Unpack
安装可以使用conda 进行安装
下面的所有程序需要在power shell下运行
下面的如何运行等等教程什么的
https://www.cnblogs.com/lsdb/p/9531338.html
Conda 安装教程
https://www.jianshu.com/p/edaa744ea47d
miniconda官网：https://conda.io/miniconda.html
下面的这些可以参考 windows10下安装conda https://www.jianshu.com/p/920a6e18cfd6
安装python3.7的minconda；
就是下载下来一步一步安装即可。
添加环境变量
换源
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/msys2/
安装openssl
在执行conda upgrade --all时，报SSLError，需要安装openssl
下载地址：
下载后直接安装就行
https://slproweb.com/products/Win32OpenSSL.html
试运行
在shell里面运行运行程序
#下面的这个就是如何使用conda对nupack进行设计的
conda install -c beliveau-lab nupack
=================================================================================
如果只是在网页是上使用，可以http://www.nupack.org/partition/new
复杂分析
分析相互作用的核酸链复合物的平衡碱基配对特性
pfunc: 计算分区函数
在集合Γ'上计算分区函数Q（φ）
pfunc [-Ttemperature] [-multi] [-pseudo] [-materialparameters][-danglestreatment]prefix
#下面就是运行的程序
(base) zhangjiandeMacBook-Pro:CleaveLand4-master zhangjian$ pfunc
No input file specified.
Requesting input manually.
% NUPACK 3.2.2
% Program: pfunc
% Start time: Wed Nov 25 10:46:58 2020
% Command: pfunc
Enter sequence:
单链计算
如果只是单条链没有其他什么参数可以直接在终端里面输入序列；
下面的就是对GGGCUGUUUUUCUCGCUGACUUUCAGCCCCAAACAAAAAAUGUCAGCA这条链进行计算；
(base) zhangjiandeMacBook-Pro:CleaveLand4-master zhangjian$ pfunc
No input file specified.
Requesting input manually.
% NUPACK 3.2.2
% Program: pfunc
% Start time: Wed Nov 25 10:46:58 2020
% Command: pfunc
Enter sequence: GGGCUGUUUUUCUCGCUGACUUUCAGCCCCAAACAAAAAAUGUCAGCA
% Sequence: GGGCUGUUUUUCUCGCUGACUUUCAGCCCCAAACAAAAAAUGUCAGCA
% v(pi): 1
% Parameters: RNA, 1995
#这里是说明序列的种类是什么rna or dna
% Dangles setting: 1
#这个是一个什么能量，是一个专有名词。（不了解）
% Temperature (C): 37.0
#这个是设置的温度
% Sodium concentration: 1.0000 M
#这个是设置的钠浓度
% Magnesium concentration: 0.0000 M
#这个是设置镁离子浓度
% Free energy (kcal/mol) and partition function:
-1.13589149e+01
1.00956434994643e+08
#这个是计算出来的自由能和一个叫什么分离函数什么的（专有名词）
上面的这个就可以对应到下面这个图的参数，如果上面的没有就不用设置的，保持默认就可以了
多条链计算
计算在23℃下由四个DNA链组成的复合物的分区函数，其中两个是无法区分的。
需要准备的输入文件如下
#第一行是说明有几种序列
#第二行到第四行为3中序列的具体参数
#第五行为每个序列的重复情况，这里就是第一条链重复一次，第二条链重复两次，第三条链重复一次。
3
AGTCTAGGATTCGGCGTGGGTTAA
TTAACCCACGCCGAATCCTAGACTCAAAGTAGTCTAGGATTCGGCGTG
AGTCTAGGATTCGGCGTGGGTTAACACGCCGAATCCTAGACTACTTTG
1 2 2 3
这里可以使用atom创建prefix.in文件
atom下载地址https://atom.io/
例如下图所示，创建的prefix.in文件
#由于项目这里是对多条链进行计算，因此这里就需要设置-multi参数，这个参数就是多条链计算参数。
Command: pfunc -T 23 -multi -material dna /Users/zhangjian/Desktop/prefix
% Sequence: AGTCTAGGATTCGGCGTGGGTTAA+TTAACCCACGCCGAATCCTAGACTCAAAGTAGTCTAGGATTCGGCGTG+TTAACCCACGCCGAATCCTAGACTCAAAGTAGTCTAGGATTCGGCGTG+AGTCTAGGATTCGGCGTGGGTTAACACGCCGAATCCTAGACTACTTTG
% v(pi): 1
% Parameters: DNA, 1998
% Dangles setting: 1
% Temperature (C): 23.0
% Sodium concentration: 1.0000 M
% Magnesium concentration: 0.0000 M
%
% Free energy (kcal/mol) and partition function:
-1.21970714e+02
1.02444390480969e+90
pairs: calculate base-pairing observables
计算碱基配对可观察值（这个翻译对不对 不一定）
Computes pair probabilities p(i n· j m) for the complex corresponding to the specified strand ordering π. When -multi is selected, also computes the expected number of base pairs E(i { A } · j { B } ).
-cutoff cutoffvalue #仅等于或大于cutoffvalue（默认值：0.001）的概率和期望值保存在输出文件中
#还使用这个文件当做输入文件
3
AGTCTAGGATTCGGCGTGGGTTAA
TTAACCCACGCCGAATCCTAGACTCAAAGTAGTCTAGGATTCGGCGTG
AGTCTAGGATTCGGCGTGGGTTAACACGCCGAATCCTAGACTACTTTG
1 2 2 3
#下面就是这个重程序运行的情况
(base) zhangjiandeMacBook-Pro:CleaveLand4-master zhangjian$ pairs -T 23 -multi -material dna -cutoff /Users/zhangjian/Desktop/prefix
Invalid cutoff
#运行结果就在运行目录下面的一个prefix.mfe文件
文件具体内容
这些稀奇古怪的文件格式，都可以使用文本编辑器进行打开，win下面可以就打开方式选择文本编辑器
% NUPACK 3.2.2
% Program: mfe
% Start time: Tue Nov 24 23:22:27 2020
% Command: mfe -T 23 -multi -material dna /Users/zhangjian/Desktop/prefix
% Sequence: AGTCTAGGATTCGGCGTGGGTTAA+TTAACCCACGCCGAATCCTAGACTCAAAGTAGTCTAGGATTCGGCGTG+TTAACCCACGCCGAATCCTAGACTCAAAGTAGTCTAGGATTCGGCGTG+AGTCTAGGATTCGGCGTGGGTTAACACGCCGAATCCTAGACTACTTTG
% v(pi): 1
% Parameters: DNA, 1998
% Dangles setting: 1
% Temperature (C): 23.0
% Sodium concentration: 1.0000 M
% Magnesium concentration: 0.0000 M
% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %
168
-119.494
.(((((((((((((((((((((((+))))))))))))))))))))))).((((((((((((((((((((((((+..(((((((((((((((((((((....((....)).............+.)))))))))))))))))))))..))))))))))))))))))))))))
2 47
3 46
4 45
5 44
6 43
7 42
8 41
9 40
10 39
11 38
12 37
13 36
14 35
15 34
16 33
17 32
18 31
19 30
20 29
21 28
22 27
23 26
24 25
49 168
50 167
51 166
52 165
53 164
54 163
55 162
56 161
57 160
58 159
59 158
60 157
61 156
62 155
63 154
64 153
65 152
66 151
67 150
68 149
69 148
70 147
71 146
72 145
75 142
76 141
77 140
78 139
79 138
80 137
81 136
82 135
83 134
84 133
85 132
86 131
87 130
88 129
89 128
90 127
91 126
92 125
93 124
94 123
95 122
100 107
101 106
% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %
mfe: find the minimum free energy (MFE) secondary structure(s)
找到具有最小自由能的二级结构
确定在复合体Γ上的序列φ的最小自由能二级结构sMFE（φ）。如果选择了简并标记，则确定所有具有最小自由能的二级结构。否则，仅返回一个MFE结构
(base) zhangjiandeMacBook-Pro:CleaveLand4-master zhangjian$ mfe -T 23 -multi -material dna -cutoff /Users/zhangjian/Desktop/prefix
Invalid cutoff
#这里输出的是没有有效的结果，可能是因为心里并不适合，同时如果没有有效的结果，返回的就是MFE的结果。
subopt：在MFE的指定自由能隙内找到所有二级结构
subopt -T 23 -multi -material dna -cutoff /Users/zhangjian/Desktop/prefix
Invalid cutoff
如果有输出的话就是一个prefix.subopt的文件，和上面的MFE输出的还差不多。
count：计算集合中二级结构的数量
计算复合体集合中二级结构的数量，|Γ|，将所有链视为不同
#比如计算下面序列的所有二级序列总和
(base) zhangjiandeMacBook-Pro:CleaveLand4-master zhangjian$ count -multi -material dna /Users/zhangjian/Desktop/prefix
% NUPACK 3.2.2
% Program: count
% Start time: Wed Nov 25 11:51:58 2020
% Command: count -multi -material dna /Users/zhangjian/Desktop/prefix
% Sequence: AGTCTAGGATTCGGCGTGGGTTAA+TTAACCCACGCCGAATCCTAGACTCAAAGTAGTCTAGGATTCGGCGTG+TTAACCCACGCCGAATCCTAGACTCAAAGTAGTCTAGGATTCGGCGTG+AGTCTAGGATTCGGCGTGGGTTAACACGCCGAATCCTAGACTACTTTG
% v(pi): 1
% Parameters: DNA, 1998
% Dangles setting: 1
% Temperature (C): 37.0
% Sodium concentration: 1.0000 M
% Magnesium concentration: 0.0000 M
%
% Total number of secondary structures:
1.88454748279349e+39
Energy：计算二级结构的自由能
输入对应的结构加上序列信息，对序列的二级结构进行换算
这里如果不知道怎么用点括号法表示核酸二级结构
可以把RNA序列放到http://rna.tbi.univie.ac.at/cgi-bin/RNAWebSuite/RNAfold.cgi
下面就是用一段序列生成的函数二级结构什么的
dna的可以使用Mfold
(base) zhangjiandeMacBook-Pro:CleaveLand4-master zhangjian$ energy -T 23 -material dna /Users/zhangjian/Desktop/prefix
% NUPACK 3.2.2
% Program: energy
% Start time: Wed Nov 25 11:57:12 2020
% Command: energy -T 23 -material dna /Users/zhangjian/Desktop/prefix
% NUPACK 3.2.2
% Program: energy
% Start time: Wed Nov 25 11:57:12 2020
% Command: energy -T 23 -material dna /Users/zhangjian/Desktop/prefix
% Sequence: GGUACUUAGGGUGCUUCAGCACCAGAAGUUGUAUGCUAAAUUUGCUAAGUGCGAGUUCUGGUUGACUUCAGUGGCAUUCUUGGGGCA
% Structure: .((.((.((((((((.(((((((((((.((((((((.......))...)))))).)))))).)).))...).)))))))).)).)).
% v(pi): 1
% Parameters: DNA, 1998
% Dangles setting: 1
% Temperature (C): 23.0
% Sodium concentration: 1.0000 M
% Magnesium concentration: 0.0000 M
%
% Energy (kcal/mol):
-8.01379493793326
prob: calculate the equilibrium probability of a secondary structure
计算二级结构的平衡概率
计算平衡概率p（φ，s），该序列在复合体Γ'内采用二级结构
输入文件是和energy计算一样的
(base) zhangjiandeMacBook-Pro:CleaveLand4-master zhangjian$ prob -T 23 -material dna /Users/zhangjian/Desktop/prefix
% NUPACK 3.2.2
% Program: prob
% Start time: Wed Nov 25 14:49:32 2020
% Command: prob -T 23 -material dna /Users/zhangjian/Desktop/prefix
% Sequence: GGUACUUAGGGUGCUUCAGCACCAGAAGUUGUAUGCUAAAUUUGCUAAGUGCGAGUUCUGGUUGACUUCAGUGGCAUUCUUGGGGCA
% Structure: .((.((.((((((((.(((((((((((.((((((((.......))...)))))).)))))).)).))...).)))))))).)).)).
% v(pi): 1
% Parameters: DNA, 1998
% Dangles setting: 1
% Temperature (C): 23.0
% Sodium concentration: 1.0000 M
% Magnesium concentration: 0.0000 M
%
% Probability:
3.175e-08
试管分析
分析相互作用的核酸链的试管的平衡碱基配对特性和浓度
complexes: calculate the partition function and equilibrium base-pairing properties for each com-plex in a test tube
络合物：计算试管中每个络合物的分配函数和平衡碱基配对属性
对于链Ψ0的集合，计算每个复合物j∈Ψ的分区函数Qj，对应于最多Lmax个链的所有复合物。可以通过命令行标志来指定重要的附加功能。复合体的输出可以用作可执行文件的输入。
输入文件示例
prefix.in文件如下
%第一行为序列种数
%第二行到第四行为3个序列的具体碱基序列
%第五行为最大复数Lmax（这里不是很清楚）
3
AGTCTAGGATTCGGCGTGGGTTAA
TTAACCCACGCCGAATCCTAGACTCAAAGTAGTCTAGGATTCGGCGTG
AGTCTAGGATTCGGCGTGGGTTAACACGCCGAATCCTAGACTACTTTG
4
prefix.list文件如下
%1到|Ψ0|范围内的L整数列表，表示复合物的链顺序
%下面的每一个数字表示上面的一条链如1就是“AGTCTAGGATTCGGCGTGGGTTAA”
%整合上面的文件中的4就是一个有4种的不同组合。
1 2 2 3 3
1 2 3 2 3
2 3 2 3 2
1 2 2 2 3 3
运行实例
#这里的-T 后面要加上温度，-material 要指明计算的核酸种类 -pairs 是按照可执行对计算碱基对可观察值 -mfe 计算每个复合体的所有MFE结构
#-cutoff cutoffvalue 在选择pairs flags时生成的输出文件中仅保存等于或大于cutoffvalue（默认值：0.001）的概率和期望值
#-timeonly 要多少时间完成计算
#-v3.0 以3.0版本运行程序
#-quiet 安静的运行程序，就是不会在屏幕上出现太多东西
(base) zhangjiandeMacBook-Pro:~ zhangjian$ complexes -T 23 -material dna -pairs -mfe -degenerate /Users/zhangjian/Desktop/prefix concentrations -pairs /Users/zhangjian/Desktop/prefix
Relative to NUPACK 3.0, the following changes were introduced to
the complexes executable:
-ordered is on by default
output files .cx and .cx-epairs are not written
the comment lines in .ocx-epairs and .ocx-mfe employ updated terminology
Use the -v3.0 option to revert to NUPACK 3.0 behavior.
Permutation generation complete.
Starting partition function calculations.
Rough time estimate for calculation: 182.77 seconds
Status: Set 1 / 37: nPerms (1) 1 / 48
Status: Set 2 / 37: nPerms (1) 2 / 48
Status: Set 3 / 37: nPerms (1) 3 / 48
Status: Set 4 / 37: nPerms (1) 4 / 48
Status: Set 5 / 37: nPerms (1) 5 / 48
Status: Set 6 / 37: nPerms (1) 6 / 48
Status: Set 7 / 37: nPerms (1) 7 / 48
Status: Set 8 / 37: nPerms (1) 8 / 48
Status: Set 9 / 37: nPerms (1) 9 / 48
Status: Set 10 / 37: nPerms (1) 10 / 48
Status: Set 11 / 37: nPerms (1) 11 / 48
Status: Set 12 / 37: nPerms (1) 12 / 48
Status: Set 13 / 37: nPerms (1) 13 / 48
Status: Set 14 / 37: nPerms (2) 14 / 48
Status: Set 15 / 37: nPerms (1) 16 / 48
Status: Set 16 / 37: nPerms (1) 17 / 48
Status: Set 17 / 37: nPerms (1) 18 / 48
Status: Set 18 / 37: nPerms (1) 19 / 48
Status: Set 19 / 37: nPerms (1) 20 / 48
Status: Set 20 / 37: nPerms (1) 21 / 48
Status: Set 21 / 37: nPerms (1) 22 / 48
Status: Set 22 / 37: nPerms (1) 23 / 48
Status: Set 23 / 37: nPerms (2) 24 / 48
Status: Set 24 / 37: nPerms (3) 26 / 48
Status: Set 25 / 37: nPerms (2) 29 / 48
Status: Set 26 / 37: nPerms (1) 31 / 48
Status: Set 27 / 37: nPerms (3) 32 / 48
Status: Set 28 / 37: nPerms (3) 35 / 48
Status: Set 29 / 37: nPerms (1) 38 / 48
Status: Set 30 / 37: nPerms (1) 39 / 48
Status: Set 31 / 37: nPerms (1) 40 / 48
Status: Set 32 / 37: nPerms (2) 41 / 48
Status: Set 33 / 37: nPerms (1) 43 / 48
Status: Set 34 / 37: nPerms (1) 44 / 48
Status: Set 35 / 37: nPerms (2) 45 / 48
Status: Set 36 / 37: nPerms (1) 47 / 48
Status: Set 37 / 37: nPerms (1) 48 / 48
Total number of terms calculated: 48 (48)
Calculation finished on: Wed Nov 25 15:08:33 2020
生成的文件
prefix.ocx文件的内容(节选）
% NUPACK 3.2.2
% Program: complexes
% Start time: Wed Nov 25 15:08:18 2020 PST
%
% Command: complexes -T 23 -material dna -pairs -mfe -degenerate -pairs /Users/zhangjian/Desktop/prefix concentrations /Users/zhangjian/Desktop/prefix
% Maximum complex size to enumerate: 4
% Number of complexes from enumeration: 44
% Additional complexes from .list file: 4
% Total number of complexes: 48
% Parameters: DNA, 1998
% Dangles setting: 1
% Temperature (C): 23.0
% Sodium concentration: 1.0000 M
% Magnesium concentration: 0.0000 M
%
% Do not change the comments below this line, as they may be read by other programs!
%
% Number of strands: 3
% id sequence
% 1 AGTCTAGGATTCGGCGTGGGTTAA
% 2 TTAACCCACGCCGAATCCTAGACTCAAAGTAGTCTAGGATTCGGCGTG
% 3 AGTCTAGGATTCGGCGTGGGTTAACACGCCGAATCCTAGACTACTTTG
% T = 23.0
1 1 1 0 0 -7.87585320e-01
2 1 0 1 0 -2.77229511e+01
3 1 0 0 1 -2.80354395e+01
4 1 2 0 0 -1.07109347e+01
5 1 1 1 0 -4.15225790e+01
6 1 1 0 1 -3.42779194e+01
7 1 0 2 0 -5.88918294e+01
8 1 0 1 1 -5.91190488e+01
9 1 0 0 2 -6.04508699e+01
10 1 3 0 0 -1.86535120e+01
11 1 2 1 0 -5.21814376e+01
12 1 2 0 1 -4.46710992e+01
13 1 1 2 0 -7.44330886e+01
14 1 1 1 1 -8.17640179e+01
14 2 1 1 1 -7.10190272e+01
15 1 1 0 2 -6.76235463e+01
16 1 0 3 0 -9.00673131e+01
17 1 0 2 1 -9.04005684e+01
18 1 0 1 2 -9.19265778e+01
19 1 0 0 3 -9.22563355e+01
20 1 4 0 0 -2.88102348e+01
21 1 3 1 0 -6.00477161e+01
22 1 3 0 1 -5.27376513e+01
23 1 2 2 0 -8.53462065e+01
23 2 2 2 0 -9.28574307e+01
24 1 2 1 1 -8.58158470e+01
24 2 2 1 1 -8.16781270e+01
24 3 2 1 1 -9.21079593e+01
refix.ocx-epairs文件内容(节选）
% NUPACK 3.2.2
% Program: complexes
% Start time: Wed Nov 25 15:08:18 2020 PST
%
% Command: complexes -T 23 -material dna -pairs -mfe -degenerate -pairs /Users/zhangjian/Desktop/prefix concentrations /Users/zhangjian/Desktop/prefix
% Maximum complex size to enumerate: 4
% Minimum output pair probability: 0.001
% Number of complexes from enumeration: 44
% Additional complexes from .list file: 4
% Total number of complexes: 48
% Parameters: DNA, 1998
% Dangles setting: 1
% Temperature (C): 23.0
% Sodium concentration: 1.0000 M
% Magnesium concentration: 0.0000 M
%
% Do not change the comments below this line, as they may be read by other programs!
%
% Number of strands: 3
% id sequence
% 1 AGTCTAGGATTCGGCGTGGGTTAA
% 2 TTAACCCACGCCGAATCCTAGACTCAAAGTAGTCTAGGATTCGGCGTG
% 3 AGTCTAGGATTCGGCGTGGGTTAACACGCCGAATCCTAGACTACTTTG
% T = 23.0
% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %
% composition1-ordering1
120
1 5 2.707e-03
1 10 4.089e-03
1 11 1.026e-02
1 17 1.924e-03
1 21 3.609e-03
1 22 2.361e-03
2 10 8.574e-03
2 12 1.171e-02
2 15 4.715e-02
3 8 2.373e-03
3 9 3.436e-02
3 14 3.927e-02
3 19 2.986e-03
4 8 5.055e-02
4 13 3.333e-02
4 14 1.877e-02
4 16 7.577e-03
4 18 1.816e-02
4 19 8.623e-02
4 20 1.839e-02
5 9 2.048e-03
5 13 5.158e-03
5 18 7.197e-02
5 19 8.534e-03
5 23 5.228e-03
prefix.ocx-key 文件的内容(节选）
% NUPACK 3.2.2
% Program: complexes
% Start time: Wed Nov 25 15:08:18 2020 PST
%
% Command: complexes -T 23 -material dna -pairs -mfe -degenerate -pairs /Users/zhangjian/Desktop/prefix concentrations /Users/zhangjian/Desktop/prefix
% Maximum complex size to enumerate: 4
% Number of complexes from enumeration: 44
% Additional complexes from .list file: 4
% Total number of complexes: 48
% Parameters: DNA, 1998
% Dangles setting: 1
% Temperature (C): 23.0
% Sodium concentration: 1.0000 M
% Magnesium concentration: 0.0000 M
%
% Do not change the comments below this line, as they may be read by other programs!
%
% Number of strands: 3
% id sequence
% 1 AGTCTAGGATTCGGCGTGGGTTAA
% 2 TTAACCCACGCCGAATCCTAGACTCAAAGTAGTCTAGGATTCGGCGTG
% 3 AGTCTAGGATTCGGCGTGGGTTAACACGCCGAATCCTAGACTACTTTG
% T = 23.0
1 1 1
2 1 2
3 1 3
4 1 1 1
5 1 1 2
6 1 1 3
7 1 2 2
8 1 2 3
9 1 3 3
10 1 1 1 1
11 1 1 1 2
12 1 1 1 3
13 1 1 2 2
14 1 1 2 3
14 2 1 3 2
15 1 1 3 3
16 1 2 2 2
17 1 2 2 3
18 1 2 3 3
19 1 3 3 3
20 1 1 1 1 1
prefix.ocx-mfe 文件的内容(节选）
% NUPACK 3.2.2
% Program: complexes
% Start time: Wed Nov 25 15:08:18 2020 PST
%
% Command: complexes -T 23 -material dna -pairs -mfe -degenerate -pairs /Users/zhangjian/Desktop/prefix concentrations /Users/zhangjian/Desktop/prefix
% Maximum complex size to enumerate: 4
% Number of complexes from enumeration: 44
% Additional complexes from .list file: 4
% Total number of complexes: 48
% Parameters: DNA, 1998
% Dangles setting: 1
% Temperature (C): 23.0
% Sodium concentration: 1.0000 M
% Magnesium concentration: 0.0000 M
%
% Do not change the comments below this line, as they may be read by other programs!
%
% Number of strands: 3
% id sequence
% 1 AGTCTAGGATTCGGCGTGGGTTAA
% 2 TTAACCCACGCCGAATCCTAGACTCAAAGTAGTCTAGGATTCGGCGTG
% 3 AGTCTAGGATTCGGCGTGGGTTAACACGCCGAATCCTAGACTACTTTG
% T = 23.0
% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %
% composition1-ordering1
24
0.00000000e+00
........................
% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %
% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %
% composition2-ordering1
48
-2.75828841e+01
......((((((((((((((((((......))))))))))))))))))
7 48
8 47
9 46
10 45
11 44
12 43
13 42
14 41
15 40
16 39
17 38
18 37
19 36
20 35
21 34
22 33
23 32
24 31
% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %
% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %
% composition3-ordering1
48
-2.77667355e+01
((((((((((((((((((......))))))))))))))))))......
1 42
2 41
3 40
4 39
5 38
6 37
7 36
8 35
9 34
10 33
11 32
12 31
13 30
14 29
15 28
16 27
17 26
18 25
% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %
% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %
% composition4-ordering1
48
-1.04023100e+01
...........((.((........+...........)).))........
12 40
13 39
15 37
16 36
% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %
% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %
prefix.ocx-ppairs 文件的内容(节选）
% NUPACK 3.2.2
% Program: complexes
% Start time: Wed Nov 25 15:08:18 2020 PST
%
% Command: complexes -T 23 -material dna -pairs -mfe -degenerate -pairs /Users/zhangjian/Desktop/prefix concentrations /Users/zhangjian/Desktop/prefix
% Maximum complex size to enumerate: 4
% Minimum output pair probability: 0.001
% Number of complexes from enumeration: 44
% Additional complexes from .list file: 4
% Total number of complexes: 48
% Parameters: DNA, 1998
% Dangles setting: 1
% Temperature (C): 23.0
% Sodium concentration: 1.0000 M
% Magnesium concentration: 0.0000 M
%
% Do not change the comments below this line, as they may be read by other programs!
%
% Number of strands: 3
% id sequence
% 1 AGTCTAGGATTCGGCGTGGGTTAA
% 2 TTAACCCACGCCGAATCCTAGACTCAAAGTAGTCTAGGATTCGGCGTG
% 3 AGTCTAGGATTCGGCGTGGGTTAACACGCCGAATCCTAGACTACTTTG
% T = 23.0
% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %
% composition1-ordering1
24
1 5 2.707e-03
1 10 4.089e-03
1 11 1.026e-02
1 17 1.924e-03
1 21 3.609e-03
1 22 2.361e-03
2 10 8.574e-03
2 12 1.171e-02
2 15 4.715e-02
3 8 2.373e-03
3 9 3.436e-02
3 14 3.927e-02
3 19 2.986e-03
4 8 5.055e-02
4 13 3.333e-02
4 14 1.877e-02
4 16 7.577e-03
4 18 1.816e-02
4 19 8.623e-02
4 20 1.839e-02
5 9 2.048e-03
5 13 5.158e-03
5 18 7.197e-02
5 19 8.534e-03
5 23 5.228e-03
6 10 4.368e-02
6 11 2.266e-02
6 17 1.248e-01
6 21 2.386e-03
6 22 1.121e-02
7 12 3.150e-02
7 15 1.720e-02
7 21 2.649e-03
8 12 5.961e-03
8 15 1.237e-01
9 17 1.644e-02
9 21 1.232e-02
9 22 5.647e-03
10 16 1.232e-02
10 20 9.301e-03
10 23 2.961e-03
10 24 2.578e-02
11 19 7.937e-03
11 23 2.459e-02
11 24 1.158e-03
12 16 9.936e-03
12 18 1.263e-01
12 19 2.621e-02
12 20 1.554e-02
13 17 2.650e-02
13 21 4.834e-03
14 21 6.112e-03
15 19 2.169e-02
15 20 8.830e-02
17 23 4.451e-03
17 24 1.161e-03
1 25 9.751e-01
2 25 9.318e-01
3 25 9.195e-01
4 25 7.670e-01
5 25 9.033e-01
6 25 7.953e-01
7 25 9.470e-01
8 25 8.165e-01
9 25 9.292e-01
10 25 8.923e-01
11 25 9.313e-01
12 25 7.728e-01
13 25 9.298e-01
14 25 9.350e-01
15 25 7.020e-01
16 25 9.695e-01
17 25 8.236e-01
18 25 7.827e-01
19 25 8.461e-01
20 25 8.668e-01
21 25 9.671e-01
22 25 9.795e-01
23 25 9.625e-01
24 25 9.709e-01
% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %
concentrations: calculate the equilibrium concentration for each complex in a test tube
计算试管中每种复合物的平衡浓度
给定用户指定的每种链物种的浓度，计算稀溶液（例如试管）中每种复杂物种或碱基对的平衡浓度（Dirks et al。，2007）。分区函数信息是从由可执行复合体生成的输出文件中读取的。
要输入的文件
prefix.ocx文件来自上面的文件计算而来
prefix.con文件来自上面的文件计算而来
%下面就prefix.con文件的内容，因为上面是三条序列因此就指定三个摩尔浓度
1 1e-6
2 1e-5
3 1e-8
(base) zhangjiandeMacBook-Pro:~ zhangjian$ concentrations -pairs /Users/zhangjian/Desktop/prefix -sort 0 /Users/zhangjian/Desktop/prefix
Relative to NUPACK 3.0, the following change was introduced to the
concentrations executable: the -ordered option is on by default.
Use the -v3.0 option to revert to NUPACK 3.0 behavior.
Error in conservation of mass: #这里报的信息是摩尔质量不失衡
7.842022e-09 Molar
1.624964e-08 Molar
1.557208e-08 Molar
Free energy = -1.825048e+02 kcal/litre of solution
Elapsed time: 0 seconds.
#-pairs 就是要指定输入文件的位置
#-sort 指定排序方法
下面是prefix.eq文件的内容
% NUPACK 3.2.2
% This is /Users/zhangjian/Desktop/prefix.eq, an output file generated for a "concentrations"
% calculation of equilibrium concentrations.
% For information on contents, see NUPACK manual.
% Program: concentrations
% Start time: Wed Nov 25 16:05:26 2020 PST
% Command: concentrations -pairs -sort 0 /Users/zhangjian/Desktop/prefix /Users/zhangjian/Desktop/prefix
% Initial monomer concentrations:
% 1: 1.000000e+00 Molar
% 2: 2.000000e+00 Molar
% 3: 3.000000e+00 Molar
% Following is the header from the input file (/Users/zhangjian/Desktop/prefix.ocx):
%
%
% NUPACK 3.2.2
% Program: complexes
% Start time: Wed Nov 25 15:08:18 2020 PST
%
% Command: complexes -T 23 -material dna -pairs -mfe -degenerate -pairs /Users/zhangjian/Desktop/prefix concentrations /Users/zhangjian/Desktop/prefix
% Maximum complex size to enumerate: 4
% Number of complexes from enumeration: 44
% Additional complexes from .list file: 4
% Total number of complexes: 48
% Parameters: DNA, 1998
% Dangles setting: 1
% Temperature (C): 23.0
% Sodium concentration: 1.0000 M
% Magnesium concentration: 0.0000 M
%
% Do not change the comments below this line, as they may be read by other programs!
%
% Number of strands: 3
% id sequence
% 1 AGTCTAGGATTCGGCGTGGGTTAA
% 2 TTAACCCACGCCGAATCCTAGACTCAAAGTAGTCTAGGATTCGGCGTG
% 3 AGTCTAGGATTCGGCGTGGGTTAACACGCCGAATCCTAGACTACTTTG
% T = 23.0
1 1 1 0 0 -7.875853e-01 2.616270e-08
2 1 0 1 0 -2.772295e+01 1.253223e-10
3 1 0 0 1 -2.803544e+01 5.793549e-02
4 1 2 0 0 -1.071093e+01 6.823000e-11
5 1 1 1 0 -4.152258e+01 2.370779e-10
6 1 1 0 1 -3.427792e+01 2.903177e-07
7 1 0 2 0 -5.889183e+01 9.902608e-20
8 1 0 1 1 -5.911905e+01 3.960408e-11
9 1 0 0 2 -6.045087e+01 1.034883e-01
10 1 3 0 0 -1.865351e+01 6.144997e-15
11 1 2 1 0 -5.218144e+01 2.157576e-12
12 1 2 0 1 -4.467110e+01 1.682233e-09
13 1 1 2 0 -7.443309e+01 3.613103e-18
14 1 1 1 1 -8.176402e+01 2.524536e-04
下面是prefix.eq文件的内容
% NUPACK 3.2.2
% This is /Users/zhangjian/Desktop/prefix.fpairs, an output file generated for a "concentrations"
% calculation of base pair fractions.
% For information on contents, see NUPACK manual.
% Program: concentrations
% Start time: Wed Nov 25 16:05:26 2020 PST
% Command: concentrations -pairs -sort 0 /Users/zhangjian/Desktop/prefix /Users/zhangjian/Desktop/prefix
% Minimum output pair fraction: 0.001
% Initial monomer concentrations:
% 1: 1.000000e+00 Molar
% 2: 2.000000e+00 Molar
% 3: 3.000000e+00 Molar
%
% Following is the header from the input file (/Users/zhangjian/Desktop/prefix.ocx):
%
% NUPACK 3.2.2
% Program: complexes
% Start time: Wed Nov 25 15:08:18 2020 PST
%
% Command: complexes -T 23 -material dna -pairs -mfe -degenerate -pairs /Users/zhangjian/Desktop/prefix concentrations /Users/zhangjian/Desktop/prefix
% Maximum complex size to enumerate: 4
% Number of complexes from enumeration: 44
% Additional complexes from .list file: 4
% Total number of complexes: 48
% Parameters: DNA, 1998
% Dangles setting: 1
% Temperature (C): 23.0
% Sodium concentration: 1.0000 M
% Magnesium concentration: 0.0000 M
%
% Do not change the comments below this line, as they may be read by other programs!
%
% Number of strands: 3
% id sequence
% 1 AGTCTAGGATTCGGCGTGGGTTAA
% 2 TTAACCCACGCCGAATCCTAGACTCAAAGTAGTCTAGGATTCGGCGTG
% 3 AGTCTAGGATTCGGCGTGGGTTAACACGCCGAATCCTAGACTACTTTG
% T = 23.0
120
1 48 4.835637e-01
1 121 5.161056e-01
2 47 9.897167e-01
2 121 9.751942e-03
3 46 9.909160e-01
3 121 8.621663e-03
4 45 9.985135e-01
4 121 1.048448e-03
5 44 9.963146e-01
5 121 3.198827e-03
6 43 9.964146e-01
6 121 3.120022e-03
7 42 9.991132e-01
8 41 9.991135e-01
9 40 9.977139e-01
9 121 1.825688e-03
10 39 9.965146e-01
10 121 3.015618e-03
11 38 9.981139e-01
11 121 1.434768e-03
12 37 9.993132e-01
13 36 9.994132e-01
14 35 9.994132e-01
15 34 9.995132e-01
16 33 9.994132e-01
17 32 9.990132e-01
18 31 9.992132e-01
19 30 9.993132e-01
distributions
在一个小盒子中计算几个复合物的平衡总体分布和期望值
给定用户定义的每种链种类的种群，可执行文件分布为包含少量链的盒子计算分区函数Qbox（Dirks等，2007）。这用于计算每种复合物种群的期望值和概率分布。分区功能信息是从由可执行复合体生成的输出文件中读取的
输入文件
%第一到底三行为123三条序列分别对应的 指定每个链种i∈Ψ0的总链总数m0i
%最后一行为 文件的最后一行包含以升为单位的盒子的体积。这可以用科学记数法输入
1 6
2 7
3 5
1.4e-18
distributions
(base) zhangjiandeMacBook-Pro:~ zhangjian$ distributions -maxstates 1e8 -writestates -sort 1 /Users/zhangjian/Desktop/prefix
Relative to NUPACK 3.0, the following change was introduced to the
distributions executable: the -ordered option is on by default.
Use the -v3.0 option to revert to NUPACK 3.0 behavior.
There are 64 populations in Lambda.
Free energy of the box: -1.667768e+01 kT, or -1.629827e-23 kcal
Elapsed time: 0 seconds.
#---maxstates 就是设置一个空间来存放计算数据
#---writestates 编写一个（通常很大的）输出文件，描述系统所有填充状态的属性
#----sort 就是结果排序的方法
输出文件
prefix.dist文件内容
% NUPACK 3.2.2
% This is /Users/zhangjian/Desktop/prefix.dist, an output file generated for a
% calculation of equilibrium complex count distributions.
% Time calculation was begun: Wed Nov 25 16:24:44 2020
% Inital monomer counts:
% 1: 1
% 2: 2
% 3: 3
% Box volume (liters): 1.400000e-18
3 1 0 0 1 -2.803544e+01 1.023065e+00 1.685686e-06 9.769415e-01 2.304693e-02 9.860647e-06
35 1 1 2 2 -1.622122e+02 9.769412e-01 2.305885e-02 9.769412e-01 0.000000e+00 0.000000e+00
27 1 1 2 1 -1.219707e+02 2.240748e-02 9.775925e-01 2.240748e-02 0.000000e+00 0.000000e+00
2 1 0 1 0 -2.772295e+01 6.514024e-04 9.993487e-01 6.512880e-04 5.719640e-08 0.000000e+00
14 1 1 1 1 -8.176402e+01 6.411420e-04 9.993589e-01 6.411420e-04 0.000000e+00 0.000000e+00
5 1 1 1 0 -4.152258e+01 9.804429e-06 9.999902e-01 9.804429e-06 0.000000e+00 0.000000e+00
9 1 0 0 2 -6.045087e+01 1.687847e-06 9.999983e-01 1.687847e-06 0.000000e+00 0.000000e+00
28 1 1 1 2 -1.153619e+02 3.497095e-07 9.999997e-01 3.497095e-07 0.000000e+00 0.000000e+00
1 1 1 0 0 -7.875853e-01 5.716051e-08 9.999999e-01 5.716051e-08 0.000000e+00 0.000000e+00
35 2 1 2 2 -1.514039e+02 1.032109e-08 1.000000e+00 1.032109e-08 0.000000e+00 0.000000e+00
8 1 0 1 1 -5.911905e+01 8.490297e-09 1.000000e+00 8.490297e-09 1.435566e-17 0.000000e+00
13 1 1 2 0 -7.443309e+01 1.414184e-09 1.000000e+00 1.414184e-09 0.000000e+00 0.000000e+00
28 2 1 1 2 -1.112604e+02 3.287730e-10 1.000000e+00 3.287730e-10 0.000000e+00 0.000000e+00
27 2 1 2 1 -1.105970e+02 9.056463e-11 1.000000e+00 9.056463e-11 0.000000e+00 0.000000e+00
6 1 1 0 1 -3.427792e+01 3.895163e-11 1.000000e+00 3.895163e-11 0.000000e+00 0.000000e+00
14 2 1 1 1 -7.101903e+01 7.542139e-12 1.000000e+00 7.542139e-12 0.000000e+00 0.000000e+00
7 1 0 2 0 -5.889183e+01 8.555047e-13 1.000000e+00 8.555047e-13 0.000000e+00 0.000000e+00
18 1 0 1 2 -9.192658e+01 6.180641e-13 1.000000e+00 6.180641e-13 0.000000e+00 0.000000e+00
19 1 0 0 3 -9.225634e+01 2.806648e-14 1.000000e+00 2.806648e-14 0.000000e+00 0.000000e+00
15 1 1 0 2 -6.762355e+01 1.383906e-14 1.000000e+00 1.383906e-14 0.000000e+00 0.000000e+00
27 3 1 2 1 -1.039379e+02 1.103362e-15 1.000000e+00 1.103362e-15 0.000000e+00 0.000000e+00
prefix.states文件内容
% NUPACK 3.2.2
% This is /Users/zhangjian/Desktop/prefix.states, an output file generated for a
% calculation of equilibrium complex count distributions.
% The contents of this file is the Lambda, the set of
% population vectors consistent with conservation of mass.
% Time calculation was begun: Wed Nov 25 16:24:44 2020
5.714489e-08 1 1 1 2 1 2 3 1 3
1.032109e-08 3 1 1 35 2 1
9.769412e-01 3 1 1 35 1 1
5.112064e-21 1 1 1 2 1 1 33 1 1
1.059172e-21 1 1 1 3 1 1 32 2 1
7.420598e-21 1 1 1 3 1 1 32 1 1
2.082922e-18 2 1 2 29 1 1
3.287708e-10 2 1 1 3 1 1 28 2 1
3.497072e-07 2 1 1 3 1 1 28 1 1
1.065891e-15 2 1 1 3 1 1 28 3 1
1.103281e-15 3 1 2 27 3 1
9.055800e-11 3 1 2 27 2 1
2.240584e-02 3 1 2 27 1 1
1.626522e-16 1 1 1 2 1 2 19 1 1
3.158972e-16 1 1 1 2 1 1 3 1 1 18 1 1
2.008982e-17 1 1 1 3 1 2 17 1 1
1.383867e-14 2 1 2 3 1 1 15 1 1
1.621705e-24 15 1 1 17 1 1
7.541490e-12 2 1 1 3 1 2 14 2 1
6.948231e-21 14 2 1 18 1 1
6.410869e-04 2 1 1 3 1 2 14 1 1
5.906551e-13 14 1 1 18 1 1
1.413874e-09 3 1 3 13 1 1
4.024326e-18 13 1 1 19 1 1
1.253896e-11 1 1 1 2 1 2 3 1 1 9 1 1
8.069547e-20 9 1 1 27 3 1
6.623534e-15 9 1 1 27 2 1
1.638793e-06 9 1 1 27 1 1
1.469396e-21 1 1 1 9 1 1 17 1 1
5.515947e-16 2 1 1 9 1 1 14 2 1
4.688995e-08 2 1 1 9 1 1 14 1 1
3.102378e-13 3 1 1 9 1 1 13 1 1
2.218333e-12 1 1 1 2 1 1 3 1 2 8 1 1
2.127116e-15 8 1 1 28 2 1
2.262573e-12 8 1 1 28 1 1
6.896216e-21 8 1 1 28 3 1
2.043825e-21 1 1 1 8 1 1 18 1 1
1.790698e-19 2 1 1 8 1 1 15 1 1
9.758546e-17 3 1 1 8 1 1 14 2 1
8.295543e-09 3 1 1 8 1 1 14 1 1
1.622518e-16 1 1 1 2 1 1 8 1 1 9 1 1
1.435240e-17 1 1 1 3 1 1 8 1 2
8.547344e-13 1 1 1 3 1 3 7 1 1
3.115492e-23 7 1 1 29 1 1
2.432841e-21 1 1 1 7 1 1 19 1 1
2.069894e-19 3 1 1 7 1 1 15 1 1
1.875493e-16 1 1 1 3 1 1 7 1 1 9 1 1
3.894719e-11 2 1 2 3 1 2 6 1 1
2.406269e-25 6 1 1 32 2 1
1.685840e-24 6 1 1 32 1 1
7.176674e-20 2 1 1 6 1 1 18 1 1
9.128166e-21 3 1 1 6 1 1 17 1 1
2.848650e-15 2 1 2 6 1 1 9 1 1
1.007939e-15 2 1 1 3 1 1 6 1 1 8 1 1
3.260634e-21 6 1 1 8 1 2
5.825456e-16 3 1 2 6 1 1 7 1 1
4.260816e-20 6 1 1 7 1 1 9 1 1
9.802088e-06 2 1 1 3 1 3 5 1 1
4.384373e-19 5 1 1 33 1 1
2.789980e-14 2 1 1 5 1 1 19 1 1
2.709299e-14 3 1 1 5 1 1 18 1 1
2.150813e-09 2 1 1 3 1 1 5 1 1 9 1 1
1.902557e-10 3 1 2 5 1 1 8 1 1
1.391556e-14 5 1 1 8 1 1 9 1 1
最后
网站上还像有一个demo 可以试找 试一下看看