- cctbxbb - phenix-online.org

Tests which randomly pass or fail (nag)
by Graeme.Winter＠diamond.ac.uk 16 Sep '14

16 Sep '14

Hi Folks Quick nag if I may... if people have tests which employ random inputs (e.g. random unit cell, random amplitudes and phases) please could they set a seed or select from some seeds which should give random values which work, or fix their tests so that all random values work (ideally!) That way when tests fail people know something is wrong, rather than everything is fine but the random values drawn are troublesome... Sorry for sounding grumpy! Cheerio 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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order bias in flex.random_permutation
by Keitaro Yamashita 11 Sep '14

11 Sep '14

Dear cctbx developers, I happened to notice that the implementation of flex.random_permutation (scitbx/random.h) results in biased order because each element is always swapped with the element randomly selected from entire range of array. For details, please see the second paragraph and the right figure of http://en.wikipedia.org/wiki/Fisher%E2%80%93Yates_shuffle#Implementation_er… I reproduced the plot using flex.random_permutation. Actually this seems to have less impact because flex.random_permutation is rarely used in cctbx or phenix as far as I know. If needed, I would commit the corrected version (using the algorithm in the wikipedia article above). Best regards, Keitaro

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IPython with cctbx
by Oliver Zeldin 09 Sep '14

09 Sep '14

Dear Devs, Has anyone tried to get IPython working with cctbx? I'd really like to be able to use IPython notebooks for examples/tutorials/documented experiments, and was wondering if anyone else had thought the same thing. Cheers, Oli

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Re: [cctbxbb] Sphinx docs for CCTBX
by Nigel Moriarty 20 Aug '14

20 Aug '14

These links don't work for me. On Mon, Aug 18, 2014 at 3:16 PM, Ian Rees <irees(a)lbl.gov> wrote: > I'm using a separate build configuration for the docs. You can view > the nightly results here: > > http://cci-vm-6.lbl.gov:8010/builders/cctbx%2Bdocs-linux-64 > > If you click the first build, you can view the log files for each > step, and view the Sphinx log file by clicking "docs:cctbx stdio", > e.g. > > > http://cci-vm-6.lbl.gov:8010/builders/cctbx%2Bdocs-linux-64/builds/6/steps/… > > I'm working through the warnings now. Mostly missing references and > import errors. > > Ian > > On Fri, Aug 15, 2014 at 8:37 AM, Nathaniel Echols <nechols(a)lbl.gov> wrote: > > On Fri, Aug 15, 2014 at 8:06 AM, Richard Gildea <rgildea(a)gmail.com> > wrote: > >> > >> I had a go at starting to document cctbx.uctbx.unit_cell, which as you > >> know is mainly a Boost.Python extension > >> (https://sourceforge.net/p/cctbx/code/20467/). Before I travel too much > >> further down this route, is this an appropriate way of documenting > >> Boost.Python extensions or is there a better way we can do this? > > > > > > I haven't had enough time to experiment to decide on the best approach. > I > > see three choices - the first is what you've done: > > > > class my_class (ext.my_class) : > > """doc""" > > > > def boosted_function (self, some_argument) : > > """function doc""" > > super(ext.my_class, self).boosted_function(some_argument) > > > > OR (2): > > > > ext.my_class.__doc__ = """doc""" > > ext.my_class.boosted_function.__func__.__doc__ = """function doc""" > > > > OR (3): > > > > put the docstrings in C++ code, for instance: > > > > .def("boosted_function", &my_class::boosted_function, "function doc") > > > > (not sure what the equivalent is for classes but it's probably pretty > > similar) > > > > My opinion is that (1) is much too prone to confusion and API conflicts > > unless we're already using this code structure (and FYI, you broke the > call > > signatures for a couple of methods). (3) is just gross. (2) is also > gross > > but has the virtue of being the least likely to break, and doesn't > require > > modifying C++ files. So I'm inclined to take that approach > > > > (For what it's worth, when modifying a class using the boost.python > > injector, we appear to be able to set __doc__ inside there; see > > iotbx.pdb.hierarchy for an example.) > > > >> It would be good to get the documentation for the core cctbx classes up > >> and running, however several of the core classes (e.g. > >> cctbx.sgtbx.space_group, cctbx.uctbx.unit_cell, flex arrays) are mostly > >> Boost.Python extensions, so it would be good to arrive at a sensible > way to > >> document these extensions. > > > > > > Agreed. I think for flex arrays we will be stuck writing the docstrings > in > > C++ - however since these are relatively stable APIs it should be > reasonably > > straightforward. > > > > -Nat > -- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov

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real-space symmetry operators
by Nathaniel Echols 18 Aug '14

18 Aug '14

Hi all-- I'm trying to figure out how to orthogonalize symmetry operators given a unit cell, which doesn't seem to be something we have code for. These appear in PDB files in the REMARK 290 section but I haven't been able to find any other software that generates them, and the relationship between the symops and the real-space equivalents is unclear. I assume this is conceptually similar to orthogonalizing fractional coordinates, but unit_cell.orthogonalize() does not quite do what I wanted. In the PDB, for P63 it has this (excerpted): REMARK 290 2555 -Y,X-Y,Z ... REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 which looks like it should be relatively straightforward, but I'm not very good with matrices. Does anyone know the correct math for this? The corresponding rt_mx object from sgtbx looks like this: r=(0.0, -1.0, 0.0, 1.0, -1.0, 0.0, 0.0, 0.0, 1.0) t=(0.0, 0.0, 0.0) (Yes, I realize that there are much easier ways to apply symmetry operators to coordinates, but I want to limit the number of matrix multiplications involved when starting from Cartesian coordinates.) thanks, Nat

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Sphinx docs for CCTBX
by Nathaniel Echols 15 Aug '14

15 Aug '14

Thanks to some superb work by Nader Morshed, Oliver Zeldin, and Ian Rees, we now have automatically updated Sphinx docs for CCTBX: http://cci.lbl.gov/cctbx_docs/ Obviously these are still pretty sparse - right now most of the formal documentation is clustered here: libtbx libtbx.utils libtbx.phil (mostly re-using Ralf's old documentation) cctbx.miller iotbx.pdb (built on Ralf's newsletter article) mmtbx.command_line These are a combination of inline docstrings and separate restructured text files in cctbx_project/sphinx. We have automatically generated rst files for some modules, but others will need to be added manually. In the end I think we'll want to curate every file, but the current layout will get us started. To facilitate additional contributions, I've modifed the installation script for base packages to include a --sphinx option. After setting up CCTBX you can then do this: cd $BUILD libtbx.configure sphinx cd $SRC/cctbx_project/sphinx make html and you will get the full documentation built locally. I am still figuring out how to use Sphinx effectively; it is definitely possible to document Boost.Python extensions but it's not quite as obvious. I don't expect us to retroactively document several hundred thousand lines of code written over a decade, but if we can get the core parts thoroughly covered that will greatly reduce the barrier for new developers. Suggestions for particular modules to focus on are appreciated; I am going to try to cover the basic PDB+reflection file functionality. I encourage anyone doing CCTBX-related development to contribute as you go. (They don't need to be your own APIs, just modules you're reasonably familiar with.) Those of you who already have a ton of undocumented code can expect me to harass you periodically about fixing this. (Note that I've cannibalized at least one newsletter article for this, and continue to do so; we should re-use existing prose descriptions as much as possible without violating copyrights.) -Nat

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Re: [cctbxbb] resend
by Mustyakimov, Marat 24 Jul '14

24 Jul '14

Loop through symops: apply each symop to the original asu, then apply unit translations to minimize its distance to the original asu, test if new asu intersects with the target 27-bricks-large box, use it, if it does. Keep in mind that asu is not always a brick, it is always a convex polyhedron in cctbx. I do not see any good reason for doing all that. I do not read cctbxbb. On Jul 24, 2014, at 2:43 PM, Alastair Fyfe <afyfe(a)soe.ucsc.edu> wrote: >> Hi Marat, my apologies if this is a duplicate. From Pavel's comment it occurred to me you might not follow posts to the cctxbb >> Alastair >> ------ >> >> Many thanks for your replies. >> >> Pavel : by "slow" I meant to (a) apply sym ops to asu and refer results >> back to unit cell thus obtaining a "full" unit cell (I expect >> "expand_to_p1()" does this?) (b) translate the cell and (c) find overlap >> with the 26-brick neighborhood of the starting brick. This should work >> but seems inefficient. >> >> Marat: applying SymOps to the basis vectors seems a great idea. >> However, it wasn't clear to me how to combine sg SymOps to yield the >> 26 adjacent bricks. Does the map expansion code do this? >> >> >

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Re: [cctbxbb] 26-fold symm expansion of asu?
by Alastair Fyfe 24 Jul '14

24 Jul '14

Many thanks for your replies. Pavel : by "slow" I meant to (a) apply sym ops to asu and refer results back to unit cell thus obtaining a "full" unit cell (I expect "expand_to_p1()" does this?) (b) translate the cell and (c) find overlap with the 26-brick neighborhood of the starting brick. This should work but seems inefficient. Marat: applying SymOps to the basis vectors seems a great idea. However, it wasn't clear to me how to combine sg SymOps to yield the 26 adjacent bricks. Does the map expansion code do this? On 07/23/2014 12:00 PM, cctbxbb-request(a)phenix-online.org wrote: > Send cctbxbb mailing list submissions to > cctbxbb(a)phenix-online.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://phenix-online.org/mailman/listinfo/cctbxbb > or, via email, send a message with subject or body 'help' to > cctbxbb-request(a)phenix-online.org > > You can reach the person managing the list at > cctbxbb-owner(a)phenix-online.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of cctbxbb digest..." > > > Today's Topics: > > 1. Re: 26-fold symm expansion of asu? (Pavel Afonine) > 2. Re: 26-fold symm expansion of asu? (Mustyakimov, Marat) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 22 Jul 2014 18:58:32 -0700 > From: Pavel Afonine <pafonine(a)lbl.gov> > To: cctbx mailing list <cctbxbb(a)phenix-online.org> > Cc: "Mustyakimov, Marat" <mustyakimovm(a)ornl.gov> > Subject: Re: [cctbxbb] 26-fold symm expansion of asu? > Message-ID: <53CF16C8.5040504(a)lbl.gov> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi Alastair, > > I think I can write a piece of code using cctbx that would do what you > want and probably that would be what you call "slow". Could you please > explain some more what it is for and why, and may be give some context? > Perhaps that helps me to see if we have something similar already > available.. > > For instance we have very efficient code that computes maps in ASU, and > also that expands map in ASU into the whole P1 box. This is something > Marat wrote recently and is very efficient. May be you can reuse that or > at least harvest ideas? > > I'm copying to Marat in case he has comments. > > Pavel > > On 7/21/14, 2:14 PM, Alastair Fyfe wrote: >> Hi, >> I'd be grateful for any pointers to clipper or cctbx code that >> addresses the following: given a "brick" of map grid coordinates that >> enclose the asu, obtain the 26 symmetry-related "bricks" which contact >> it. Calculating this by successively generating symmetry mates and >> testing seems slow; I was wondering whether there was a better way. >> thank you, >> Alastair Fyfe >> UCSC >> _______________________________________________ >> cctbxbb mailing list >> cctbxbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/cctbxbb > > > ------------------------------ > > Message: 2 > Date: Wed, 23 Jul 2014 14:01:13 +0000 > From: "Mustyakimov, Marat" <mustyakimovm(a)ornl.gov> > To: Pavel Afonine <pafonine(a)lbl.gov> > Cc: cctbx mailing list <cctbxbb(a)phenix-online.org> > Subject: Re: [cctbxbb] 26-fold symm expansion of asu? > Message-ID: <9457BEEC-4821-4BBB-8D91-E903AAFAE7F0(a)ornl.gov> > Content-Type: text/plain; charset="iso-8859-1" > > The fast way to generate symmetry equivalent ASU: > Apply symmetry operation to unit vectors: ex = SymOp*(1,0,0), ey=SymOp*(0,1,0) and ez=SymOp*(0,0,1); > Then every map point of the symmetry related asu is obtained from the original one: > new_ijk = i*ex + j*ey + k*ez where (i,j,k) is the grid point in the original ASU. > > Marat Mustyakimov > P.O. Box 2008, Bldg. 8600, MS-6475 > Oak Ridge National Lab > Oak Ridge TN 37831 USA > e-mail: mustyakimovm(a)ornl.gov<mailto:[email protected]> > e-mail: marat.mustyakimov(a)gmail.com<mailto:[email protected]> > Tel: +1-865-253-3924 > > On Jul 22, 2014, at 9:58 PM, Pavel Afonine <pafonine(a)lbl.gov<mailto:[email protected]>> wrote: > > Hi Alastair, > > I think I can write a piece of code using cctbx that would do what you want and probably that would be what you call "slow". Could you please explain some more what it is for and why, and may be give some context? Perhaps that helps me to see if we have something similar already available.. > > For instance we have very efficient code that computes maps in ASU, and also that expands map in ASU into the whole P1 box. This is something Marat wrote recently and is very efficient. May be you can reuse that or at least harvest ideas? > > I'm copying to Marat in case he has comments. > > Pavel > > On 7/21/14, 2:14 PM, Alastair Fyfe wrote: > Hi, > I'd be grateful for any pointers to clipper or cctbx code that addresses the following: given a "brick" of map grid coordinates that enclose the asu, obtain the 26 symmetry-related "bricks" which contact it. Calculating this by successively generating symmetry mates and testing seems slow; I was wondering whether there was a better way. > thank you, > Alastair Fyfe > UCSC > _______________________________________________ > cctbxbb mailing list > cctbxbb(a)phenix-online.org<mailto:[email protected]> > http://phenix-online.org/mailman/listinfo/cctbxbb > > > > > ------------------------------ > > _______________________________________________ > cctbxbb mailing list > cctbxbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/cctbxbb > > > End of cctbxbb Digest, Vol 64, Issue 2 > **************************************

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26-fold symm expansion of asu?
by Alastair Fyfe 23 Jul '14

23 Jul '14

Hi, I'd be grateful for any pointers to clipper or cctbx code that addresses the following: given a "brick" of map grid coordinates that enclose the asu, obtain the 26 symmetry-related "bricks" which contact it. Calculating this by successively generating symmetry mates and testing seems slow; I was wondering whether there was a better way. thank you, Alastair Fyfe UCSC

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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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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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building cctbx with external boost
by Marcin Wojdyr 19 Dec '13

19 Dec '13

Hi I vaguely remember a discussion some time ago about building cctbx with stand-alone boost libraries. Do you know what boost versions are compatible? Is using the --scan-boost option enough? I see that Gentoo has extra patch to unbundle boost from cctbx: http://sources.gentoo.org/cgi-bin/viewvc.cgi/gentoo-x86/sci-libs/cctbx/file… Is it necessary? I'm asking because at this moment we have in CCP4 two versions of boost, one in cctbx and the other for building DSSP (it uses different subset of boost libs than cctbx). It would make sense to use a single version for both, if possible. Cheers Marcin

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Re: [cctbxbb] cctbxbb Digest, Vol 59, Issue 1
by Zhenwei Luo 09 Dec '13

09 Dec '13

Hi Nat, Thanks for your reply! I have tried the first method you mentioned--adding an index value to the return method. It did work if I only needed a single array for future calculation. But I found it's not very convenient for my program. It's convenient and more efficient if other classes in it could process all the one-dimensional arrays at the same time. Otherwise, I needed to write more control code in python, and the c++ part could only deal with a single array now. Therefore, I hoped that I could pass such a multidimensional array in my program. Sincerely, Zhenwei On Sun, Dec 8, 2013 at 2:00 PM, <cctbxbb-request(a)phenix-online.org> wrote: > Send cctbxbb mailing list submissions to > cctbxbb(a)phenix-online.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://phenix-online.org/mailman/listinfo/cctbxbb > or, via email, send a message with subject or body 'help' to > cctbxbb-request(a)phenix-online.org > > You can reach the person managing the list at > cctbxbb-owner(a)phenix-online.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of cctbxbb digest..." > > > Today's Topics: > > 1. Passing array between python and C++ (Zhenwei Luo) > 2. Re: Passing array between python and C++ (Nathaniel Echols) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 7 Dec 2013 22:25:08 -0600 > From: Zhenwei Luo <tluozhenwei(a)gmail.com> > To: cctbxbb(a)phenix-online.org > Subject: [cctbxbb] Passing array between python and C++ > Message-ID: <90518A19-AC1B-493B-8B27-79D31EDDF055(a)gmail.com> > Content-Type: text/plain; charset=us-ascii > > Hello Everyone, > > I am writing a refinement program using the cctbx. I have > encountered with a problem when I wanted to pass an array between c++ and > python. The type of array I used in my c++ source file is > af::shared<af::shared<vec3> >, I would like to pass it into my python > script, thus I could do some other operations to this array. > I wrote a method in my class to return this array. > > af::shared<af::shared<vec3<double> > return_modes( ) { return modes; } > > I wrote another method in the *_ext file to wrap this method to make it > callable from python. > > .def("return_modes", &nm_init::return_modes) > > But when I use it in python, > eigenvector = nm_init_manager.return_modes() > > It gave me an error: > > TypeError: No to_python (by-value) converter found for c++ type: > scitbx::af::shared<scitbx::af::shared<scitbx::vec3<double> > > > > What I want to realize is just creating an two dimensional array using > vec3 as its element. I can also using the select method in this array to > select some elements from its column, just like in the > af::shared<vec3<double> > array. Namely, the column of this array should > have some same properties like af::shared<vec3<double> >. Can anyone help > me figure out what I should do? > > Thank you very much! Any help will be greatly appreciated. > > Sincerely, > Zhenwei Luo > Rice University > > > ------------------------------ > > Message: 2 > Date: Sat, 7 Dec 2013 20:45:10 -0800 > From: Nathaniel Echols <nechols(a)lbl.gov> > To: cctbx mailing list <cctbxbb(a)phenix-online.org> > Subject: Re: [cctbxbb] Passing array between python and C++ > Message-ID: > <CALeAa1MOL1wbW5Vb=M= > jXsnGTaCBQNJjcOzDwMhM27x5PP+XNA(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > On Sat, Dec 7, 2013 at 8:25 PM, Zhenwei Luo <tluozhenwei(a)gmail.com> wrote: > > > I am writing a refinement program using the cctbx. I have > > encountered with a problem when I wanted to pass an array between c++ and > > python. The type of array I used in my c++ source file is > > af::shared<af::shared<vec3> >, I would like to pass it into my python > > script, thus I could do some other operations to this array. > > I wrote a method in my class to return this array. > > > > af::shared<af::shared<vec3<double> > return_modes( ) { return modes; } > > > > I wrote another method in the *_ext file to wrap this method to make it > > callable from python. > > > > .def("return_modes", &nm_init::return_modes) > > > > But when I use it in python, > > eigenvector = nm_init_manager.return_modes() > > It gave me an error: > > TypeError: No to_python (by-value) converter found for c++ type: > > scitbx::af::shared<scitbx::af::shared<scitbx::vec3<double> > > > > > > What that error means is that boost.python doesn't know how to present this > new type to Python. For the data structures that we pass back and forth, > we have to explicitly provide wrappers for them - including new > instantiations of scitbx::array_family templates. > > What I want to realize is just creating an two dimensional array using vec3 > > as its element. I can also using the select method in this array to > select > > some elements from its column, just like in the af::shared<vec3<double> > > > array. Namely, the column of this array should have some same properties > > like af::shared<vec3<double> >. Can anyone help me figure out what I > should > > do? > > > > In general the scitbx::array_family templates aren't really intended to > every be multidimensional; for inherently 2D and 3D data types like images > and maps, we use flex.grid to provide a multi-dimensional accessor on top > of the 1D array. The grid may not be the most appropriate in your case but > if I'm making the correct assumptions about the data you're trying to pass > back and forth, I think it might be easiest to simply define a custom class > that contains a std::vector of af::shared<vec3> arrays, and add an index > parameter to the return_modes method, which would be modified to return > only a single array of modes at a time. You can also do things like > wrapping a method as __getitem__ with boost.python, which would mimic a 2D > array. (I can probably dig up/cook up some code examples tomorrow if this > is unclear, since it was certainly not intuitive to me when I started > working with CCTBX and it would be nice to have documentation for the > future.) > > -Nat >

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Passing array between python and C++
by Zhenwei Luo 08 Dec '13

08 Dec '13

Hello Everyone, I am writing a refinement program using the cctbx. I have encountered with a problem when I wanted to pass an array between c++ and python. The type of array I used in my c++ source file is af::shared<af::shared<vec3> >, I would like to pass it into my python script, thus I could do some other operations to this array. I wrote a method in my class to return this array. af::shared<af::shared<vec3<double> > return_modes( ) { return modes; } I wrote another method in the *_ext file to wrap this method to make it callable from python. .def("return_modes", &nm_init::return_modes) But when I use it in python, eigenvector = nm_init_manager.return_modes() It gave me an error: TypeError: No to_python (by-value) converter found for c++ type: scitbx::af::shared<scitbx::af::shared<scitbx::vec3<double> > > What I want to realize is just creating an two dimensional array using vec3 as its element. I can also using the select method in this array to select some elements from its column, just like in the af::shared<vec3<double> > array. Namely, the column of this array should have some same properties like af::shared<vec3<double> >. Can anyone help me figure out what I should do? Thank you very much! Any help will be greatly appreciated. Sincerely, Zhenwei Luo Rice University

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libtbx.run_tests_parallel
by Graeme.Winter＠diamond.ac.uk 14 Nov '13

14 Nov '13

Folks, Would anyone mind if I added an option to libtbx.run_tests_parallel to automatically make a temporary directory, chdir to there and run? It would mean I could write a little update / build / run tests script more easily. auto_run_dir=true springs to mind as a Phil option. Any thoughts? Thanks & best wishes, 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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iotbx newbie question
by wtempel 07 Nov '13

07 Nov '13

Hello all, please consider the scenario of a manuscript that, among other things, describes 20 crystal structures. Suppose the journal editor requires a Table 1. I now looking for a tool to prepare such table with high accuracy and little effort. My PDB deposition workflow includes the preparation of mmcif coordinates with pdb_extract. The mmcif file is complete in the sense that after upload to RCSB-ADIT, virtually no additional information is required for deposition. My intuition was to combine CSV and IOTBX python modules and produce the table via input of a list of mmcif files. The current phenix table_1 tool provides some, but not all of that functionality, and I thought once familiar with the python modules, I would quickly write the script. After confirming that the example at http://cctbx.sourceforge.net/iotbx_cif/ works with my cctbx installation, I attempted to transform that code to read in PDB mmcif coordinates: <code> test_structure = iotbx.cif.reader( file_path="/tmp/1NXC.cif").build_crystal_structures()["1NXC"] </code> which throws an exception: <output> Traceback (most recent call last): File "1NXC.py", line 3, in <module> test_structure = iotbx.cif.reader(file_path="/tmp/1NXC.cif").build_crystal_structures()["1NXC"] KeyError: '1NXC' </output> How do I need to write the code so that it returns a python object with access to all the cif items? Thank you, Wolfram Tempel

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