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deprecation prep #1399

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deprecation prep #1399

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736da67
deprecation prep
jamesmkrieger Aug 1, 2021
1b1732a
more deprec fixes
jamesmkrieger Aug 1, 2021
08468b7
bug fix on tobytes deprec
jamesmkrieger Aug 5, 2021
34aa0f7
except ImportError
jamesmkrieger Oct 25, 2021
66decac
PY3K deprec
jamesmkrieger Oct 25, 2021
8f163f3
select ImportError
jamesmkrieger Oct 25, 2021
d2be9de
Merge branch 'master' of github.com:prody/ProDy into deprec
jamesmkrieger Dec 20, 2021
74256a0
merge update
jamesmkrieger Jan 31, 2023
dee7bdc
Merge branch 'main' of github.com:prody/ProDy into deprec
jamesmkrieger Sep 19, 2024
43422da
Merge branch 'main' into deprec
jamesmkrieger Jul 28, 2026
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12 changes: 10 additions & 2 deletions prody/dynamics/nmdfile.py
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Original file line number Diff line number Diff line change
Expand Up @@ -272,7 +272,11 @@ def parseNMD(filename, type=NMA):

line, coords = atomic.pop('coordinates', None)
if coords is not None:
coords = np.fromstring(coords, dtype=float, sep=' ')
try:
coords = np.fromstring(coords, dtype=float, sep=' ')
except:
coords = np.frombuffer(coords, dtype=float, sep=' ')

dof = coords.shape[0]
if dof % 3 != 0:
LOGGER.warn('Coordinate data in {0} at line {1} is corrupt '
Expand Down Expand Up @@ -325,7 +329,11 @@ def parseNMD(filename, type=NMA):
eigvals = []
count = 0
for i, (line, mode) in enumerate(modes):
mode = np.fromstring(mode, dtype=float, sep=' ')
try:
mode = np.fromstring(mode, dtype=float, sep=' ')
except:
mode = np.frombuffer(mode, dtype=float, sep=' ')

diff = len(mode) - dof
if diff < 0 or diff > 2:
LOGGER.warn('Mode data in {0} at line {1} is corrupt.'
Expand Down
31 changes: 26 additions & 5 deletions prody/sequence/msa.py
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Original file line number Diff line number Diff line change
Expand Up @@ -153,8 +153,16 @@ def __getitem__(self, index):
if isinstance(rows, list):
rows = self.getIndex(rows) or rows
elif isinstance(rows, int):
return Sequence(self._msa[rows, cols].tobytes(),
self._labels[rows])
if PY3K:
try:
return Sequence(self._msa[rows, cols].tostring().decode(),
self._labels[rows])
except:
return Sequence(self._msa[rows, cols].tobytes().decode(),
self._labels[rows])
else:
return Sequence(self._msa[rows, cols].tostring(),
self._labels[rows])
elif isinstance(rows, str):
try:
rows = self._mapping[rows]
Expand All @@ -163,8 +171,12 @@ def __getitem__(self, index):
.format(index))
else:
if isinstance(rows, int):
return Sequence(self._msa[rows, cols].tobytes(),
self._labels[rows])
try:
return Sequence(self._msa[rows, cols].tostring(),
self._labels[rows])
except:
return Sequence(self._msa[rows, cols].tobytes(),
self._labels[rows])

@SHZ66 SHZ66 Sep 30, 2021

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Same issue with these lines. Maybe use PY3K macro to check this?

@jamesmkrieger jamesmkrieger Oct 25, 2021 •
edited
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We have the following block in the Sequence object, on which we could maybe base these:

        if PY3K:
            try:
                return self._array.tostring().decode()
            except:
                return self._array.tobytes().decode()
        else:
            return self._array.tostring()

@jamesmkrieger jamesmkrieger Oct 25, 2021

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I've now tried this


if cols is None:
msa = self._msa[rows]
Expand Down Expand Up @@ -545,7 +557,16 @@ def refineMSA(msa, index=None, label=None, rowocc=None, seqid=None, colocc=None,
from prody.utilities import GAP_PENALTY, GAP_EXT_PENALTY, ALIGNMENT_METHOD

chseq = chain.getSequence()
algn = alignBioPairwise(pystr(arr[index].tobytes().upper()), pystr(chseq),

if PY3K:
try:
arr2 = arr[index].tostring().decode()
except:
arr2 = arr[index].tobytes().decode()
else:
arr2 = arr[index].tostring()

algn = alignBioPairwise(pystr(arr2.upper()), pystr(chseq),
"local",
MATCH_SCORE, MISMATCH_SCORE,
GAP_PENALTY, GAP_EXT_PENALTY,
Expand Down
8 changes: 6 additions & 2 deletions prody/sequence/msafile.py
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Original file line number Diff line number Diff line change
Expand Up @@ -435,8 +435,12 @@ def setSlice(self, slice):
raise TypeError('invalid slice: ' + repr(slice))
else:
self._slice = slice
self._slicer = lambda seq, slc=slice: fromstring(seq,
'|S1')[slc].tobytes()
try:
self._slicer = lambda seq, slc=slice: fromstring(seq,
'|S1')[slc].tostring()
except:
self._slicer = lambda seq, slc=slice: fromstring(seq,
'|S1')[slc].tobytes()
else:
self._slice = slice
self._slicer = lambda seq, slc=slice: seq[slc]
Expand Down
5 changes: 4 additions & 1 deletion prody/sequence/sequence.py
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Original file line number Diff line number Diff line change
Expand Up @@ -48,7 +48,10 @@ def _array(self):
def __str__(self):

if PY3K:
return self._array.tobytes().decode()
try:
return self._array.tostring().decode()
except:
return self._array.tobytes().decode()
else:
return self._array.tobytes()

Expand Down
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