From db36e8a51cf454121e29a4d57c836cb3862169a2 Mon Sep 17 00:00:00 2001 From: gph82 Date: Sun, 21 Apr 2024 14:07:31 +0200 Subject: [PATCH] [docs and README] update outputs to new table formats, also a "getting started" section --- README.rst | 2 +- doc/basic_usage.rst | 18 ++++++++--------- doc/highlights.rst | 47 ++++++++++++++++++++++---------------------- doc/index.rst | 22 +++++++++++---------- doc/installation.rst | 25 +++++++++++++++++++---- 5 files changed, 66 insertions(+), 48 deletions(-) diff --git a/README.rst b/README.rst index c95bb24f..a8b156a6 100644 --- a/README.rst +++ b/README.rst @@ -41,7 +41,7 @@ System Requirements =================== ``mdciao`` is developed in GNU/Linux, and CI-tested via `github actions `_ 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. diff --git a/doc/basic_usage.rst b/doc/basic_usage.rst index ce32afe6..2da73536 100644 --- a/doc/basic_usage.rst +++ b/doc/basic_usage.rst @@ -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: ./neighborhood.overall@4.0_Ang.pdf ./neighborhood.LEU394@4.0_Ang.dat diff --git a/doc/highlights.rst b/doc/highlights.rst index bbaf654f..9d6fb814 100644 --- a/doc/highlights.rst +++ b/doc/highlights.rst @@ -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 R385@G.H5.17 - Q229@5.68x68 344 956 1.00 - 1.00 D381@G.H5.13 - Q229@5.68x68 340 956 2.00 - 1.00 Q384@G.H5.16 - I135@3.54x54 343 865 3.00 - 1.00 D381@G.H5.13 - K232@5.71x71 340 959 4.00 - 0.99 T350@G.h4s6.03 - R239@ICL3 309 966 4.99 - 0.98 E392@G.H5.24 - T274@6.36x36 351 976 5.97 - 0.96 R385@G.H5.17 - K232@5.71x71 344 959 6.93 - + The 44-th contact has a frequency of 0.42. + freq label residues fragments sum + 1 1.00 R385@G.H5.17 - Q229@5.68x68 344 - 956 0 - 3 1.00 + 2 1.00 Q384@G.H5.16 - I135@3.54x54 343 - 865 0 - 3 2.00 + 3 1.00 D381@G.H5.13 - Q229@5.68x68 340 - 956 0 - 3 3.00 + 4 1.00 D381@G.H5.13 - K232@5.71x71 340 - 959 0 - 3 4.00 + 5 0.99 T350@G.h4s6.03 - R239@ICL3 309 - 966 0 - 3 4.99 + 6 0.98 E392@G.H5.24 - T274@6.36x36 351 - 976 0 - 3 5.97 + 7 0.96 R385@G.H5.17 - K232@5.71x71 344 - 959 0 - 3 6.93 ... The following files have been created: ./interface.overall@4.0_Ang.xlsx @@ -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: ... @@ -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: ... diff --git a/doc/index.rst b/doc/index.rst index 83d7df14..7c74dca8 100644 --- a/doc/index.rst +++ b/doc/index.rst @@ -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: ./neighborhood.overall@4.0_Ang.pdf - ./neighborhood.LEU394@4.0_Ang.dat - ./neighborhood.LEU394.time_trace@4.0_Ang.pdf + ./neighborhood.LEU394@frag0@4.0_Ang.dat + ./neighborhood.LEU394@frag0.time_trace@4.0_Ang.pdf + You can also invoke:: diff --git a/doc/installation.rst b/doc/installation.rst index 1bf886e7..47173169 100644 --- a/doc/installation.rst +++ b/doc/installation.rst @@ -17,13 +17,30 @@ Installation via package manager We recommend you install ``mdciao`` via the `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`_. @@ -83,7 +100,7 @@ Operating systems and Python versions ------------------------------------- ``mdciao`` is developed in GNU/Linux, and CI-tested via `github actions `_ 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.