buildH

Build hydrogen atoms from united-atom molecular dynamics of lipids and calculate the order parameters

Features

BuildH can :

• Reconstruct hydrogens from a united-atom structure file (PDB, GRO) or a trajectory.
• Calculate the order parameter based on the reconstructed hydrogens.
• Write a new structure/trajectory file with the reconstructed hydrogens.

BuildH works in two modes :

1. A slow mode when an output trajectory (e.g. in xtc format) is requested by the user. In this case, the whole trajectory including newly built hydrogens are written to this trajectory.
2. A fast mode without any output trajectory.

Requirements

Python >= 3.6 is mandatory for running buildH.

buildH is written in Python 3 and needs the modules numpy, pandas, MDAnalysis and Numba.

Installation

A simple installation with pip will do the trick:

python3 -m pip install buildh

All dependencies (modules) will be installed automatically by pip.

More details on installation here.

For installing a developement version, see here.

Launching buildH

Once installed with pip as shown above, a simple invocation of buildH will launch the program ($ represents the Unix prompt):

$ buildH
usage: buildH [-h] -c COORD [-t TRAJ] -l LIPID [-lt LIPID_TOPOLOGY [LIPID_TOPOLOGY ...]] -d DEFOP
              [-opx OPDBXTC] [-o OUT] [-b BEGIN] [-e END] [-pi PICKLE]
buildH: error: the following arguments are required: -c/--coord, -l/--lipid, -d/--defop

The minimal command for launching buildH can ressemble this:

buildH -c start_128popc.pdb -t popc0-25ns_dt1000.xtc -l Berger_POPC -d Berger_POPC.def

The different arguments mean the following: -c start_128popc.pdb is a pdb file with 128 POPC, -t popc0-25ns_dt1000.xtc is a trajectory with 25 frames, -l Berger_POPC indicates the united-atom force field and the type of lipid to be analyzed, -d Berger_POPC.def indicates what C-H are considered for H building and order parameter calculation. This latter file can be found here. The final order parameters averaged over the trajectory will be written to the default output name OP_buildH.out

Some other commented examples as well as a Notebook showing a full analysis on a trajectory of 2500 frames can be found on the documentation part.

Important: sometimes, when performing MD, some molecules are split over periodic boundary conditions (PBC). buildH takes as input whole structure (pdb, gro, xtc, etc.). If broken molecules are supplied, it will most likely generate nonsense results. So it is up to the user to take care of making molecules whole before running buildH (e.g. by using a tool like trjconv in GROMACS with flag -pbc mol).

Invoking buildH with the -h flag will display some help to the screen and tell the user which lipids are supported by buildH.

$ buildH -h
usage: buildH [-h] -c COORD [-t TRAJ] -l LIPID [-lt LIPID_TOPOLOGY [LIPID_TOPOLOGY ...]] -d DEFOP
              [-opx OPDBXTC] [-o OUT] [-b BEGIN] [-e END] [-pi PICKLE]
[...]
The list of supported lipids (-l option) are: Berger_POPC, Berger_PLA, Berger_POP, CHARMM36_POPC.

Documentation

The full documentation is available on readthedocs.

Contributors

• Patrick Fuchs
• Amélie Bacle
• Hubert Santuz
• Pierre Poulain

Licence

buildH is licensed under the BSD License.

Dev

1.3.1

• Fix setup.cfg to include json files in python package archive

1.3.0

• Complete documentation
• Accelerate functions within geometry.py with Numba
• Implement the use of buildH as a module
• Simplify calculation of CH on an sp3 carbon
• Use MyST parser for documentation (handles latex equations)
• Clarify some error messages
• Fix residue number exceeding 9999
• Add POPE def and json files
• Add Notebook01 (basic buildH analysis on a Berger traj)
• Add Notebook02 (+trajectory output)
• Add Notebook03 (analysis on a mixture POPC/POPE)
• Move CHARMM36 POPC validation to Zenodo

1.2.0

• Build docs
• Rename '-x/--xtc' flag to -t/--traj' one to be more generic
• Replace mandatory topology argument to '-c/--coord' flag
• Improve performance of control functions.
• Move misc functions to a module utils.py
• Improve Exception handling & add proper exits
• Improve PEP8 & PEP257 compliance
• Improve test coverage
• Fix bug when a trajectory was written when only a pdb was provided.
• Add sanity checks for the various input files
• Use json files instead of python module to read lipid topologies.
• Optimize package for better performance

1.1.0

• Create Python package structure
• Create conda environment
• Fix tests
• Separate entry point
• Update README for dev version installation
• Handle version with bump2version

BSD 3-Clause License

Copyright (c) 2019, Patrick FUCHS All rights reserved.

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

• Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.

• Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.

• Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.