From d38202cb97e24da486ccba72b83da686e109251a Mon Sep 17 00:00:00 2001 From: Sebastian Ehlert <28669218+awvwgk@users.noreply.github.com> Date: Tue, 12 Jan 2021 19:20:57 +0100 Subject: [PATCH] Update documentation in README and add SPDX-Identifiers --- README.md | 45 ++++++++++++++++++++++++++++++++++++++++++++ app/main.f90 | 1 + app/meson.build | 1 + app/targ.f90 | 1 + config/meson.build | 1 + meson.build | 1 + src/meson.build | 1 + src/rmsd.f90 | 1 + src/rmsd/config.f90 | 1 + src/rmsd/filter.f90 | 1 + src/rmsd/ls.f90 | 1 + src/rmsd/meson.build | 1 + src/rmsd/toml.f90 | 1 + src/rmsd/version.f90 | 1 + test/meson.build | 1 + 15 files changed, 59 insertions(+) diff --git a/README.md b/README.md index f6ecfca..c26c48e 100644 --- a/README.md +++ b/README.md @@ -27,6 +27,51 @@ You can run the projects testsuite with meson test -C _build --print-errorlogs ``` +If the testsuite passes you can install with + +``` +meson configure _build --prefix=/path/to/install +meson install -C _build +``` + +This might require administrator access depending on the chosen install prefix. +Now you are ready to use ``mctc-rmsd``. + + +## Usage + +To calculate the RMSD between two structures use the [``mctc-rmsd(1)``](man/mctc-rmsd.1.adoc) program with + +``` +mctc-rmsd struc-a.xyz struc-b.xyz +``` + +The RMSD is calculated relative to the first provided structure. +Multiple structures can be provided to perform additional RMSD calculations, + +``` +mctc-rmsd coord conf-1.xyz conf-2.xyz conf-3.xyz +``` + +To select a subset of atoms use a filter + +``` +mctc-rmsd xrd.pdb opt.pdb --filter heavy +``` + +The heavy atom RMSD (excluding all H atoms) is built-in by default. +New filter can be defined in the ``mctc.toml`` configuration file in the current directory or in your home directory with: + +```toml +[rmsd.filter] +# Definition of the built-in heavy atom filter +heavy.exclude = ["H", "h"] +# Include all carbon, nitrogen and oxygen atoms +organic.include = [6, 7, 8] +``` + +For more details look up [the manual page](man/mctc-rmsd.1.adoc). + ## License diff --git a/app/main.f90 b/app/main.f90 index e3f1457..bc1cfe9 100644 --- a/app/main.f90 +++ b/app/main.f90 @@ -1,4 +1,5 @@ ! This file is part of mctc-rmsd. +! SPDX-Identifier: LGPL-3.0-or-later ! ! mctc-rmsd is free software: you can redistribute it and/or modify it under ! the terms of the GNU Lesser General Public License as published by diff --git a/app/meson.build b/app/meson.build index f5b5a51..de5e57f 100644 --- a/app/meson.build +++ b/app/meson.build @@ -1,4 +1,5 @@ # This file is part of mctc-rmsd. +# SPDX-Identifier: LGPL-3.0-or-later # # mctc-rmsd is free software: you can redistribute it and/or modify it under # the terms of the GNU Lesser General Public License as published by diff --git a/app/targ.f90 b/app/targ.f90 index 46c065b..8340c48 100644 --- a/app/targ.f90 +++ b/app/targ.f90 @@ -1,3 +1,4 @@ +! SPDX-Identifier: LGPL-3.0-or-later module targ use tomlf implicit none diff --git a/config/meson.build b/config/meson.build index 1ba46cc..f12ed62 100644 --- a/config/meson.build +++ b/config/meson.build @@ -1,4 +1,5 @@ # This file is part of mctc-rmsd. +# SPDX-Identifier: LGPL-3.0-or-later # # mctc-rmsd is free software: you can redistribute it and/or modify it under # the terms of the GNU Lesser General Public License as published by diff --git a/meson.build b/meson.build index df8ad48..da0e794 100644 --- a/meson.build +++ b/meson.build @@ -1,4 +1,5 @@ # This file is part of mctc-rmsd. +# SPDX-Identifier: LGPL-3.0-or-later # # mctc-rmsd is free software: you can redistribute it and/or modify it under # the terms of the GNU Lesser General Public License as published by diff --git a/src/meson.build b/src/meson.build index 4aa44b3..5690d50 100644 --- a/src/meson.build +++ b/src/meson.build @@ -1,4 +1,5 @@ # This file is part of mctc-rmsd. +# SPDX-Identifier: LGPL-3.0-or-later # # mctc-rmsd is free software: you can redistribute it and/or modify it under # the terms of the GNU Lesser General Public License as published by diff --git a/src/rmsd.f90 b/src/rmsd.f90 index 85ef828..c51e28e 100644 --- a/src/rmsd.f90 +++ b/src/rmsd.f90 @@ -1,4 +1,5 @@ ! This file is part of mctc-rmsd. +! SPDX-Identifier: LGPL-3.0-or-later ! ! mctc-rmsd is free software: you can redistribute it and/or modify it under ! the terms of the GNU Lesser General Public License as published by diff --git a/src/rmsd/config.f90 b/src/rmsd/config.f90 index 80f7ea4..f71d8c8 100644 --- a/src/rmsd/config.f90 +++ b/src/rmsd/config.f90 @@ -1,4 +1,5 @@ ! This file is part of mctc-rmsd. +! SPDX-Identifier: LGPL-3.0-or-later ! ! mctc-rmsd is free software: you can redistribute it and/or modify it under ! the terms of the GNU Lesser General Public License as published by diff --git a/src/rmsd/filter.f90 b/src/rmsd/filter.f90 index e63291d..78b233c 100644 --- a/src/rmsd/filter.f90 +++ b/src/rmsd/filter.f90 @@ -1,4 +1,5 @@ ! This file is part of mctc-rmsd. +! SPDX-Identifier: LGPL-3.0-or-later ! ! mctc-rmsd is free software: you can redistribute it and/or modify it under ! the terms of the GNU Lesser General Public License as published by diff --git a/src/rmsd/ls.f90 b/src/rmsd/ls.f90 index a60d3ef..87c61a5 100644 --- a/src/rmsd/ls.f90 +++ b/src/rmsd/ls.f90 @@ -1,4 +1,5 @@ ! This file is part of mctc-rmsd. +! SPDX-Identifier: LGPL-3.0-or-later ! ! Copyright (C) 2004, 2005 Chaok Seok, Evangelos Coutsias and Ken Dill ! UCSF, Univeristy of New Mexico, Seoul National University diff --git a/src/rmsd/meson.build b/src/rmsd/meson.build index 11e893b..f777da9 100644 --- a/src/rmsd/meson.build +++ b/src/rmsd/meson.build @@ -1,4 +1,5 @@ # This file is part of mctc-rmsd. +# SPDX-Identifier: LGPL-3.0-or-later # # mctc-rmsd is free software: you can redistribute it and/or modify it under # the terms of the GNU Lesser General Public License as published by diff --git a/src/rmsd/toml.f90 b/src/rmsd/toml.f90 index 1a40600..ab9c8d7 100644 --- a/src/rmsd/toml.f90 +++ b/src/rmsd/toml.f90 @@ -1,4 +1,5 @@ ! This file is part of mctc-rmsd. +! SPDX-Identifier: LGPL-3.0-or-later ! ! mctc-rmsd is free software: you can redistribute it and/or modify it under ! the terms of the GNU Lesser General Public License as published by diff --git a/src/rmsd/version.f90 b/src/rmsd/version.f90 index cf11c91..f3c6d63 100644 --- a/src/rmsd/version.f90 +++ b/src/rmsd/version.f90 @@ -1,4 +1,5 @@ ! This file is part of mctc-rmsd. +! SPDX-Identifier: LGPL-3.0-or-later ! ! mctc-rmsd is free software: you can redistribute it and/or modify it under ! the terms of the GNU Lesser General Public License as published by diff --git a/test/meson.build b/test/meson.build index 0c3fcae..c0411bb 100644 --- a/test/meson.build +++ b/test/meson.build @@ -1,4 +1,5 @@ # This file is part of mctc-rmsd. +# SPDX-Identifier: LGPL-3.0-or-later # # mctc-rmsd is free software: you can redistribute it and/or modify it under # the terms of the GNU Lesser General Public License as published by