Dear Tom and All, During the last months, I have been improving in chimera's world by using helps and flying through the scripts as you told me to do last year (and obviously by sending you tons of queries). I am now getting with a small group of students with whom we are developping some scripts from different level of complexity. I think that for some of them it is easier to understand the whole architecture through the programmer's reference. Thanks a lot for trying to get it back on the web. All the best, JD Dr. Jean-Didier Maréchal Lecturer Computational Biotechnological Chemistry @ Transmet Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal@uab.es ----- Missatge original ----- De: chimera-dev-request@cgl.ucsf.edu Data: Divendres, Juliol 31, 2009 9:00 pm Assumpte: Chimera-dev Digest, Vol 66, Issue 12

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Today's Topics:

1. Re: Programmer's reference (Thomas Goddard)

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Message: 1 Date: Thu, 30 Jul 2009 17:21:40 -0700 From: Thomas Goddard <goddard@cgl.ucsf.edu> Subject: Re: [chimera-dev] Programmer's reference To: chimera-dev@cgl.ucsf.edu Message-ID: <4A723914.9030202@cgl.ucsf.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Hi JD,

We decided at or Chimera developer meeting today that we would revive the programmer's reference on the web. It will still be auto- generated from code comments, probably from a newer version of HappyDoc. Eric Pettersen will look into it. It may be many months away since we have lots of higher priority projects.

Tom

-------- Original Message -------- Subject: Re: [chimera-dev] Programmer's reference From: Thomas Goddard To: chimera-dev@cgl.ucsf.edu Date: 7/27/09 4:58 PM

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Hi JD,

The automatically generated programmer's reference was removed from the Chimera distribution because it was large and rarely useful. When it was taken out of the distribution we did not set up a daily automated build for a web site reference guide. I believe that used to come from the automatic Chimera distribution builds. We'll discuss whether we should bring this back at this Thursday's developer meeting.

For development here we use dir() and help() in the IDLE shell as described previously http://www.cgl.ucsf.edu/pipermail/chimera-users/2008- February/002354.html> Also we look directly at Python code files which are included with all Chimera distributions under the chimera/share directory (Chimera.app/Contents/Resources/share on Mac) and we look at the C++ header files which are included in distributions under chimera/include. Of course we work all the time on Chimera code so these methods may not be ideal for your less frequent programming needs.

While we ponder this, you can use the Chimera 1.3 programmer's reference included with the distribution in

share/chimera/helpdir/ProgrammersGuide

Tom

-------- Original Message -------- Subject: Re: [chimera-dev] Programmer's reference From: Thomas Goddard To: chimera-dev@cgl.ucsf.edu Date: 7/27/09 1:34 PM

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Hi Tom and All,

thanks for the answer. I knew the pdf was removed, but not the full reference. Though it was complicated sometime to get to the right place, I finally got used to it and it was useful to me.

Do you think of posting another kind of reference in the future or will you stop to provide any?

all the best, JD

-------- Original Message -------- Subject: Re: [chimera-dev] Programmer's refere <goddard@cgl.ucsf.edu>>> To: Jean Didier Marechal Date: 7/24/09 10:10 PM

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Hi JD,

I believe we no longer provide the programmer's reference guide. It was automatically generated from source code comments using HappyDoc. It's quality was so poor we stopped generating it.

Tom

-------- Original Message -------- Subject: [chimera-dev] Programmer's reference From: Jean Didier Pie Marechal To: chimera-dev@cgl.ucsf.edu Date: 7/24/09 2:34 AM

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Dear All,

It seems that we have a problem in getting to the programmer's reference. Is there something wrong with the server?

All the best, JD

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