Download by catalog: Difference between revisions

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= Downloading 3D lead-like models from a particular catalog =
= Downloading 3D lead-like models from a particular catalog =


* 1. get the script.  http://files.docking.org/catalogs/getfiles.csh
* 1. get the script.
  http://files.docking.org/catalogs/getleadlike.csh
or
http://files.docking.org/catalogs/getfraglike.csh


* 2. get the mapping from ZINC ID to catalog codes. Say ChemBridge, thus chbr.  Also ChemDiv cdiv.
* 2. get the mapping from ZINC ID to catalog codes. Say ChemBridge, thus chbr.  Also ChemDiv cdiv.
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* 5. Download the 3D models.
* 5. Download the 3D models.
  cd lead-like; csh ../getfiles.csh
  cd lead-like; csh ../getleadlike.csh
or
cd frag-like; csh ../getfraglike.csh


Any errors, problems, suggestions, please John.
Any errors, problems, suggestions, please John.

Revision as of 19:19, 20 September 2016

Downloading 3D lead-like models from a particular catalog

  • 1. get the script.
http://files.docking.org/catalogs/getleadlike.csh

or

http://files.docking.org/catalogs/getfraglike.csh
  • 2. get the mapping from ZINC ID to catalog codes. Say ChemBridge, thus chbr. Also ChemDiv cdiv.
http://files.docking.org/catalogs/50/chbr/chbr-zinc.txt.gz

Where 50,40,30,20,10,1 are different purchasability levels. The columns are: vendor code, ZINC ID, InChIKey (for cross-referencing)

  • 3. Get the data for each lead-like tranche
http://files.docking.org/catalogs/50/chbr/lead-like.tgz
  • 4. Uncompress lead-like.tgz
tar xzf lead-like.tgz
  • 5. Download the 3D models.
cd lead-like; csh ../getleadlike.csh

or

cd frag-like; csh ../getfraglike.csh

Any errors, problems, suggestions, please John. The same procedure can be followed for ChemDiv (cdiv) and FCH Group (fchgroup).

The same procedure can be followed for frag-like as well as lead-like. Other vendors can and will be prepared, but they take time. Please write me to expedite certain catalogs.

Note that we only export for lead-like and frag-like, as they are relevant for docking.