Assuming RINmaker is on $PATH:
RINmaker [OPTIONS] SUBCOMMANDA brief help is available with -h or --help.
RINmaker -i 6j8j.pdb -o testrun.graphml rinWill parse the first model in the 6j8j pdb.
RINmaker v1.0.1 build Aug 4 2023 11:42:57 (Linux) [DEBUG]
(C) 2020-23 Ca' Foscari University of Venice
Usage: ./RINmaker [OPTIONS] SUBCOMMAND
Options:
-h,--help Print this help message and exit
-H,--help-expanded Print this help message (expanded) and exit
--version Display program version information and exit
-i,--input TEXT:FILE REQUIRED Path to .pdb or .cif file
-o,--output TEXT REQUIRED Output file (or directory if -d flag is specified)
-d Use -o argument as a directory
-l,--log TEXT=./main.txt Log file
--csv-out Output in CSV format rather than GraphML. This will output two CSV files per model, one for the nodes and one for the edges of the RIN
-v,--verbose Log also to stdout
-n,--no-hydrogen Skip hydrogen fixing
-w,--keep-water Keep water residues
-s,--sequence-separation INT:POSITIVE=3 Minimum sequence separation
--illformed ENUM:{fail,kall,kres,sres}=sres Behaviour in case of malformed ring or ionic group
Subcommands:
rin Compute the residue interaction network
cmap Compute the contact map of the protein
| Param. | Abbr. | Default | Meaning |
|---|---|---|---|
--help |
-h |
all |
Print a brief helper and exit. |
--help-expanded |
-H |
3.5 | Print the full helper and exit. |
--input |
-i |
REQUIRED | Path to either a .pdb or a .cif file. |
--output |
-o |
REQUIRED | If -d is not used, then it represents the path to the output file. If -d is used, it will be used as a directory for the resulting graphs. |
-d |
not set | It's a flag. By default, it is not set and the program will analyse only the first model of the protein. If used, then all the models in the PDB/mmCIF will be analysed instead and multiple graphs will be produced. | |
--log |
-l |
"./main.txt" | Maximum distance between two aromatic rings (in ångström; centre of mass is considered) to be tested for bonding conditions. |
--verbose |
-v |
not set | It's a flag. If used, logs will be mirrored to standard output. |
--no-hydrogen |
-n |
not set | Skip hydrogen fixing. |
--keep-water |
-w |
not set | Keep water residues |
--sequence-separation |
-s |
3 | Minimum sequence separation |
--illformed |
-f |
sres |
|
| Param. | Default | Meaning |
|---|---|---|
--policy |
all |
|
--hydrogen-bond |
3.5 | Maximum distance between atoms (in ångström) for a pair donor-acceptor to be tested for hydrogen bond. |
--vdw-bond |
0.5 | Maximum distance (in ångström) between the surfaces of the spheres marked by two atoms' Van der Waals radii. |
--ionic-bond |
4.0 | Maximum distance between two ionic groups (in ångström; centre of mass is considered) to be tested for bonding conditions. |
--pication-bond |
5.0 | Maximum distance between a cation and an aromatic ring (in ångström; centre of mass is considered) to be considered bond candidates. |
--pipistack-bond |
6.5 | Maximum distance between two aromatic rings (in ångström; centre of mass is considered) to be tested for bonding conditions. |
--h-bond-realistic |
not set | It's a flag; if used, it keeps only MC-MC hydrogen bonds with minimum energy before filtering by policy. |
--h-bond-angle |
63 | Angle (degrees) for hydrogen bonds. |
--pication-angle |
45 | Angle for cation-pi bonds. |
--pipistack-normal-normal |
30 | Angle range from normal to normal for pi-pi stackings. |
--pipistack-normal-centre |
60 | Angle range from normal to centre for pi-pi stackings. |
| Param. | Default | Meaning |
|---|---|---|
--type |
ca |
|
--distance |
3.5 | Query distance between alpha/beta carbons. |
You will need:
cmake- A suitable C++ compiler. For *nix systems
g++; for Windows, you can useMSVC.
CMake will automatically fetch the following dependencies:
Clone and initialize the project:
git clone -b dev https://github.com/RINmaker/RINmaker.git
cd RINmaker
git submodule update --init --recursive
cmake -S . -B buildcmake --build build --target RINmakerThe application's executable will be located at: ./build/app/RINmaker.
Hydrogen fixing is performed internally by the third-party library GEMMI. It needs an additional non-software dependency, that is a suitable monomer library. The GEMMI documentation suggests to use the CCP4 monomer library, which we do not distribute. There are at least 3 ways to get it.
-
(git) In your terminal, move where the
RINmakerexecutable is located and prompt:git clone --depth=1 --branch ccp4-8.0.011 https://github.com/MonomerLibrary/monomers.git. -
(breezy) In your terminal, move where the
RINmakerexecutable is located and prompt:brz checkout https://ccp4serv6.rc-harwell.ac.uk/anonscm/bzr/monomers/trunk monomers(see this paper, section 6. Open research data: availability and reproducibility). -
(CCP4 download) The monomer library should be included in your local copy of the CCP4 software suite.
The monomers directory must always reside alongside the RINmaker executable.
cmake --build build --target RINmaker_testTo run the full test suite (assuming you are in the project's root):
./build/test/RINmaker_testRINmaker: a fast, versatile and reliable tool to determine residue interaction networks in proteins.
Alvise Spanò, Lorenzo Fanton, Davide Pizzolato, Jacopo Moi, Francesco Vinci, Alberto Pesce, Cedrix J. Dongmo Foumthuim, Achille Giacometti, Marta Simeoni
![allcontributors[bot] avatar](https://avatars.githubusercontent.com/in/23186?v=4 "allcontributors[bot]")
![dependabot[bot] avatar](https://avatars.githubusercontent.com/in/29110?v=4 "dependabot[bot]")
![pre-commit-ci[bot] avatar](https://avatars.githubusercontent.com/in/68672?v=4 "pre-commit-ci[bot]")
React
Typescript
Django
Laravel
Facebook
Microsoft
Google
Alibaba
D3
Tencent