AttributeError: Segment has no attribute name

[fabricecarles]

Hi,
I am interested by your tools, but unfortunately when a want to use it against the structure 1atp (rename here test1atp.pdb) I get the following error:

kinconform test1atp.pdb 
Traceback (most recent call last):
  File "/bin/kinconform", line 169, in <module>
    results = do_one(args)
  File "/bin/kinconform", line 133, in do_one
    temp,posn = get_sequence(x)
  File "/bin/kinconform", line 55, in get_sequence
    chains = [x.name for x in prot.segments]
  File "/usr/lib64/python2.7/site-packages/MDAnalysis/core/groups.py", line 2709, in __getattr__
    "".format(cls=self.__class__.__name__, attr=attr))
AttributeError: Segment has no attribute name

Any idea ? could you provide the exact version of each dependencies ? I suspect an issue with version of MDAnalysis.
For your intention I have install the last MDAnalysis version using pip

 pip install --upgrade MDAnalysis
Collecting MDAnalysis
  Downloading MDAnalysis-0.16.2.tar.gz (2.6MB)
    100% |████████████████████████████████| 2.6MB 285kB/s 

Sincerely

[dmcskim]

Hi! I'm glad you're playing with my program. It does look like MDAnalysis has changed some commands. Namely, the 'name' attribute is now 'resname', and it no longer has a 'sequence' method to extract a fasta formatted sequence. I've made the necessary changes and pushed them to the github respository. Note, this program requires MapGaps (not widely used) for aligning kinases to the supplied profiles. Thanks, Daniel

…

On Tue, Jul 25, 2017 at 11:20 AM, fabricecarles ***@***.***> wrote: Hi, I am interested by your tools, but unfortunately when a want to use it against the structure 1atp (rename here test1atp.pdb) I get the following error: kinconform test1atp.pdb Traceback (most recent call last): File "/bin/kinconform", line 169, in <module> results = do_one(args) File "/bin/kinconform", line 133, in do_one temp,posn = get_sequence(x) File "/bin/kinconform", line 55, in get_sequence chains = [x.name for x in prot.segments] File "/usr/lib64/python2.7/site-packages/MDAnalysis/core/groups.py", line 2709, in __getattr__ "".format(cls=self.__class__.__name__, attr=attr)) AttributeError: Segment has no attribute name Any idea ? could you provide the exact version of each dependencies ? I suspect an issue with version of MDAnalysis. For your intention I have install the last MDAnalysis version using pip pip install --upgrade MDAnalysis Collecting MDAnalysis Downloading MDAnalysis-0.16.2.tar.gz (2.6MB) 100% |████████████████████████████████| 2.6MB 285kB/s Sincerely — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#2>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AB1HovephKsw8Sgydnw-0E9CW_1ICJFiks5sRgepgaJpZM4Oith0> .

[fabricecarles]

Hi Daniel,
Thank a lot for this quick patch.
Now I have a mistake with an other fonction...
I have add in my bashrc the mapgaps1.0.1 bin executable after extraction of the tar.gz
export PATH=$PATH:/home/carles/Documents/sources/mapgaps1_0_1/bin
Then I run a test from mapgaps1_0_1/example/run_example shell script and everything seem to be ok.
Unfortunately when I try to run kinconform from my /home I get the following error.

kinconform struct1atp.pdb 
struct1atp.pdb
Traceback (most recent call last):
  File "/bin/kinconform", line 179, in <module>
    results = do_one(args)
  File "/bin/kinconform", line 150, in do_one
    mapping = align_and_map_fasta('pdbs.fasta', positions, basedir)
  File "/bin/kinconform", line 83, in align_and_map_fasta
    mapping = make_mapfile(fasta+'_aln.cma',positions)
  File "/bin/kinconform", line 25, in make_mapfile
    block = cma.read(aligned_seq)
  File "build/bdist.linux-x86_64/egg/biocma/sugar.py", line 12, in read
  File "build/bdist.linux-x86_64/egg/biocma/cma.py", line 16, in parse
  File "/usr/lib64/python2.7/contextlib.py", line 17, in __enter__
    return self.gen.next()
  File "build/bdist.linux-x86_64/egg/biocma/sugar.py", line 34, in maybe_open
IOError: [Errno 2] No such file or directory: 'pdbs.fasta_aln.cma'

Did I miss something on the configuration of my environnement ?
where is supposed to be the pdbs.fasta_aln.cma file ?

Fabrice

[dmcskim]

Hey Fabrice, Hm.. the default output file from run_gaps should be <input file name>_aln.cma. So kinconform is taking your pdbs, extracting the sequences and placing them in a local file named pdbs.fasta. These are aligned with run_gaps, which should produce a file called pdbs.fasta_aln.cma. Are the files pdbs.fasta and pdbs.fasta_aln.cma being created? Note, you may need to specify the base directory of kinconform (with the --base command line argument) if you are not running kinconform in that directory. In the test Makefile, you can see that the basedir is specified as the parent directory. Thanks,

…

On Wed, Jul 26, 2017 at 10:02 AM, fabricecarles ***@***.***> wrote: Hi Daniel, Thank a lot for this quick patch. Now I have a mistake with an other fonction... I have add in my bashrc the mapgaps1.0.1 bin executable after extraction of the tar.gz export PATH=$PATH:/home/carles/Documents/sources/mapgaps1_0_1/bin Then I run a test from mapgaps1_0_1/example/run_example shell script and everything seem to be ok. Unfortunately when I try to run kinconform from my /home I get the following error. kinconform struct1atp.pdb struct1atp.pdb Traceback (most recent call last): File "/bin/kinconform", line 179, in <module> results = do_one(args) File "/bin/kinconform", line 150, in do_one mapping = align_and_map_fasta('pdbs.fasta', positions, basedir) File "/bin/kinconform", line 83, in align_and_map_fasta mapping = make_mapfile(fasta+'_aln.cma',positions) File "/bin/kinconform", line 25, in make_mapfile block = cma.read(aligned_seq) File "build/bdist.linux-x86_64/egg/biocma/sugar.py", line 12, in read File "build/bdist.linux-x86_64/egg/biocma/cma.py", line 16, in parse File "/usr/lib64/python2.7/contextlib.py", line 17, in __enter__ return self.gen.next() File "build/bdist.linux-x86_64/egg/biocma/sugar.py", line 34, in maybe_open IOError: [Errno 2] No such file or directory: 'pdbs.fasta_aln.cma' Did I miss something on the configuration of my environnement ? where is supposed to be the pdbs.fasta_aln.cma file ? Fabrice — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#2 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AB1HoqW6JiVcwzGzsDYn_DUw41I0R3Ysks5sR0cRgaJpZM4Oith0> .

[fabricecarles]

Thank again for your quick answer,
I runed again your test with makefile. I got the pdbs.fasta file but not pdbs.fasta_aln.cma
I think there is a problem with fasta format and carriage return since the ">Name of sequence" has to be separate from the sequence by '\n' as well as each new sequence. Moreover file should finish with "\n" again.

[zencore]

Hi @fabricecarles

I've made some fixes in the kinconform script might also fix the errors you were facing. I've sent a pull request to @dmcskim, or you can check out my fork of kinconform.

[dmcskim]

Thanks zencore! Updates were merged.

[pschmidtke]

Hi I also tried a recent install. Tried with latest MDanalysis and also run in this segment error stated in the beginning of the issue. I tried to go back to 0.16.2 but still the same error. Can you please specify which version you were using by the time of development or if there's a conda or docker version available?