LCOV - code coverage report
Current view: top level - src - topology_pdb.F (source / functions) Coverage Total Hit
Test: CP2K Regtests (git:42dac4a) Lines: 97.2 % 176 171
Test Date: 2025-07-25 12:55:17 Functions: 100.0 % 2 2

            Line data    Source code
       1              : !--------------------------------------------------------------------------------------------------!
       2              : !   CP2K: A general program to perform molecular dynamics simulations                              !
       3              : !   Copyright 2000-2025 CP2K developers group <https://cp2k.org>                                   !
       4              : !                                                                                                  !
       5              : !   SPDX-License-Identifier: GPL-2.0-or-later                                                      !
       6              : !--------------------------------------------------------------------------------------------------!
       7              : 
       8              : ! **************************************************************************************************
       9              : !> \brief Handles PDB files
      10              : !>
      11              : !> PDB Format Description Version 2.2 from http://www.rcsb.org
      12              : !> COLUMNS       DATA TYPE       FIELD         DEFINITION
      13              : !>
      14              : !>  1 -  6       Record name     "ATOM  "
      15              : !>  7 - 11       Integer         serial        Atom serial number.
      16              : !> 13 - 16       Atom            name          Atom name.
      17              : !> 17            Character       altLoc        Alternate location indicator.
      18              : !> 18 - 20       Residue name    resName       Residue name.
      19              : !> 22            Character       chainID       Chain identifier.
      20              : !> 23 - 26       Integer         resSeq        Residue sequence number.
      21              : !> 27            AChar           iCode         Code for insertion of residues.
      22              : !> 31 - 38       Real(8.3)       x             Orthogonal coordinates for X in
      23              : !>                                             Angstroms.
      24              : !> 39 - 46       Real(8.3)       y             Orthogonal coordinates for Y in
      25              : !>                                             Angstroms.
      26              : !> 47 - 54       Real(8.3)       z             Orthogonal coordinates for Z in
      27              : !>                                             Angstroms.
      28              : !> 55 - 60       Real(6.2)       occupancy     Occupancy.
      29              : !> 61 - 66       Real(6.2)       tempFactor    Temperature factor.
      30              : !> 73 - 76       LString(4)      segID         Segment identifier, left-justified.
      31              : !> 77 - 78       LString(2)      element       Element symbol, right-justified.
      32              : !> 79 - 80       LString(2)      charge        Charge on the atom.
      33              : !>
      34              : !> 81 -          Real(*)         Charge Ext.   This last field is an extenstion to
      35              : !>                                             standard PDB to provide a full charge
      36              : !>                                             without limitation of digits.
      37              : !>
      38              : !>  1 -  6       Record name    "CRYST1"
      39              : !>  7 - 15       Real(9.3)      a (Angstroms)
      40              : !> 16 - 24       Real(9.3)      b (Angstroms)
      41              : !> 25 - 33       Real(9.3)      c (Angstroms)
      42              : !> 34 - 40       Real(7.2)      alpha (degrees)
      43              : !> 41 - 47       Real(7.2)      beta (degrees)
      44              : !> 48 - 54       Real(7.2)      gamma (degrees)
      45              : !> 56 - 66       LString        Space group
      46              : !> 67 - 70       Integer        Z value
      47              : ! **************************************************************************************************
      48              : MODULE topology_pdb
      49              :    USE cell_types,                      ONLY: get_cell
      50              :    USE cp2k_info,                       ONLY: compile_revision,&
      51              :                                               cp2k_version,&
      52              :                                               r_datx,&
      53              :                                               r_host_name,&
      54              :                                               r_user_name
      55              :    USE cp_log_handling,                 ONLY: cp_get_default_logger,&
      56              :                                               cp_logger_type
      57              :    USE cp_output_handling,              ONLY: cp_print_key_finished_output,&
      58              :                                               cp_print_key_generate_filename,&
      59              :                                               cp_print_key_unit_nr
      60              :    USE cp_parser_methods,               ONLY: parser_get_next_line
      61              :    USE cp_parser_types,                 ONLY: cp_parser_type,&
      62              :                                               parser_create,&
      63              :                                               parser_release
      64              :    USE cp_units,                        ONLY: cp_unit_to_cp2k
      65              :    USE input_constants,                 ONLY: do_conn_user
      66              :    USE input_section_types,             ONLY: section_get_rval,&
      67              :                                               section_vals_get_subs_vals,&
      68              :                                               section_vals_type,&
      69              :                                               section_vals_val_get
      70              :    USE kinds,                           ONLY: default_path_length,&
      71              :                                               default_string_length,&
      72              :                                               dp
      73              :    USE memory_utilities,                ONLY: reallocate
      74              :    USE message_passing,                 ONLY: mp_para_env_type
      75              :    USE physcon,                         ONLY: angstrom
      76              :    USE qmmm_ff_fist,                    ONLY: qmmm_ff_precond_only_qm
      77              :    USE string_table,                    ONLY: id2str,&
      78              :                                               s2s,&
      79              :                                               str2id
      80              :    USE topology_types,                  ONLY: atom_info_type,&
      81              :                                               topology_parameters_type
      82              : #include "./base/base_uses.f90"
      83              : 
      84              :    IMPLICIT NONE
      85              : 
      86              :    CHARACTER(len=*), PARAMETER, PRIVATE :: moduleN = 'topology_pdb'
      87              : 
      88              :    PRIVATE
      89              :    PUBLIC :: read_coordinate_pdb, write_coordinate_pdb
      90              : 
      91              : CONTAINS
      92              : 
      93              : ! **************************************************************************************************
      94              : !> \brief ...
      95              : !> \param topology ...
      96              : !> \param para_env ...
      97              : !> \param subsys_section ...
      98              : !> \par History
      99              : !>      TLAINO 05.2004 - Added the TER option to use different non-bonded molecules
     100              : ! **************************************************************************************************
     101         2412 :    SUBROUTINE read_coordinate_pdb(topology, para_env, subsys_section)
     102              :       TYPE(topology_parameters_type)                     :: topology
     103              :       TYPE(mp_para_env_type), POINTER                    :: para_env
     104              :       TYPE(section_vals_type), POINTER                   :: subsys_section
     105              : 
     106              :       CHARACTER(len=*), PARAMETER :: routineN = 'read_coordinate_pdb'
     107              :       INTEGER, PARAMETER                                 :: nblock = 1000
     108              : 
     109              :       CHARACTER(LEN=default_path_length)                 :: line
     110              :       CHARACTER(LEN=default_string_length)               :: record, root_mol_name, strtmp
     111              :       INTEGER                                            :: handle, id0, inum_mol, istat, iw, natom, &
     112              :                                                             newsize
     113              :       LOGICAL                                            :: my_end
     114              :       REAL(KIND=dp)                                      :: pfactor
     115              :       TYPE(atom_info_type), POINTER                      :: atom_info
     116              :       TYPE(cp_logger_type), POINTER                      :: logger
     117              :       TYPE(cp_parser_type)                               :: parser
     118              : 
     119          804 :       NULLIFY (logger)
     120         1608 :       logger => cp_get_default_logger()
     121              :       iw = cp_print_key_unit_nr(logger, subsys_section, "PRINT%TOPOLOGY_INFO/PDB_INFO", &
     122          804 :                                 extension=".subsysLog")
     123          804 :       CALL timeset(routineN, handle)
     124              : 
     125          804 :       pfactor = section_get_rval(subsys_section, "TOPOLOGY%MEMORY_PROGRESSION_FACTOR")
     126          804 :       atom_info => topology%atom_info
     127          804 :       CALL reallocate(atom_info%id_molname, 1, nblock)
     128          804 :       CALL reallocate(atom_info%id_resname, 1, nblock)
     129          804 :       CALL reallocate(atom_info%resid, 1, nblock)
     130          804 :       CALL reallocate(atom_info%id_atmname, 1, nblock)
     131          804 :       CALL reallocate(atom_info%r, 1, 3, 1, nblock)
     132          804 :       CALL reallocate(atom_info%atm_mass, 1, nblock)
     133          804 :       CALL reallocate(atom_info%atm_charge, 1, nblock)
     134          804 :       CALL reallocate(atom_info%occup, 1, nblock)
     135          804 :       CALL reallocate(atom_info%beta, 1, nblock)
     136          804 :       CALL reallocate(atom_info%id_element, 1, nblock)
     137              : 
     138          804 :       IF (iw > 0) THEN
     139              :          WRITE (UNIT=iw, FMT="(T2,A)") &
     140            1 :             "BEGIN of PDB data read from file "//TRIM(topology%coord_file_name)
     141              :       END IF
     142              : 
     143          804 :       id0 = str2id(s2s(""))
     144          804 :       topology%molname_generated = .FALSE.
     145              : 
     146          804 :       CALL parser_create(parser, topology%coord_file_name, para_env=para_env)
     147              : 
     148          804 :       natom = 0
     149          804 :       inum_mol = 1
     150          804 :       WRITE (UNIT=root_mol_name, FMT='(A3,I0)') "MOL", inum_mol
     151              :       DO
     152       440697 :          line = ""
     153       440697 :          CALL parser_get_next_line(parser, 1, at_end=my_end)
     154       440697 :          IF (my_end) EXIT
     155       440197 :          line = parser%input_line(1:default_path_length)
     156       440197 :          record = line(1:6)
     157              :          record = TRIM(record)
     158              : 
     159       440197 :          IF ((record == "ATOM") .OR. (record == "HETATM")) THEN
     160       397997 :             natom = natom + 1
     161       397997 :             topology%natoms = natom
     162       397997 :             IF (natom > SIZE(atom_info%id_atmname)) THEN
     163          500 :                newsize = INT(pfactor*natom)
     164          500 :                CALL reallocate(atom_info%id_molname, 1, newsize)
     165          500 :                CALL reallocate(atom_info%id_resname, 1, newsize)
     166          500 :                CALL reallocate(atom_info%resid, 1, newsize)
     167          500 :                CALL reallocate(atom_info%id_atmname, 1, newsize)
     168          500 :                CALL reallocate(atom_info%r, 1, 3, 1, newsize)
     169          500 :                CALL reallocate(atom_info%atm_mass, 1, newsize)
     170          500 :                CALL reallocate(atom_info%atm_charge, 1, newsize)
     171          500 :                CALL reallocate(atom_info%occup, 1, newsize)
     172          500 :                CALL reallocate(atom_info%beta, 1, newsize)
     173          500 :                CALL reallocate(atom_info%id_element, 1, newsize)
     174              :             END IF
     175              :          END IF
     176              : 
     177          500 :          SELECT CASE (record)
     178              :          CASE ("ATOM", "HETATM")
     179       397997 :             READ (UNIT=line(13:16), FMT=*) strtmp
     180       397997 :             atom_info%id_atmname(natom) = str2id(s2s(strtmp))
     181       397997 :             READ (UNIT=line(18:20), FMT=*, IOSTAT=istat) strtmp
     182       397997 :             IF (istat == 0) THEN
     183       394831 :                atom_info%id_resname(natom) = str2id(s2s(strtmp))
     184              :             ELSE
     185         3166 :                atom_info%id_resname(natom) = id0
     186              :             END IF
     187       397997 :             READ (UNIT=line(23:26), FMT=*, IOSTAT=istat) atom_info%resid(natom)
     188       397997 :             READ (UNIT=line(31:38), FMT=*, IOSTAT=istat) atom_info%r(1, natom)
     189       397997 :             READ (UNIT=line(39:46), FMT=*, IOSTAT=istat) atom_info%r(2, natom)
     190       397997 :             READ (UNIT=line(47:54), FMT=*, IOSTAT=istat) atom_info%r(3, natom)
     191       397997 :             READ (UNIT=line(55:60), FMT=*, IOSTAT=istat) atom_info%occup(natom)
     192       397997 :             READ (UNIT=line(61:66), FMT=*, IOSTAT=istat) atom_info%beta(natom)
     193       397997 :             READ (UNIT=line(73:76), FMT=*, IOSTAT=istat) strtmp
     194       397997 :             IF (istat == 0) THEN
     195       239544 :                atom_info%id_molname(natom) = str2id(s2s(strtmp))
     196              :             ELSE
     197       158453 :                atom_info%id_molname(natom) = str2id(s2s(root_mol_name))
     198       158453 :                topology%molname_generated = .TRUE.
     199              :             END IF
     200       397997 :             READ (UNIT=line(77:78), FMT=*, IOSTAT=istat) strtmp
     201       397997 :             IF (istat == 0) THEN
     202       160397 :                atom_info%id_element(natom) = str2id(s2s(strtmp))
     203              :             ELSE
     204       237600 :                atom_info%id_element(natom) = id0
     205              :             END IF
     206       397997 :             atom_info%atm_mass(natom) = 0.0_dp
     207       397997 :             atom_info%atm_charge(natom) = -HUGE(0.0_dp)
     208       397997 :             IF (topology%charge_occup) atom_info%atm_charge(natom) = atom_info%occup(natom)
     209       397997 :             IF (topology%charge_beta) atom_info%atm_charge(natom) = atom_info%beta(natom)
     210       397997 :             IF (topology%charge_extended) THEN
     211         3188 :                READ (UNIT=line(81:), FMT=*, IOSTAT=istat) atom_info%atm_charge(natom)
     212              :             END IF
     213              : 
     214       397997 :             IF (atom_info%id_element(natom) == id0) THEN
     215              :                ! Element is assigned on the basis of the atm_name
     216       237600 :                topology%aa_element = .TRUE.
     217       237600 :                atom_info%id_element(natom) = atom_info%id_atmname(natom)
     218              :             END IF
     219              : 
     220       397997 :             IF (iw > 0) THEN
     221              :                WRITE (UNIT=iw, FMT="(A6,I5,T13,A4,T18,A3,T23,I4,T31,3F8.3,T73,A4,T77,A2)") &
     222            6 :                   record, natom, &
     223            6 :                   TRIM(id2str(atom_info%id_atmname(natom))), &
     224            6 :                   TRIM(id2str(atom_info%id_resname(natom))), &
     225            6 :                   atom_info%resid(natom), &
     226            6 :                   atom_info%r(1, natom), &
     227            6 :                   atom_info%r(2, natom), &
     228            6 :                   atom_info%r(3, natom), &
     229            6 :                   ADJUSTL(TRIM(id2str(atom_info%id_molname(natom)))), &
     230           12 :                   ADJUSTR(TRIM(id2str(atom_info%id_element(natom))))
     231              :             END IF
     232       397997 :             atom_info%r(1, natom) = cp_unit_to_cp2k(atom_info%r(1, natom), "angstrom")
     233       397997 :             atom_info%r(2, natom) = cp_unit_to_cp2k(atom_info%r(2, natom), "angstrom")
     234       397997 :             atom_info%r(3, natom) = cp_unit_to_cp2k(atom_info%r(3, natom), "angstrom")
     235              :          CASE ("TER")
     236        41508 :             inum_mol = inum_mol + 1
     237        41508 :             WRITE (UNIT=root_mol_name, FMT='(A3,I0)') "MOL", inum_mol
     238              :          CASE ("REMARK")
     239          280 :             IF (iw > 0) WRITE (UNIT=iw, FMT=*) TRIM(line)
     240              :          CASE ("END")
     241       440197 :             EXIT
     242              :          CASE DEFAULT
     243              :          END SELECT
     244              :       END DO
     245          804 :       CALL parser_release(parser)
     246              : 
     247          804 :       CALL reallocate(atom_info%id_molname, 1, natom)
     248          804 :       CALL reallocate(atom_info%id_resname, 1, natom)
     249          804 :       CALL reallocate(atom_info%resid, 1, natom)
     250          804 :       CALL reallocate(atom_info%id_atmname, 1, natom)
     251          804 :       CALL reallocate(atom_info%r, 1, 3, 1, natom)
     252          804 :       CALL reallocate(atom_info%atm_mass, 1, natom)
     253          804 :       CALL reallocate(atom_info%atm_charge, 1, natom)
     254          804 :       CALL reallocate(atom_info%occup, 1, natom)
     255          804 :       CALL reallocate(atom_info%beta, 1, natom)
     256          804 :       CALL reallocate(atom_info%id_element, 1, natom)
     257              : 
     258          804 :       IF (topology%conn_type /= do_conn_user) THEN
     259          940 :          IF (.NOT. topology%para_res) atom_info%resid(:) = 1
     260              :       END IF
     261              : 
     262          804 :       IF (iw > 0) THEN
     263              :          WRITE (UNIT=iw, FMT="(T2,A)") &
     264            1 :             "END of PDB data read from file "//TRIM(topology%coord_file_name)
     265              :       END IF
     266              : 
     267          804 :       topology%natoms = natom
     268              :       CALL cp_print_key_finished_output(iw, logger, subsys_section, &
     269          804 :                                         "PRINT%TOPOLOGY_INFO/PDB_INFO")
     270          804 :       CALL timestop(handle)
     271              : 
     272         2412 :    END SUBROUTINE read_coordinate_pdb
     273              : 
     274              : ! **************************************************************************************************
     275              : !> \brief ...
     276              : !> \param file_unit ...
     277              : !> \param topology ...
     278              : !> \param subsys_section ...
     279              : ! **************************************************************************************************
     280          318 :    SUBROUTINE write_coordinate_pdb(file_unit, topology, subsys_section)
     281              : 
     282              :       INTEGER, INTENT(IN)                                :: file_unit
     283              :       TYPE(topology_parameters_type)                     :: topology
     284              :       TYPE(section_vals_type), POINTER                   :: subsys_section
     285              : 
     286              :       CHARACTER(len=*), PARAMETER :: routineN = 'write_coordinate_pdb'
     287              : 
     288              :       CHARACTER(LEN=120)                                 :: line
     289              :       CHARACTER(LEN=default_string_length)               :: my_tag1, my_tag2, my_tag3, my_tag4, &
     290              :                                                             record
     291              :       INTEGER                                            :: handle, i, id1, id2, idres, iw, natom
     292              :       LOGICAL                                            :: charge_beta, charge_extended, &
     293              :                                                             charge_occup, ldum
     294              :       REAL(KIND=dp)                                      :: angle_alpha, angle_beta, angle_gamma
     295              :       REAL(KIND=dp), DIMENSION(3)                        :: abc
     296              :       TYPE(atom_info_type), POINTER                      :: atom_info
     297              :       TYPE(cp_logger_type), POINTER                      :: logger
     298              :       TYPE(section_vals_type), POINTER                   :: print_key
     299              : 
     300           53 :       NULLIFY (logger)
     301           53 :       logger => cp_get_default_logger()
     302              :       iw = cp_print_key_unit_nr(logger, subsys_section, "PRINT%TOPOLOGY_INFO/PDB_INFO", &
     303           53 :                                 extension=".subsysLog")
     304           53 :       print_key => section_vals_get_subs_vals(subsys_section, "TOPOLOGY%DUMP_PDB")
     305           53 :       CALL timeset(routineN, handle)
     306              : 
     307           53 :       CALL section_vals_val_get(print_key, "CHARGE_OCCUP", l_val=charge_occup)
     308           53 :       CALL section_vals_val_get(print_key, "CHARGE_BETA", l_val=charge_beta)
     309           53 :       CALL section_vals_val_get(print_key, "CHARGE_EXTENDED", l_val=charge_extended)
     310          212 :       i = COUNT((/charge_occup, charge_beta, charge_extended/))
     311           53 :       IF (i > 1) &
     312            0 :          CPABORT("Either only CHARGE_OCCUP, CHARGE_BETA, or CHARGE_EXTENDED can be selected")
     313              : 
     314           53 :       atom_info => topology%atom_info
     315              :       record = cp_print_key_generate_filename(logger, print_key, &
     316              :                                               extension=".pdb", &
     317           53 :                                               my_local=.FALSE.)
     318              : 
     319           53 :       IF (iw > 0) WRITE (UNIT=iw, FMT=*) "    Writing out PDB file ", TRIM(record)
     320              : 
     321              :       ! Write file header
     322              :       WRITE (UNIT=file_unit, FMT="(A6,T11,A)") &
     323           53 :          "TITLE ", "PDB file created by "//TRIM(cp2k_version)//" (revision "//TRIM(compile_revision)//")", &
     324          106 :          "AUTHOR", TRIM(r_user_name)//"@"//TRIM(r_host_name)//" "//r_datx(1:19)
     325              :       ! Write cell information
     326           53 :       CALL get_cell(cell=topology%cell, alpha=angle_alpha, beta=angle_beta, gamma=angle_gamma, abc=abc)
     327              :       WRITE (UNIT=file_unit, FMT="(A6,3F9.3,3F7.2)") &
     328          212 :          "CRYST1", abc(1:3)*angstrom, angle_alpha, angle_beta, angle_gamma
     329              : 
     330           53 :       natom = topology%natoms
     331           53 :       idres = 0
     332           53 :       id1 = 0
     333           53 :       id2 = 0
     334              : 
     335        28984 :       DO i = 1, natom
     336              : 
     337        28931 :          IF (topology%para_res) THEN
     338        28235 :             idres = atom_info%resid(i)
     339              :          ELSE
     340          696 :             IF ((id1 /= atom_info%map_mol_num(i)) .OR. (id2 /= atom_info%map_mol_typ(i))) THEN
     341           49 :                idres = idres + 1
     342           49 :                id1 = atom_info%map_mol_num(i)
     343           49 :                id2 = atom_info%map_mol_typ(i)
     344              :             END IF
     345              :          END IF
     346              : 
     347        28931 :          line = ""
     348        28931 :          my_tag1 = id2str(atom_info%id_atmname(i)); ldum = qmmm_ff_precond_only_qm(my_tag1)
     349        28931 :          my_tag2 = id2str(atom_info%id_resname(i)); ldum = qmmm_ff_precond_only_qm(my_tag2)
     350        28931 :          my_tag3 = id2str(atom_info%id_molname(i)); ldum = qmmm_ff_precond_only_qm(my_tag3)
     351        28931 :          my_tag4 = id2str(atom_info%id_element(i)); ldum = qmmm_ff_precond_only_qm(my_tag4)
     352              : 
     353        28931 :          WRITE (UNIT=line(1:6), FMT="(A6)") "ATOM  "
     354        28931 :          WRITE (UNIT=line(7:11), FMT="(I5)") MODULO(i, 100000)
     355        28931 :          WRITE (UNIT=line(13:16), FMT="(A4)") ADJUSTL(my_tag1(1:4))
     356        28931 :          WRITE (UNIT=line(18:20), FMT="(A3)") TRIM(my_tag2)
     357        28931 :          WRITE (UNIT=line(23:26), FMT="(I4)") MODULO(idres, 10000)
     358       115724 :          WRITE (UNIT=line(31:54), FMT="(3F8.3)") atom_info%r(1:3, i)*angstrom
     359        28931 :          IF (ASSOCIATED(atom_info%occup)) THEN
     360        28652 :             WRITE (UNIT=line(55:60), FMT="(F6.2)") atom_info%occup(i)
     361              :          ELSE
     362          279 :             WRITE (UNIT=line(55:60), FMT="(F6.2)") 0.0_dp
     363              :          END IF
     364        28931 :          IF (ASSOCIATED(atom_info%beta)) THEN
     365        28652 :             WRITE (UNIT=line(61:66), FMT="(F6.2)") atom_info%beta(i)
     366              :          ELSE
     367          279 :             WRITE (UNIT=line(61:66), FMT="(F6.2)") 0.0_dp
     368              :          END IF
     369        28931 :          IF (ASSOCIATED(atom_info%atm_charge)) THEN
     370        28931 :             IF (ANY((/charge_occup, charge_beta, charge_extended/)) .AND. &
     371              :                 (atom_info%atm_charge(i) == -HUGE(0.0_dp))) &
     372            0 :                CPABORT("No atomic charges found yet (after the topology setup)")
     373        28931 :             IF (charge_occup) THEN
     374            0 :                WRITE (UNIT=line(55:60), FMT="(F6.2)") atom_info%atm_charge(i)
     375        28931 :             ELSE IF (charge_beta) THEN
     376            0 :                WRITE (UNIT=line(61:66), FMT="(F6.2)") atom_info%atm_charge(i)
     377        28931 :             ELSE IF (charge_extended) THEN
     378            0 :                WRITE (UNIT=line(81:), FMT="(F20.16)") atom_info%atm_charge(i)
     379              :             ELSE
     380              :                ! Write no atomic charge
     381              :             END IF
     382              :          END IF
     383        28931 :          WRITE (UNIT=line(73:76), FMT="(A4)") ADJUSTL(my_tag3)
     384        28931 :          WRITE (UNIT=line(77:78), FMT="(A2)") TRIM(my_tag4)
     385        28984 :          WRITE (UNIT=file_unit, FMT="(A)") TRIM(line)
     386              :       END DO
     387           53 :       WRITE (UNIT=file_unit, FMT="(A3)") "END"
     388              : 
     389           53 :       IF (iw > 0) WRITE (UNIT=iw, FMT=*) "  Exiting "//routineN
     390              : 
     391              :       CALL cp_print_key_finished_output(iw, logger, subsys_section, &
     392           53 :                                         "PRINT%TOPOLOGY_INFO/PDB_INFO")
     393              : 
     394           53 :       CALL timestop(handle)
     395              : 
     396           53 :    END SUBROUTINE write_coordinate_pdb
     397              : 
     398              : END MODULE topology_pdb
        

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