prolint2 0.0.3

Ultra-Fast Contacts Calculation.

ProLint v2: an optimized tool for the analysis of lipid protein interactions.

The Ultra-Fast Contact Calculation (UFCC) tool calculates the distance-based contacts between two references from molecular dynamics simulations. This release of ufcc is a demo version with a reduced number of features to test how it behaves with different use cases.

Installation

To install ufcc we recommend creating a new conda environment as follows:

   conda create -n ufcc python=3.8 #(or higher)
   conda activate ufcc

Then you can install ufcc via pip:

   pip install ufcc==0.0.7

Basic example (from the command-line):

   ufcc coordinates.gro trajectory.xtc -c 7 

The previous line calculates the contacts using a cutoff of 7 Angstroms between all lipids and proteins in the system, and give you a link to launch the visualization dashboard on a browser.

ufcc selection interface:

You can enter in the interactive selection mode by selecting the -i option.

ufcc operates on atom selection called groups. ufcc defines two refence groups: the Query and the Database. ufcc calculates contacts between the atoms in the Query group and the atoms in the Database group at the level of residue. By default, ufcc will extract proteins into the Query groups, and lipids into the Database group (if your membrane has lipids with resnames different to those recognized by default by ufcc [POPC, DPPC, DOPC, CHOL, CHL1, POPS, POPE] you can add them using the -al option). The current interface allows you to customize these selections based on your needs. We have created a few default selections and user-friendly actions that you can perform on them to reach a high level of especificity in the selections. Note that when you have created a group with the especific selection that you need, you can update either the Database or Query groups, as follow:

db Group_ID

or

qr Group_ID

You can see a detailed list of the action keys below:

db  :  update database group for contacts calculation. (i.e. >> db Group_ID) where Group_ID is the identifier of the group on the list of groups.
qr  :  update query group for contacts calculation. (i.e. >> qr Group_ID) where Group_ID is the identifier of the group on the list of groups.
gb :  create subgroups grouped by any topology attribute ("names", "resnames", "masses", etc). (i.e. >> gp Group_ID resnames) creates new groups for every different resname in the Group_ID selected.
sl  :  create new groups by splitting a previous group at the desired level ("segment", "residue", "atom", "molecule"). (i.e. >> sl Group_ID residue) splits the Group_ID selected into all the residues that make it up, and create a new group for each of them.
add:  merge two or more groups and create a new group with the combination. (i.e. >> add Group_ID1 Group_ID2 ... Group_IDn) creates a new group for the combination of the groups Group_ID1 Group_ID2 ... Group_IDn.
del:  delete a group from the list of groups. (i.e. >> del Group_ID) remove the Group_ID selected.
lg :  print the list of groups.
h  :  print the help for all the available action keys.
e  :  exit interactive selection and calculate de contacts between the Query and Database groups. 

As for explaining the capabilities of this selection interface we will show some examples below using a membrane made up POPS, CHOL and POPE and a single protein:

Example 1: Using only two types of protein residues (ARG and LEU) as Query and all the lipids in the membrane as Database:

• Default groups:

Database and Query groups:

Database --> 7824 atoms
Query --> 5216 atoms
-----------------------------------------------------

Selection groups:

(0) : System --> 23820 atoms
(1) : Protein --> 2956 atoms
(2) : Lipids --> 20864 atoms
(3) : POPS --> 7824 atoms
(4) : CHOL --> 5216 atoms
(5) : POPE --> 7824 atoms

• Grouping by resnames the Protein group:

gb 1 resnames

(0) : System --> 23820 atoms
(1) : Protein --> 2956 atoms
(2) : Lipids --> 20864 atoms
(3) : POPS --> 7824 atoms
(4) : CHOL --> 5216 atoms
(5) : POPE --> 7824 atoms
(6) : ALA grouped by resnames from Protein --> 52 atoms
(7) : GLU grouped by resnames from Protein --> 224 atoms
(8) : THR grouped by resnames from Protein --> 192 atoms
(9) : PHE grouped by resnames from Protein --> 352 atoms
(10) : ASP grouped by resnames from Protein --> 112 atoms
(11) : HIS grouped by resnames from Protein --> 112 atoms
(12) : GLN grouped by resnames from Protein --> 80 atoms
(13) : TYR grouped by resnames from Protein --> 160 atoms
(14) : ARG grouped by resnames from Protein --> 192 atoms
(15) : ASN grouped by resnames from Protein --> 104 atoms
(16) : SER grouped by resnames from Protein --> 144 atoms
(17) : MET grouped by resnames from Protein --> 96 atoms
(18) : GLY grouped by resnames from Protein --> 76 atoms
(19) : LYS grouped by resnames from Protein --> 168 atoms
(20) : TRP grouped by resnames from Protein --> 140 atoms
(21) : VAL grouped by resnames from Protein --> 208 atoms
(22) : LEU grouped by resnames from Protein --> 240 atoms
(23) : ILE grouped by resnames from Protein --> 176 atoms
(24) : CYS grouped by resnames from Protein --> 64 atoms
(25) : PRO grouped by resnames from Protein --> 64 atoms

• Merging ARG and LEU groups:

add 14 22

(0) : System --> 23820 atoms
(1) : Protein --> 2956 atoms
(2) : Lipids --> 20864 atoms
(3) : POPS --> 7824 atoms
(4) : CHOL --> 5216 atoms
(5) : POPE --> 7824 atoms
(6) : ALA grouped by resnames from Protein --> 52 atoms
(7) : GLU grouped by resnames from Protein --> 224 atoms
(8) : THR grouped by resnames from Protein --> 192 atoms
(9) : PHE grouped by resnames from Protein --> 352 atoms
(10) : ASP grouped by resnames from Protein --> 112 atoms
(11) : HIS grouped by resnames from Protein --> 112 atoms
(12) : GLN grouped by resnames from Protein --> 80 atoms
(13) : TYR grouped by resnames from Protein --> 160 atoms
(14) : ARG grouped by resnames from Protein --> 192 atoms
(15) : ASN grouped by resnames from Protein --> 104 atoms
(16) : SER grouped by resnames from Protein --> 144 atoms
(17) : MET grouped by resnames from Protein --> 96 atoms
(18) : GLY grouped by resnames from Protein --> 76 atoms
(19) : LYS grouped by resnames from Protein --> 168 atoms
(20) : TRP grouped by resnames from Protein --> 140 atoms
(21) : VAL grouped by resnames from Protein --> 208 atoms
(22) : LEU grouped by resnames from Protein --> 240 atoms
(23) : ILE grouped by resnames from Protein --> 176 atoms
(24) : CYS grouped by resnames from Protein --> 64 atoms
(25) : PRO grouped by resnames from Protein --> 64 atoms
(26) : Group combined from ['14', '22'] --> 432 atoms

• Updating the Query with the previously created group:

qr 26

• Exiting the interactive selection mode:

e

Example 2: Using only a single bead (PO4) of a single type of lipid in the membrane (POPS) as Database, and the whole protein as Query:

• Default groups:

Database and Query groups:

Database --> 7824 atoms
Query --> 5216 atoms
-----------------------------------------------------

Selection groups:

(0) : System --> 23820 atoms
(1) : Protein --> 2956 atoms
(2) : Lipids --> 20864 atoms
(3) : POPS --> 7824 atoms
(4) : CHOL --> 5216 atoms
(5) : POPE --> 7824 atoms

• Grouping by names the POPS group:

gb 1 names

(0) : System --> 23820 atoms
(1) : Protein --> 2956 atoms
(2) : Lipids --> 20864 atoms
(3) : POPE --> 7824 atoms
(4) : POPS --> 7824 atoms
(5) : CHOL --> 5216 atoms
(6) : D2A grouped by names from POPS --> 652 atoms
(7) : C4B grouped by names from POPS --> 652 atoms
(8) : C1B grouped by names from POPS --> 652 atoms
(9) : C1A grouped by names from POPS --> 652 atoms
(10) : C3A grouped by names from POPS --> 652 atoms
(11) : GL1 grouped by names from POPS --> 652 atoms
(12) : PO4 grouped by names from POPS --> 652 atoms
(13) : C4A grouped by names from POPS --> 652 atoms
(14) : GL2 grouped by names from POPS --> 652 atoms
(15) : CNO grouped by names from POPS --> 652 atoms
(16) : C3B grouped by names from POPS --> 652 atoms
(17) : C2B grouped by names from POPS --> 652 atoms

• Updating the Database with the group corresponding the bead PO4:

db 12

• Exiting the interactive selection mode:

e

How to contribute?

If you find a bug in the source code, you can help us by submitting an issue to our GitHub repo. Even better, you can submit a Pull Request with a fix.

We really appreciate your feedback!

License

Source code included in this project is available under the MIT License.

Copyright

Copyright (c) 2022, Daniel P. Ramirez & Besian I. Sejdiu

Acknowledgements

The respository structure of UFCC is based on the Computational Molecular Science Python Cookiecutter version 1.6.