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Commit a3d9620b authored by Studer Gabriel's avatar Studer Gabriel
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Manual Python 3 port of doc example code

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modules/base/doc/generic.rst
+ 5
− 5
View file @ a3d9620b
......@@ -54,7 +54,7 @@ already exists, it will be overwritten. To check if it exists, use:
.. code-block:: python
exists=atom.HasProp("myfloatprop")
print exists
print(exists)
To access the value of a generic property, we first check if the property exists
and then access it, using the method suitable for the data type of the property.
......@@ -65,7 +65,7 @@ level:
for atom in entity.GetAtomList():
if atom.HasProp("myfloatprop"):
print atom.GetFloatProp("myfloatprop")
print(atom.GetFloatProp("myfloatprop"))
When trying to access a property that has not been set, or one that has been
set, but at a different level, an error is thrown. The same is true when trying
......@@ -75,13 +75,13 @@ to access a property of a different data type, e.g.:
# all of the following lines will throw errors
# error because the property does not exist
print atom.GetFloatProp("unknownprop")
print(atom.GetFloatProp("unknownprop"))
# error because the property was set at another level
print entity.GetFloatProp("myfloatprop")
print(entity.GetFloatProp("myfloatprop"))
# error because the data type of the property is different
print atom.GetStringProp("myfloatprop")
print(atom.GetStringProp("myfloatprop"))
Use of Generic Properties in Queries
......
modules/base/doc/logging.rst
+ 2
− 2
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......@@ -106,7 +106,7 @@ You can change the verbosity level with the following two methods:
ost.LogLevel.Info
# Outputs: ost._ost_base.LogLevel.Info
print ost.LogLevel.Info
print(ost.LogLevel.Info)
# Outputs: Info
int(ost.LogLevel.Info)
......@@ -267,7 +267,7 @@ terminal (or the python shell in DNG). The logger also prints the current time.
levels=['ERROR', 'WARNING', 'SCRIPT', 'INFO',
'VERBOSE', 'DEBUG', 'TRACE']
level=levels[severity]
print '%s[%s]: %s' % (level, str(datetime.datetime.now()), message),
print('%s[%s]: %s' % (level, str(datetime.datetime.now()), message))
py_logger=PyLogger()
ost.PushLogSink(py_logger)
......
modules/bindings/doc/dssp.rst
+ 1
− 1
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......@@ -39,7 +39,7 @@ using the mmCIF interface.
for chain in ent.chains:
if chain.is_polypeptide:
for res in chain.residues:
print res.GetFloatProp('relative_solvent_accessibility')
print(res.GetFloatProp('relative_solvent_accessibility'))
DSSP bindings Usage
......
modules/bindings/doc/hhblits.rst
+ 3
− 3
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......@@ -54,7 +54,7 @@ First query by sequence:
with open(hit_file) as hit_fh:
header, hits = hhblits.ParseHHblitsOutput(hit_fh)
for hit in hits:
print hit.aln
print(hit.aln)
# cleanup
hh.Cleanup()
......@@ -82,7 +82,7 @@ Very similar going by file:
with open(hit_file) as hit_fh:
header, hits = hhblits.ParseHHblitsOutput(hit_fh)
for hit in hits:
print hit.aln
print(hit.aln)
# cleanup
hh.Cleanup()
......@@ -106,7 +106,7 @@ so one may want to extract them:
# note that ParseA3M is not a class method but a module function
output = hhblits.ParseA3M(open(a3m_file))
print output['msa']
print(output['msa'])
# cleanup
hh.Cleanup()
......
modules/bindings/doc/tmtools.rst
+ 5
− 5
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......@@ -61,9 +61,9 @@ structures and print the RMSD as well as the GDT_TS and GDT_HA similarity measur
pdb1=io.LoadPDB('1ake.pdb', restrict_chains='A')
pdb2=io.LoadPDB('4ake.pdb', restrict_chains='A')
result=tmtools.TMScore(pdb1, pdb2)
print result.rmsd_below_five # 1.9
print result.gdt_ha # 0.41
print result.gdt_ts # 0.56
print(result.rmsd_below_five) # 1.9
print(result.gdt_ha) # 0.41
print(result.gdt_ts) # 0.56
Usage of TMalign
--------------------------------------------------------------------------------
......@@ -96,8 +96,8 @@ generated in order to call the executable.
pdb2=io.LoadPDB('4ake.pdb').Select("peptide=true")
result = bindings.WrappedTMAlign(pdb1.chains[0], pdb2.chains[0],
fast=True)
print result.tm_score
print result.alignment.ToString(80)
print(result.tm_score)
print(result.alignment.ToString(80))
.. class:: TMAlignResult(rmsd, tm_score, aligned_length, transform, alignment)
......
modules/conop/doc/compoundlib.rst
+ 1
− 1
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......@@ -194,7 +194,7 @@ In this example we will translate the three-letter-codes given in the SEQRES rec
compound=compound_lib.FindCompound(tlc)
if compound:
sequence+=compound.one_letter_code
print sequence # prints 'AGMVF'
print(sequence) # prints 'AGMVF'
.. _mmcif-convert:
......
modules/doc/external.rst
+ 8
− 8
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......@@ -26,7 +26,7 @@ As an example, we would like to obtain the full path of the msms executable (a p
from ost import settings
exe_path = settings.Locate('msms', search_paths=['/opt/app','/home/app'],
env_name='MSMS', search_system_paths=True)
print exe_path
print(exe_path)
The :func:`~ost.settings.Locate` command looks for the program with the name
`msms`. If env_name is set, it first looks if an environment variable with the
......@@ -52,12 +52,12 @@ An example how to generate a temporary directory, open a file in this directory
# generate a temporary directory
tmp_dir_name = tempfile.mkdtemp()
print 'temporary directory:',tmp_dir_name
print('temporary directory:',tmp_dir_name)
# generate and open a file in the temp directory
tmp_file_name = os.path.join(tmp_dir_name,"entity")
tmp_file_handle = open(tmp_file_name, 'w')
print 'temporary file:',tmp_file_handle
print('temporary file:',tmp_file_handle)
# write position and radius of all atoms to file
for a in entity.GetAtomList():
......@@ -82,7 +82,7 @@ To run the external program msms from the above example, with the temporary file
# set the command to execute
command = "%s -if %s -of %s" % (exe_path,
tmp_file_name, tmp_file_name)
print 'command:',command
print('command:',command)
# run the executable with the command
proc = subprocess.Popen(command, shell=True, stdout=subprocess.PIPE)
......@@ -90,11 +90,11 @@ To run the external program msms from the above example, with the temporary file
# check for successful completion of msms
if proc.returncode != 0:
print "WARNING: msms error\n", stdout_value
print("WARNING: msms error\n", stdout_value)
raise subprocess.CalledProcessError(proc.returncode, command)
# print everything written to the command line (stdout)
print stdout_value
print(stdout_value)
Read Generated Output
--------------------------------------------------------------------------------
......@@ -106,8 +106,8 @@ Here we first print the command line output and then load the generated msms sur
.. code-block:: python
# print everything written to the command line (stdout)
print stdout_value
print(stdout_value)
# read msms surface from file
surface = io.LoadSurface(tmp_file_name, "msms")
print 'number of vertices:',len(surface.GetVertexIDList())
print('number of vertices:',len(surface.GetVertexIDList()))
modules/doc/intro-01.rst
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− 9
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......@@ -47,9 +47,9 @@ The loaded structure is an instance of :class:`~ost.mol.EntityHandle` which offe
.. code-block:: python
print len(fragment.chains), fragment.chains
print len(fragment.residues), fragment.residues
print len(fragment.atoms), fragment.atoms
print(len(fragment.chains), fragment.chains)
print(len(fragment.residues), fragment.residues)
print(len(fragment.atoms), fragment.atoms)
As you can see, our fragment consists of one peptide chain of 12 amino acids and
has 81 atoms in total. Now let's examine our fragment in more detail. Enter the
......@@ -58,9 +58,9 @@ command
.. code-block:: python
for residue in fragment.residues:
print residue, 'has', len(residue.atoms), 'atom(s).'
print(residue, 'has', len(residue.atoms), 'atom(s).')
for atom in residue.atoms:
print ' ', atom.name, atom.pos
print(' ', atom.name, atom.pos)
This will group the atoms by residue. And, for completeness, we will first group them by chain, then by residues.
......@@ -68,11 +68,11 @@ This will group the atoms by residue. And, for completeness, we will first group
.. code-block:: python
for chain in fragment.chains:
print 'chain', chain.name, 'has', len(chain.residues), 'residue(s)'
print('chain', chain.name, 'has', len(chain.residues), 'residue(s)')
for residue in chain.residues:
print ' ', residue, 'has', len(residue.atoms), 'atom(s).'
print(' ', residue, 'has', len(residue.atoms), 'atom(s).')
for atom in residue.atoms:
print ' ', atom.name, atom.pos
print(' ', atom.name, atom.pos)
A protein fragment would not be complete without bonds. Let's see
what bonds we have in there:
......@@ -80,7 +80,7 @@ what bonds we have in there:
.. code-block:: python
for bond in fragment.bonds:
print bond
print(bond)
Let There Be Shiny Graphics
--------------------------------------------------------------------------------
......
modules/doc/intro-02.rst
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......@@ -30,7 +30,7 @@ Now let's inspect what we just loaded:
.. code-block:: python
print map.GetPixelSampling(), map.GetSize()
print(map.GetPixelSampling(), map.GetSize())
We can see that the sampling is set to 1.0 Angstrom in all three dimensions. The loaded map is an instance of :class:`~ost.img.ImageHandle`, a class to represent images in one, two and three dimensions.
......
modules/doc/table.rst
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− 6
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......@@ -42,14 +42,14 @@ Iterating over table items:
# iterate over all rows
for row in tab.rows:
# print complete row
print row
print(row)
# print value for column 'foo'
print row[idx]
print(row[idx])
# iterate over all rows of selected columns
for foo, bar in tab.Zip('foo','bar'):
print foo, bar
print(foo, bar)
Doing element wise mathematical operations on entire colums:
......@@ -63,7 +63,7 @@ Doing element wise mathematical operations on entire colums:
# addition of column foo and column bar
tab.AddCol('qux', 'f', tab['foo']+tab['bar'])
print tab
print(tab)
Select part of the table based on a query:
......@@ -76,11 +76,11 @@ Select part of the table based on a query:
# select all rows where foo>=2 and bar<10
subtab = tab.Select('foo>=2 and bar<10')
print subtab
print(subtab)
# select all rows where foo>3 or bar=1
subtab = tab.Select('foo>3 or bar=1')
print subtab
print(subtab)
Functions You Might be Interested In
......
modules/geom/doc/mat.rst
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− 3
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......@@ -11,8 +11,8 @@ the following code examples:
.. code-block:: python
m=geom.Mat2(1, 2, 3, 4)
print m # will print {{1,2},{3,4}}
print m[(0,0)], m[(0,1)], m[(1,0)], m[(1,1)] # will print 1, 2, 3, 4
print(m) # will print {{1,2},{3,4}}
print(m[(0,0)], m[(0,1)], m[(1,0)], m[(1,1)]) # will print 1, 2, 3, 4
Matrices support arithmetic via overloaded operators. The following operations are
supported:
......@@ -164,4 +164,4 @@ Functions Operating on Matrices
(0, 0, 0).
:param vec: A vector of arbitrary length
:type vec: :class:`Vec3`
\ No newline at end of file
:type vec: :class:`Vec3`
modules/geom/doc/vec.rst
+ 7
− 7
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......@@ -16,9 +16,9 @@ This is shown in the following example:
vec_a=geom.Vec2(1, 0)
vec_b=geom.Vec2(0, 1)
print vec_a, vec_b
print vec_a+vec_b
print vec_a*3-vec_b
print(vec_a, vec_b)
print(vec_a+vec_b)
print(vec_a*3-vec_b)
The standard vector operations are implemented as :ref:`free standing functions
<vector-functions>`:
......@@ -29,12 +29,12 @@ The standard vector operations are implemented as :ref:`free standing functions
vec_a=geom.Vec3(1, 0, 0)
vec_b=geom.Vec3(0, 1, 0)
print geom.Dot(vec_a, vec_b)
print geom.Cross(vec_a, vec_b)
print(geom.Dot(vec_a, vec_b))
print(geom.Cross(vec_a, vec_b))
print geom.Normalize(geom.Vec3(1, 1, 0))
print(geom.Normalize(geom.Vec3(1, 1, 0)))
print geom.Length(geom.Vec3(1, 1, 1))
print(geom.Length(geom.Vec3(1, 1, 1)))
Vector Classes
......
modules/gui/doc/python_cpp.rst
+ 1
− 1
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......@@ -12,7 +12,7 @@ which wraps the Object into a Python SIP Object.
seq_viewer = gui.SequenceViewer() # Create SequenceViewer Object
qobj = seq_viewer.qobject #Get Python SIP Object
print qobj.size() # Call function on QWidget
print(qobj.size()) # Call function on QWidget
The other way around, each boost::python Qt Object accepts Python objects as
input for Qt Objects. It handles the cast to a C++ Qt Object internally.
......
modules/img/base/doc/point-size-extent.rst
+ 2
− 2
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......@@ -39,7 +39,7 @@ Point
..code-block:: python
p=img.Point(1,2,3)
print p
print(p)
p[1]=5
.. method:: ToVec3()
......@@ -140,4 +140,4 @@ Extent
# visits all the pixels in the extent and
# prints out their values
for pixel in ei:
print i.GetReal(pixel)
\ No newline at end of file
print(i.GetReal(pixel))
modules/io/doc/io.rst
+ 0
− 22
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......@@ -478,28 +478,6 @@ Saving Density Maps
io.SaveImage(image, 'new_map.map', CCP4())
.. testsetup:: io
from ost import io
.. testcode:: io
:hide:
from ost import io,seq
ent = io.LoadPDB('./examples/entity/fragment.pdb')
print ent.atom_count
myseq = seq.SequenceFromChain('t',ent.chains[0])
print myseq.GetLength()
.. testoutput:: io
:hide:
81
12
Stereochemical Parameters
--------------------------------------------------------------------------------
......
modules/mol/alg/doc/lddt.rst
+ 1
− 1
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......@@ -240,7 +240,7 @@ One can replicate the binary using simple python script:
#
# Check consistency
is_cons = ResidueNamesMatch(model_view, references[0], True)
print "Consistency check: ", "OK" if is_cons else "ERROR"
print("Consistency check: ", "OK" if is_cons else "ERROR")
#
# Calculate lDDT
LocalDistDiffTest(model_view,
......
modules/mol/alg/doc/molalg.rst
+ 1
− 1
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......@@ -576,7 +576,7 @@ Local Distance Test scores (lDDT, DRMSD)
#
# Calculate lDDT
scorer = lDDTScorer(references=references, model=model_view, settings=settings)
print "Global score:", scorer.global_score
print("Global score:", scorer.global_score)
scorer.PrintPerResidueStats()
:param references: Sets :attr:`references`
......
modules/mol/base/doc/entity.rst
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− 14
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......@@ -58,7 +58,7 @@ The Handle Classes
.. code-block:: python
for res in ent.residues:
print res.name, res.atom_count
print(res.name, res.atom_count)
Also available as :meth:`GetResidueList`. To access a single residue, use
:meth:`FindResidue`.
......@@ -380,7 +380,7 @@ The Handle Classes
chain=ent.FindChain("A")
for res in chain.residues:
print res.name, res.atom_count
print(res.name, res.atom_count)
Also available as :meth:`GetResidueList`. To access a single residue, use
:meth:`FindResidue`.
......@@ -394,12 +394,12 @@ The Handle Classes
.. code-block:: python
chain=ent.FindChain("A")
print chain.residues # [A.GLY1, A.GLY2, A.GLY4A, A.GLY4B]
print chain.in_sequence # prints true
print(chain.residues) # [A.GLY1, A.GLY2, A.GLY4A, A.GLY4B]
print(chain.in_sequence) # prints true
chain=ent.FindChain("B")
print chain.residues # [B.GLY1, B.GLY4, B.GLY3]
print chain.in_sequence # prints false
print(chain.residues) # [B.GLY1, B.GLY4, B.GLY3]
print(chain.in_sequence) # prints false
.. attribute:: residue_count
......@@ -537,7 +537,7 @@ The Handle Classes
.. code-block:: python
print ''.join([r.one_letter_code for r in chain.residues])
print(''.join([r.one_letter_code for r in chain.residues]))
:type: str
......@@ -1063,7 +1063,7 @@ The View Classes
.. code-block:: python
for res in ent.residues:
print res.name, res.atom_count
print(res.name, res.atom_count)
Also available as :meth:`GetResidueList`. To access a single residue, use
:meth:`FindResidue`.
......@@ -1410,7 +1410,7 @@ The View Classes
chain=ent.FindChain("A")
for res in chain.residues:
print res.name, res.atom_count
print(res.name, res.atom_count)
Also available as :meth:`GetResidueList`. To access a single residue, use
:meth:`FindResidue`.
......@@ -1424,12 +1424,12 @@ The View Classes
.. code-block:: python
chain=ent.FindChain("A")
print chain.residues # [A.GLY1, A.GLY2, A.GLY4A, A.GLY4B]
print chain.in_sequence # prints true
print(chain.residues) # [A.GLY1, A.GLY2, A.GLY4A, A.GLY4B]
print(chain.in_sequence) # prints true
chain=ent.FindChain("B")
print chain.residues # [B.GLY1, B.GLY4, B.GLY3]
print chain.in_sequence # prints false
print(chain.residues) # [B.GLY1, B.GLY4, B.GLY3]
print(chain.in_sequence) # prints false
.. attribute:: atoms
......@@ -1653,7 +1653,7 @@ The View Classes
.. code-block:: python
print ''.join([r.one_letter_code for r in chain.residues])
print(''.join([r.one_letter_code for r in chain.residues]))
:type: str
......
modules/seq/alg/doc/seqalg.rst
+ 8
− 8
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......@@ -60,14 +60,14 @@ Algorithms for Alignments
aln_a = seq.CreateAlignment()
aln_a.AddSequence(seq_a1)
aln_a.AddSequence(seq_a2)
print aln_a
print(aln_a)
# >>> A1 acdefghikl-mn
# >>> A2 atd-fghikllmn
aln_b = seq.CreateAlignment()
aln_b.AddSequence(seq_b1)
aln_b.AddSequence(seq_b2)
print aln_b
print(aln_b)
# >>> B1 acdefg-hiklmn
# >>> B2 acd---qhirlmn
......@@ -76,7 +76,7 @@ Algorithms for Alignments
aln_list.append(aln_b)
merged_aln = ost.seq.alg.MergePairwiseAlignments(aln_list, ref_seq)
print merged_aln
print(merged_aln)
# >>> ref acdefg-hikl-mn
# >>> A2 atd-fg-hikllmn
# >>> B2 acd---qhirl-mn
......@@ -121,7 +121,7 @@ Algorithms for Alignments
seq_a = seq.CreateSequence('A', 'acdefghiklmn')
seq_b = seq.CreateSequence('B', 'acdhiklmn')
alns = seq.alg.LocalAlign(seq_a, seq_b, seq.alg.BLOSUM62)
print alns[0].ToString(80)
print(alns[0].ToString(80))
# >>> A acdefghiklmn
# >>> B acd---hiklmn
......@@ -150,7 +150,7 @@ Algorithms for Alignments
seq_a = seq.CreateSequence('A', 'acdefghiklmn')
seq_b = seq.CreateSequence('B', 'acdhiklmn')
alns = seq.alg.GlobalAlign(seq_a, seq_b, seq.alg.BLOSUM62)
print alns[0].ToString(80)
print(alns[0].ToString(80))
# >>> A acdefghiklmn
# >>> B acd---hiklmn
......@@ -193,11 +193,11 @@ Algorithms for Alignments
seq_a = seq.CreateSequence('A', 'abcdefghijklmnok')
seq_b = seq.CreateSequence('B', 'cdehijk')
alns = seq.alg.GlobalAlign(seq_a, seq_b, seq.alg.BLOSUM62)
print alns[0].ToString(80)
print(alns[0].ToString(80))
# >>> A abcdefghijklmnok
# >>> B --cde--hi-----jk
alns = seq.alg.SemiGlobalAlign(seq_a, seq_b, seq.alg.BLOSUM62)
print alns[0].ToString(80)
print(alns[0].ToString(80))
# >>> A abcdefghijklmnok
# >>> B --cde--hijk-----
......@@ -370,7 +370,7 @@ differences between the structures.
dist_to_mean = seq.alg.CreateDist2Mean(d_map)
# report min. and max. variances
print "MIN-MAX:", var_map.Min(), "-", var_map.Max()
print("MIN-MAX:", var_map.Min(), "-", var_map.Max())
# get data and json-strings for further processing
var_map_data = var_map.GetData()
var_map_json = var_map.GetJsonString()
......
modules/seq/base/doc/seq.rst
+ 10
− 10
View file @ a3d9620b
......@@ -56,7 +56,7 @@ input methods, sequences can also be loaded from a string:
seq_string = '''>sequence
abcdefghiklmnop'''
s = io.SequenceFromString(seq_string, 'fasta')
print s.name, s # will print "sequence abcdefghiklmnop"
print(s.name, s) # will print "sequence abcdefghiklmnop"
Note that, in that case specifying the format is mandatory.
......@@ -92,8 +92,8 @@ The SequenceHandle
.. code-block:: python
s=seq.CreateSequence("A", "abc---def")
print s.GetPos(1) # prints 1
print s.GetPos(3) # prints 6
print(s.GetPos(1)) # prints 1
print(s.GetPos(3)) # prints 6
The reverse mapping, that is from position in the sequence to residue index
can be achieved with :meth:`GetResidueIndex`.
......@@ -108,12 +108,12 @@ The SequenceHandle
.. code-block:: python
s=seq.CreateSequence("A", "abc--def")
print s.GetResidueIndex(1) # prints 1
print s.GetResidueIndex(6) # prints 4
print(s.GetResidueIndex(1)) # prints 1
print(s.GetResidueIndex(6)) # prints 4
# the following line raises an exception of type
# Error with the message "requested position contains
# a gap"
print s.GetResidueIndex(3)
print(s.GetResidueIndex(3))
.. method:: GetResidue(pos)
......@@ -319,11 +319,11 @@ an alignment:
aln=io.LoadAlignment('aln.fasta')
# iterate over the columns
for col in aln:
print col
print(col)
# iterate over the sequences
for s in aln.sequences:
print s
print(s)
.. function:: CreateAlignment()
......@@ -376,7 +376,7 @@ an alignment:
aln.AddSequence(seq.CreateSequence("A", "abcdefghik"))
aln.AddSequence(seq.CreateSequence("B", "1234567890"))
# The following command will print the output given below
print aln.ToString(7)
print(aln.ToString(7))
# A abcde
# B 12345
#
......@@ -431,7 +431,7 @@ an alignment:
aln.AddSequence(seq.CreateSequence("B", "1234567890"))
aln.Cut(4, 7)
print aln.ToString(80)
print(aln.ToString(80))
# will print
# A abcdhik
# B 1234890
......
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