Update documentation in README and add SPDX-Identifiers

grimme-lab · Jan 12, 2021 · d38202c · d38202c
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diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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