Hi,
As per the previous mail in taking a snapshot of chemical structure or reaction
,the reaction image is rendered as (Ex.) HH if we input H2 in the reaction how
to resolve this and also please let me know where can i find all the cdk
properties like "ReactionConditions" in
rxn.setProperty("cdk:ReactionConditions", "Reaction Text"); As i am new to this
library
P.S. John, I am really very sorry to bother you ,as i am very new to this and
dont know where to use what ,and i thought the mail would go to the cdk-user
group. And now i am aware of this :)Thanks
On Friday, 27 January 2017 6:51 PM, Rajesh C <[email protected]> wrote:
Hi JohnThanks for the reply,but i am not using SMILE format, instead i am
using a textfile with data(.mol or .rxn.. please refer attchment).basically i
am using openscience/jchempaint to read and capture the image
here code snippet for jchempaintpanel properties Renderer rr=
panel.getRenderPanel().getRenderer(); RendererModel rrm =
rr.getRenderer2DModel(); rrm.setZoomFactor(1);//setting the zoom factor
rrm.setBondDistance(0.1);//setting the length between 2 bonds of the double or
triple bonds rrm.setBondWidth(1);//setting the width of the bond
rrm.setBondLength(1); rrm.setShowEndCarbons(true);//show end carbons only
rrm.setWedgeWidth(0.2);//setting the width of wedge rrm.setMargin(20);
rrm.setScale(1); rrm.setArrowHeadWidth(1);//arrow head width
On Friday, 27 January 2017 5:24 PM,
"[email protected]"
<[email protected]> wrote:
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Today's Topics:
1. Re: Cdk-user post from [email protected] requires approval
(John Mayfield)
----------------------------------------------------------------------
Message: 1
Date: Fri, 27 Jan 2017 11:54:08 +0000
From: John Mayfield <[email protected]>
Subject: Re: [Cdk-user] Cdk-user post from [email protected] requires
approval
To: cdkuser <[email protected]>, Rajesh C
<[email protected]>
Message-ID:
<CAFdOP2s13gq05B25iB=skrh4yptk6o2amr20jv0bo-e1x5c...@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Hi Rajesh,
Not sure why this message didn't come though to my inbox after being
approved.
A subset of text positions are supported, you can put text in a depiction
as:
- molecule title
- reaction title
- reaction conditions
- atom annotations
- bond annotations
Beyond that you will have to roll on your own and either draw on the raster
image with AWT or append elements to the SVG.
For you described use case it looks like you actually don't want text at
all but rather list agents.
[H][H].C>>[H][H]
https://cdkdepict-openchem.rhcloud.com/depict/bow/svg?smi=[H][H].C%3E%3E[H][H]&abbr=on&suppressh=true&showtitle=false&zoom=1.3&annotate=none
[image: Inline images 7]
vs
[H][H].C>CCO>[H][H]
https://cdkdepict-openchem.rhcloud.com/depict/bow/svg?smi=[H][H].C%3ECCO%3E[H][H]&w=210&h=50&abbr=on&suppressh=true&showtitle=false&zoom=2.05&annotate=none
[image: Inline images 6]
If you want to describe reaction conditions set the property
'cdk:ReactionConditions' on the molecule.
[H][H].C>CCO>[H][H] |SgD::cdk:ReactionConditions:RT|
https://cdkdepict-openchem.rhcloud.com/depict/bow/svg?smi=[H][H].C%3ECCO%3E[H][H]%20%7CSgD%3A%3Acdk%26%2358%3BReactionConditions%3ART%7C&w=210&h=50&abbr=on&suppressh=true&showtitle=false&zoom=2.05&annotate=none
[image: Inline images 8]
John
On 25 January 2017 at 20:18, <[email protected]> wrote:
> As list administrator, your authorization is requested for the
> following mailing list posting:
>
> List: [email protected]
> From: [email protected]
> Subject: Store image with text elements
> Reason: Post by non-member to a members-only list
>
> At your convenience, visit:
>
> https://lists.sourceforge.net/lists/admindb/cdk-user
>
> to approve or deny the request.
>
>
> ---------- Forwarded message ----------
> From: Rajesh C <[email protected]>
> To: "[email protected]" <[email protected]>
> Cc:
> Date: Wed, 25 Jan 2017 20:15:34 +0000 (UTC)
> Subject: Store image with text elements
> Hi cdk user,
> Can you please help me in storing a structural as an jpeg image(read from
> Mol) with text in it.
>
> Thanks
>
>
>
>
> ---------- Forwarded message ----------
> From: [email protected]
> To:
> Cc:
> Date:
> Subject: confirm 1c371a42b7079c73c06ec8042d6960f2473c995d
> If you reply to this message, keeping the Subject: header intact,
> Mailman will discard the held message. Do this if the message is
> spam. If you reply to this message and include an Approved: header
> with the list password in it, the message will be approved for posting
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> of the body of the reply.
>
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