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[docs and README] update outputs to new table formats, also a "gettin…
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gph82 committed Apr 21, 2024
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2 changes: 1 addition & 1 deletion README.rst
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Expand Up @@ -41,7 +41,7 @@ System Requirements
===================
``mdciao`` is developed in GNU/Linux, and CI-tested via `github actions <https://github.com/gph82/mdciao/actions?query=workflow%3A%22Python+package%22>`_ for GNU/Linux and MacOs. Tested python versions are:

* GNU/Linux: 3.7, 3.8, 3.9, 3.10
* GNU/Linux: 3.7, 3.8, 3.9, 3.10, 3.11
* MacOs: 3.7, 3.8, 3.9

So everything should work *out of the box* in these conditions.
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18 changes: 8 additions & 10 deletions doc/basic_usage.rst
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Expand Up @@ -25,16 +25,14 @@ This basic command::
will print the following to the terminal (some headers have been left out)::

...
#idx freq contact fragments res_idxs ctc_idx Sum
1: 0.96 LEU394-ARG389 0-0 353-348 30 0.96
2: 0.92 LEU394-LEU388 0-0 353-347 29 1.88
3: 0.79 LEU394-LEU230 0-0 353-957 51 2.67
4: 0.71 LEU394-ARG385 0-0 353-344 26 3.38
5: 0.50 LEU394-LYS270 0-0 353-972 65 3.88
These 5 contacts capture 3.88 (~90%) of the total frequency 4.31 (over 74 input contacts)
As orientation value, the first 5 ctcs already capture 90.0% of 4.31.
The 5-th contact has a frequency of 0.50

The following 5 contacts capture 3.88 (~90%) of the total frequency 4.31 (over 7 contacts with nonzero frequency).
[...]
freq label residues fragments sum
1 0.96 L394 - R389 353 - 348 0 - 0 0.96
2 0.92 L394 - L388 353 - 347 0 - 0 1.88
3 0.79 L394 - L230 353 - 957 0 - 0 2.67
4 0.71 L394 - R385 353 - 344 0 - 0 3.38
5 0.50 L394 - K270 353 - 972 0 - 0 3.88
The following files have been created:
./[email protected]_Ang.pdf
./[email protected]_Ang.dat
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47 changes: 24 additions & 23 deletions doc/highlights.rst
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Expand Up @@ -153,19 +153,17 @@ Highlights

>>> mdc_interface.py prot.pdb traj.xtc -fg1 0 -fg2 3 --GPCR adrb2_human --CGN GNAS2_HUMAN -t "3SN6 beta2AR-Galpha interface" -ni
...
These 50 contacts capture 35.56 (~96%) of the total frequency 36.88 (over 20307 input contacts)
The following 50 contacts capture 35.56 (~96%) of the total frequency 36.88 (over 75 contacts with nonzero frequency).
As orientation value, the first 44 ctcs already capture 90.0% of 36.88.
The 44-th contact has a frequency of 0.42

freq label residue idxs sum
1.00 [email protected] - [email protected] 344 956 1.00
1.00 [email protected] - [email protected] 340 956 2.00
1.00 [email protected] - [email protected] 343 865 3.00
1.00 [email protected] - [email protected] 340 959 4.00
0.99 [email protected] - R239@ICL3 309 966 4.99
0.98 [email protected] - [email protected] 351 976 5.97
0.96 [email protected] - [email protected] 344 959 6.93

The 44-th contact has a frequency of 0.42.
freq label residues fragments sum
1 1.00 [email protected] - [email protected] 344 - 956 0 - 3 1.00
2 1.00 [email protected] - [email protected] 343 - 865 0 - 3 2.00
3 1.00 [email protected] - [email protected] 340 - 956 0 - 3 3.00
4 1.00 [email protected] - [email protected] 340 - 959 0 - 3 4.00
5 0.99 [email protected] - R239@ICL3 309 - 966 0 - 3 4.99
6 0.98 [email protected] - [email protected] 351 - 976 0 - 3 5.97
7 0.96 [email protected] - [email protected] 344 - 959 0 - 3 6.93
...
The following files have been created:
./[email protected]_Ang.xlsx
Expand Down Expand Up @@ -276,11 +274,13 @@ Highlights

>>> mdc_neighborhoods.py 3SN6.pdb 3SN6.pdb -r R131 -o 3SN6 -nf -o 3SN6.X
...
#idx freq contact fragments res_idxs ctc_idx Sum
1: 1.00 ARG131-TYR391 0-0 1007-345 14 1.00
2: 1.00 ARG131-TYR326 0-0 1007-1174 111 2.00
3: 1.00 ARG131-ILE278 0-0 1007-1126 97 3.00
These 3 contacts capture 3.00 (~100%) of the total frequency 3.00 (over 120 contacts)
The following 3 contacts capture 3.00 (~100%) of the total frequency 3.00 (over 3 contacts with nonzero frequency).
As orientation value, the first 3 ctcs already capture 90.0% of 3.00.
The 3-th contact has a frequency of 1.00.
freq label residues fragments sum
1 1.0 R131 - I278 1007 - 1126 0 - 0 1.0
2 1.0 R131 - Y326 1007 - 1174 0 - 0 2.0
3 1.0 R131 - Y391 1007 - 345 0 - 0 3.0
...
The following files have been created:
...
Expand All @@ -290,12 +290,13 @@ Highlights

>>> mdc_neighborhoods.py prot.pdb traj.xtc -r R131 -nf -o 3SN6.MD
...
#idx freq contact fragments res_idxs ctc_idx Sum
1: 0.88 ARG131-TYR391 0-0 861-350 11 0.88
2: 0.69 ARG131-TYR326 0-0 861-1028 95 1.56
3: 0.44 ARG131-TYR219 0-0 861-946 65 2.00
4: 0.12 ARG131-ILE278 0-0 861-980 84 2.12
These 4 contacts capture 2.12 (~100%) of the total frequency 2.12 (over 104 input contacts)
The following 4 contacts capture 2.12 (~100%) of the total frequency 2.12 (over 5 contacts with nonzero frequency).
...
freq label residues fragments sum
1 0.88 R131 - Y391 861 - 350 0 - 0 0.88
2 0.69 R131 - Y326 861 - 1028 0 - 0 1.56
3 0.44 R131 - Y219 861 - 946 0 - 0 2.00
4 0.12 R131 - I278 861 - 980 0 - 0 2.12
...
The following files have been created:
...
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22 changes: 12 additions & 10 deletions doc/index.rst
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Expand Up @@ -41,18 +41,20 @@ and calculates the time-traces of residue-residue distances, and from there, **

mdc_neighborhoods.py prot.pdb traj.xtc --residues L394
[...]
#idx freq contact fragments res_idxs ctc_idx Sum
1: 0.96 LEU394-ARG389 0-0 353-348 30 0.96
2: 0.92 LEU394-LEU388 0-0 353-347 29 1.88
3: 0.79 LEU394-LEU230 0-0 353-957 51 2.67
4: 0.71 LEU394-ARG385 0-0 353-344 26 3.38
5: 0.50 LEU394-LYS270 0-0 353-972 65 3.88
These 5 contacts capture 3.88 (~90%) of the total frequency 4.31 (over 74 input contacts)
[...]
The following 5 contacts capture 3.88 (~90%) of the total frequency 4.31 (over 7 contacts with nonzero frequency).
As orientation value, the first 5 ctcs already capture 90.0% of 4.31.
The 5-th contact has a frequency of 0.50.
freq label residues fragments sum
1 0.96 L394@frag0 - R389@frag0 353 - 348 0 - 0 0.96
2 0.92 L394@frag0 - L388@frag0 353 - 347 0 - 0 1.88
3 0.79 L394@frag0 - L230@frag3 353 - 957 0 - 3 2.67
4 0.71 L394@frag0 - R385@frag0 353 - 344 0 - 0 3.38
5 0.50 L394@frag0 - K270@frag3 353 - 972 0 - 3 3.88
The following files have been created:
./[email protected]_Ang.pdf
./[email protected]_Ang.dat
./[email protected]_Ang.pdf
./neighborhood.LEU394@[email protected]_Ang.dat
./[email protected][email protected]_Ang.pdf


You can also invoke::

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25 changes: 21 additions & 4 deletions doc/installation.rst
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Expand Up @@ -17,13 +17,30 @@ Installation via package manager

We recommend you install ``mdciao`` via the `pip <https://pypi.org/project/pip/>`_ Python package installer::

pip install mdciao
>>> pip install mdciao

Getting started
~~~~~~~~~~~~~~~
For the impatient, you can directly issue afterwards::

mdc_examples
>>> mdc_examples.py

for built-in command-line examples to choose from. For a bit more of context, check the :ref:`CLI Tutorial`, the :ref:`API Jupyter Notebook Tutorial`, and the :ref:`Jupyter Notebook Gallery` for real-life, more elaborated notebooks.
for built-in command-line examples to choose from. For live Jupyter notebooks with examples for scripting and API calls, type::

>>> mdc_notebooks.py
>>> cd mdciao_notebooks
>>> ls -1
Tutorial.ipynb
MSA_via_Consensus_Labels.ipynb
Missing_Contacts.ipynb
Manuscript.ipynb
Flareplot_Schemes.ipynb
EGFR_Kinase_Inhibitors.ipynb
Comparing_CGs_Flares.ipynb
Comparing_CGs_Bars.ipynb


Alternatively, check the :ref:`CLI Tutorial`, the :ref:`API Jupyter Notebook Tutorial`, and the :ref:`Jupyter Notebook Gallery`.

.. note::
As almost any Python module, ``mdciao`` comes with some dependencies that will be installed along when installing ``mdciao``. If you don't want ``mdciao`` to alter the existing python installation, we highly recommend to create a separate, virtual python environment to install ``mdciao`` into. More info on how to do this in the note about the `Python interpreter and environment`_.
Expand Down Expand Up @@ -83,7 +100,7 @@ Operating systems and Python versions
-------------------------------------
``mdciao`` is developed in GNU/Linux, and CI-tested via `github actions <https://github.com/gph82/mdciao/actions?query=workflow%3A%22Python+package%22>`_ for GNU/Linux and MacOs. Tested python versions are:

* GNU/Linux: 3.7, 3.8, 3.9, 3.10
* GNU/Linux: 3.7, 3.8, 3.9, 3.10, 3.11
* MacOs: 3.7, 3.8, 3.9

So everything should work *out of the box* in these conditions. Please see this warning_ for problems during installation from source.
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