Building blocks - Revision history

Frodo: asdf

2015-06-11T19:45:36Z

asdf

← Older revision		Revision as of 19:45, 11 June 2015
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	http://zinc15.docking.org/substances/subsets/bb.sdf:zinc_id,mwt,logp?structure-contains=[CX4][ND1]&~structure-contains=C(=O)[OD1]&purchasability=for-sale&count=1000		http://zinc15.docking.org/substances/subsets/bb.sdf:zinc_id,mwt,logp?structure-contains=[CX4][ND1]&~structure-contains=C(=O)[OD1]&purchasability=for-sale&count=1000
	</pre>		</pre>

			There may be some duplicates in these later queries. We're aware of that and we're working to fix it.

	We hope you find this useful.		We hope you find this useful.

Frodo: asdf

2015-06-11T19:43:42Z

asdf

← Older revision		Revision as of 19:43, 11 June 2015
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	Perhaps you were really only interested in a particular functional group. For instance, primary amines:		Perhaps you were really only interested in a particular functional group. For instance, primary amines:
	<pre>		<pre>
	http://zinc15.docking.org/substances/subsets/bb.~~smi~~:zinc_id,mwt,logp?structure-contains=[CX4][ND1]&purchasability=for-sale&count=1000		http://zinc15.docking.org/substances/subsets/bb.sdf:zinc_id,mwt,logp?structure-contains=[CX4][ND1]&purchasability=for-sale&count=1000
	</pre>		</pre>
	That is, 1000 building blocks that are for sale and containing a primary amine, in 2D SDF format containing data tags for ZINC ID, molecular weight and logP.		That is, 1000 building blocks that are for sale and containing a primary amine, in 2D SDF format containing data tags for ZINC ID, molecular weight and logP.

			Oh, wait, when you look at them, you realize that you want only molecules containing a primary amine, but without a carboxylate. So do this.

			<pre>
			http://zinc15.docking.org/substances/subsets/bb.sdf:zinc_id,mwt,logp?structure-contains=[CX4][ND1]&~structure-contains=C(=O)[OD1]&purchasability=for-sale&count=1000
			</pre>

	We hope you find this useful.		We hope you find this useful.

Frodo: asdf

2015-06-11T19:40:41Z

asdf

← Older revision		Revision as of 19:40, 11 June 2015
Line 31:		Line 31:
	Perhaps you were really only interested in a particular functional group. For instance, primary amines:		Perhaps you were really only interested in a particular functional group. For instance, primary amines:
	<pre>		<pre>
	"http://zinc15.docking.org/substances/subsets/bb.smi:zinc_id,mwt,logp?structure-contains=[CX4][ND1]&purchasability=for-sale&count=1000"		http://zinc15.docking.org/substances/subsets/bb.smi:zinc_id,mwt,logp?structure-contains=[CX4][ND1]&purchasability=for-sale&count=1000
	</pre>		</pre>
	That is, 1000 building blocks that are for sale and containing a primary amine, in 2D SDF format containing data tags for ZINC ID, molecular weight and logP.		That is, 1000 building blocks that are for sale and containing a primary amine, in 2D SDF format containing data tags for ZINC ID, molecular weight and logP.

Frodo: asdf

2015-06-11T19:40:24Z

asdf

← Older revision		Revision as of 19:40, 11 June 2015
Line 30:		Line 30:

	Perhaps you were really only interested in a particular functional group. For instance, primary amines:		Perhaps you were really only interested in a particular functional group. For instance, primary amines:
			<pre>
	"http://zinc15.docking.org/substances/subsets/bb.smi:zinc_id,mwt,logp?structure-contains=[CX4][ND1]&purchasability=for-sale&count=1000"		"http://zinc15.docking.org/substances/subsets/bb.smi:zinc_id,mwt,logp?structure-contains=[CX4][ND1]&purchasability=for-sale&count=1000"
			</pre>
	That is, 1000 building blocks that are for sale and containing a primary amine, in 2D SDF format containing data tags for ZINC ID, molecular weight and logP.		That is, 1000 building blocks that are for sale and containing a primary amine, in 2D SDF format containing data tags for ZINC ID, molecular weight and logP.

Frodo: asdf

2015-06-11T19:39:40Z

asdf

← Older revision		Revision as of 19:39, 11 June 2015
Line 31:		Line 31:
	Perhaps you were really only interested in a particular functional group. For instance, primary amines:		Perhaps you were really only interested in a particular functional group. For instance, primary amines:

	http://zinc15.docking.org/substances/subsets/bb.smi:zinc_id,mwt,logp?structure-contains=[CX4][ND1]&purchasability=for-sale&count=1000		"http://zinc15.docking.org/substances/subsets/bb.smi:zinc_id,mwt,logp?structure-contains=[CX4][ND1]&purchasability=for-sale&count=1000"

	That is, 1000 building blocks that are for sale and containing a primary amine, in 2D SDF format containing data tags for ZINC ID, molecular weight and logP.		That is, 1000 building blocks that are for sale and containing a primary amine, in 2D SDF format containing data tags for ZINC ID, molecular weight and logP.

Frodo: asdf

2015-06-11T19:38:56Z

asdf

← Older revision		Revision as of 19:38, 11 June 2015
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	Is that what you wanted? Perhaps you wanted only purchasable building blocks?		Is that what you wanted? Perhaps you wanted only purchasable building blocks?

	~~wget -o log -O bb.smi "~~http://zinc15.docking.org/substances/subsets/~~purchasable+~~bb.smi?count=1000"		http://zinc15.docking.org/substances/subsets/bb.smi?purchasability=for-sale&count=1000

	Is that right? Perhaps you only wanted ones that are in stock for 2-week delivery. In this case, use		Is that right? Perhaps you only wanted ones that are in stock for 2-week delivery. In this case, use

	~~wget -o log -O bb.smi "~~http://zinc15.docking.org/substances/subsets/~~in-stock+~~bb.smi?count=1000"		http://zinc15.docking.org/substances/subsets/bb.smi?purchasability=in-stock&count=1000

	Did you want some extra information for each one, like molecular weight and logP?		Did you want some extra information for each one, like molecular weight and logP?

	~~wget -o log -O bb.smi "~~http://zinc15.docking.org/substances/subsets/~~in-stock+~~bb.smi:zinc_id,mwt,logp?count=1000"		http://zinc15.docking.org/substances/subsets/bb.smi:zinc_id,mwt,logp?purchasability=for-sale&count=1000

	Now, perhaps you wanted 2D SDF format, for use in DataWarrior or InstantJchem?		Now, perhaps you wanted 2D SDF format, for use in DataWarrior or InstantJchem?

	~~wget~~ -~~o log -O bb~~.~~smi "~~http://zinc15.docking.org/substances/subsets/~~in-stock+~~bb.~~sdf~~:zinc_id,mwt,logp?count=1000"		http://zinc15.docking.org/substances/subsets/bb.sdf?purchasability=for-sale&count=1000

			Finally, you are ready to download them all. Change 1000 to all. It will take a while, since there are millions of qualifying molecules.

			Perhaps you were really only interested in a particular functional group. For instance, primary amines:

			http://zinc15.docking.org/substances/subsets/bb.smi:zinc_id,mwt,logp?structure-contains=[CX4][ND1]&purchasability=for-sale&count=1000

			That is, 1000 building blocks that are for sale and containing a primary amine, in 2D SDF format containing data tags for ZINC ID, molecular weight and logP.

	We hope you find this useful.		We hope you find this useful.

Frodo: asdf

2015-06-11T19:33:45Z

asdf

← Older revision		Revision as of 19:33, 11 June 2015
Line 1:		Line 1:
	Our users often write us asking about building blocks. In [[ZINC15]] there are some improved ways to do this.		Our users often write us asking about building blocks. In [[ZINC15]] there are some improved ways to do this.

	I am trying to download the csh mol2 script for Unix but the file is not being found. Could you please fix the file? Or is there another way to download the zbb database?		I am trying to download the csh mol2 script for Unix but the file is not being found.
			Could you please fix the file? Or is there another way to download the zbb database?

	First, you might just want to browse them and see what you're going to get.		First, you might just want to browse them and see what you're going to get.

Frodo: asdf

2015-06-11T19:33:34Z

asdf

New page

Our users often write us asking about building blocks. In [[ZINC15]] there are some improved ways to do this.

I am trying to download the csh mol2 script for Unix but the file is not being found. Could you please fix the file? Or is there another way to download the zbb database?

First, you might just want to browse them and see what you're going to get.
http://zinc15.docking.org/substances/subsets/bb

Once you are ready to download, begin with 1000 SMILES:

wget -o log -O bb.smi "http://zinc15.docking.org/substances/subsets/bb.smi?count=1000"

Is that what you wanted? Perhaps you wanted only purchasable building blocks?

wget -o log -O bb.smi "http://zinc15.docking.org/substances/subsets/purchasable+bb.smi?count=1000"

Is that right? Perhaps you only wanted ones that are in stock for 2-week delivery. In this case, use

wget -o log -O bb.smi "http://zinc15.docking.org/substances/subsets/in-stock+bb.smi?count=1000"

Did you want some extra information for each one, like molecular weight and logP?

wget -o log -O bb.smi "http://zinc15.docking.org/substances/subsets/in-stock+bb.smi:zinc_id,mwt,logp?count=1000"

Now, perhaps you wanted 2D SDF format, for use in DataWarrior or InstantJchem?

wget -o log -O bb.smi "http://zinc15.docking.org/substances/subsets/in-stock+bb.sdf:zinc_id,mwt,logp?count=1000"

We hope you find this useful.

[[Category:ZINC15]]
[[Category:Tutorials]]