Latest revision as of 21:08, 23 May 2024

We define middleware here to mean whatever comes between your application and the operating system. If you have a better name for it, tell us.

Essential

Installing AMSOL AMSOL - atomic charge and desolvation penalty calculations required for database building.
Omega by OpenEye - conformation generation required for database building.
Matplotlib - currently only needed for analysis plots (enrichment)
MSMS - currently only needed by be_blasti

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 We define middleware here to mean whatever comes between your application and the operating system. If you have a better name for it, tell us.
+{{TOCright}}
 = Essential =
-* [[Python]] - 2.7 series
+* [[Installing AMSOL]]  [[AMSOL]] - atomic charge and desolvation penalty calculations required for database building.
-* [[AMSOL]] - atomic charge and desolvation penalty calculations required for database building.
 * [[Omega]] by [[OpenEye]] - [[conformation generation]] required for database building.
-* 3D modeling - [[PyMol]] or [[Chimera]]
 * [[Matplotlib]] - currently only needed for analysis plots (enrichment)
 * [[MSMS]] - currently only needed by [[be_blasti]]
 = Recommended =
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 * [[OGS/GE]] - queuing system.  OpenGridEngine is included in [[Centos]] and you do not need to install it separately.
+Set up psql/rdkit from scratch
+Psql.
+rdkit.
+Drupal.
-Psql. rdkit. Drupal. Chemaxon. mysql. openbabel.
+* [[PyMol]]
+* [[Chimera]]
+* [[Knime]]
+* [[Marvin]]  and [[InstantJChem]] from [[ChemAxon]]
+* [[OpenBabel]]
+* [[rdkit]]
+* [[psql]] and [[MySQL]]
+== Feeware ==
+* [[pgf]]
+* [[CSD]]
+* [[Chemaxon]]
+* [[OpenEye]]
+* [[AMSOL]]
+* [[Epik]] and [[ligprep]] from Schrodinger
+* [[OpenEye]]
+Chemaxon.
+mysql.
+openbabel.
+wiki
+Return to [[So you want to set up a lab]].
 [[Category:Internal]]
 [[Category:Sysadmin]]
 [[Category:Docking]]
+[[Category:Software]]