H)
Distance (2.OD1 5.H)
Distance (2.OD1 6.H)
Distance (2.O 4.H)
Distance (2.O 5.H)
Distance (2.O 6.H)
Torsion (4.H 4.N 5.N 5.H)
Torsion (5.H 5.N 6.N 6.H)
Torsion (2.OD2 2.CG 2.OD1 4.H)
Torsion (2.OD2 2.CG 2.OD1 5.H)
Torsion (2.OD2 2.CG 2.OD1 6.H)
Torsion (1.N 2.C 2.O 4.H)
Torsion (1.N 2.C 2.O 5.H)
Torsion (1.N 2.C 2.O 6.H)
Torsion (2.OD1 4.H 4.N 4.CA)
Torsion (2.OD1 5.H 5.N 5.CA)
Torsion (2.OD1 6.H 6.N 6.CA)
Torsion (2.O 4.H 4.N 4.CA)
Torsion (2.O 5.H 5.N 5.CA)
Torsion (2.O 6.H 6.N 6.CA)
Torsion (3.C 4.N 4.CA 4.C)
Torsion (4.N 4.CA 4.C 5.N)
Torsion (4.C 5.N 5.CA 5.C)
Torsion (5.N 5.CA 5.C 6.N)
Torsion (5.C 6.N 6.CA 6.C)
Torsion (6.N 6.CA 6.C 7.N)
Angle (4.N 5.N 6.N)
Angle (2.CG 2.OD1 4.H)
Angle (2.CG 2.OD1 5.H)
Angle (2.CG 2.OD1 6.H)
Angle (2.C 2.O 4.H)
Angle (2.C 2.O 5.H)
Angle (2.C 2.O 6.H)
Angle (2.OD1 4.H 4.N)
Angle (2.OD1 5.H 5.N)
Angle (2.OD1 6.H 6.N)
Angle (2.O 4.H 4.N)
Angle (2.O 5.H 5.N)
Angle (2.O 6.H 6.N)
and this is the output following the script
pdbid motif Distance Distance Distance DistanceDistance
Distance Torsion Torsion Torsion Torsion Torsion Torsion TorsionT
orsion Torsion Torsion Torsion Torsion Torsion Torsion Torsion Torsion TorsionT
orsion Torsion Torsion Angle Angle Angle Angle Angle Angle AngleAng
le Angle Angle Angle Angle Angle
Processing : 119lH
119lH betabulgeloop5 19-25 1.95 2.67 1.90 3.00 2.04 3.8365.3
2 -54.19 -94.03 -160.58 80.14 -137.34 -117.13 -85.60 -59.81 105.35-8
1.00 -124.02 -27.89 -135.91 -95.32 -2.55 88.85 12.87 -92.54 147.7711
3.89 113.09 150.33 132.24 62.82 110.17 86.94 142.55 107.98 159.5284
.78 159.86 111.37
Processing : 153lH
Processing : 16pkH
Processing : 19hcAH
Processing : 1a12AH
1a12AH betabulgeloop5 309-315 2.14 3.15 2.01 2.82 2.76 3.6177.3
7 -46.03 -106.65 -130.77 59.67 -137.92 -131.89 -88.89 -46.58 110.8023
.19 -133.02 97.28 -119.25 -116.48 22.26 82.45 19.06 -108.80 138.0511
5.29 107.02 156.40 150.05 65.21 117.84 99.39 154.80 95.05 157.9610
4.92 156.45 140.60
Processing : 1a1yIH
1a1yIH betabulgeloop5 70-76 2.18 2.84 2.09 3.01 2.07 3.6666.4
2 -44.27 -104.04 -162.09 74.11 -141.25 -127.73 -87.15 -52.69 105.17-3
8.72 -119.20 16.61 -131.22 -89.99 0.18 66.48 31.02 -100.90 154.7211
6.85 109.19 149.82 140.47 62.43 115.93 96.72 131.12 102.97 159.0789
.99 153.93 124.64
Processing : 1a28BH
Processing : 1a2pAH
Processing : 1a2zAH
Processing : 1a3aDH
Processing : 1a4iBH
Processing : 1a62H
Processing : 1a6mH
Processing : 1a73AH
Processing : 1a7sH
Processing : 1a8dH
1a8dH betabulgeloop5 142-148 1.90 2.56 1.87 2.90 2.36 3.8364.0
0 -61.05 -101.06 -147.88 63.21 -140.87 -129.33 -92.34 -51.73 109.47-7
7.57 -130.89 19.05 -118.11 -107.58 5.69 98.09 3.84 -77.43 145.7711
8.94 106.73 156.92 132.61 63.22 111.39 93.26 147.59 103.25 161.5999
.28 171.42 114.57
Processing : 1a8eH
Processing : 1a8iH
Processing : 1a92AH
Processing : 1aacH
Processing : 1aayH
Processing : 1abaH
Processing : 1adsH
Processing : 1agjAH
1agjAH betabulgeloop5 92-98 1.88 2.54 1.87 2.94 2.25 3.8671.6
1 -61.47 -109.41 179.39 54.84 -139.48 -125.66 -88.51 -56.65 109.81-9
2.58 -125.70 47.92 -124.90 -102.23 7.99 88.86 6.68 -83.42 117.1111
6.87 107.90 159.77 119.83 60.23 114.10 91.77 134.59 97.58 163.3992
.50 169.26 116.95
Traceback (most recent call last):
File "Tailor/Script.py", line 221, in ?
run.run()
File "/users/brc/jeddahbi/Tailor-1.2/Tailor/Run.py", line 102, in run
result = measure.measure(motif)
File "/users/brc/jeddahbi/Tailor-1.2/Tailor/Measure.py", line 127, in measure
a = feature.findFeature(self.descriptionA).center
AttributeError: 'NoneType' object has no attribute 'center'
art.dcs.gla.ac.uk{jeddahbi}3: python Tailor/Script.py scripts/betabulge5.scr>out
putbeta5
Processing : 119lH
Processing : 153lH
Processing : 16pkH
Processing : 19hcAH
Processing : 1a12AH
Processing : 1a1yIH
Processing : 1a28BH
Processing : 1a2pAH
Processing : 1a2zAH
Processing : 1a3aDH
Processing : 1a4iBH
Processing : 1a62H
Processing : 1a6mH
Processing : 1a73AH
Processing : 1a7sH
Processing : 1a8dH
Processing : 1a8eH
Processing : 1a8iH
Processing : 1a92AH
Processing : 1aacH
Processing : 1aayH
Processing : 1abaH
Processing : 1adsH
Processing : 1agjAH
Traceback (most recent call last):
File "Tailor/Script.py", line 221, in ?
run.run()
File "/users/brc/jeddahbi/Tailor-1.2/Tailor/Run.py", line 102, in run
result = measure.measure(motif)
File "/users/brc/jeddahbi/Tailor-1.2/Tailor/Measure.py", line 127, in measure
a = feature.findFeature(self.descriptionA).center
AttributeError: 'NoneType' object has no attribute 'center'
art.dcs.gla.ac.uk{jeddahbi}4:
Can you please tell me what is wrong, I tried to figure it out but I couldnt. I tried to seek help but no one works on python.
Thanks
Fawzia