PyMOL Users:
 
Questions have been raised about Quantum Pharmaceuticals http://q-pharm.com a Moscow company developing products obviously based on PyMOL (circa 0.98).  They recently posted on CCL, eliciting the response below from me.  Hopefully this information will be helpful for anyone considering derivative use of the PyMOL source (hence this foward to pymol-users).
 
For the record, there is no relationship whatsoever between Quantum Pharmaceuticals and DeLano Scientific LLC, and we have no opinion on their products either way.  Quantum is merely using the PyMOL source code as intended in a completely independent development effort, and with a couple of minor changes in practice, they will be in full compliance with the PyMOL open-source licensing terms.
 
By the way, with respect to future efforts, the PyMOL source and API are still not matured to the point of being able to serve as a robust foundations for development of derivative products.  Regardless, much progress has being made in the past few years, especially in terms of eliminating global state and providing for Python-free use of the graphics capacity.  Such improvements can enable embedded or componentized use of PyMOL from within Java and other GUI frameworks, so if you have interests along these lines and resources to commit in support of such effort, please do not hesistate to make contact! 
 
Cheers,
Warren
 

From: owner-chemistry@ccl.net [mailto:owner-chemistry@ccl.net]
Sent: Saturday, June 09, 2007 9:28 AM
To: Warren DeLano
Subject: CCL: Download free trial of a new generation computer aided drug design software (Quantum 3.3.)

Dear Maxim,
 
Congratulations on your product release!  It is quite gratifying to see another company taking PyMOL seriously as a development platform, despite its shortcomings.  Quantum is an impressive early example of one of the many types of things the unrestricted open-source PyMOL source code is intended to enable.  In fact, I am astounded by all that your company has accomplished independently using PyMOL, with nary a word from Moscow! 
 
However, one condition from the PyMOL open-source (top-level) LICENSE file seems to have been inadvertently overlooked (note text between asterisks):   “Permission to use, copy, modify, distribute, and distribute modified versions of this software and its documentation for any purpose and without fee is hereby granted, **** provided that the above copyright notice appears in all copies and that both the copyright notice and this permission notice appear in supporting documentation, ****”
 
Please remedy this (presumed unintentional) breach of the Copyright terms as soon as practical by (1) enclosing a copy of PyMOL’s original LICENSE file in all product distributions (buried in a Quantum subdirectory is fine), and by (2) including the text of the PyMOL copyright and permission notices somewhere in the supporting documentation (fine as an appendix at the end of the manual).  Prompt action will surely alleviate concerns that have been raised regarding the legal status of the Quantum product vis-à-vis PyMOL. 
 
Just to reiterate, so that everyone is clear: 
 
In addition to development of new free and open-source tools, it is also my desire to see new independent commercial products built on the PyMOL foundation.  PyMOL is BSD-ish rather than GPL-ish for precisely that reason, and I do hope that Quantum and other like efforts will prove successful and have numerous positive impacts on the field.  However, it is of critical import that such efforts rest on a solid foundation of compliance with the very minimal legal requirements associated with derivative use of the PyMOL open-source code. 
 
If ever there is any doubt regarding terms, the best way to achieve certainty is to check in with me in advance of product release (before it becomes a public matter).  Another reason to talk to me early on is that, in some cases, I may even be available to help with the development work.
 
Thank you and everyone else for compliance with the PyMOL open-source terms!
 
Cheers,
 
Warren L. DeLano, Ph.D.
warren/./delsci.com
Author of PyMOL
Founder of DeLano Scientific LLC


From: owner-chemistry/./ccl.net [mailto:owner-chemistry/./ccl.net]
Sent: Friday, June 08, 2007 8:33 AM
To: Warren DeLano
Subject: CCL: Download free trial of a new generation computer aided drug design software (Quantum 3.3.)

Dear Colleagues,
 
Let me introduce you a  free trial of new CADD software, which is  all CCL community is
invited to download, compare and discuss at CCL.

Quantum  contains modules for  industrial strength docking / virtual
screening of compound libraries  on  flexible proteins, accurate IC50 calculations and chemical properties
prediction tools (Water and DMSO solubility and LogP) and protein analysis
tools.

 QUANTUM software employs advanced molecular simulations techniques rather
 than statistically trained scores to obtain binding free energies of the
 docked compounds. As a result QUANTUM can be used as a robust and accurate
 in silico tool for hit identification and lead optimization.

This physically-solid approach provides a number of definite advantages and
opens new opportunities in drug discovery. The main of them are as follows:

1. ACCURACY

2. PREDICTION OF NEW CLASSES OF INHIBITORS

3. POSSIBILITY TO IDENTIFY INHIBITORS FOR TARGETS WITH NO KNOWN LIGANDS.

4. DRAMATICAL REDUCTION IN FALSE POSITIVES

5. FULL PROTEIN FLEXIBILITY IS TAKEN INTO CONSIDERATION

6. NO TRAINING SETS

7. UNDERSTANDING OF NATURE OF PROTEIN-LIGAND INTERACTIONS


 You can evaluate QUANTUM software immediately by downloading free trial at
 
www.q-pharm.com.

A detailed description of technology, and  variety of Computer Aided Drug Design products and services can also be found at www.q-pharm.com and www.q-lead.com
 
 
 
Feel free to post or contact me directly at maxim.kholin-at--q-pharm.com
 
Kindest regards,
Maxim