pdbio

November 18, 2022 · View on GitHub

The Protein Data Bank (pdb) file format is a textual file format describing the three-dimensional structures of molecules held in the Protein Data Bank. The pdb format accordingly provides for description and annotation of protein and nucleic acid structures including atomic coordinates, secondary structure assignments, as well as atomic connectivity. In addition experimental metadata are stored. The units are in Ångströms.

TITLE     Two water molecules, t= 0.0
REMARK    THIS IS A SIMULATION BOX
CRYST1   18.206   18.206   18.206  90.00  90.00  90.00 P 1           1
MODEL        1
ATOM      1  OW1 WAT A   1       1.260  16.240  16.790  1.00  0.00           O  
ATOM      2  HW2 WAT A   1       1.900  16.610  17.470  1.00  0.00           H  
ATOM      3  HW3 WAT A   1       1.770  15.680  16.130  1.00  0.00           H  
ATOM      4  OW1 WAT A   2      12.750   0.530   6.220  1.00  0.00           O  
ATOM      5  HW2 WAT A   2      13.370   0.020   6.800  1.00  0.00           H  
ATOM      6  HW3 WAT A   2      13.260   1.200   5.680  1.00  0.00           H  
TER
ENDMDL

PDB files contais all sort of metadata we are only interested with keywordATOM or HETATM tha contain atom infromation. Lines contain the following information:

Record type,
Atom serial number,
Atom name,
Alternate location indicator,
Residue name.
Chain identifier,
Residue sequence number,
Code for insertions of residues,
Orthogonal coordinates for x, y, and z,
Occupancy,
Temperature factor,
Segment identifier,
Element symbol,
and atoms charge

Fortran format: (6x,i5,1x,a4,a1,a3,x,a1,i4,a1,3x,3f8.3,2f6.2,10x,a2,i2)

For more information please see reference.

`pdb_open`

Open file for reading and checked. Frame offset table is constructed (byte position where frame starts). Move to selected frame with fseek. If the function fails stat is a positive number, otherwise it is set to zero. If stat is not present end error occurs error stop is raised.

call pdb_open (file, unit, nframes, offset, stat, errmsg)

Parameters

character(*), intent(IN) :: file

Input file name.

integer, intent(OUT) :: unit

Fortran file unit.

integer, intent(OUT) :: nframes

Number of frames in file.

integer(INT64), allocatable, dimension(:), intent(INOUT) :: offset

Frame offset table. Array size same as nframes.

integer, intent(OUT), optional :: stat

Error status code. Returns zero if no error.

character(*), intent(OUT), optional :: errmsg

Error status message. Empty if no error.

`pdb_close`

Close opened file.

call pdb_close (unit, stat, errmsg)

integer, intent(IN) :: unit

Fortran file unit.

integer, intent(OUT), optional :: stat

Error status code. Returns zero if no error.

character(*), intent(OUT), optional :: errmsg

Error status message. Empty if no error.

`pdb_get_natoms`

Count num. of atoms in current PDB frame i.e. count occurance of "ATOM" and "HETATOM" keywords. File must be opened as Fortran 'formatted stream'.

call pdb_get_natoms (unit, natoms, stat, errmsg)

integer, intent(IN) :: unit

Fortran file unit.

integer, intent(OUT) :: natoms

Number of atoms.

integer, intent(OUT), optional :: stat

Error status code. Returns zero if no error.

character(*), intent(OUT), optional :: errmsg

Error status message. Empty if no error.

`pdb_read_data`

Read data in PDB format.

call pdb_read_data (unit, natoms, atomi, atomn, resi, resn, chain, resic, &
& altloc, qfact, bfact, element, charge, coor, box, stat, errmsg)

integer, intent(IN) :: unit

Fortran file unit.

integer, intent(IN) :: natoms

Number of atoms.

integer, dimension(natoms), intent(OUT) :: atomi, resi

Atom and residue index.

character(*), dimension(natoms), intent(OUT) :: atomn, resn

Atom and residue name.

character(*), intent(OUT) :: chain

Chain identifier.

character(*), intent(OUT) :: resic

Code for insertions of residues

real, dimension(DIM,natoms), intent(OUT) :: coor

Atom cartesian coordinates in Å.

real, dimension(natoms), intent(OUT) :: qfact, bfact

Occupancy and temperature factor.

character(*), dimension(natoms), intent(OUT) :: element

Element symbol.

integer, dimension(natoms), intent(OUT) :: charge

Elemental charge.

integer, intent(OUT), optional :: stat

Error status code. Returns zero if no error.

character(*), intent(OUT), optional :: errmsg

Error status message. Empty if no error.

`pdb_read_coor`

Read ONLY coordinate data in PDB format.

call pdb_read_coor (unit, natoms, coor, stat, errmsg)

integer, intent(IN) :: unit

Fortran file unit.

integer, intent(IN) :: natoms

Number of atoms.

real, dimension(DIM,natoms), intent(OUT) :: coor

Atom cartesian coordinates in Å.

integer, intent(OUT), optional :: stat

Error status code. Returns zero if no error.

character(*), intent(OUT), optional :: errmsg

Error status message. Empty if no error.

`pdb_skip_data`

Read through file (skip) in PDB format but do not store any data.

call pdb_skip_data (unit, natoms, stat, errmsg)

integer, intent(IN) :: unit

Fortran file unit.

integer, intent(IN) :: natoms

Number of atoms.

integer, intent(OUT), optional :: stat

Error status code. Returns zero if no error.

character(*), intent(OUT), optional :: errmsg

Error status message. Empty if no error.

`pdb_write`

Read data in PDB format.

call pdb_write (unit, natoms, atomi, atomn, resi, resn, chain, resic, &
& altloc, qfact, bfact, element, charge, coor, box, stat, errmsg)

integer, intent(IN) :: unit

Fortran file unit.

integer, intent(IN) :: natoms

Number of atoms.

integer, dimension(natoms), intent(IN) :: atomi, resi

Atom and residue index.

character(*), dimension(natoms), intent(IN) :: atomn, resn

Atom and residue name.

character(*), intent(IN) :: chain

Chain identifier.

character(*), intent(IN) :: resic

Code for insertions of residues

real, dimension(DIM,natoms), intent(IN) :: coor

Atom cartesian coordinates in Å.

real, dimension(natoms), intent(IN) :: qfact, bfact

Occupancy and temperature factor.

character(*), dimension(natoms), intent(IN) :: element

Element symbol.

integer, dimension(natoms), intent(IN) :: charge

Elemental charge.

integer, intent(IN), optional :: stat

Error status code. Returns zero if no error.

character(*), intent(IN), optional :: errmsg

Error status message. Empty if no error.

Example

Example of reading PDB file.

program main
  use atomlib_pdbio
  use iso_fortran_env, only: INT64
  implicit none
  integer, parameter :: DIM = 3
  integer(INT64), allocatable :: offset(:)
  integer, allocatable :: atomi(:), resi(:), charge(:)
  character(6), allocatable :: atomn(:), resn(:), chain(:), resic(:), altloc(:), element(:)
  real, allocatable :: qfact(:), bfact(:), coor(:,:)
  real :: box(DIM,DIM)
  integer :: i, unit, nframes, natoms, status

    call pdb_open (arg, unit, nframes, offset, STAT=status, ERRMSG=message)
    if (status /= 0) error stop message

    call pdb_get_natoms (unit, natoms, STAT=status, ERRMSG=message)
    if (status /= 0) error stop message

    allocate (atomi(natoms), atomn(natoms), resi(natoms), resn(natoms), chain(natoms), resic(natoms), &
    & altloc(natoms), qfact(natoms), bfact(natoms), element(natoms), charge(natoms), coor(DIM,natoms))

    call pdb_read_data (unit, natoms, atomi, atomn, resi, resn, chain, resic, &
    & altloc, qfact, bfact, element, charge, coor, box, STAT=status, ERRMSG=message)
    if (status /= 0) error stop message

    call pdb_close (unit, STAT=status, ERRMSG=message)
    if (status /= 0) error stop message 

end program main