Version 1.0 of the API is now available. What would you like to see in version 2.0?
I am very happy to declare that version 1.0 of the CSD Python API makes some of these aspects more widely available:
A new docking module, based on the GOLD docking engine, is under development and is available to associated collaborators.
Further details can be found in the API user guide.
It should be as simple as typing in a console window:
pip install matplotlib
There are other installation options described at http://matplotlib.org/users/installing.html
Any of the recent versions should work. I'd suggest 1.5.0 is as good a choice as any.
Version 1.0 of the CSD Python API is in testing now. This marks a level of maturity in the product, established over the past few years, that we believe makes it ready for wide-spread use. Active development of the API is not going to stop now. On the contrary, we have some exciting developments lined up as we push more of the CCDC's extensive scientific technology into this interface.
Hitting the notable 1.0 milestone encourages us to pause for a moment and to think about how it might best help users do their jobs. You might have some ideas or priorities that are beyond our current thoughts.
What features or enhancements would you most like to see in the future CSD Python API?
Are there any parts you would like to see improved: more functionality, faster, easier to use? Are there any specific CCDC tools that you'd like to access via the API? Are there any important tasks that you can't yet complete with the API?
We are listening...
We do most of our development inside virtualenvs, so they should work without issue. Your use of Python 2.7.5 is fine, we fully support that. It was quite easy to reproduce your error report - we clearly have a problem with Anaconda on OS X.
It seems that this problem is common in Anaconda. There are various workarounds proposed on the web, but we will endeavour to update the installer to overcome this. Your suggestion that this is a linking problem is correct.
Your other errors (RuntimeError: Welcome to the CSD Python API...) are a result of the API not finding a valid CSD license. Assuming that you have the CSDS installed and working, you need to ensure that the CSDHOME envvar points at the correct location. e.g.:
$ export CSDHOME=/home/my/software/csds_v536/
When reading the documentation, you are likely to notice that some portions of the API are annotated as being available only to associated collaborators. These are parts of the API that are currently undergoing further development and external testing. These features will become more broadly available in future releases.
The three features that are currently available to associated collaborators only are listed in the following table:
|Crystal Packing Similarity||0.7|
|Field-based Ligand Screener||0.6|
If you are interested in contributing to the development of these features please contact email@example.com
Suppose you have installed the API exactly as described in the installation instructions. When you try to run the tests, you might find that many tests fail with messages like:
IOError: Test file xxxxxxx does not exist in /mypath/tests/testdata or /mypath/doc/example_files
Sorry, this is because the installation instructions are unclear. To run the tests, you need to extract the full archive, not just the 'tests' directory out of the archive.
We will update future versions of the documentation.
I guess that it falls to me for the first introduction.
I'm Stewart, and I work at the CCDC, where I lead the Life Sciences software development team. Collectively, we are responsible for bringing you various products, including the CSD Python API.
My background is in protein modelling and cheminformatics, although I've worked for most of the past decade as a scientific software engineer. The CSD Python API excites me because it opens up many of the CSD-based technologies. Until now these were only available in our desktop tools. With the API you can choose how to apply these technologies to solve your own problems rather than being able to apply them only how we thought you wanted.
I can hardly wait to see what amazing things everyone builds, and what scientific challenges they overcome, with our API!
Welcome to the CSD Python API forum. We hope that this will grow into a valuable resource for anyone looking at our Python API..
We would like this to become a friendly, welcoming and encouraging forum. It should be a place where anyone can come to share their Python API stories - both success and failures. Anyone with problems to solve, or recommendations to give, should feel comfortable posting here. Hopefully, this can become a source of inspiration and a hub of innovation.
I invite you to introduce yourself in this thread. Who are you? What do you work on? What problems will the CSD Python API let you solve?
My recommendation is the PyCharm Educational Edition.
PyCharm is an integrated development environment used by some software developers at the CCDC. You can think of it as a Python-aware text editor with various useful features like one-click execution of your Python scripts. It is a free download, and that particular version comes with a built-in tutorial that teaches the most basic parts of the Python syntax.
It is used in schools, so is quite simple and intuitive.
Once you've been through that, I think that the best way to learn is to do! Just pick a simple task (make a list of all entries containing caffeine, say) and write a script to do it. If you get stuck, please don't hesitate in posting questions on this forum or on a Python-specific forum such as http://www.python-forum.org/