Author: bugman
Date: Mon Oct 1 22:12:24 2012
New Revision: 17629
URL: http://svn.gna.org/viewcvs/relax?rev=17629&view=rev
Log:
Python 3 - a number of fixes for running the ScientificPython modules in
relax on Python 2 and 3.
This includes relative imports, converting raise statements to function
calls, removal of the use of
many string module functions which do not exist in Python 3, etc.
Modified:
trunk/extern/scientific_python/Geometry/TensorModule.py
trunk/extern/scientific_python/Geometry/__init__.py
trunk/extern/scientific_python/IO/ArrayIO.py
trunk/extern/scientific_python/IO/FortranFormat.py
trunk/extern/scientific_python/IO/PDB.py
trunk/extern/scientific_python/IO/TextFile.py
Modified: trunk/extern/scientific_python/Geometry/TensorModule.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/extern/scientific_python/Geometry/TensorModule.py?rev=17629&r1=17628&r2=17629&view=diff
==============================================================================
--- trunk/extern/scientific_python/Geometry/TensorModule.py (original)
+++ trunk/extern/scientific_python/Geometry/TensorModule.py Mon Oct 1
22:12:24 2012
@@ -208,7 +208,7 @@
ev, vectors = eigenvectors(self.array)
return ev, Tensor(vectors)
else:
- raise ValueError, 'Undefined operation'
+ raise ValueError('Undefined operation')
def inverse(self):
"""
Modified: trunk/extern/scientific_python/Geometry/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/extern/scientific_python/Geometry/__init__.py?rev=17629&r1=17628&r2=17629&view=diff
==============================================================================
--- trunk/extern/scientific_python/Geometry/__init__.py (original)
+++ trunk/extern/scientific_python/Geometry/__init__.py Mon Oct 1 22:12:24
2012
@@ -21,12 +21,12 @@
# Pretend that Vector and Tensor are defined directly
# in Scientific.Geometry.
-import VectorModule
+import extern.scientific_python.Geometry.VectorModule
Vector = VectorModule.Vector
isVector = VectorModule.isVector
del VectorModule
-import TensorModule
+import extern.scientific_python.Geometry.TensorModule
Tensor = TensorModule.Tensor
isTensor = TensorModule.isTensor
del TensorModule
@@ -52,7 +52,7 @@
import sys
if 'epydoc' in sys.modules:
- import VectorModule, TensorModule
+ import extern.scientific_python.Geometry.VectorModule,
extern.scientific_python.Geometry.TensorModule
Vector = VectorModule.Vector
isVector = VectorModule.isVector
vm_name = VectorModule.__name__
Modified: trunk/extern/scientific_python/IO/ArrayIO.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/extern/scientific_python/IO/ArrayIO.py?rev=17629&r1=17628&r2=17629&view=diff
==============================================================================
--- trunk/extern/scientific_python/IO/ArrayIO.py (original)
+++ trunk/extern/scientific_python/IO/ArrayIO.py Mon Oct 1 22:12:24 2012
@@ -49,7 +49,7 @@
if len(line) == 0 and len(data) > 0:
break
if line[0] != '#':
- data.append(map(eval, string.split(line)))
+ data.append(map(eval, line.split()))
a = Numeric.array(data)
if a.shape[0] == 1 or a.shape[1] == 1:
a = Numeric.ravel(a)
@@ -68,7 +68,7 @@
data = []
for line in TextFile(filename):
if line[0] != '#':
- data.append(map(string.atof, string.split(line)))
+ data.append(map(string.atof, line.split()))
a = Numeric.array(data)
if a.shape[0] == 1 or a.shape[1] == 1:
a = Numeric.ravel(a)
@@ -87,7 +87,7 @@
data = []
for line in TextFile(filename):
if line[0] != '#':
- data.append(map(string.atoi, string.split(line)))
+ data.append(map(string.atoi, line.split()))
a = Numeric.array(data)
if a.shape[0] == 1 or a.shape[1] == 1:
a = Numeric.ravel(a)
Modified: trunk/extern/scientific_python/IO/FortranFormat.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/extern/scientific_python/IO/FortranFormat.py?rev=17629&r1=17628&r2=17629&view=diff
==============================================================================
--- trunk/extern/scientific_python/IO/FortranFormat.py (original)
+++ trunk/extern/scientific_python/IO/FortranFormat.py Mon Oct 1 22:12:24
2012
@@ -150,7 +150,7 @@
@returns: C{True} if the line contains only whitespace
@rtype: C{bool}
"""
- return len(string.strip(self.text)) == 0
+ return len(self.text.strip()) == 0
def _input(self):
text = self.text
@@ -165,7 +165,7 @@
if type == 'A':
value = s
elif type == 'I':
- s = string.strip(s)
+ s = s.strip()
if len(s) == 0:
value = 0
else:
@@ -178,8 +178,8 @@
except:
value = None
elif type == 'D' or type == 'E' or type == 'F' or type == 'G':
- s = string.lower(string.strip(s))
- n = string.find(s, 'd')
+ s = s.strip().lower()
+ n = s.find('d')
if n >= 0:
s = s[:n] + 'e' + s[n+1:]
if len(s) == 0:
@@ -215,7 +215,7 @@
s = repr(value)
elif type == 'D':
s = ('%'+repr(length)+'.'+repr(fraction)+'e') % value
- n = string.find(s, 'e')
+ n = s.find('e')
s = s[:n] + 'D' + s[n+1:]
elif type == 'E':
s = ('%'+repr(length)+'.'+repr(fraction)+'e') % value
@@ -225,9 +225,9 @@
s = ('%'+repr(length)+'.'+repr(fraction)+'g') % value
else:
raise ValueError('Not yet implemented')
- s = string.upper(s)
+ s = s.upper()
self.text = self.text + ((length*' ')+s)[-length:]
- self.text = string.rstrip(self.text)
+ self.text = self.text.rstrip()
#
# The class FortranFormat represents a format specification.
@@ -252,34 +252,34 @@
@param nested: I{for internal use}
"""
fields = []
- format = string.strip(format)
+ format = format.strip()
while format and format[0] != ')':
n = 0
while format[0] in string.digits:
n = 10*n + string.atoi(format[0])
format = format[1:]
if n == 0: n = 1
- type = string.upper(format[0])
+ type = format[0].upper()
if type == "'":
- eof = string.find(format, "'", 1)
+ eof = format.find("'", 1)
text = format[1:eof]
format = format[eof+1:]
else:
- format = string.strip(format[1:])
+ format = format[1:].strip()
if type == '(':
subformat = FortranFormat(format, 1)
fields = fields + n*subformat.fields
format = subformat.rest
- eof = string.find(format, ',')
+ eof = format.find(',')
if eof >= 0:
format = format[eof+1:]
else:
- eof = string.find(format, ',')
+ eof = format.find(',')
if eof >= 0:
field = format[:eof]
format = format[eof+1:]
else:
- eof = string.find(format, ')')
+ eof = format.find(')')
if eof >= 0:
field = format[:eof]
format = format[eof+1:]
@@ -289,7 +289,7 @@
if type == "'":
field = (type, text)
else:
- dot = string.find(field, '.')
+ dot = field.find('.')
if dot > 0:
length = string.atoi(field[:dot])
fraction = string.atoi(field[dot+1:])
Modified: trunk/extern/scientific_python/IO/PDB.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/extern/scientific_python/IO/PDB.py?rev=17629&r1=17628&r2=17629&view=diff
==============================================================================
--- trunk/extern/scientific_python/IO/PDB.py (original)
+++ trunk/extern/scientific_python/IO/PDB.py Mon Oct 1 22:12:24 2012
@@ -66,9 +66,9 @@
from extern.scientific_python.IO.TextFile import TextFile
from extern.scientific_python.IO.FortranFormat import FortranFormat,
FortranLine
+from extern.scientific_python.IO.PDBExportFilters import export_filters
from extern.scientific_python.Geometry import Vector, Tensor
from extern.scientific_python import N
-from PDBExportFilters import export_filters
import copy, string
#
@@ -162,7 +162,7 @@
self.file = TextFile(file_or_filename, mode)
else:
self.file = file_or_filename
- self.output = string.lower(mode[0]) == 'w'
+ self.output = mode[0].lower() == 'w'
self.export_filter = None
if subformat is not None:
export = export_filters.get(subformat, None)
@@ -200,49 +200,49 @@
line = self.file.readline()
if not line: return ('END', '')
if line[-1] == '\n': line = line[:-1]
- line = string.strip(line)
+ line = line.strip()
if line: break
- line = string.ljust(line, 80)
- type = string.strip(line[:6])
+ line = line.ljust(80)
+ type = line[:6].strip()
if type == 'ATOM' or type == 'HETATM':
line = FortranLine(line, atom_format)
data = {'serial_number': line[1],
'name': line[2],
- 'alternate': string.strip(line[3]),
- 'residue_name': string.strip(line[4]),
- 'chain_id': string.strip(line[5]),
+ 'alternate': line[3].strip(),
+ 'residue_name': line[4].strip(),
+ 'chain_id': line[5].strip(),
'residue_number': line[6],
- 'insertion_code': string.strip(line[7]),
+ 'insertion_code': line[7].strip(),
'position': Vector(line[8:11]),
'occupancy': line[11],
'temperature_factor': line[12],
- 'segment_id': string.strip(line[13]),
- 'element': string.strip(line[14]),
- 'charge': string.strip(line[15])}
+ 'segment_id': line[13].strip(),
+ 'element': line[14].strip(),
+ 'charge': line[15].strip()}
return type, data
elif type == 'ANISOU':
line = FortranLine(line, anisou_format)
data = {'serial_number': line[1],
'name': line[2],
- 'alternate': string.strip(line[3]),
- 'residue_name': string.strip(line[4]),
- 'chain_id': string.strip(line[5]),
+ 'alternate': line[3].strip(),
+ 'residue_name': line[4].strip(),
+ 'chain_id': line[5].strip(),
'residue_number': line[6],
- 'insertion_code': string.strip(line[7]),
+ 'insertion_code': line[7].strip(),
'u': 1.e-4*Tensor([[line[8], line[11], line[12]],
[line[11], line[9], line[13]],
[line[12], line[13], line[10]]]),
- 'segment_id': string.strip(line[14]),
- 'element': string.strip(line[15]),
- 'charge': string.strip(line[16])}
+ 'segment_id': line[14].strip(),
+ 'element': line[15].strip(),
+ 'charge': line[16].strip()}
return type, data
elif type == 'TER':
line = FortranLine(line, ter_format)
data = {'serial_number': line[1],
- 'residue_name': string.strip(line[2]),
- 'chain_id': string.strip(line[3]),
+ 'residue_name': line[2].strip(),
+ 'chain_id': line[3].strip(),
'residue_number': line[4],
- 'insertion_code': string.strip(line[5])}
+ 'insertion_code': line[5].strip()}
return type, data
elif type == 'CONECT':
line = FortranLine(line, conect_format)
@@ -314,7 +314,7 @@
line = line + [data.get('serial_number', 1),
data.get('name'),
data.get('alternate', ''),
- string.rjust(data.get('residue_name', ''), 3),
+ data.get('residue_name', '').rjust(3),
data.get('chain_id', ''),
data.get('residue_number', 1),
data.get('insertion_code', ''),
@@ -322,7 +322,7 @@
data.get('occupancy', 0.),
data.get('temperature_factor', 0.),
data.get('segment_id', ''),
- string.rjust(data.get('element', ''), 2),
+ data.get('element', '').rjust(2),
data.get('charge', '')]
elif type == 'ANISOU':
format = anisou_format
@@ -332,18 +332,18 @@
line = line + [data.get('serial_number', 1),
data.get('name'),
data.get('alternate', ''),
- string.rjust(data.get('residue_name'), 3),
+ data.get('residue_name').rjust(3),
data.get('chain_id', ''),
data.get('residue_number', 1),
data.get('insertion_code', '')] \
+ u \
+ [data.get('segment_id', ''),
- string.rjust(data.get('element', ''), 2),
+ data.get('element', '').rjust(2),
data.get('charge', '')]
elif type == 'TER':
format = ter_format
line = line + [data.get('serial_number', 1),
- string.rjust(data.get('residue_name'), 3),
+ data.get('residue_name').rjust(3),
data.get('chain_id', ''),
data.get('residue_number', 1),
data.get('insertion_code', '')]
@@ -391,7 +391,7 @@
@type text: C{str}
"""
while text:
- eol = string.find(text, '\n')
+ eol = text.find('\n')
if eol == -1:
eol = len(text)
self.file.write('REMARK %s \n' % text[:eol])
@@ -419,7 +419,7 @@
type = 'HETATM'
else:
type = 'ATOM'
- name = string.upper(name)
+ name = name.upper()
if element != '' and len(element) == 1 and name and name[0] ==
element:
name = ' ' + name
self.data['name'] = name
@@ -445,7 +445,7 @@
information in order to use different atom or
residue names in terminal residues.
"""
- name = string.upper(name)
+ name = name.upper()
if self.export_filter is not None:
name, number = self.export_filter.processResidue(name, number,
terminus)
@@ -544,7 +544,7 @@
self.properties['element'] = name[0]
else:
self.properties['element'] = name[0:2]
- self.name = string.strip(name)
+ self.name = name.strip()
self.parent = None
def __getitem__(self, item):
@@ -808,7 +808,7 @@
def __init__(self, name, atoms = None, number = None):
self.pdbname = name
- name = string.strip(name)
+ name = name.strip()
if name[0] != 'D' and name[0] != 'R':
name = 'D' + name
Residue.__init__(self, name, atoms, number)
Modified: trunk/extern/scientific_python/IO/TextFile.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/extern/scientific_python/IO/TextFile.py?rev=17629&r1=17628&r2=17629&view=diff
==============================================================================
--- trunk/extern/scientific_python/IO/TextFile.py (original)
+++ trunk/extern/scientific_python/IO/TextFile.py Mon Oct 1 22:12:24 2012
@@ -14,7 +14,7 @@
gzip = None
try:
_version = map(string.atoi,
- string.split(string.split(sys.version)[0], '.'))
+ sys.version.split()[0], '.').split()
if _version >= [1, 5, 2]:
try:
import gzip
@@ -48,7 +48,7 @@
@param mode: file access mode: 'r' (read), 'w' (write), or 'a'
(append)
@type mode: C{str}
"""
- if string.find(filename, ':/') > 1: # URL
+ if filename.find(':/') > 1: # URL
if mode != 'r':
raise IOError("can't write to a URL")
import urllib
r17629 - in /trunk/extern/scientific_python: Geometry/ IO/