Source code for adaptivemd.io

# IO for ACEMD
# write and read for bincoor format

import numpy as np

# this is taken from HTMD code so MAKE SURE we are allowed to use this!


# htmd/htmd/molecule/writers.py

def BINCOORwrite(coords, filename):
    import struct
    natoms = np.array([coords.shape[0]])
    f = open(filename, 'wb')

    dat = coords[:, :, 0]
    dat = dat.reshape(dat.shape[0] * 3).astype(np.float64)

    fmt1 = 'i' * natoms.shape[0]
    bin1 = struct.pack(fmt1, *natoms)
    fmt2 = 'd' * dat.shape[0]
    bin2 = struct.pack(fmt2, *dat)
    f.write(bin1)
    f.write(bin2)
    f.close()


# htmd/htmd/molecule/writers.py

def BINCOORread(filename):
    import struct
    f = open(filename, 'rb')
    dat = f.read(4)
    fmt = 'i'
    natoms = struct.unpack(fmt, dat)[0]
    dat = f.read(natoms * 3 * 8)
    fmt = 'd' * (natoms * 3)
    coords = struct.unpack(fmt, dat)
    coords = np.array(coords, dtype=np.float32).reshape((natoms, 3, 1))
    f.close()
    return coords