-
Notifications
You must be signed in to change notification settings - Fork 26
/
Copy pathINSTALL
142 lines (102 loc) · 5.19 KB
/
INSTALL
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
--- Requirements ---
AlGDock is a third-party python extension.
The required programs and extensions should be installed and tested prior to AlGDock.
It is recommended to use a scientific distribution of python.
These include:
Enthought Canopy Python (tested with version 2.7.6)
https://www.enthought.com/products/epd/
or
Anaconda Scientific Python
https://store.continuum.io/cshop/anaconda/
Unfortunately, due to the issue with a dependency, Scientific Python,
AlGDock requires that numpy is prior to 1.9.
This means that the latest versions of other packages cannot be used.
Here are versions of packages in a working version of AlGDock.
algdock 0.0.1 <pip>
curl 7.30.0 2
cython 0.24 py27_0
dateutil 2.4.1 py27_0
freetype 2.4.10 1
hdf5 1.8.9 2
jpeg 8d 1
lcms 1.19 0
libnetcdf 4.2.1.1 2
libpng 1.5.13 1
matplotlib 1.4.0 np18py27_0
mmtk 2.7.9 <pip>
netcdf4 1.1.1 np18py27_0
numpy 1.8.2 py27_0
openssl 1.0.2h 1
pil 1.1.7 py27_1
pip 8.1.2 py27_0
pymbar 3.0.0.dev0 <pip>
pyparsing 2.0.1 py27_0
python 2.7.11 0
python-dateutil 2.4.1 <pip>
pytz 2016.4 py27_0
readline 6.2 2
scientificpython 2.9.4 <pip>
scipy 0.14.0 np18py27_0
setuptools 23.0.0 py27_0
six 1.10.0 py27_0
sqlite 3.13.0 0
tk 8.5.18 0
wheel 0.29.0 py27_0
zlib 1.2.8 3
After installing a scientific python distribution, the following extensions are also required:
Scientific Python (tested with version 2.9.2)
http://dirac.cnrs-orleans.fr/plone/software/scientificpython/
Molecular Modeling ToolKit (MMTK) (tested with version 2.7.9)
http://dirac.cnrs-orleans.fr/MMTK
pymbar (tested with version 2.0beta)
https://github.com/choderalab/pymbar
OpenMM (tested with version 7.0)
Finally, AlGDock requires the following external programs:
Not Another Molecular Dynamics (NAMD), tested with version 2.9
http://www.ks.uiuc.edu/Research/namd/
--- Installation of AlGDock ---
To install AlGDock, first modify AlGDock/_external_paths.py to point to the locations of the relevant programs. In AlGDock/_external_paths.py, search_paths['MMTK'] should point to the source directory that contains the Include subdirectory.
Then run the commands:
python setup.py build
python setup.py install
--- Complete installation of AlGDock and associated packages with miniconda/anaconda ---
To install AlGDock with conda, follow these steps:
1. Create a conda environment
conda create --name algdock numpy=1.8.1 netcdf4 six cython scipy requests munkres
source activate algdock
2. Install OpenMM and pymbar. This can be done with conda.
conda install -c omnia openmm
conda install -c omnia pymbar
3. Install Scientific python
Identify the NETCDF_PREFIX.
(algdock) Minh-IIT-MBP:ScientificPython-2.9.4 dminh$ which python
/miniconda2/envs/algdock/bin/python
export NETCDF_PREFIX=/miniconda2/envs/algdock/
Download, extract, and change to the scientific python directory. Then enter:
python setup.py install
After changing the directory again,
python -c 'import Scientific.IO.NetCDF'
should work.
If not, you might need a symbolic link to the netcdf dynamic library. Here is an example.
sudo mkdir -p /opt/anaconda1anaconda2anaconda3/lib/
sudo ln -s /Users/dminh/Applications/miniconda2/envs/algdock/lib/libnetcdf.7.dylib /opt/anaconda1anaconda2anaconda3/lib/libnetcdf.7.dylib
4. Install MMTK and pymbar
Download, extract, and change to the MMTK directory. Then enter:
python setup.py install
5. Install AlGDock
Download, extract, and change to the AlGDock directory. Then enter:
python setup.py install
6. (Optional) Install packages for analysis tools.
conda install matplotlib numpy=1.8
TODO: The following may mess up NetCDF compatibility
conda install PIL numpy=1.8
7. (Optional) To prepare a binary with DistTools/Distribute.sh, you will need
pyinstaller, setuptools. Fortunately they can all be installed with conda.
conda install pyinstaller
conda install setuptools=19.2
--- Testing ---
In the AlGDock/Example/ subdirectory, you may test the program with:
test_python.py
or
test_terminal.sh
It should generate output in the dock and cool subdirectories. The dock and cool subdirectories should be removed before testing.