sh-3.2# port install py26-MMTK @2.7.4
---> Computing dependencies for sqlite3
---> Fetching archive for sqlite3
---> Attempting to fetch sqlite3-3.7.12.1_0.darwin_11.x86_64.tbz2 from http://packages.macports.org/sqlite3
---> Attempting to fetch sqlite3-3.7.12.1_0.darwin_11.x86_64.tbz2.rmd160 from http://packages.macports.org/sqlite3
---> Installing sqlite3 @3.7.12.1_0
---> Cleaning sqlite3
---> Computing dependencies for sqlite3
---> Deactivating sqlite3 @3.7.12_0
---> Cleaning sqlite3
---> Activating sqlite3 @3.7.12.1_0
---> Cleaning sqlite3
---> Computing dependencies for py26-distribute
---> Fetching archive for py26-distribute
---> Attempting to fetch py26-distribute-0.6.27_0.darwin_11.x86_64.tbz2 from http://packages.macports.org/py26-distribute
---> Attempting to fetch py26-distribute-0.6.27_0.darwin_11.x86_64.tbz2.rmd160 from http://packages.macports.org/py26-distribute
---> Installing py26-distribute @0.6.27_0
---> Cleaning py26-distribute
---> Computing dependencies for py26-distribute
---> Deactivating py26-distribute @0.6.26_0
---> Cleaning py26-distribute
---> Activating py26-distribute @0.6.27_0
---> Cleaning py26-distribute
---> Computing dependencies for py26-MMTK
---> Dependencies to be installed: py26-scientific
---> Fetching distfiles for py26-scientific
---> Verifying checksum(s) for py26-scientific
---> Extracting py26-scientific
---> Configuring py26-scientific
---> Building py26-scientific
---> Staging py26-scientific into destroot
---> Installing py26-scientific @2.9.1_0
---> Activating py26-scientific @2.9.1_0
---> Cleaning py26-scientific
---> Fetching archive for py26-MMTK
---> Attempting to fetch py26-MMTK-2.7.4_1.darwin_11.x86_64.tbz2 from http://packages.macports.org/py26-MMTK
---> Fetching distfiles for py26-MMTK
---> Verifying checksum(s) for py26-MMTK
---> Extracting py26-MMTK
---> Configuring py26-MMTK
---> Building py26-MMTK
---> Staging py26-MMTK into destroot
---> Installing py26-MMTK @2.7.4_1
---> Activating py26-MMTK @2.7.4_1
---> Cleaning py26-MMTK
---> Updating database of binaries: 100.0%
---> Scanning binaries for linking errors: 100.0%
---> No broken files found.
2012年5月18日 星期五
安裝 ROCR
先進入 R
Lee-Kevinteki-MacBook:~ kevet$ R
安裝 ROCR
> install.packages("ROCR", repos = "http://cran.csie.ntu.edu.tw")
測試呼叫
> library(ROCR)
Loading required package: gplots
Loading required package: gtools
Loading required package: gdata
gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.
gdata: read.xls support for 'XLSX' (Excel 2007+) files ENABLED.
Attaching package: ‘gdata’
The following object(s) are masked from ‘package:stats’:
nobs
The following object(s) are masked from ‘package:utils’:
object.size
Loading required package: caTools
Loading required package: bitops
Loading required package: grid
Loading required package: KernSmooth
KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
Attaching package: ‘gplots’
The following object(s) are masked from ‘package:stats’:
lowess
在醫學上診斷疾病所使用的檢查產生了多種類型的結果,有一些結果僅簡單的
呈現陽性或陰性,而有一些檢驗的結果為一個連續的數值Ƕ在這兩種的情況下,指
定一個分界點(cut-point)來區分檢驗的陽性與陰性可能都是任意的Ƕ這個分界點的
指定會影響到診斷工作的敏感度(sensitivity)及特異度(specificity),其中敏感度表示
有病者被判為陽性的機率,而特異度表示無病者被判為陰性的機率Ƕ在處理這些問
題的時候,很多時候常利用 ROC 曲線(Receiver operating characteristic curve)來評估Ƕ
ROC 曲線為一個用來呈現篩檢試驗敏感度(sensitivity)及1-特異度(specificity)的圖形,
其中 X 軸為 1-特異度,又稱為偽陽性率(false positive),而 Y 軸為敏感度(ture positive)
,任何一個在曲線上的點都會對應到一個檢驗的用以區分陽性或陰性的分界點Ƕ
ROC 曲線在判別時,會以對角線為一個參考線,若是檢驗工具的 ROC 曲線剛
好落在對角的參考線上,則表示檢驗工具對於此疾病的診斷沒有鑑別性Ƕ若是 ROC
曲線愈往圖形的左上方移動表示檢驗工具對於疾病的敏感度愈高ǵ且偽陽性率愈低,
亦即此工具的鑑別力較佳Ƕ
一般在判別檢驗工具的好壞時,除了看曲線的圖形之外,也可以利用曲線下的
面積(Area Under Curve, AUC)來判別 ROC 曲線的鑑別力,AUC 數值的範圍從 0 到
1,數值愈大愈好Ƕ以下為 AUC 數值一般的判別規則如下:
AUC = 0.5 幾乎沒有判別力( no discrimination)
0.7ɩAUC < 0.8 可接受的判別力(acceptable discrimination)
0.8ɩAUC < 0.9 好的判別力(excellent discrimination)
AUC ɪ0.9 非常好的判別力(outstanding discrimination)
Lee-Kevinteki-MacBook:~ kevet$ R
安裝 ROCR
> install.packages("ROCR", repos = "http://cran.csie.ntu.edu.tw")
測試呼叫
> library(ROCR)
Loading required package: gplots
Loading required package: gtools
Loading required package: gdata
gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.
gdata: read.xls support for 'XLSX' (Excel 2007+) files ENABLED.
Attaching package: ‘gdata’
The following object(s) are masked from ‘package:stats’:
nobs
The following object(s) are masked from ‘package:utils’:
object.size
Loading required package: caTools
Loading required package: bitops
Loading required package: grid
Loading required package: KernSmooth
KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
Attaching package: ‘gplots’
The following object(s) are masked from ‘package:stats’:
lowess
註解
在醫學上診斷疾病所使用的檢查產生了多種類型的結果,有一些結果僅簡單的
呈現陽性或陰性,而有一些檢驗的結果為一個連續的數值Ƕ在這兩種的情況下,指
定一個分界點(cut-point)來區分檢驗的陽性與陰性可能都是任意的Ƕ這個分界點的
指定會影響到診斷工作的敏感度(sensitivity)及特異度(specificity),其中敏感度表示
有病者被判為陽性的機率,而特異度表示無病者被判為陰性的機率Ƕ在處理這些問
題的時候,很多時候常利用 ROC 曲線(Receiver operating characteristic curve)來評估Ƕ
ROC 曲線為一個用來呈現篩檢試驗敏感度(sensitivity)及1-特異度(specificity)的圖形,
其中 X 軸為 1-特異度,又稱為偽陽性率(false positive),而 Y 軸為敏感度(ture positive)
,任何一個在曲線上的點都會對應到一個檢驗的用以區分陽性或陰性的分界點Ƕ
ROC 曲線在判別時,會以對角線為一個參考線,若是檢驗工具的 ROC 曲線剛
好落在對角的參考線上,則表示檢驗工具對於此疾病的診斷沒有鑑別性Ƕ若是 ROC
曲線愈往圖形的左上方移動表示檢驗工具對於疾病的敏感度愈高ǵ且偽陽性率愈低,
亦即此工具的鑑別力較佳Ƕ
一般在判別檢驗工具的好壞時,除了看曲線的圖形之外,也可以利用曲線下的
面積(Area Under Curve, AUC)來判別 ROC 曲線的鑑別力,AUC 數值的範圍從 0 到
1,數值愈大愈好Ƕ以下為 AUC 數值一般的判別規則如下:
AUC = 0.5 幾乎沒有判別力( no discrimination)
0.7ɩAUC < 0.8 可接受的判別力(acceptable discrimination)
0.8ɩAUC < 0.9 好的判別力(excellent discrimination)
AUC ɪ0.9 非常好的判別力(outstanding discrimination)
pymol 1.5 + pyETV plugin
sh-3.2# port install pymol @1.5
sh-3.2# pymol
PyMOL(TM) Molecular Graphics System, Version 1.5.0.3.
Copyright (c) Schrodinger, LLC.
All Rights Reserved.
Created by Warren L. DeLano, Ph.D.
PyMOL is user-supported open-source software. Although some versions
are freely available, PyMOL is not in the public domain.
If PyMOL is helpful in your work or study, then please volunteer
support for our ongoing efforts to create open and affordable scientific
software by purchasing a PyMOL Maintenance and/or Support subscription.
More information can be found at "http://www.pymol.org".
Enter "help" for a list of commands.
Enter "help" for information on a specific command.
Hit ESC anytime to toggle between text and graphics.
Detected OpenGL version 2.0 or greater. Shaders available.
Detected GLSL version 1.20.
OpenGL graphics engine:
GL_VENDOR: NVIDIA Corporation
GL_RENDERER: NVIDIA GeForce 9400M OpenGL Engine
GL_VERSION: 2.1 NVIDIA-7.18.11
Detected 2 CPU cores. Enabled multithreaded rendering.
OpenGL quad-buffer stereo 3D detected and enabled.
PyMOL: normal program termination.
sh-3.2# pymol
PyMOL(TM) Molecular Graphics System, Version 1.5.0.3.
Copyright (c) Schrodinger, LLC.
All Rights Reserved.
Created by Warren L. DeLano, Ph.D.
PyMOL is user-supported open-source software. Although some versions
are freely available, PyMOL is not in the public domain.
If PyMOL is helpful in your work or study, then please volunteer
support for our ongoing efforts to create open and affordable scientific
software by purchasing a PyMOL Maintenance and/or Support subscription.
More information can be found at "http://www.pymol.org".
Enter "help" for a list of commands.
Enter "help
Hit ESC anytime to toggle between text and graphics.
Detected OpenGL version 2.0 or greater. Shaders available.
Detected GLSL version 1.20.
OpenGL graphics engine:
GL_VENDOR: NVIDIA Corporation
GL_RENDERER: NVIDIA GeForce 9400M OpenGL Engine
GL_VERSION: 2.1 NVIDIA-7.18.11
Detected 2 CPU cores. Enabled multithreaded rendering.
OpenGL quad-buffer stereo 3D detected and enabled.
PyMOL: normal program termination.
Deactivating and Activating python
---> Deactivating python26 @2.6.7_3
---> Cleaning python26
---> Activating python26 @2.6.8_0
To make python 2.6 the default (i.e. the version you get when you run 'python'), please run:
sudo port select --set python python26
---> Cleaning python26
---> Activating python26 @2.6.8_0
To make python 2.6 the default (i.e. the version you get when you run 'python'), please run:
sudo port select --set python python26
CE align
linux 下安裝 http://cl.sdsc.edu/ce/ce_align.html
Mac 下安裝 可用 port
因要讀取 scratch file 設定 path 給 ce
>> ce - 1a0j.pdb A 1ixe.pdb A /Users/kevet/scratch
Structure Alignment Calculator, version 1.02, last modified: Mar 13, 2003.
CE Algorithm, version 1.00, 1998.
Chain 1: 1a0j.pdb:A (Size=223)
Chain 2: 1ixe.pdb:A (Size=377)
Alignment length = 57 Rmsd = 5.93A Z-Score = 1.2 Gaps = 52(91.2%) CPU = 3s Sequence identities = 7.0%
Chain 1: 124 LSGSSSNYPD--TLR--------CL--DLPILSSSSCNSAYPGQITSNMFCAGFMEGGKD----------
Chain 2: 229 MIQEIGTPERAREWVREKLAKKERIMGMGHRVYKAFDPRAGV-----------------LEKLARLVAEK
Chain 1: 172 --------SCQGDSG--GPVVCNGQLQGVVSWGYGCAQR
Chain 2: 282 HGHSKEYQILKIVEEEAGKVLN---PRGIYPNVDFYSGV
X2 = (-0.962516)*X1 + ( 0.270705)*Y1 + (-0.016798)*Z1 + ( 14.622005)
Y2 = (-0.195940)*X1 + (-0.651186)*Y1 + ( 0.733188)*Z1 + ( 50.781464)
Z2 = ( 0.187539)*X1 + ( 0.708996)*Y1 + ( 0.679819)*Z1 + ( 89.564117)
Mac 下安裝 可用 port
因要讀取 scratch file 設定 path 給 ce
>> ce - 1a0j.pdb A 1ixe.pdb A /Users/kevet/scratch
Structure Alignment Calculator, version 1.02, last modified: Mar 13, 2003.
CE Algorithm, version 1.00, 1998.
Chain 1: 1a0j.pdb:A (Size=223)
Chain 2: 1ixe.pdb:A (Size=377)
Alignment length = 57 Rmsd = 5.93A Z-Score = 1.2 Gaps = 52(91.2%) CPU = 3s Sequence identities = 7.0%
Chain 1: 124 LSGSSSNYPD--TLR--------CL--DLPILSSSSCNSAYPGQITSNMFCAGFMEGGKD----------
Chain 2: 229 MIQEIGTPERAREWVREKLAKKERIMGMGHRVYKAFDPRAGV-----------------LEKLARLVAEK
Chain 1: 172 --------SCQGDSG--GPVVCNGQLQGVVSWGYGCAQR
Chain 2: 282 HGHSKEYQILKIVEEEAGKVLN---PRGIYPNVDFYSGV
X2 = (-0.962516)*X1 + ( 0.270705)*Y1 + (-0.016798)*Z1 + ( 14.622005)
Y2 = (-0.195940)*X1 + (-0.651186)*Y1 + ( 0.733188)*Z1 + ( 50.781464)
Z2 = ( 0.187539)*X1 + ( 0.708996)*Y1 + ( 0.679819)*Z1 + ( 89.564117)
Scwrl 4
Target:
protein 1BGA -> Q216D
Try to test the Q216D will impede the neighbor same charged residue D289 to rotate its side chain.
Useage:
>> Scwrl4 -i D216_1bga.pdb -o 1bga_D216.pdb
Using parameters from /usr/local/bin/scwrl4/Scwrl4.ini
Using rotamer library: /usr/local/bin/scwrl4/bbDepRotLib.bin
Residue A 448 is being treated as C-terminal
Total number of subrotamer interactions = 7308602
Total number of subrotamer interactions = 0
Running Goldstein's DEE (version G)
:::::::::::::::::::::::::::::::::::
Initial number of residues - 368
Initial number of rotamers - 4907
1526 redundant edges eliminated
Isolated residues removed - 4
round 1:
199 redundant edges eliminated
Isolated residues removed - 90
Rotamers eliminated - 3118
round 2:
55 redundant edges eliminated
Isolated residues removed - 43
Rotamers eliminated - 489
round 3:
28 redundant edges eliminated
Isolated residues removed - 15
Rotamers eliminated - 148
round 4:
8 redundant edges eliminated
Isolated residues removed - 9
Rotamers eliminated - 36
round 5:
2 redundant edges eliminated
Isolated residues removed - 5
Rotamers eliminated - 17
round 6:
0 redundant edges eliminated
Isolated residues removed - 0
Rotamers eliminated - 0
Energy accumulated during DEE = 305.91
Searching for clusters... 6 clusters found
Processing cluster of 4 vertices
Redundant nodes eliminated : 1
Tree-decomposition has been built. Width+1 = 1
Total combinations to search = 3.6e+1
2 : -> 312 3
1( 2 ) : 312 -> 316
0( 2 ) : 3 -> 1
ArtPts = 0 MaxDegree = 2 MaxBag = 1 AvgBag = 2
===============================
Launching bottom-to-top process
Combinations:
in intersections - 6
in exclusions - 103.2
total to search - 28
Maximal size of a key is 4 elements
Processing nodes ..
Number of combinations = 8
Energy of this cluster = 28.0031
Processing cluster of 186 vertices
Redundant nodes eliminated : 36
Tree-decomposition has been built. Width+1 = 8
Total combinations to search = 4.61771e+7
149( 91 ) : 100 26 164 135 136 123 99 -> 117
148( 33 ) : 14 26 143 140 102 -> 150 331
147( 148 ) : 14 26 331 102 140 -> 15
146( 147 ) : 14 15 331 140 102 -> 101
145( 146 ) : 15 331 140 102 101 -> 323
144( 37 ) : 68 81 17 22 85 -> 43 20
143( 145 ) : 140 102 101 323 -> 137 138
142( 149 ) : 100 26 117 164 136 123 99 -> 66
141( 143 ) : 137 138 101 140 323 -> 288 239
140( 32 ) : 81 17 47 50 85 -> 46
139( 140 ) : 81 46 47 50 85 -> 84
138( 141 ) : 239 137 288 101 323 -> 61
137( 113 ) : 135 133 99 123 127 -> 174
136( 100 ) : 100 26 117 110 66 -> 104
135( 137 ) : 135 133 174 99 123 -> 124
134( 62 ) : 164 135 136 203 204 -> 178
133( 68 ) : 195 218 203 199 219 -> 216
132( 144 ) : 68 81 22 43 20 -> 21
131( 142 ) : 100 117 66 99 123 -> 120
130( 141 ) : 239 288 138 140 323 -> 180
129( 100 ) : 100 117 164 110 136 -> 162
128( 28 ) : 143 203 155 219 251 -> 147
127( 99 ) : 68 17 14 26 22 -> 65
126( 51 ) : 82 133 123 99 130 -> 97
125( 139 ) : 46 47 84 50 -> 88
124( 32 ) : 43 47 20 50 -> 51
123( 148 ) : 150 143 331 140 -> 144
122( 28 ) : 195 218 155 251 -> 221
121( 138 ) : 137 288 239 61 -> 287
120( 127 ) : 14 26 22 65 -> 24
119( 120 ) : 14 26 22 24 -> 27
118( 135 ) : 135 133 174 124 -> 177
117( 134 ) : 164 203 178 204 -> 163
116( 118 ) : 133 174 124 177 -> 170
115( 133 ) : 195 216 203 199 -> 198
114( 121 ) : 137 61 287 -> 96
113( 91 ) : 82 135 123 99 85 -> 133 127
112( 114 ) : 61 287 96 -> 285 322
111( 112 ) : 285 61 322 96 -> 132
110( 51 ) : 82 127 130 85 -> 86
109( 117 ) : 164 178 163 204 -> 208
108( 130 ) : 239 288 180 323 -> 241
107( 124 ) : 43 20 51 -> 44
106( 107 ) : 44 43 51 -> 345
105( 106 ) : 44 51 345 -> 45
104( 105 ) : 45 51 345 -> 347
103( 104 ) : 347 45 51 -> 48
102( 103 ) : 48 347 51 -> 52
101( 87 ) : 143 203 199 252 251 -> 195 218
100( 142 ) : 100 26 117 66 164 136 -> 110
99( 98 ) : 14 26 82 85 -> 68 17 22
98( 85 ) : 100 26 143 82 140 85 -> 14
97( 81 ) : 338 -> 289 306 309 305
96( 120 ) : 14 26 65 24 -> 103
95( 97 ) : 289 306 309 338 -> 321
94( 115 ) : 216 203 198 -> 213
93( 94 ) : 198 213 -> 202
92( 93 ) : 202 213 -> 206
91 : -> 100 26 82 164 135 136 123 99 85
90( 92 ) : 206 202 -> 280 279
89( 133 ) : 195 218 216 -> 215
88( 109 ) : 163 208 -> 231
87( 62 ) : 143 203 140 -> 199 252 251
86( 88 ) : 231 -> 160 227
85( 91 ) : 100 26 82 164 136 135 85 -> 143 140
84( 86 ) : 160 227 -> 225 112
83( 123 ) : 150 331 144 -> 149
82( 106 ) : 44 43 345 -> 41
81( 102 ) : 347 52 -> 339 338
80( 136 ) : 26 110 104 -> 25
79( 80 ) : 110 104 25 -> 108
78( 81 ) : 52 339 338 -> 353
77( 97 ) : 306 305 338 -> 302
76( 77 ) : 302 306 338 -> 352
75( 111 ) : 132 285 96 -> 236
74( 75 ) : 132 285 236 -> 320
73( 74 ) : 285 320 236 -> 283
72( 134 ) : 136 178 204 -> 139
71( 76 ) : 302 352 338 -> 350
70( 71 ) : 302 352 350 -> 299
69( 70 ) : 302 350 299 -> 336
68( 101 ) : 195 143 218 203 199 251 -> 219
67( 69 ) : 336 350 -> 340 327
66( 74 ) : 132 320 236 -> 176
65( 114 ) : 137 61 96 -> 98
64( 137 ) : 174 123 127 -> 125
63( 64 ) : 125 174 -> 173
62( 85 ) : 143 164 135 136 140 -> 203 204
61( 63 ) : 125 173 -> 121 169
60( 64 ) : 125 123 127 -> 126
59( 60 ) : 126 127 123 -> 79
58( 145 ) : 15 331 323 -> 330
57( 59 ) : 126 79 127 -> 83
56( 74 ) : 132 285 320 -> 10
55( 95 ) : 289 309 321 -> 240
54( 95 ) : 306 321 338 -> 356
53( 110 ) : 130 86 -> 95
52( 89 ) : 195 218 -> 253
51( 113 ) : 82 133 123 127 99 85 -> 130
50( 61 ) : 169 -> 172 168
49( 50 ) : 172 168 -> 171
48( 49 ) : 168 171 -> 232
47( 90 ) : 202 279 -> 276
46( 90 ) : 206 280 -> 210
45( 84 ) : 160 227 -> 212
44( 84 ) : 160 112 -> 161
43( 140 ) : 17 46 -> 42
42( 81 ) : 347 339 -> 326
41( 42 ) : 347 326 -> 49
40( 82 ) : 41 345 -> 40
39( 67 ) : 336 340 -> 294
38( 54 ) : 306 -> 355
37( 99 ) : 68 17 22 82 85 -> 81
36( 38 ) : 355 -> 365 367
35( 56 ) : 132 10 -> 94
34( 55 ) : 309 240 -> 243
33( 98 ) : 100 14 143 26 140 -> 102
32( 144 ) : 81 17 43 20 85 -> 47 50
31( 22 ) : 311 -> 313 271
30( 31 ) : 313 271 -> 317
29( 30 ) : 271 317 -> 275
28( 68 ) : 195 143 218 203 219 251 -> 155
27( 29 ) : 275 -> 278 318
26( 58 ) : 331 330 -> 332
25( 26 ) : 332 331 -> 264
24( 25 ) : 332 264 -> 335
23( 24 ) : 332 335 -> 35
22( 34 ) : 243 -> 269 311
21( 22 ) : 269 243 -> 267
20( 23 ) : 35 335 -> 334
19( 20 ) : 35 334 -> 36
18( 21 ) : 269 243 -> 272
17( 130 ) : 180 140 -> 200
16( 96 ) : 14 26 -> 329
15( 18 ) : 243 272 -> 183
14( 57 ) : 83 -> 129
13( 131 ) : 120 -> 70
12( 119 ) : 27 -> 23
11( 79 ) : 25 -> 106
10( 11 ) : 106 -> 28
9( 46 ) : 206 -> 211
8( 107 ) : 20 -> 19
7( 102 ) : 51 -> 55
6( 39 ) : 336 -> 292
5( 6 ) : 292 -> 263
4( 77 ) : 305 -> 262
3( 36 ) : 365 -> 363
2( 22 ) : 311 -> 268
1( 54 ) : 356 -> 359
0( 15 ) : 183 -> 184
ArtPts = 0 MaxDegree = 4 MaxBag = 8 AvgBag = 4.33333
===============================
Launching bottom-to-top process
Combinations:
in intersections - 2.6e+06
in exclusions - 53733.2
total to search - 4.2e+07
Maximal size of a key is 508032 elements
Processing nodes .....................................................................................................................................................
Number of combinations = 4.57229e+6
Energy of this cluster = 654.853
Processing cluster of 4 vertices
Redundant nodes eliminated : 2
Tree-decomposition has been built. Width+1 = 2
Total combinations to search = 1.2e+1
1 : -> 254 196 245
0( 1 ) : 245 -> 244
ArtPts = 0 MaxDegree = 1 MaxBag = 2 AvgBag = 2.5
===============================
Launching bottom-to-top process
Combinations:
in intersections - 2
in exclusions - 23.2
total to search - 4
Maximal size of a key is 2 elements
Processing nodes .
Number of combinations = 8
Energy of this cluster = 8.94757
Processing cluster of 3 vertices
Redundant nodes eliminated : 2
Tree-decomposition has been built. Width+1 = 2
Total combinations to search = 4.8e+1
0 : -> 255 248 246
ArtPts = 0 MaxDegree = 0 MaxBag = 2 AvgBag = 3
Number of combinations = 4.8e+1
Energy of this cluster = 6.82758
Processing cluster of 3 vertices
Redundant nodes eliminated : 2
Tree-decomposition has been built. Width+1 = 2
Total combinations to search = 2.4e+1
0 : -> 351 298 297
ArtPts = 0 MaxDegree = 0 MaxBag = 2 AvgBag = 3
Number of combinations = 2.4e+1
Energy of this cluster = 8.7144
Processing cluster of 2 vertices
Redundant nodes eliminated : 1
Tree-decomposition has been built. Width+1 = 1
Total combinations to search = 8
0 : -> 187 192
ArtPts = 0 MaxDegree = 0 MaxBag = 1 AvgBag = 2
Number of combinations = 8
Energy of this cluster = 4.51308
Total minimal energy of the graph = 1017.77
Deleting workspace.
真是落落長 ! 而且差很多 ~
protein 1BGA -> Q216D
Try to test the Q216D will impede the neighbor same charged residue D289 to rotate its side chain.
Useage:
>> Scwrl4 -i D216_1bga.pdb -o 1bga_D216.pdb
Using parameters from /usr/local/bin/scwrl4/Scwrl4.ini
Using rotamer library: /usr/local/bin/scwrl4/bbDepRotLib.bin
Residue A 448 is being treated as C-terminal
:::::::::::::::::::::::::::::::::::
Initial number of residues - 368
Initial number of rotamers - 4907
1526 redundant edges eliminated
Isolated residues removed - 4
round 1:
199 redundant edges eliminated
Isolated residues removed - 90
Rotamers eliminated - 3118
round 2:
55 redundant edges eliminated
Isolated residues removed - 43
Rotamers eliminated - 489
round 3:
28 redundant edges eliminated
Isolated residues removed - 15
Rotamers eliminated - 148
round 4:
8 redundant edges eliminated
Isolated residues removed - 9
Rotamers eliminated - 36
round 5:
2 redundant edges eliminated
Isolated residues removed - 5
Rotamers eliminated - 17
round 6:
0 redundant edges eliminated
Isolated residues removed - 0
Rotamers eliminated - 0
Energy accumulated during DEE = 305.91
Searching for clusters... 6 clusters found
Processing cluster of 4 vertices
Redundant nodes eliminated : 1
Tree-decomposition has been built. Width+1 = 1
Total combinations to search = 3.6e+1
2 : -> 312 3
1( 2 ) : 312 -> 316
0( 2 ) : 3 -> 1
ArtPts = 0 MaxDegree = 2 MaxBag = 1 AvgBag = 2
===============================
Launching bottom-to-top process
Combinations:
in intersections - 6
in exclusions - 103.2
total to search - 28
Maximal size of a key is 4 elements
Processing nodes ..
Processing cluster of 186 vertices
Redundant nodes eliminated : 36
Tree-decomposition has been built. Width+1 = 8
Total combinations to search = 4.61771e+7
149( 91 ) : 100 26 164 135 136 123 99 -> 117
148( 33 ) : 14 26 143 140 102 -> 150 331
147( 148 ) : 14 26 331 102 140 -> 15
146( 147 ) : 14 15 331 140 102 -> 101
145( 146 ) : 15 331 140 102 101 -> 323
144( 37 ) : 68 81 17 22 85 -> 43 20
143( 145 ) : 140 102 101 323 -> 137 138
142( 149 ) : 100 26 117 164 136 123 99 -> 66
141( 143 ) : 137 138 101 140 323 -> 288 239
140( 32 ) : 81 17 47 50 85 -> 46
139( 140 ) : 81 46 47 50 85 -> 84
138( 141 ) : 239 137 288 101 323 -> 61
137( 113 ) : 135 133 99 123 127 -> 174
136( 100 ) : 100 26 117 110 66 -> 104
135( 137 ) : 135 133 174 99 123 -> 124
134( 62 ) : 164 135 136 203 204 -> 178
133( 68 ) : 195 218 203 199 219 -> 216
132( 144 ) : 68 81 22 43 20 -> 21
131( 142 ) : 100 117 66 99 123 -> 120
130( 141 ) : 239 288 138 140 323 -> 180
129( 100 ) : 100 117 164 110 136 -> 162
128( 28 ) : 143 203 155 219 251 -> 147
127( 99 ) : 68 17 14 26 22 -> 65
126( 51 ) : 82 133 123 99 130 -> 97
125( 139 ) : 46 47 84 50 -> 88
124( 32 ) : 43 47 20 50 -> 51
123( 148 ) : 150 143 331 140 -> 144
122( 28 ) : 195 218 155 251 -> 221
121( 138 ) : 137 288 239 61 -> 287
120( 127 ) : 14 26 22 65 -> 24
119( 120 ) : 14 26 22 24 -> 27
118( 135 ) : 135 133 174 124 -> 177
117( 134 ) : 164 203 178 204 -> 163
116( 118 ) : 133 174 124 177 -> 170
115( 133 ) : 195 216 203 199 -> 198
114( 121 ) : 137 61 287 -> 96
113( 91 ) : 82 135 123 99 85 -> 133 127
112( 114 ) : 61 287 96 -> 285 322
111( 112 ) : 285 61 322 96 -> 132
110( 51 ) : 82 127 130 85 -> 86
109( 117 ) : 164 178 163 204 -> 208
108( 130 ) : 239 288 180 323 -> 241
107( 124 ) : 43 20 51 -> 44
106( 107 ) : 44 43 51 -> 345
105( 106 ) : 44 51 345 -> 45
104( 105 ) : 45 51 345 -> 347
103( 104 ) : 347 45 51 -> 48
102( 103 ) : 48 347 51 -> 52
101( 87 ) : 143 203 199 252 251 -> 195 218
100( 142 ) : 100 26 117 66 164 136 -> 110
99( 98 ) : 14 26 82 85 -> 68 17 22
98( 85 ) : 100 26 143 82 140 85 -> 14
97( 81 ) : 338 -> 289 306 309 305
96( 120 ) : 14 26 65 24 -> 103
95( 97 ) : 289 306 309 338 -> 321
94( 115 ) : 216 203 198 -> 213
93( 94 ) : 198 213 -> 202
92( 93 ) : 202 213 -> 206
91 : -> 100 26 82 164 135 136 123 99 85
90( 92 ) : 206 202 -> 280 279
89( 133 ) : 195 218 216 -> 215
88( 109 ) : 163 208 -> 231
87( 62 ) : 143 203 140 -> 199 252 251
86( 88 ) : 231 -> 160 227
85( 91 ) : 100 26 82 164 136 135 85 -> 143 140
84( 86 ) : 160 227 -> 225 112
83( 123 ) : 150 331 144 -> 149
82( 106 ) : 44 43 345 -> 41
81( 102 ) : 347 52 -> 339 338
80( 136 ) : 26 110 104 -> 25
79( 80 ) : 110 104 25 -> 108
78( 81 ) : 52 339 338 -> 353
77( 97 ) : 306 305 338 -> 302
76( 77 ) : 302 306 338 -> 352
75( 111 ) : 132 285 96 -> 236
74( 75 ) : 132 285 236 -> 320
73( 74 ) : 285 320 236 -> 283
72( 134 ) : 136 178 204 -> 139
71( 76 ) : 302 352 338 -> 350
70( 71 ) : 302 352 350 -> 299
69( 70 ) : 302 350 299 -> 336
68( 101 ) : 195 143 218 203 199 251 -> 219
67( 69 ) : 336 350 -> 340 327
66( 74 ) : 132 320 236 -> 176
65( 114 ) : 137 61 96 -> 98
64( 137 ) : 174 123 127 -> 125
63( 64 ) : 125 174 -> 173
62( 85 ) : 143 164 135 136 140 -> 203 204
61( 63 ) : 125 173 -> 121 169
60( 64 ) : 125 123 127 -> 126
59( 60 ) : 126 127 123 -> 79
58( 145 ) : 15 331 323 -> 330
57( 59 ) : 126 79 127 -> 83
56( 74 ) : 132 285 320 -> 10
55( 95 ) : 289 309 321 -> 240
54( 95 ) : 306 321 338 -> 356
53( 110 ) : 130 86 -> 95
52( 89 ) : 195 218 -> 253
51( 113 ) : 82 133 123 127 99 85 -> 130
50( 61 ) : 169 -> 172 168
49( 50 ) : 172 168 -> 171
48( 49 ) : 168 171 -> 232
47( 90 ) : 202 279 -> 276
46( 90 ) : 206 280 -> 210
45( 84 ) : 160 227 -> 212
44( 84 ) : 160 112 -> 161
43( 140 ) : 17 46 -> 42
42( 81 ) : 347 339 -> 326
41( 42 ) : 347 326 -> 49
40( 82 ) : 41 345 -> 40
39( 67 ) : 336 340 -> 294
38( 54 ) : 306 -> 355
37( 99 ) : 68 17 22 82 85 -> 81
36( 38 ) : 355 -> 365 367
35( 56 ) : 132 10 -> 94
34( 55 ) : 309 240 -> 243
33( 98 ) : 100 14 143 26 140 -> 102
32( 144 ) : 81 17 43 20 85 -> 47 50
31( 22 ) : 311 -> 313 271
30( 31 ) : 313 271 -> 317
29( 30 ) : 271 317 -> 275
28( 68 ) : 195 143 218 203 219 251 -> 155
27( 29 ) : 275 -> 278 318
26( 58 ) : 331 330 -> 332
25( 26 ) : 332 331 -> 264
24( 25 ) : 332 264 -> 335
23( 24 ) : 332 335 -> 35
22( 34 ) : 243 -> 269 311
21( 22 ) : 269 243 -> 267
20( 23 ) : 35 335 -> 334
19( 20 ) : 35 334 -> 36
18( 21 ) : 269 243 -> 272
17( 130 ) : 180 140 -> 200
16( 96 ) : 14 26 -> 329
15( 18 ) : 243 272 -> 183
14( 57 ) : 83 -> 129
13( 131 ) : 120 -> 70
12( 119 ) : 27 -> 23
11( 79 ) : 25 -> 106
10( 11 ) : 106 -> 28
9( 46 ) : 206 -> 211
8( 107 ) : 20 -> 19
7( 102 ) : 51 -> 55
6( 39 ) : 336 -> 292
5( 6 ) : 292 -> 263
4( 77 ) : 305 -> 262
3( 36 ) : 365 -> 363
2( 22 ) : 311 -> 268
1( 54 ) : 356 -> 359
0( 15 ) : 183 -> 184
ArtPts = 0 MaxDegree = 4 MaxBag = 8 AvgBag = 4.33333
===============================
Launching bottom-to-top process
Combinations:
in intersections - 2.6e+06
in exclusions - 53733.2
total to search - 4.2e+07
Maximal size of a key is 508032 elements
Processing nodes .....................................................................................................................................................
Processing cluster of 4 vertices
Redundant nodes eliminated : 2
Tree-decomposition has been built. Width+1 = 2
Total combinations to search = 1.2e+1
1 : -> 254 196 245
0( 1 ) : 245 -> 244
ArtPts = 0 MaxDegree = 1 MaxBag = 2 AvgBag = 2.5
===============================
Launching bottom-to-top process
Combinations:
in intersections - 2
in exclusions - 23.2
total to search - 4
Maximal size of a key is 2 elements
Processing nodes .
Processing cluster of 3 vertices
Redundant nodes eliminated : 2
Tree-decomposition has been built. Width+1 = 2
Total combinations to search = 4.8e+1
0 : -> 255 248 246
ArtPts = 0 MaxDegree = 0 MaxBag = 2 AvgBag = 3
Processing cluster of 3 vertices
Redundant nodes eliminated : 2
Tree-decomposition has been built. Width+1 = 2
Total combinations to search = 2.4e+1
0 : -> 351 298 297
ArtPts = 0 MaxDegree = 0 MaxBag = 2 AvgBag = 3
Processing cluster of 2 vertices
Redundant nodes eliminated : 1
Tree-decomposition has been built. Width+1 = 1
Total combinations to search = 8
0 : -> 187 192
ArtPts = 0 MaxDegree = 0 MaxBag = 1 AvgBag = 2
Total minimal energy of the graph = 1017.77
真是落落長 ! 而且差很多 ~
2012年5月14日 星期一
my Mac ~/.bash_profile
# export LSCOLORS=gxfxbEaEBxxEhEhBaDaCaD
PS1="\$(date +%H:%M) \[\033[1;32m\]\u@\[\033[0m\h\[\033[0m\]\[\033[1;36m\]:\w\[\033[0m\]$"
LSCOLORS="DxGxFxdxCxegedabagacad"
export PS1 LSCOLORS
alias ls="ls -GF"
##
# Your previous /Users/kevet/.bash_profile file was backed up as /Users/kevet/.bash_profile.macports-saved_2012-05-17_at_17:26:03
##
# MacPorts Installer addition on 2012-05-17_at_17:26:03: adding an appropriate PATH variable for use with MacPorts.
export PATH=/opt/local/bin:/opt/local/sbin:/opt/local/lib/gromacs/bin/:/usr/local/bin/scwrl4/:$PATH
# Finished adapting your PATH environment variable for use with MacPorts.
ps.
PS1="\$(date +%H:%M) \[\033[1;32m\]\u@\[\033[0m\h\[\033[0m\]\[\033[1;36m\]:\w\[\033[0m\]$"
LSCOLORS="DxGxFxdxCxegedabagacad"
export PS1 LSCOLORS
alias ls="ls -GF"
##
# Your previous /Users/kevet/.bash_profile file was backed up as /Users/kevet/.bash_profile.macports-saved_2012-05-17_at_17:26:03
##
# MacPorts Installer addition on 2012-05-17_at_17:26:03: adding an appropriate PATH variable for use with MacPorts.
export PATH=/opt/local/bin:/opt/local/sbin:/opt/local/lib/gromacs/bin/:/usr/local/bin/scwrl4/:$PATH
# Finished adapting your PATH environment variable for use with MacPorts.
ps.
Mac path >> sudo vim /etc/paths
http://keveting.blogspot.com/2008/11/mac-os-x-105xpath.html
2012年5月6日 星期日
CSB Core Lab
Link
ACCESS: Surface Accessibility
DEFINE_S: Define Protein Secondary Structure
http://www.csb.yale.edu/download/volume/volume.tar.ZDDMP: Difference Distance Matrix Plot
OS: Occluded Surface and Packing Analysis
VOLUME : Residue Voronoi Volumes
2012年5月5日 星期六
Natasha Bedingfield 新專輯 4.30
但是還是老歌好聽
Link
Staring at the blank page before you
仔細端詳眼前的青春白皮書
Open up the dirty window
推開污濁的窗
Let the sun illuminate the words that you can not find
讓陽光照亮筆墨不及的字
Reaching for something in the distance
追尋遠方的目標
So close you can almost taste it
千里之遠也會成為咫尺之遙
Release your inhibitions
放手往前衝
Feel the rain on your skin
感受打在身上的雨
No one else can feel it for you
沒有人能替你感受
Only you can let it in
只有你能體會
No one else, no one else
沒有人 沒有人能可以
Can speak the words on your lips
奪去你口中的話
Drench yourself in words unspoken
把自己浸在無形的語言中
Live your life with arms wide open
場開雙臂迎接你的生命
Today is where your book begins
今天是你青春白皮書的首頁
The rest is still unwritten
之後就交由你天馬行空
I break tradition, sometimes my tries, are outside the lines
我挑戰傳統 有時我的限制 超越了界限
We've been conditioned to not make mistakes, but I can't live that way
我們被限制 沒有犯錯的空間 但我無法這樣子生活
Feel the rain on your skin
感受打在身上的雨
No one else can feel it for you
沒有人能替你感受
Only you can let it in
只有你能體會
No one else, no one else
沒有人 沒有人能可以
Can speak the words on your lips
奪去你口中的話
Drench yourself in words unspoken
把自己浸在無形的語言中
Live your life with arms wide open
場開雙臂迎接你的生命
Today is where your book begins
今天是你青春白皮書的首頁
The rest is still unwritten
之後就交由你天馬行空
Link
I am unwritten, can't read my mind, I'm undefined
我的青春任我天馬行空 沒人抓得住我的心思
I'm just beginning, the pen's in my hand, ending unplanned
生命還沒被定義 人生才剛開始 筆握在我的手中 結局如何還未定
我的青春任我天馬行空 沒人抓得住我的心思
I'm just beginning, the pen's in my hand, ending unplanned
生命還沒被定義 人生才剛開始 筆握在我的手中 結局如何還未定
Staring at the blank page before you
仔細端詳眼前的青春白皮書
Open up the dirty window
推開污濁的窗
Let the sun illuminate the words that you can not find
讓陽光照亮筆墨不及的字
Reaching for something in the distance
追尋遠方的目標
So close you can almost taste it
千里之遠也會成為咫尺之遙
Release your inhibitions
放手往前衝
Feel the rain on your skin
感受打在身上的雨
No one else can feel it for you
沒有人能替你感受
Only you can let it in
只有你能體會
No one else, no one else
沒有人 沒有人能可以
Can speak the words on your lips
奪去你口中的話
Drench yourself in words unspoken
把自己浸在無形的語言中
Live your life with arms wide open
場開雙臂迎接你的生命
Today is where your book begins
今天是你青春白皮書的首頁
The rest is still unwritten
之後就交由你天馬行空
I break tradition, sometimes my tries, are outside the lines
我挑戰傳統 有時我的限制 超越了界限
We've been conditioned to not make mistakes, but I can't live that way
我們被限制 沒有犯錯的空間 但我無法這樣子生活
Staring at the blank page before you
仔細端詳眼前的青春白皮書
Open up the dirty window
推開污濁的窗
Let the sun illuminate the words that you can not find
讓陽光照亮筆墨不及的字
Reaching for something in the distance
追尋遠方的目標
So close you can almost taste it
千里之遠也會成為咫尺之遙
Release your inhibitions
放手往前衝
仔細端詳眼前的青春白皮書
Open up the dirty window
推開污濁的窗
Let the sun illuminate the words that you can not find
讓陽光照亮筆墨不及的字
Reaching for something in the distance
追尋遠方的目標
So close you can almost taste it
千里之遠也會成為咫尺之遙
Release your inhibitions
放手往前衝
Feel the rain on your skin
感受打在身上的雨
No one else can feel it for you
沒有人能替你感受
Only you can let it in
只有你能體會
No one else, no one else
沒有人 沒有人能可以
Can speak the words on your lips
奪去你口中的話
Drench yourself in words unspoken
把自己浸在無形的語言中
Live your life with arms wide open
場開雙臂迎接你的生命
Today is where your book begins
今天是你青春白皮書的首頁
The rest is still unwritten
之後就交由你天馬行空
2012年5月1日 星期二
菜英文 (1)
"except" 後面可以接名詞、代名詞、動詞、副詞、介詞片語或子句,而 "except for" 僅能接名詞或代名詞。
在 all, any, every, no, none, anything, anybody, anyone, everything, everybody, everyone, nobody, nothing 等表示總括的不定代名詞之後,一般都用 "except" 而不用 "except for"。
except 用於表示同類事物之間的關係,而 except for 表示非同類事物進行比較。
"except for" 可置於句首,但 "except" 不行。
"except for" 在表示對整體大部分的肯定和對小部分的否定 -- 亦即包含大部分,除去小部分。
僅 "except for" 有「若非;要不是」的意思,"except" 並無此意思。
在 all, any, every, no, none, anything, anybody, anyone, everything, everybody, everyone, nobody, nothing 等表示總括的不定代名詞之後,一般都用 "except" 而不用 "except for"。
except 用於表示同類事物之間的關係,而 except for 表示非同類事物進行比較。
"except for" 可置於句首,但 "except" 不行。
"except for" 在表示對整體大部分的肯定和對小部分的否定 -- 亦即包含大部分,除去小部分。
僅 "except for" 有「若非;要不是」的意思,"except" 並無此意思。
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