gstn-caruso / codnasq Goto Github PK

E. g.:
'Longitude' to 'Length'
'Species' to 'Organism'
'Cluster' to 'Cluster ID'
etc.
the changes will be done using the new names file

Ligand code (1-3 characters) followed by ligand's name inside parenthesis

e.g>

PDB ID:
1wuq

old ligands:
ZN zinc ion, 8GT 8-oxo-guanosine-5'-triphosphate

new ligands:
ZN (zinc ion), 8GT (8-oxo-guanosine-5'-triphosphate)

Add>

'Oligomeric state' filter

Switch>

Names of filters (make iqual to home page filters)

Groups:

a >> 'Tertiary deformations'
b >> 'Mixed motions'
c >> 'Rigid-body displacements'

https://about.gitlab.com/solutions/github/

make more narrow?

switch Average number of conformers per protein

old > 15.09

new > 5.15

Relacionado con #6 , necesitamos tener una idea de qué necesitamos presentar ante el equipo de redes de la UNQ para poder tener la aplicación andando y luego #5 para poder acceder.

##Outcome

Create a route where you pass the protein id and you get the protein details page.

Setup project

• Outcome: pck ready to import with the web server running and a basic landing page

Precondición:

• pertenecen al mismo cluster
• comparamos solamente dos conformers

aceptación:

• datos de cada conformer
• datos del par

The following could be added to the home page:

CoDNaS-Q is a high-quality collection of homo-oligomeric conformers obtained from the Protein Data Bank (PDB). It allows the exploration of conformational diversity and its determinants at the quaternary level, for a large number of proteins determined under different experimental conditions and from a wide variety of families and species. Find out more about CoDNaS-Q in the About and Help pages.

(include links to About and Help pages)

Relacionado con #4 esto nos permitiría acceder a la aplicación desde una url provista por el equipo de redes de la UNQ.

As part of #55.

The question is, how to tell which row should be highlighted?

Nota bene: There is .is-selected css class which changes the background-color

When resizing the browser to less than 1024 px wide, the sections on the header dissapear.

e.g. http://localhost:8080/cluster/show/CQ2vcq

add:
max RMSD Q the same mentionated below on 'Maximum RMSD Pair information'
average RMSD Q
max RMSD T
average RMSD T
Group

Subsection "Representative conformer":
'Description' of main conformer (in this case title of 2vcq "Complex structure of prostaglandin D2 synthase at 1.95A.")
'length'
'Species'

if it's posible Standar deviation of RMSD Q and RMSD T, https://www.mathsisfun.com/data/standard-deviation-formulas.html

link in 'Conformer numbers' (in this case 18 ) that scroll down to 'Conformers' list

http://localhost:8080/cluster/search?query=HOMO+SAPIENS&criteria=source&page=4

actual>
Page 4
Total pages: 290

new>
Total 2900
Page 4
Total pages: 290

shown when specie from 'conformer lists' is clicked

same thing with 'name' is clicked

add>

-last page button
-conformer quantity column
-maxRMSD-Q of clusters column
-show only 1 result per cluster
-fix empty last page

delete>

-Biological Assembly column
-Resolution

Outcome

To have a handy way to find proteins by code 1 / code 2.

In the footer, the section Rooms 31-33, Department of Science & Technology, UNQ links to:
http://ufq.unq.edu.ar/sbg/files/map_sbg-unq.png

This is incorrect. It should read images instead of files. as follows:
http://ufq.unq.edu.ar/sbg/images/map_sbg-unq.png

on this page, we will be able to search the clusters ordened by certain criteria (e. g. organism, family, etc.)

Outcome

To have a base image with all the "Data".

Requires #11

Outcome

To have a basic form with a file selector to insert a csv with a protein list.

add>

-scroll bar on list box (or something like that)

modify>

-rename title 'Conformers' to 'Conformers in cluster'

delete>

-cluster column (is allways the same cluster here)

Outcome

For demo purposes and as an easy way to see how the navigation is, we want 3 examples below main search bar.

This would work like:

Blocked by #9 issue

'not found' legend when the search is not successful

Follow https://en.wikipedia.org/wiki/Protein_quaternary_structure#Nomenclature

What

Split protein class, into conformer, protein pair, cluster and each repository.

Given that Cluster and conformers uses the same ID, we want to distinguish between Cluster id and Conformer id, so we'll add CQ before cluster id.

description of what we can find on this website

When searching from the home page with a PDB code (e.g. 2ff2) the results are different according to the search field selected:

• If searching for "All fields", the table of search results is returned:
  http://codnasq.ddns.net/cluster/search?query=2ff2&criteria=all

• If searching for "PDB", the cluster view is returned.
  http://codnasq.ddns.net/cluster/search?query=2ff2&criteria=pdb

This should be consistent and it should always direct to search results (i.e. as if searching in "All fields").

Only if the user enters a cluster ID (e.g. CQ2ff2) it may lead to the cluster view directly.

Criterio de aceptación

en la vista de detalle de un conformero tengo que ver la cantidad de integrantes del mismo cluster

fixes #26

Conformer information page

rename 'Longitude' -> 'Length'
rename 'Siblings' -> 'Other conformers'
mark somehow the row of opened conformer of the list

Cluster information

remove 'Average RMSD Tertiary' (we dont have that data)
add 'Representative conformer type:' (with the title of the conformer. People wanna know what kind of cluster are they seeing)
add space between number and Å in Max RMSD Quaternary

Maximum RMSD Pair information

add chains of query and target for 'RMSD Tertiary' row (included in the csv file)

Conformers in cluster

delete 'Cluster' column
rename 'Longitude' -> 'Length'

Statistics page

resize images

how to use the site

-switch 'conformer type' to 'name'

-switch 'conformer source' to 'species' if the string is a part of the species text, should show all that in results

-switch 'cluster ID' to 'PDB' *when a pdb code is written here, the page shows the cluster belonging to the code pdb *

-switch examples>
Example entries: 2vcq | hydrolase | mus musculus

-add 'All fields' by default

-if no text is ingresed, the search shows all results for that field

Estuve haciendo algunas pruebas locales y logré dockerizar la aplicación:

Preparamos un directorio hacemos:

mkdir cuis-docker
cd cuis-docker

wget -O cogspur.tgz https://github.com/OpenSmalltalk/opensmalltalk-vm/releases/download/201807260206/squeak.cog.spur_linux64x64_201807260206.tar.gz
git clone --depth 1 https://github.com/Cuis-Smalltalk/Cuis-Smalltalk-Dev.git

tar -zxvf cogspur.tgz
rm cogspur.tgz
mv ./sqcogspur64linuxht ./cogspur

Probablemente se pueden borrar varios archivos de Cuis-Smalltalk-Dev.

Sobre el mismo directorio crear un Dockerfile con:

FROM debian:9-slim
WORKDIR /opt/cuis
COPY . .
CMD cogspur/squeak -vm-display-null -vm-sound-null Cuis-Smalltalk-Dev/Cuis5.0-3665.image

Después buildeamos la imagen con:

docker build -t "cuis_web:testing" ./
docker run -p 8080:8080 cuis_web:testing

Y con eso ya tenemos el servidor levantado, si la imagen estaba en condiciones (con el webserver levantado).

As part of #55.

The big question is, how to get the chains?

add>

-max RMSD Tertiary pair information (next to the Quaternary)
-'pH' (row)
-'Temperature' (row)

modify>

-rename title, to 'max RMSD Quaternary pair information'
-rename 'Source' row to 'Organism'
-rename 'Sequence identity' to 'Sequence identity (%)'
-rename 'Structural similarity' to 'Structural similarity (%)'
-rename 'RMSD' to ''RMSD (Å)' (angstrom symbol= Unicode Character 'ANGSTROM SIGN' (U+212B))
-new value 'Structural similarity (%)' defined as: Structural similarity * 100 / Structurally equivalent residue pairs
-move 'Sequence identity (%)' below 'Organism'
-move 'Structurally equivalent residue pairs' below 'Sequence identity (%)'

delete>

-Permutations
-Type of alignment
-rank of alignment

• conformero referente (por defecto el que tiene el mismo PDB id)
• Máximo RMSD
• minimo RMSD
• promedio RMSD
• Uniprot del cluster
• Type del conformero referente
• cantidad de conformeros del cluster

add>

-'Ligands'
-'pH'
-'Temperature'
-'Description' (title)
-'Type of Movement' (a,b,c)

modify>

-rename 'siblings' por 'other conformers'
-rename 'Longitude' as 'length'
-diferent colour, font for the opened conformer in the list

delete>

-'cluster' column (because all here are inside the same cluster)

get the '|' separator and show it as ','

replacing 'XXXX' with the PDB code
https://www.rcsb.org/structure/XXXX

Display conformer pair with max rmsd on cluster with each conformer details and properties of comparison