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# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under the Lesser GNU Public Licence, v2.1 or any higher version
#
# Please cite your use of MDAnalysis in published work:
#
# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler,
# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein.
# MDAnalysis: A Python package for the rapid analysis of molecular dynamics
# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th
# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy.
# doi: 10.25080/majora-629e541a-00e
#
# N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein.
# MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations.
# J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
#
from libc.stdlib cimport free
from libc.stdint cimport uintptr_t
from libc.stdio cimport SEEK_SET, SEEK_CUR, SEEK_END
import cython
cimport numpy as cnp
cnp.import_array()
# Tell cython about the off_t type. It doesn't need to match exactly what is
# defined since we don't expose it to python but the cython compiler needs to
# know about it.
cdef extern from 'sys/types.h':
ctypedef int off_t
ctypedef int fio_fd
ctypedef off_t fio_size_t
cdef extern from 'include/fastio.h':
int fio_open(const char * filename, int mode, fio_fd * fd)
int fio_fclose(fio_fd fd)
fio_size_t fio_ftell(fio_fd fd)
fio_size_t fio_fseek(fio_fd fd, fio_size_t offset, int whence)
cdef extern from 'include/readdcd.h':
int read_dcdheader(fio_fd fd, int * natoms, int * nsets, int * istart,
int * nsavc, double * delta, int * nfixed, int ** freeind,
float ** fixedcoords, int * reverse_endian, int * charmm,
char ** remarks, int * len_remarks)
void close_dcd_read(int * freeind, float * fixedcoords)
int read_dcdstep(fio_fd fd, int natoms, float * X, float * Y, float * Z,
double * unitcell, int num_fixed,
int first, int * indexes, float * fixedcoords,
int reverse_endian, int charmm)
int read_dcdsubset(fio_fd fd, int natoms, int lowerb, int upperb,
float * X, float * Y, float * Z,
double * unitcell, int num_fixed,
int first, int * indexes, float * fixedcoords,
int reverse_endian, int charmm)
int write_dcdheader(fio_fd fd, const char * remarks, int natoms,
int istart, int nsavc, double delta, int with_unitcell,
int charmm)
int write_dcdstep(fio_fd fd, int curframe, int curstep,
int natoms, const float * x, const float * y, const float * z,
const double * unitcell, int charmm)
cdef class DCDFile:
"""DCDFile(fname, mode='r')
File like wrapper for DCD files
This class can be similar to the normal file objects in python. The read()
function will return a frame and all information in it instead of a single
line. Additionally the context-manager protocol is supported as well.
"""
# DCD file pointer
cdef fio_fd fp
# File name
cdef readonly fname
# Starting timestep of dcd file
cdef int istart
# Timesteps between dcd saves
cdef int nsavc
# Trajectory timestep
cdef double delta
# Number of atoms
cdef int natoms
# Number of fixed atoms
cdef int nfixed
# Free indices
cdef int * freeind
# Fixed coordinates
cdef float * fixedcoords
# Are we reverse endian?
cdef int reverse_endian
# Is the DCD file CHARMM style
cdef int charmm
# Is the file periodic
cdef readonly int is_periodic
# String data in the file
cdef remarks
# File mode
cdef str mode
# Number of dimensions in
cdef readonly int ndims
# The number of frames
cdef readonly int n_frames
# Flag to indicate if header has been read
cdef bint b_read_header
# The current DCD frame
cdef int current_frame
# size of the first DCD frame
cdef readonly fio_size_t _firstframesize
# Size of a DCD frame
cdef readonly fio_size_t _framesize
# Size of the DCD header
cdef readonly fio_size_t _header_size
# Is the file open?
cdef int is_open
# Have we reached the end of the file
cdef int reached_eof
# Have we written the header?
cdef int wrote_header
# Are buffers set up?
cdef int _buffers_setup
# buffer for reading coordinates
cdef cnp.ndarray _coordinate_buffer
# buffer for reading unitcell
cdef cnp.ndarray _unitcell_buffer
# fortran contiguious memoryviews of the buffers to pass to the C code
cdef float[::1] xview
cdef float[::1] yview
cdef float[::1] zview
cdef double[::1] unitcellview
cdef void _setup_buffers(self)
cdef void _read_header(self)
# Estimate the number of frames
cdef int _estimate_n_frames(self)
# Helper to read current DCD frame
cdef int c_readframes_helper(self, float[::1] x,
float[::1] y, float[::1] z,
double[::1] unitcell, int first_frame)
# Helper in readframes to copy given a specific memory layout
cdef void copy_in_order(float[:, :] source, float[:, :, :] target, int order, int index)
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