Installation of Related Packages

Choose a directory for all the packages or apps, for example: ~/apps/

Anaconda

1. Download Anaconda
2. Use bash Anaconda-xxx.sh command to install Anaconda as given on Anaconda page.
3. In the process of installing Anaconda, change the installation path to ~/apps/anaconda/

Kcombu

1. Download kcombu
2. Install pkcombu following the instruction: pkcombu, assume the path of pkcombu is ~/apps/pkcombu.

RDKit

1. conda install python=3.5.2 if you use python 3 and python version is 3.6 or higher.
2. conda install -c rdkit rdkit=2015.09.2

eMolFrag

1. tar -zxf eMolFrag-xxx.tar.gz
2. cd eMolFrag-xxx, assume current path is ~/apps/eMolFrag_2017_01_18_01/
3. Run configuration script: python ConfigurePath.py
4. Type ~/apps/eMolFrag_2017_01_18_01/ as the eMolFrag path when told to.
5. Type ~/apps/pkcombu as the pkcombu path when told to.

Openbabel

1. Download Openbabel
2. tar -zxf openbabel-2.3.1.tar.gz # For example: *.tar.gz in ~/Download/
3. cd ~/apps/
4. mkdir openbabel-2.3.1
5. cd ~/Download/openbabel-2.3.1/
6. cmake ../openbabel-2.3.1 -DCMAKE_INSTALL_PREFIX=~/apps/openbabel-2.3.1/
7. make && make install

(Optional) If you meet some errors when running babel like: .../lib/libstdc++.so.6: version GLIBCXX_3.4.21' not found (required by babel), conda install libgccmight be able to solve the problem.

gsl

1. Install from source file or use yum on Red Hat system or use apt-get on Ubuntu system.

eSynth

1. Download eSynth.
2. tar -zxf esynth-1.1.gz
3. cp -r esynth-1.1 ~/apps/esynth
4. cd ~/apps/esynth
5. vim Makefile and edit the paths for openbabel and gsl. Paths may need to be changed: OB_INC, OB_LIB, GSL_LIB, GSL_INC.
6. make