LowCarb

With little carbo-hydrates and lots of protein!

PREREQUISITES

This project requires:

Cross-platform Make (CMake) v2.6.2+
GNU Make or equivalent.
GCC or an alternative, reasonably conformant C++ compiler.

BUILDING

The olden way:

$ ./configure && make

Possible configure options are:

DEBUG
PROFILE
COVERAGE
OPTIMIZE
SSE2
OPENMP

of which optimization, sse and openmp are set to ON by default.

To make use of the python3 build script you might have to install certain requirements:

$ pip3 install --user -r requirements.txt

Compilation:

$ python3 cc clean compile # use 'cc' instead of 'clean compile'

Testing:

$ ./sync-test-data down # data required for unittests
$ python3 cc --check-unittests --check-coupling compile

To run the coverage tests, make sure to run unittests!

RUNNING

Allowed options:

-h [ --help ]           produce help message
-c [ --config ] PATH    config file path
-o [ --output ] PATH    output file path
-d [ --debug ]          print debug output

Example:

./bin/low-carb --config test/resources/integration/config.ini -o output

CONFIGURATION

There are several configuration options available. Example:

[General]
ENSEMBLE_SIZE = 2000
SEGMENT_SIZE  = 20
TEMPERATURE   = 120.0

[Fitting]
AVERAGE_BIN_LENGTH = 1.0
MINIMUM_LENGTH = 6.0
MAXIMUM_LENGTH = 12.0
USE_SLOW_FITTING = true
SLOW_MINIMUM_LENGTH = 11.0
SLOW_MAXIMUM_LENGTH = 20.0

[Files]
DSSP = 1a6g.dssp
PROTEIN = mb_ca.pdb
TRAJECTORIES = mb_ca-1.dcd,mb_ca-2.dcd

Some values have defaults, others are not required. Please refer to the following list for more information.

Section: General

ENSEMBLE_SIZE:

Type: Integer
Default: 2000
Required: No
Description: Maximum number of frames per ensemble.

SEGMENT_SIZE:

Type: Integer
Default: 20
Required: No
Description: Maximum number of residues per segment.

TEMPERATURE:

Type: Double
Required: Yes
Description: Temperature at which the trajectory data was accquired.

CRYSTAL_INFORMATION:

Type: Boolean
Default: false
Required: Yes, if true.
Description: If trajectory files contain crystal information.

Section: Files

PROTEIN:

Type: String
Allowed formats: pdb
Required: Yes
Description: Path to the protein file (allowed formats: pdb)

TRAJECTORIES:

Type: String
Allowed formats: dcd, xtc
Required: Yes, if NMA_COVARIANCE is absent.
Description: Comma seperated list of paths to files containing trajectory
             data.

NMA_COVARIANCE:

Type: String
Allowed formats: csv
Required: No
Description: Path to covariance input file to be used instead of trajectory
             file(s). Please refer to nma covariance section for more
             information.

REDUCTION:

Type: String
Required: No
Description: Path to a file containing a reduction scheme. For more
             information refer to section about reduction.

SECONDARY_STRUCTURE:

Type: String
Allowed formats: dssp
Required: No
Description: Path to a file containing secondary structure information.

Section: Fitting

AVERAGE_BIN_LENGTH:

Type: Double
Default: 1.0
Required: No
Description: **TODO**

MINIMUM_LENGTH:

Type: Double
Default: 6.0
Required: No
Description: **TODO**

MAXIMUM_LENGTH:

Type: Double
Default: 12.0
Required: No
Description: **TODO**

SLOW_MINIMUM_LENGTH:

Type: Double
Default: 11.0
Required: No
Description: **TODO**

SLOW_MAXIMUM_LENGTH:

Type: Double
Default: 20.0
Required: No
Description: **TODO**

Section: Threading

THREADS:

Type: Integer
Default: 0
Required: No
Description: Maximum number of threads where 0 is unlimited.

DYNAMIC:

Type: Boolean
Default: true
Required: No
Description: Whether to enable openmp dynamic teams.
             Deactivating will fix the number of threads used by openmp.

EIGEN_THREADS:

Type: Integer
Default: 0
Required: No
Description: Maximum number of threads to be used by Eigen where 0 is unlimited.

Section: Logging

LEVEL:

Type: Integer
Default: 4
Choices: 0-6
Required: No
Description: Log output level, choose from 0-6 where 0 is no output at all
             and 6 prints everything.

Reduction

It is possible to reduce the Protein Model through projecting all Residua on the remaining Residua. You specify the remaining Residua in a textfile.

Example:

1,2,3,5-7,10-end

NMA Covariance input

TODO

Known Issues

CSVWriter class will not show any errors if it fails to write anything (e.g. into a non existing folder). This will be caught by the ConfigParser.

External Libraries

_Plog 1.0.0: https://github.com/SergiusTheBest/plog
_Boost 1.59.0: http://www.boost.org/
_xdrfile 1.1.4: http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library
_fast_cpp_csv_parser: https://github.com/ben-strasser/fast-cpp-csv-parser

Name		Name	Last commit message	Last commit date
Latest commit History 1 Commits
docs		docs
include		include
src		src
test		test
thirdparty		thirdparty
tools		tools
.gitignore		.gitignore
AUTHORS		AUTHORS
CMakeLists.txt		CMakeLists.txt
COPYING		COPYING
Doxyfile		Doxyfile
INSTALL		INSTALL
LICENSE		LICENSE
README.rst		README.rst
cc		cc
configure		configure
requirements.txt		requirements.txt

License

Licenses found

AFriemann/LowCarb

Folders and files

Latest commit

History

Repository files navigation