From: Michael S. <mik...@ho...> - 2002-12-12 06:00:45
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Hello all, I share in Warren's vision of extending PyMol into a "complete platform for crystallography, computational chemistry, modeling, and informatics". However, I believe this can only come about by cooperation and integration with other python based molecule toolkits. MMTK has code which may be expanded into a general molecular mechanics engine. Frowns toolkit allows for detailed chemical analysis based on topology, including useful tools such as substructure searching (required for forcefield atom typing). PyQuante allows for Quantum Chemical calculations. It seems to be in everyone's interest to allow easy interoperation between the toolkits. However, in my experience it is a frustrating and difficult task, even for relatively simple tasks. Does anyone else feel the same frustration? And if so, does anyone have a solution? I believe that a common set of core modules is required. The most important feature is the molecule. Each toolkit uses a different molecule, each with a different interface, holding different information and optimised for specialised work. If a common molecule definition can be agreed upon by the major authors of the toolkits concerned, interoperability will be made MUCH easier. Other multipurpose molecular modelling programs (MOE, Sybyl) seem to get by using a common molecule definition, so I believe that it is theoretically possible. The aim would be to define a molecule that contains all the functionality required for the multiple toolkits and to maintain the interfaces used by the toolkits as much as possible. The question is whether the will exists to do this? Many of the toolkits are relatively young. I feel that the longer the problem is ignored, the less likely that it will be possible to combine features from various toolkits. I am interested in other people's thoughts on this matter. Michael Sorich PhD Student School of Pharmaceutical, Molecular and Biomedical Sciences University of South Australia Email: mic...@po... mik...@ho... --- Outgoing mail is certified Virus Free. Checked by AVG anti-virus system (http://www.grisoft.com). Version: 6.0.408 / Virus Database: 230 - Release Date: 24/10/2002 |
From: Jules J. <jo...@he...> - 2002-12-12 10:33:51
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I completely agree here, an integrated total platform would be immensely useful. I think that the problem is not necessarily all that far from a solution- currently there is a collaborative computing project for NMR (CCPN) http://www.bio.cam.ac.uk/nmr/ccp/ The core of this program is the data model in which each atom in a molecule is defined. The next layer are the conversion scripts which take the molecule data from the model and pipe them out to whatever format is needed for the various data manipulation programs (Aqua, XPLOR and the like). Seeing as this model is in existance and will be tightly integrated with the PDB databank for their structural checking procedures prior to accepting a model it would make sense that this be used as an industrial standard. Jules Jules Jacobsen MRC Centre for Protein Engineering Cambridge Laboratory of Molecular Biology On Thu, 12 Dec 2002, Michael Sorich wrote: > Hello all, > > I share in Warren's vision of extending PyMol into a "complete platform > for crystallography, computational chemistry, modeling, and > informatics". However, I believe this can only come about by cooperation > and integration with other python based molecule toolkits. MMTK has code > which may be expanded into a general molecular mechanics engine. Frowns > toolkit allows for detailed chemical analysis based on topology, > including useful tools such as substructure searching (required for > forcefield atom typing). PyQuante allows for Quantum Chemical > calculations. > > It seems to be in everyone's interest to allow easy interoperation > between the toolkits. However, in my experience it is a frustrating and > difficult task, even for relatively simple tasks. > > Does anyone else feel the same frustration? And if so, does anyone have > a solution? > > I believe that a common set of core modules is required. The most > important feature is the molecule. Each toolkit uses a different > molecule, each with a different interface, holding different information > and optimised for specialised work. If a common molecule definition can > be agreed upon by the major authors of the toolkits concerned, > interoperability will be made MUCH easier. Other multipurpose molecular > modelling programs (MOE, Sybyl) seem to get by using a common molecule > definition, so I believe that it is theoretically possible. The aim > would be to define a molecule that contains all the functionality > required for the multiple toolkits and to maintain the interfaces used > by the toolkits as much as possible. > > The question is whether the will exists to do this? Many of the toolkits > are relatively young. I feel that the longer the problem is ignored, the > less likely that it will be possible to combine features from various > toolkits. > > I am interested in other people's thoughts on this matter. > > > Michael Sorich > PhD Student > School of Pharmaceutical, Molecular and Biomedical Sciences > University of South Australia > Email: mic...@po... > mik...@ho... > > > > --- > Outgoing mail is certified Virus Free. > Checked by AVG anti-virus system (http://www.grisoft.com). > Version: 6.0.408 / Virus Database: 230 - Release Date: 24/10/2002 > > > > ------------------------------------------------------- > This sf.net email is sponsored by: > With Great Power, Comes Great Responsibility > Learn to use your power at OSDN's High Performance Computing Channel > http://hpc.devchannel.org/ > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > |
From: Michael B. <mb...@gm...> - 2002-12-12 16:05:58
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On Thu, Dec 12, 2002 at 10:33:47AM +0000, Jules Jacobsen wrote: > I completely agree here, an integrated total platform would be immensely > useful. > I think that the problem is not necessarily all that far from a solution- > currently there is a collaborative computing project for NMR (CCPN) > > http://www.bio.cam.ac.uk/nmr/ccp/ Looks interesting, but I couldn't find a License. What's the License for CCPN, please? thanks, Michael |
From: Michael B. <mb...@gm...> - 2002-12-12 17:46:03
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Hi again, Ok, so the license is available at http://www.bio.cam.ac.uk/nmr/ccp/project/about_ccpn/licensing/licensing.html Unfortunately, this looks quite incompatible to the GPL: (2) Conditions for DISTRIBUTION of SOFTWARE to MEMBERS (2.1) An individual or ORGANISATION must be a MEMBER of CCPN in order to receive any SOFTWARE from CCPN, and must adhere to the MEMBERSHIP, DISTRIBUTION and RE-DISTRIBUTION rules. Under these conditions, any previously DISTRIBUTED SOFTWARE may be used in for the lifetime of the SOFTWARE even if MEMBERSHIP of CCPN lapses. (4) Conditions for MEMBERSHIP of CCPN MEMBERSHIP for an individual or ORGANISATION shall be based on registration and payment of annual fee as required and detailed below. The annual fee may be reviewed from time to time. The current scale of fees are as follows: a. individuals and not for profit ORGANISATIONs - nil b. ORGANISATIONs with annual turnover less than 200000 pounds Sterling - nil c. ORGANISATIONs with annual turnover between 200000 pounds Sterling and 1 million pounds Sterling - 1000 pounds Sterling d. ORGANISATIONs with annual turnover larger than one million pounds Sterling - 7000 pounds Sterling This makes the software not freely distributable, IMHO Furthermore, it violates one of the definitions of Open-Source Software, namely 'No Discrimination Against Persons or Groups', see http://www.opensource.org/docs/definition.php. Please correct me if I'm wrong. thanks, Michael |
From: Richard G. <re...@co...> - 2002-12-12 17:02:31
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Jules Jacobsen wrote: > ... stuff deleted > The core of this program is the data model in which each atom in a > molecule is defined. The next layer are the conversion scripts which take > the molecule data from the model and pipe them out to whatever format is > needed for the various data manipulation programs (Aqua, XPLOR and the > like). Seeing as this model is in existance and will be tightly integrated > with the PDB databank for their structural checking procedures prior to > accepting a model it would make sense that this be used as an industrial > standard. My two cents: One of the reasons I have stuck with OpenDX (www.opendx.org) for visualization for so long is the general (object-oriented) data model. It has its limitations, but it has proven very powerful. Users can define a wide variety of data in hierarchical forms. Modules can be quite smart about the data structures they recieve: for example the isosurface module can accept groups of 2D and 3D grids and will produce corresponding groups of lines and surfaces. It was also easy for me to create a RenderMan/BlueMoon module that allowed OpenDX users to seamlessly access almost all the features of the renderer without modifying any OpenDX code. Same was true of the MatLab module a student and I created. This was all possible because of the general data model (which, by the way, was designed with parallelism in mind from the start). I'm not neccessarily trying to plug the OpenDX model (though I strongly enourage folks to take careful look), but I think that any future system should put a great deal of work into developing a strong underlying general data model, not just for molecules, but for all kinds of scientific data: grids, vector fields, polygonal surfaces, trees etc. Just leaving things open to general objects is not a good idea ... there needs to be some structure and standardization so that 3rd-party modules can be intelligent and interoperable. Anyone ever checked out the Object Management Group (OMG)? I went to one of their meetings (Objects ion Bio- & Chem-Informatics 2001) a while back and was impressed with the concept. They are basically a non-profit consortium that sets open industry standards for objects across all different languages. CORBA is one of their babies. The PDB is also involved with OMG as are a number of bio/macromolecule groups (Michel Sanner of Scripps gave a nice talk on his Python-based modeling system). Worth looking into. Richard Gillilan MacCHESS, Cornell |