Allow usage of template input to amend geometry information (#11)

- transfer lattice, periodicity, bonds and other annotations
- the template structure is read before the input structure from STDIN
- error if template and input structure mismatch in the number of atoms

CMakeLists.txt

@@ -18,7 +18,7 @@ get_directory_property(is-subproject PARENT_DIRECTORY)
 project(
   "mctc-lib"
   LANGUAGES "Fortran"
-  VERSION "0.2.0"
+  VERSION "0.2.1"
   DESCRIPTION "Modular computation tool chain"
 )
 

app/main.f90

@@ -37,18 +37,36 @@ program main
    implicit none
    character(len=*), parameter :: prog_name = "mctc-convert"
 
-   character(len=:), allocatable :: input, output
-   integer, allocatable :: input_format, output_format
+   character(len=:), allocatable :: input, output, template
+   integer, allocatable :: input_format, output_format, template_format
    type(structure_type) :: mol
+   type(structure_type), allocatable :: mol_template
    type(error_type), allocatable :: error
    logical :: normalize
 
-   call get_arguments(input, input_format, output, output_format, normalize, error)
+   call get_arguments(input, input_format, output, output_format, normalize, &
+      & template, template_format, error)
    if (allocated(error)) then
       write(error_unit, '(a)') error%message
       error stop
    end if
 
+   if (allocated(template)) then
+      allocate(mol_template)
+      if (template == "-") then
+         if (.not.allocated(template_format)) then
+            template_format = merge(output_format, filetype%xyz, allocated(output_format))
+         end if
+         call read_structure(mol_template, input_unit, template_format, error)
+      else
+         call read_structure(mol_template, template, error, template_format)
+      end if
+      if (allocated(error)) then
+         write(error_unit, '(a)') error%message
+         error stop
+      end if
+   end if
+
    if (input == "-") then
       if (.not.allocated(input_format)) input_format = filetype%xyz
       call read_structure(mol, input_unit, input_format, error)
@@ -60,6 +78,22 @@ program main
       error stop
    end if
 
+   if (allocated(mol_template)) then
+      if (mol%nat /= mol_template%nat) then
+         write(error_unit, '(*(a, 1x))') &
+            "Number of atoms missmatch in", template, "and", input
+         error stop
+      end if
+
+      ! move_alloc can also move non-allocated objects
+      call move_alloc(mol_template%lattice, mol%lattice)
+      call move_alloc(mol_template%periodic, mol%periodic)
+      call move_alloc(mol_template%bond, mol%bond)
+      call move_alloc(mol_template%comment, mol%comment)
+      call move_alloc(mol_template%pdb, mol%pdb)
+      call move_alloc(mol_template%sdf, mol%sdf)
+   end if
+
    if (normalize) then
       mol%sym = to_symbol(mol%num)
    end if
@@ -95,6 +129,9 @@ subroutine help(unit)
       "-i, --input <format>", "Hint for the format of the input file", &
       "-o, --output <format>", "Hint for the format of the output file", &
       "--normalize", "Normalize all element symbols to capitalized format", &
+      "--template <file>", "File to use as template to fill in meta data", &
+      "", "(useful to add back SDF or PDB annotions)", &
+      "--template-format <format>", "", "", "Hint for the format of the template file", &
       "--version", "Print program version and exit", &
       "--help", "Show this help message"
 
@@ -115,7 +152,7 @@ end subroutine version
 
 
 subroutine get_arguments(input, input_format, output, output_format, normalize, &
-      & error)
+      & template, template_format, error)
 
    !> Input file name
    character(len=:), allocatable :: input
@@ -129,6 +166,12 @@ subroutine get_arguments(input, input_format, output, output_format, normalize,
    !> Output file format
    integer, allocatable, intent(out) :: output_format
 
+   !> Template file name
+   character(len=:), allocatable :: template
+
+   !> Template file format
+   integer, allocatable, intent(out) :: template_format
+
    !> Normalize element symbols
    logical, intent(out) :: normalize
 
@@ -180,6 +223,21 @@ subroutine get_arguments(input, input_format, output, output_format, normalize,
          output_format = get_filetype("."//arg)
       case("--normalize")
          normalize = .true.
+      case("--template")
+         iarg = iarg + 1
+         call get_argument(iarg, template)
+         if (.not.allocated(template)) then
+            call fatal_error(error, "Missing argument for template file")
+            exit
+         end if
+      case("--template-format")
+         iarg = iarg + 1
+         call get_argument(iarg, arg)
+         if (.not.allocated(arg)) then
+            call fatal_error(error, "Missing argument for template format")
+            exit
+         end if
+         template_format = get_filetype("."//arg)
       end select
    end do
 

fpm.toml

@@ -1,5 +1,5 @@
 name = "mctc-lib"
-version = "0.2.0"
+version = "0.2.1"
 license = "Apache-2.0"
 maintainer = ["@awvwgk"]
 author = ["Sebastian Ehlert"]

man/mctc-convert.1.adoc

@@ -13,6 +13,9 @@ mctc-convert - Convert between supported input formats of the tool chain library
 
 Read structure from input file and writes it to output file.
 The format is determined by the file extension or the format hint.
+The input structure can be read from standard input by providing - as argument.
+Similarly, the output structure can be written to standard output with - as argument.
+Standard input and standard output should be combined with a format hint option.
 
 Supported formats:
 
@@ -36,6 +39,16 @@ Hint for the format of the output file
 *--normalize*::
 Normalize all element symbols to capitalized format
 
+*--template* _file_::
+File to use as template to fill in meta data (useful to add back SDF or PDB annotions).
+Transfers lattice, periodicity, comments and format specific annotations from the template
+to the input structure.
+If the standard input, -, is provided the template structure will
+be read _before_ the input structure.
+
+*--template-format* _format_::
+Hint for the format of the template file (only used if template file name is provided)
+
 *--version*::
 Print program version and exit
 

meson.build

@@ -15,7 +15,7 @@
 project(
   'mctc-lib',
   'fortran',
-  version: '0.2.0',
+  version: '0.2.1',
   license: 'Apache-2.0',
   meson_version: '>=0.53',
   default_options: [

src/mctc/io/read/pdb.f90

@@ -97,7 +97,7 @@ subroutine read_pdb(self, unit, error)
    end if
 
    call new(self, sym(:iatom), xyz(:, :iatom))
-   !self%pdb = pdb(:iatom)
+   self%pdb = pdb(:iatom)
    self%charge = sum(pdb(:iatom)%charge)
 
    if (.not.all(self%num > 0)) then

src/mctc/version.f90

@@ -21,10 +21,10 @@ module mctc_version
 
 
    !> String representation of the mctc-lib version
-   character(len=*), parameter :: mctc_version_string = "0.2.0"
+   character(len=*), parameter :: mctc_version_string = "0.2.1"
 
    !> Numeric representation of the mctc-lib version
-   integer, parameter :: mctc_version_compact(3) = [0, 2, 0]
+   integer, parameter :: mctc_version_compact(3) = [0, 2, 1]
 
 
 contains