- cctbxbb - phenix-online.org

Phenix dependencies in CCTBX code
by Graeme.Winter＠diamond.ac.uk 22 Jun '14

22 Jun '14

Dear All, In cctbx_project/iotbx/pdb/multimer_reconstruction.py there is a dependency on Phenix from phenix.command_line.simple_ncs_from_pdb import simple_ncs_from_pdb from phenix.command_line.simple_ncs_from_pdb import ncs_master_params Please could someone remove this? I just had a look at cleaning things up so that this was encapsulated but was not obvious and figured risk of breaking was more substantial. This is breaking our nightly build tests at Diamond as we don’t check out phenix :o( Thanks Graeme -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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Re: [cctbxbb] Boost Import Error
by Magnus Andersson 19 Jun '14

19 Jun '14

Hi all, In case anyone else runs into the same problems (which is not unlikely), the following worked for me: > svn co https://pymol.svn.sourceforge.net/svnroot/pymol/trunk/pymol > cd pymol > cctbx.python setup.py build > cctbx.python setup.py install > Thanks to Luc & Nat for being helpful and persistent! Cheers, Magnus > > On 17 Jun 2014, at 21:34, Luc Bourhis <luc_j_bourhis(a)mac.com> wrote: > >> Hi, >> >> it's a bit late here in Paris but I can at least fix one point: >> >>> port select --set python27 >>> Error: The 'set' command expects two arguments: <group>, <version> >> >>> I tried to figure this out but without success... sorry to bug you with syntax issues. >> >> I'm the one to be sorry here as I pulled it from the top of my head and got it wrong. It's >> >> port select --set python python27 >> >> As for your original problem, I'll try to regroup and think through our former exchange to see what I may have missed. >> >> Best wishes, >> >> Luc >> >

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Boost Import Error
by Magnus Andersson 17 Jun '14

17 Jun '14

Hi, I've installed the cctbx package from the selfextracting file found in http://cci.lbl.gov/cctbx_build/ but I run into problems when importing cctbx in my python script: import iotbx.pdb File "/Users/magnus/Downloads/cctbx_sources/iotbx/pdb/__init__.py", line 2, in <module> from cctbx.array_family import flex File "/Users/magnus/Downloads/cctbx_sources/cctbx/array_family/flex.py", line 2, in <module> import scitbx.array_family.flex File "/Users/magnus/Downloads/cctbx_sources/scitbx/array_family/flex.py", line 2, in <module> import boost.optional # import dependency ImportError: No module named boost.optional It is flex.py that wants to import boost.optional and does not find it. However, I find these three files: optional.hpp optional_fwd.hpp optional_io.hpp in the following directory: /Users/magnus/Downloads/cctbx_sources/boost/boost/optional which suggests that it's present. What am I missing here? I'm using Mac OS X Version 10.9.3 and Python2.7. Cheers, Magnus

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sparse matrix
by David Waterman 10 Jun '14

10 Jun '14

Hi, I have a problem where the use of a sparse matrix is appropriate, so I was pretty happy to grep cctbx for "sparse" and discover the code in scitbx/sparse. I'm just browsing through the code and tests to get a feel for how to use these types. In my existing Python code I set the values for some columns using flex.double vectors, then ultimately fill a flex.double(flex.grid(n,m)) by these columns using matrix_paste_column_in_place. It seems to me I can use a very similar pattern by replacing the flex.doubles with sparse.matrix_columns and setting columns in the sparse.matrix using slice notation: mat[:,0] = column. So far so good. The issue is that I'm not sure how best to go about setting the values in the matrix_column in the first place. At the moment I'm making a lot of use of flex.size_t selections and the set_selected method of flex.double to efficiently (from Python) set elements of one flex.double from another. It appears that there is no similar functionality for sparse.matrix_column. Am I right? Possibly the best I can do is construct a Python dictionary consisting of the indices from my size_t selection and the values from my flex.double array and use these to construct the matrix_column, as done in tst_sparse, e.g. sparse.matrix_column(m, {1:0.1, 2:0.2}). Without having tried this, I sense it might be a burden. I have a lot of values to set and don't really want to convert from flex.double via a dictionary. Are there any philosophical/technical/other reasons for not writing a set_selected method for sparse.vector? If not, I might try to do this. Thanks -- David

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where is the mmtbx.mp_geo command
by Sun, Miao 13 Mar '14

13 Mar '14

Hi, I have installed cctbx software, however, I cant find the command mmtbx.mp_geo. I wanna to validate the backbone bond and angles. Is there any other command could do that? Thanks. -Miao

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Re: [cctbxbb] Adding columns to new *unmerged* MTZ object
by Graeme.Winter＠diamond.ac.uk 13 Feb '14

13 Feb '14

In related news…. Should void object::adjust_column_array_sizes(int new_nref) { CMtz::MTZ* p = ptr(); if (!p->refs_in_memory) return; if (new_nref > p->nref) { reserve(new_nref); for(int i=0;i<p->nxtal;i++) { for(int j=0;j<p->xtal[i]->nset;j++) { for(int k=0;k<p->xtal[i]->set[j]->ncol;k++) { CMtz::MTZCOL* col_k = p->xtal[i]->set[j]->col[k]; int old_size = column_array_size(col_k); if (new_nref > old_size) { ccp4array_resize(col_k->ref, new_nref); for(int iref=old_size;iref<new_nref;iref++) { *(reinterpret_cast<union float_uint_uchar*>( &col_k->ref[iref])) = not_a_number_value_; } } } } } } } assign nref? otherwise repeated calling of this will keep on re-allocating the arrays Thanks Graeme On 12 Feb 2014, at 10:40, Graeme Winter <graeme.winter(a)diamond.ac.uk> wrote: > All, > > By adding > > m_out.adjust_column_array_sizes(len(mi)) > > to the bpl wrapper and defining > > m_out.set_n_reflections(len(mi)) > > in the object.h and bpl wrapper I can do what I want… > > I will add some tests and some warnings that this may make nonsense of the values… however before committing any comments on the interface? or behaviour? > > Thanks Graeme > > > > On 12 Feb 2014, at 09:11, <Graeme.Winter(a)diamond.ac.uk> <Graeme.Winter(a)diamond.ac.uk> wrote: > >> Hi Folks, >> >> I am trying to create a new MTZ file containing unmerged and it seems to be less simple than I would think - set_reals() on a column requires a set of Miller indices and values and does a lookup internally (which I don’t want for unmerged values) and set_values() requires that the array is already the right size - when it starts off as size 0 and I have no idea how to make enough room in there from the Python API… >> >> Any clues? I have done quite a chunk of grepping around to try and figure this one out and have run out of ideas… >> >> Thanks Graeme_______________________________________________ >> cctbxbb mailing list >> cctbxbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/cctbxbb >

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Adding columns to new *unmerged* MTZ object
by Graeme.Winter＠diamond.ac.uk 12 Feb '14

12 Feb '14

Hi Folks, I am trying to create a new MTZ file containing unmerged and it seems to be less simple than I would think - set_reals() on a column requires a set of Miller indices and values and does a lookup internally (which I don’t want for unmerged values) and set_values() requires that the array is already the right size - when it starts off as size 0 and I have no idea how to make enough room in there from the Python API… Any clues? I have done quite a chunk of grepping around to try and figure this one out and have run out of ideas… Thanks Graeme

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building with external boost
by Marcin Wojdyr 30 Jan '14

30 Jan '14

Hi all, would it be ok if I added an option to use installed boost libraries? Debian and gentoo patches add boolean --use_system_libs flag. I could use the same, but with a list of arguments (at first only --use_system_libs=boost). Marcin

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boost python and metaclass inheritance
by David Waterman 10 Jan '14

10 Jan '14

Hi, Does anyone know how to use __metaclass__ specification alongside inheritance from boost python classes? This code illustrates the problem: import abc > from scitbx.lstbx import normal_eqns > class Refinery(object): > __metaclass__ = abc.ABCMeta > pass > class AdaptLstbx(Refinery, normal_eqns.non_linear_ls): > pass The result is Traceback (most recent call last): > File "<stdin>", line 1, in <module> > File "/usr/lib/python2.7/abc.py", line 87, in __new__ > cls = super(ABCMeta, mcls).__new__(mcls, name, bases, namespace) > TypeError: Error when calling the metaclass bases > metaclass conflict: the metaclass of a derived class must be a > (non-strict) subclass of the metaclasses of all its bases The real Refinery is a class that has one method that must be supplied by a concrete subclass. I like the idea of making it impossible to instantiate a base Refinery rather than relying on e.g. raise NotImplementedError() in that method definition. This is what ABCMeta would give me, if only I could get it to work here. Google found me some answers that require me to know the __metaclass__ of the bases (as suggested by the error message), but normal_eqns.non_linear_ls.__metaclass__ does not exist. I don't terribly mind the raise NotImplementedError() alternative, but I thought that if I can easily use ABCMeta, I'd like to. Cheers -- David

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cctbx.python unnecessarily unfriendly
by James Stroud 10 Jan '14

10 Jan '14

Hello CCTBX developers, I noticed in the cctbx.python script the following lines that call the python interpreter if [ -n "$LIBTBX__VALGRIND_FLAG__" ]; then exec $LIBTBX_VALGRIND "$LIBTBX_PYEXE" -Qnew "$@" elif [ $# -eq 0 ]; then exec "$LIBTBX_PYEXE" -Qnew else exec "$LIBTBX_PYEXE" -Qnew "$@" fi Here, the “-Qnew” flag forces the python interpreter to work with new division (where “/“ does not strictly mean integer division). This flag basically overrides the expected python behavior to which python programmers have been writing code for over a decade, wrecks some dependencies, and stifles new code that itself depends on cctbx. It is highly frustrating to work around this highly unnecessary flag!! Fortunately, python has a better way to handle this problem by just having “from __future__ import division” at the top of .py files. In fact, I have spot-checked several files in the cctbx source tree and noticed that the ALL have this line at the top. So why does the -Qnew flag still exist in the cctbx.python script? It is entirely unnecessary and requires any and all dependencies to be programmed to a behavior that is not standard for the language. James p.s. It is not reasonable to ask users who install your packages to patch the cctbx.python script or to patch dependencies that don’t conform to this non-standard behavior.

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