diff --git a/doc/html/_modules/index.html b/doc/html/_modules/index.html index a6fe610d2108e076dc2d0670304919ea9f17e382..55d1bb8bef5c5357a052d139b4f15a1d04ad8e4e 100644 --- a/doc/html/_modules/index.html +++ b/doc/html/_modules/index.html @@ -85,7 +85,7 @@ </div> <div class="footer"> © Copyright 2013, Bienchen. - Last updated on Sep 18 16:30, 2014. + Last updated on Sep 25 11:22, 2014. Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3. </div> </body> diff --git a/doc/html/_modules/promod3/core/argcheck.html b/doc/html/_modules/promod3/core/argcheck.html index fb384b8db28f4c3cb0a22e2a887d9e74429d4b4e..334fc4083cb6e5815431d9b89fb4e030b07ae73d 100644 --- a/doc/html/_modules/promod3/core/argcheck.html +++ b/doc/html/_modules/promod3/core/argcheck.html @@ -193,7 +193,7 @@ </div> <div class="footer"> © Copyright 2013, Bienchen. - Last updated on Sep 18 16:30, 2014. + Last updated on Sep 25 11:22, 2014. Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3. </div> </body> diff --git a/doc/html/_sources/buildsystem.txt b/doc/html/_sources/buildsystem.txt index b6f3b861a29daabaee4c662e69d60d5fbf0e1420..4e01a700031f053d686d62d0e2e5c8b8a64e18f6 100644 --- a/doc/html/_sources/buildsystem.txt +++ b/doc/html/_sources/buildsystem.txt @@ -106,7 +106,7 @@ special targets: .. _cmake: http://www.cmake.org/ .. _python: https://www.python.org/ .. _boost: http://www.boost.org/ -.. _eigen3: http://eigen.tuxfamily.org/ +.. _eigen3: http://eigen.tuxfamily.org/index.php?title=Main_Page .. _lapack: http://www.netlib.org/lapack/ .. LocalWords: cmake makefiles CMakeLists txt DOCTEST LINKCHECK conf html diff --git a/doc/html/_sources/contributing.txt b/doc/html/_sources/contributing.txt index b9bd37f83a2caf79ad5b82a0da3e5b81bc53da76..d536b3ff6619c56d093554eac5454f97916a33b9 100644 --- a/doc/html/_sources/contributing.txt +++ b/doc/html/_sources/contributing.txt @@ -199,7 +199,8 @@ only running unit tests from all modules in |project|. Actually ``make check`` does nothing more but invoking ``doctest``, ``linkcheck`` and ``codetest`` as dependencies. You could even go with running tests gathered in a single file: assuming you have :file:`your_module/tests/test_awesome_feature.py`, |cmake| -will provide you with a target ``test_awesome_feature.py_run``. +will provide you with a target ``test_awesome_feature.py_run``. If your module +has |C++| tests, those will be available by ``test_suite_your_module_run``. -------------------------------------------------------------------------------- Writing Documentation diff --git a/doc/html/buildsystem.html b/doc/html/buildsystem.html index ba044996fd463d1e8cb312396d164624bc9083e0..1104805e43f56c44b8399d655d5dd3a6154e3dd3 100644 --- a/doc/html/buildsystem.html +++ b/doc/html/buildsystem.html @@ -62,7 +62,7 @@ 1.4, and <a class="reference external" href="http://swissmodel.expasy.org/qmean/cgi/index.cgi?">QMEAN</a>. To create the build system, <a class="reference external" href="http://www.cmake.org/">CMake</a> is required in version 2.8.7 or higher. <a class="reference external" href="https://www.python.org/">Python</a> works well from version 2.7. For OST and the C++ bit of ProMod3, <a class="reference external" href="http://www.boost.org/">Boost</a> is required in version 1.47.0 (the same as -used for OST). Also <a class="reference external" href="http://eigen.tuxfamily.org/">Eigen 3</a> and <a class="reference external" href="http://www.netlib.org/lapack/">LAPACK</a> are needed. To build +used for OST). Also <a class="reference external" href="http://eigen.tuxfamily.org/index.php?title=Main_Page">Eigen 3</a> and <a class="reference external" href="http://www.netlib.org/lapack/">LAPACK</a> are needed. To build documentation, <a class="reference external" href="http://sphinx-doc.org/">Sphinx</a> 1.2b1 is used.</p> <ul class="simple"> <li><a class="reference external" href="http://www.OpenStructure.org">OST</a> 1.4</li> @@ -71,7 +71,7 @@ documentation, <a class="reference external" href="http://sphinx-doc.org/">Sphin <li><a class="reference external" href="https://www.python.org/">Python</a> 2.7</li> <li><a class="reference external" href="http://www.boost.org/">Boost</a> 1.47.0</li> <li><a class="reference external" href="http://sphinx-doc.org/">Sphinx</a> 1.2b1</li> -<li><a class="reference external" href="http://eigen.tuxfamily.org/">Eigen 3</a> 3.2.1</li> +<li><a class="reference external" href="http://eigen.tuxfamily.org/index.php?title=Main_Page">Eigen 3</a> 3.2.1</li> <li><a class="reference external" href="http://www.netlib.org/lapack/">LAPACK</a> 3.0</li> </ul> </div> @@ -212,7 +212,7 @@ builder</li> </div> <div class="footer"> © Copyright 2013, Bienchen. - Last updated on Sep 18 15:50, 2014. + Last updated on Sep 25 11:22, 2014. Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3. </div> </body> diff --git a/doc/html/contributing.html b/doc/html/contributing.html index 53a7130141e00994bd7ebe9d59a06b60a8c215f6..dd5d620840f960a7dbbef11cca3e6a77b04db738 100644 --- a/doc/html/contributing.html +++ b/doc/html/contributing.html @@ -228,7 +228,8 @@ only running unit tests from all modules in ProMod3. Actually <tt class="docutil does nothing more but invoking <tt class="docutils literal"><span class="pre">doctest</span></tt>, <tt class="docutils literal"><span class="pre">linkcheck</span></tt> and <tt class="docutils literal"><span class="pre">codetest</span></tt> as dependencies. You could even go with running tests gathered in a single file: assuming you have <tt class="file docutils literal"><span class="pre">your_module/tests/test_awesome_feature.py</span></tt>, CMake -will provide you with a target <tt class="docutils literal"><span class="pre">test_awesome_feature.py_run</span></tt>.</p> +will provide you with a target <tt class="docutils literal"><span class="pre">test_awesome_feature.py_run</span></tt>. If your module +has C++ tests, those will be available by <tt class="docutils literal"><span class="pre">test_suite_your_module_run</span></tt>.</p> </div> <div class="section" id="writing-documentation"> <h2>Writing Documentation<a class="headerlink" href="#writing-documentation" title="Permalink to this headline">¶</a></h2> @@ -794,7 +795,7 @@ contributions to web pages using ProMod3.</p> </div> <div class="footer"> © Copyright 2013, Bienchen. - Last updated on Sep 18 16:30, 2014. + Last updated on Sep 25 11:22, 2014. Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3. </div> </body> diff --git a/doc/html/developers.html b/doc/html/developers.html index 819b82bb7fce017d436561806a81b6138be4d066..62874d5948d7c5dc0269c94925e6b7add3c23e91 100644 --- a/doc/html/developers.html +++ b/doc/html/developers.html @@ -140,7 +140,7 @@ </div> <div class="footer"> © Copyright 2013, Bienchen. - Last updated on Sep 18 16:30, 2014. + Last updated on Sep 25 11:22, 2014. Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3. </div> </body> diff --git a/doc/html/genindex.html b/doc/html/genindex.html index ac9b0837ccadba64e776ce63343a5e0a826ee285..873f86cb88c47efb4b5aaf240adb09cd1ced1257 100644 --- a/doc/html/genindex.html +++ b/doc/html/genindex.html @@ -334,7 +334,7 @@ </div> <div class="footer"> © Copyright 2013, Bienchen. - Last updated on Sep 18 16:30, 2014. + Last updated on Sep 25 11:22, 2014. Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3. </div> </body> diff --git a/doc/html/index.html b/doc/html/index.html index 8623365555d9781658169f03b3cd8add1959a207..de372cdc663e3f328c84468a401834cab57580a8 100644 --- a/doc/html/index.html +++ b/doc/html/index.html @@ -132,7 +132,7 @@ </div> <div class="footer"> © Copyright 2013, Bienchen. - Last updated on Sep 18 16:30, 2014. + Last updated on Sep 25 11:22, 2014. Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3. </div> </body> diff --git a/doc/html/objects.inv b/doc/html/objects.inv index 9c6f756aba1760165d3008b970d3d82700805f0a..5f98c7dd8eb9661333612747ad89492cf38764c1 100644 --- a/doc/html/objects.inv +++ b/doc/html/objects.inv @@ -2,6 +2,5 @@ # Project: ProMod3 # Version: 0.1 # The remainder of this file is compressed using zlib. -xڥTMo�0��+*m�fC�q�IH�4�)��6"U� -��KZ�ƺ ��"����ű� �!�3�3TI:M�c�O� ��7��dC��/�6zB4���eb;�m��w��t6�}b�:f�)�����7��"�O�3F��L\�DZ�]. -;�".��Kk"�ge��pά�"��u]6���5��B���Z��{��Wk�7 �����he�ֽ Z2��R���𭅜�ɬ"�����:�ֹ���B��2�*y&�!Ta\�����!���&�:��ᵄ,����ɺ��F���?�8���ߜ�Po[�4$�8��r�m%;i��添+`��+EL������e��S���[�?^�o!7�ҙ�[��x�S�=�#�m \ No newline at end of file +xڥT�n�0����kܢD%�V��{�x���������J��ܢ��xf�YmA�C� f�g��t���T�XAZ�%o*��*�&9�_@m��hZ=r'��Ʀvj�4 �<�I�l��� �0h�����$��7�}��1\`b� +&�2�rQ�ر�py 4^Z�>+#(~O�Κ/y]���T����R�x �u8���}��\p8![��V�l����r��y ϕ�d��o#�DNfa�6������5v���"���`���]�t������<�o�H�����ld��u���Z{�~q��1S�9o��B%FF��r0��b'M�[A��v��R�t��:�]��>��|�e��U�r���4ߺ�LJ��ߘ��Ϩm \ No newline at end of file diff --git a/doc/html/py-modindex.html b/doc/html/py-modindex.html index f8a56c37d9356b512d3bbd3fddc0a0d3dc84fa2a..d39d332e052bc1adf428453b8673521947e9de41 100644 --- a/doc/html/py-modindex.html +++ b/doc/html/py-modindex.html @@ -113,7 +113,7 @@ </div> <div class="footer"> © Copyright 2013, Bienchen. - Last updated on Sep 18 16:30, 2014. + Last updated on Sep 25 11:22, 2014. Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3. </div> </body> diff --git a/doc/html/search.html b/doc/html/search.html index 3a763dc10db069283d10e35381264b64879337a5..72ed3117c048d4a43b05d273560b6fa0274d9330 100644 --- a/doc/html/search.html +++ b/doc/html/search.html @@ -99,7 +99,7 @@ </div> <div class="footer"> © Copyright 2013, Bienchen. - Last updated on Sep 18 16:30, 2014. + Last updated on Sep 25 11:22, 2014. Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3. </div> </body> diff --git a/doc/html/searchindex.js b/doc/html/searchindex.js index 87a8913917062b5c258ee4cb3006ce7b9c9e54d9..7aeb31c4266540ce82ed9b7d7c0d4e687769cdf7 100644 --- a/doc/html/searchindex.js +++ b/doc/html/searchindex.js @@ -1 +1 @@ -Search.setIndex({envversion:42,terms:{aln:6,all:[8,0,1,4,6],code:[8,0,4],forget:[8,4],chain:[4,6],messi:4,skip:4,forbidden:4,sidechains_unit_test:4,ost:[0,1,2,3,4,5,6,7,8,9,10],disable_document:[8,4],prefix:[4,0],concept:4,subclass:4,abil:4,follow:[4,6],middl:4,structuralgap:1,readabl:4,init:4,program:7,under:4,introduc:4,sourc:[8,0,4],everi:[4,6],string:0,fals:[4,0,1,6],internet:4,candid:1,worst:4,failur:[4,0],veri:[4,0],affect:4,relev:8,tri:6,four:1,magic:4,solver:4,did:4,list:[8,0,1,4,6],assertequ:4,item:[4,6],fileextens:0,smallish:[8,4],align:6,dir:4,malici:4,promod_gcc_45:4,your_modul:4,direct:4,past:4,second:6,design:0,pass:4,download:8,acid:6,even:[8,4],index:[4,3],what:[8,0,4],hide:4,sub:4,resembl:4,sum:1,invok:[8,4],anywai:4,current:4,delet:6,version:[8,4],"new":[4,1,6],boost:[0,1,2,3,4,5,6,7,8,9,10],method:1,meld:5,subtre:4,submodule1:4,honour:1,gener:4,never:4,here:[8,0,4,6],lib_stage_path:4,let:4,set_directory_properti:4,path:[8,0,4],along:4,modifi:[4,6,5],implicit:8,valu:[8,0],wait:4,test_someth:4,search:[8,3,4],executable_output_path:4,setup_boost:4,shader:[],promod3_version_minor:4,doctest:[8,4],action:4,implement:4,pack:1,honor:6,chanc:4,methionin:6,via:4,extra:4,solut:4,modul:5,submodul:4,ask:4,unix:4,api:[],instal:[8,4],total:1,unit:8,highli:8,fed:4,from:[0,1,5,6,8,9,4],describ:0,would:[8,4],regist:4,two:4,next:4,everybodi:4,few:[8,4,1,6],live:4,call:[8,4],recommend:8,loadalign:6,checkout:4,tell:[4,0],tightli:4,more:[8,4,6],sort:1,trustworthi:4,peopl:4,relat:4,notic:4,warn:4,flag:[4,0],include_directori:4,particular:4,known:0,rare:4,hold:[1,6],cach:[8,4],must:4,ost_double_precis:8,py_run:4,hous:4,setup:[4,5],work:[8,4],histori:4,remain:6,paragraph:4,can:[8,0,4,6],torsion_scor:1,purpos:4,root:4,fetch:[4,0],def:4,control:4,give:4,process:4,add_argu:0,indic:0,topic:4,abort:4,want:[8,4],phrase:4,backbonelist:1,hydrogen:6,packing_scor:1,alwai:4,gcc:4,cours:4,end:[8,0,1,4],thing:[8,4],rather:4,peptid:[1,6],comfort:0,calpha_onli:6,"__init__":4,opt:0,instead:[8,0,4],config:4,updat:4,python_vers:4,product:4,entityhandl:[1,6],rebas:4,mess:4,dive:4,after:[8,4],usabl:4,sortbyscor:1,befor:4,wrong:8,attent:4,date:4,multipl:4,data:4,grow:6,man:[8,4],subsequ:6,"short":4,essenti:4,practic:4,mol_alg:4,sit:4,correspond:[4,1],stash:4,exclud:4,alias:4,"switch":4,maintain:4,environ:4,allow:4,exclus:4,order:1,origin:4,promod3_version_major:4,eigen:[8,4],over:[8,4,6],insight:4,becaus:[8,4],increas:1,through:4,files_to_be_remov:4,gitignor:4,still:4,pointer:8,disable_disable_doctest:4,entiti:[4,1],perfect:4,output_vari:4,binari:4,fix:[4,0],selenium:6,structuralgaplist:6,runnabl:4,carri:[4,0],complex:4,onc:4,python_doc_url:4,therefor:4,easier:1,linkcheck:[8,4],them:4,good:4,"return":[0,1,6],thei:[8,4,1],python:[0,1,2,3,4,5,6,7,8,9,10],dai:0,exot:4,"break":4,framework:4,conquer:4,clash_bb_scor:1,verifi:0,front:[8,0,4],now:[4,6],minimalist:6,cmake_cxx_flags_releas:4,libexec_stage_path:4,name:[4,0],rmsd:1,anyth:[8,4],level:[8,4],separ:4,easili:4,achiev:4,each:4,debug:4,found:4,went:4,higher:8,side:4,mean:[8,0,4],compil:4,monolith:4,parwis:6,strip:6,idea:[4,5],realli:[8,0,4],runtest:4,member:[4,6],"static":4,coord:1,our:4,extract:4,special:[8,4],out:[8,4],variabl:[8,4],shown:4,goe:[8,4],promod3_unittest:4,crucial:4,content:[4,3,10],reader:4,print:[8,6],got:8,exec_program:4,clone:4,common:[4,0],model:7,make_directori:4,runtimeerror:[1,6],given:[0,1],free:4,standard:8,headlin:4,reason:4,base:[0,6],term:4,put:[8,0,4],org:4,basi:4,could:[4,6],keep:4,turn:[4,0],clash_sc_scor:1,place:4,think:4,first:[4,5],oper:4,softwar:4,major:4,suffix:0,obviou:4,prevent:4,feel:4,sidechains_pymod:4,number:[1,6],yourself:[8,4],restrict:4,mai:[8,4,6],alreadi:4,done:4,messag:[4,0],blank:4,stabl:4,miss:[0,1,6],straight:4,exit_statu:0,differ:[8,4],script:[8,0,4],top:[8,4],perfectli:4,mkdir:4,system:[8,4,5],least:[8,4],tradition:0,attach:6,stori:4,master:4,too:4,termin:0,scheme:4,"final":[4,6],store:[4,1,6],shell:[8,0],option:[8,0,4],tool:0,copi:[4,6],restrict_chain:6,openstructur:[0,1,2,3,4,5,6,7,8,9,10],part:4,pars:0,boost_include_dir:4,mostli:4,rst:4,conop:4,exactli:8,than:4,kind:4,grep:8,target:[8,4],whenev:4,provid:[8,4],seamlessli:4,tree:4,unrecognis:0,project:4,find_packag:4,reus:6,str:[0,6],were:4,posit:[0,1],toward:4,markup:4,pre:4,python_binari:4,sometim:4,mind:4,argument:8,packag:4,manner:4,have:[8,4,1,6],"__main__":4,need:[8,0,4],fasta:6,tidi:4,cmake_current_source_dir:4,optimis:4,rmsdto:1,imagin:4,built:4,advic:4,inform:6,diverg:4,self:4,also:[8,0,4,6],without:[4,0,6],take:[4,6],which:[8,4,6,7],thoroughli:4,noth:4,singl:[4,6],"_opt":4,sure:4,distribut:4,clash:1,track:0,buildrawmodel:6,compress:0,strict:4,somethingtest:4,fragment:1,eigen3_found:4,hotfix:4,"class":[4,9,1,6,7],charg:4,renam:5,url:4,doc:[8,4],later:4,cover:[4,0,7],doe:[4,0,6],ext:0,declar:4,clean:[8,4],usual:[8,4],someth:4,came:4,cmakelist:[8,4],show:4,dbg:4,attachview:6,bring:4,permiss:4,add_doc_sourc:4,fine:4,find:4,help:[8,4],involv:4,access:1,onli:[4,0,6],locat:8,explain:4,configur:[8,4],activ:4,state:[8,4],should:[4,0],score:1,suppos:[4,1],templat:6,folder:4,move:4,hit:4,unus:4,variou:8,get:[8,4],watch:4,soon:4,cannot:4,loadpdb:6,report:[4,6],toolbox:4,requir:[8,4,1],setup_compiler_flag:4,add_changelog_to_doc:4,candit:1,enabl:0,"2b1":8,gather:[4,7],whether:0,"float":1,integr:4,contain:[8,0,4,6,9],python_root:8,where:4,remov:8,view:4,user:[],set:[8,0,1,4,6],project_nam:4,seq:4,allatom_scor:1,frame:4,around:4,ost_include_dir:4,see:4,temporarili:4,mandatori:4,result:[8,4,6],smng:5,arg:4,testcas:4,close:4,sport:4,subject:4,awar:4,statu:4,detect:0,parent:6,review:4,version_great:4,enumer:4,label:4,figur:4,header_stage_path:4,subdir:4,simplest:4,"import":[8,0,4,6],awai:4,paramet:[0,1,6],approach:4,attribut:4,accord:4,extend:4,sole:4,cmake_cxx_compiler_vers:4,test_your_modul:4,solv:4,come:[4,0],addit:[4,0],fail:[4,1],extens:[0,1],howev:1,disable_doctest:[8,4],promod3_version_patch:4,tutori:4,grain:4,fno:4,modif:6,whole:[4,6],pdb:[0,6],comment:4,sidechains_rst:4,"1ake":6,point:[8,4,1],cxx:4,overview:4,unittest:4,argumentpars:0,pop:4,walk:4,residu:[1,6],header:[8,4],param:1,codetest:4,test_submodule1:4,assum:4,torsion:1,quit:4,template_structur:6,evalu:4,coupl:4,rebuild:[8,4],three:4,been:4,sinc:[8,0,4],compon:4,trigger:4,besid:8,treat:[4,6],basic:[8,4,6],ost_root:[8,4],popul:[8,4],seq_alg:4,tini:4,quickli:4,life:[4,1],convert:6,ani:4,coordin:[],togeth:4,input:0,fileexist:0,educ:4,those:[8,4],"case":4,cmake_c_compiler_vers:4,uncertain:4,look:[4,0],raw:[],testfileexistsfals:4,disable_disable_linkcheck:4,servic:4,properti:4,commerci:4,formatt:4,calcul:1,match:[4,6],abov:4,error:0,dost_root:[8,4],loop:[],stage_dir:4,spawn:4,real:4,test_sidechain:4,helper:1,readi:8,sidechain:[4,1,6],henc:4,non:4,itself:4,clutter:4,conf:[8,4],protein:[9,6],vanish:4,dedic:[8,4],sever:[8,4],reviv:4,disabl:4,develop:[],fedora:4,etc:4,author:4,suggest:4,belong:4,savepdb:6,same:[8,4,1],"while":[4,0],promod3_version_str:4,funni:8,drawback:4,admir:4,document:[8,5],start:8,conflict:4,complet:[4,6],http:4,again:[8,4],optim:[8,4],bienchen:4,argpars:0,hand:8,driven:4,moment:4,rais:[1,6],disable_linkcheck:[8,4],initi:5,kic:4,respons:4,stack:4,expand:4,recent:4,task:4,off:[4,6],pymod:4,nevertheless:4,macro:4,builder:8,well:[8,4,1,6],exampl:[8,4,6],command:[],branchnam:4,thi:[0,1,6,7,8,9,4],endif:4,gzip:0,everyth:4,academ:4,loss:4,spend:4,latest:8,cmake_support:4,clash_scor:1,just:[8,4],entri:4,mol:4,reduced_scor:1,obtain:6,reserv:0,legal:4,touch:4,rest:[0,1,2,3,4,5,6,7,8,9,10],web:[8,4],loopcandid:1,lapack:[8,4],restructuredtext:[0,1,2,3,4,5,6,7,8,9,10],makefil:[8,4],except:4,littl:4,add:[4,1],eigen3:4,densiti:1,els:4,save:4,boost_root:8,bin:4,advis:4,format:4,handl:6,specimen:0,setup_stag:4,piec:4,source2:4,source1:4,know:8,background:8,elabor:4,bit:[8,4],cmake_compiler_is_gnucxx:4,mod:4,eigen3_include_dir:[8,4],insert:[1,6],like:[8,4,6],success:[0,1],incred:6,manual:[8,4],html:[8,4,5],test_:4,test_awesome_featur:4,"boolean":0,either:[4,6],output:[4,0],hook:4,page:[8,3,4],www:4,drop:4,often:[4,0],acknowledg:4,some:[8,0,4],begin:4,resolv:4,intern:4,proper:4,librari:4,qmean:[8,4],thu:0,txt:[8,4],lead:0,avoid:4,definit:4,per:[4,7],exit:0,select:6,recognis:4,sequenc:[9,1,6],condit:4,amino:6,core:0,plu:4,cmake_source_dir:4,backbon:[1,6],step:4,promot:4,repositori:[4,5],"__name__":4,cmake_minimum_requir:4,intervent:4,mmcif:0,stage:8,chapter:4,src:4,about:[4,6],actual:[4,1],most:[4,0,6],materi:4,manag:4,coars:4,commit:4,ost_doc_url:4,produc:8,qmean_root:[8,4],within:[8,4],automat:[4,0],due:[1,6],right:[8,4],empti:4,cmake_cxx_flag:4,cmake_module_path:4,announc:4,your:8,merg:4,git:[8,5],fill:4,log:4,wai:[8,4],pictur:4,qmean_include_dir:4,support:[4,0],renumb:6,custom:4,avail:[8,4],lost:4,sortbycorrel:1,much:[4,6],interfac:4,includ:[4,0,5],lot:[4,0],suit:4,forward:4,parse_arg:0,unfortun:4,"function":0,headach:4,unexpect:8,enough:4,tupl:0,forg:4,wno:4,back:4,link:[8,4],atom:[1,6],don:[8,4],line:[],inlin:4,"true":[4,0,1,6],bug:4,pull:[8,4],tripl:0,immedi:4,consist:4,possibl:[4,6],"default":[8,4],type:[0,1,6],insertinto:1,displai:0,below:4,otherwis:4,problem:4,similar:8,eigenvector:4,testutil:4,featur:4,creat:[8,4],"int":0,certain:8,utilis:[4,0],fellow:4,incomplet:6,exist:[4,0,1],file:8,dqmean_root:[8,4],deuterium:6,check:[8,0,4],probabl:[8,4],echo:4,cmakecach:8,calpha:6,when:[4,6],detail:[4,6],other:[8,4,6],bool:[0,1],seem:4,test:8,you:[8,0,4],phosphoserin:6,nice:4,correl:1,bb_list:1,toentiti:1,additional_make_clean_fil:4,extern:4,determin:0,rawmodelingresult:6,devot:7,cmake_build_typ:4,add_subdirectori:4,briefli:4,eigenvalu:4,consid:4,gap:[1,6],homolog:7,doptim:4,fatal_error:4,stai:4,reduc:1,sphinx:[0,1,2,3,4,5,6,7,8,9,10],algorithm:[4,6],project_binary_dir:4,directori:8,descript:4,pseudo:6,rule:4,ignor:6,time:[4,6],push:4},objtypes:{"0":"py:module","1":"py:function","2":"py:method","3":"py:attribute","4":"py:class"},objnames:{"0":["py","module","Python module"],"1":["py","function","Python function"],"2":["py","method","Python method"],"3":["py","attribute","Python attribute"],"4":["py","class","Python class"]},filenames:["core/argcheck","meld/loop","users","index","contributing","changelog","meld/rawmodel","core/index","buildsystem","meld/index","developers"],titles:["<tt class=\"docutils literal\"><span class=\"pre\">argcheck</span></tt> - Standard tests for command line arguments","Loop Modeling","Documentation For Users","Welcome to ProMod3’s documentation!","Contributing","Changelog","Raw Coordinate Modeling","<tt class=\"docutils literal\"><span class=\"pre\">core</span></tt> - ProMod3 core functionality","Building ProMod3","<tt class=\"docutils literal\"><span class=\"pre\">meld</span></tt> - Coordinate modeling","Documentation For Developes"],objects:{"promod3.core.argcheck":{FileExtension:[0,1,1,""],FileExists:[0,1,1,""]},"sm.meld.LoopCandidate":{correl:[1,3,1,""],clash_score:[1,3,1,""],allatom_score:[1,3,1,""],score:[1,3,1,""],reduced_score:[1,3,1,""],torsion_score:[1,3,1,""],InsertInto:[1,2,1,""],gap:[1,3,1,""],clash_sc_score:[1,3,1,""],ToEntity:[1,2,1,""],clash_bb_score:[1,3,1,""],coords:[1,3,1,""],packing_score:[1,3,1,""],RmsdTo:[1,2,1,""]},"sm.meld":{LoopCandidate:[1,4,1,""],LoopCandidates:[1,4,1,""],BuildRawModel:[6,1,1,""],RawModelingResult:[6,4,1,""]},"sm.meld.RawModelingResult":{model:[6,3,1,""],gaps:[6,3,1,""]},"sm.meld.LoopCandidates":{SortByScore:[1,2,1,""],model:[1,3,1,""],SortByCorrel:[1,2,1,""],Add:[1,2,1,""]},promod3:{core:[7,0,0,"-"],meld:[9,0,0,"-"]}},titleterms:{own:4,modul:4,argument:0,indic:3,raw:6,api:[1,6],file:0,tabl:3,argcheck:0,your:4,unit:4,git:4,develop:10,welcom:3,start:4,parti:4,make:8,write:4,how:4,build:8,branch:4,test:[4,0],document:[4,3,10,2],promod3:[8,3,7],meld:9,"function":7,core:7,run:8,contribut:4,standard:0,coordin:[9,6],user:2,releas:5,cmake:[8,4],line:0,model:[9,1,6],stage:4,third:4,changelog:5,directori:4,introduct:[0,6],structur:4,issu:4,command:0,chang:5,licens:4,loop:1,depend:8}}) \ No newline at end of file +Search.setIndex({envversion:42,terms:{aln:6,all:[8,0,1,4,6],code:[8,0,4],forget:[8,4],chain:[4,6],messi:4,skip:4,forbidden:4,sidechains_unit_test:4,ost:[0,1,2,3,4,5,6,7,8,9,10],disable_document:[8,4],prefix:[4,0],concept:4,legal:4,abil:4,follow:[4,6],middl:4,structuralgap:1,readabl:4,init:4,program:7,under:4,introduc:4,sourc:[8,0,4],everi:[4,6],string:0,fals:[4,0,1,6],internet:4,candid:1,worst:4,failur:[4,0],veri:[4,0],affect:4,runnabl:4,tri:6,four:1,magic:4,solver:4,did:4,list:[8,0,1,4,6],assertequ:4,item:[4,6],fileextens:0,align:6,dir:4,malici:4,promod_gcc_45:4,your_modul:4,direct:4,past:4,second:6,design:0,pass:4,download:8,acid:6,even:[8,4],index:[4,5],what:[8,0,4],hide:4,sub:4,resembl:4,sum:1,calcul:1,find:4,current:4,delet:6,version:[8,4],"new":[4,1,6],boost:[0,1,2,3,4,5,6,7,8,9,10],method:1,meld:3,subtre:4,submodule1:4,honour:1,gener:4,never:4,here:[8,0,4,6],sphinx:[0,1,2,3,4,5,6,7,8,9,10],save:4,lib_stage_path:4,let:4,set_directory_properti:4,path:[8,0,4],along:4,modifi:[4,6,3],implicit:8,valu:[8,0],wait:4,headlin:4,search:[8,5,4],produc:8,executable_output_path:4,setup_boost:4,shader:[],promod3_version_minor:4,doctest:[8,4],within:[8,4],action:4,implement:4,stage_dir:4,honor:6,chanc:4,argpars:0,spawn:4,via:4,extra:4,activ:4,modul:3,submodul:4,put:[8,0,4],unix:4,api:[],instal:[8,4],total:1,unit:[],highli:8,fed:4,from:[0,1,3,6,8,9,4],describ:0,would:[8,4],regist:4,two:4,next:4,everybodi:4,few:[8,4,1,6],live:4,call:[8,4],recommend:8,loadalign:6,checkout:4,tell:[4,0],tightli:4,more:[8,4,6],sort:1,chapter:4,peopl:4,relat:4,notic:4,warn:4,flag:[4,0],include_directori:4,particular:4,known:0,actual:[4,1],hold:[1,6],cach:[8,4],must:4,ost_double_precis:8,py_run:4,hous:4,setup:[4,3],work:[8,4],histori:4,remain:6,paragraph:4,can:[8,0,4,6],torsion_scor:1,purpos:4,root:4,fetch:[4,0],def:4,control:4,give:4,process:4,add_argu:0,indic:0,topic:4,abort:4,want:[8,4],phrase:4,backbonelist:1,hydrogen:6,packing_scor:1,alwai:4,gcc:4,cours:4,end:[8,0,1,4],thing:[8,4],rather:4,comfort:0,sever:[8,4],verifi:0,config:4,updat:4,python_vers:4,product:4,entityhandl:[1,6],rebas:4,mess:4,clone:4,after:[8,4],usabl:4,sortbyscor:1,befor:4,wrong:8,attent:4,mai:[8,4,6],multipl:4,data:4,grow:6,man:[8,4],"short":4,essenti:4,practic:4,ost_doc_url:4,sit:4,correspond:[4,1],stash:4,exclud:4,alias:4,"switch":4,maintain:4,environ:4,allow:4,exclus:4,order:1,origin:4,promod3_version_major:4,eigen:[8,4],over:[8,4,6],insight:4,becaus:[8,4],report:[4,6],through:4,same:[8,4,1],gitignor:4,still:4,pointer:8,disable_disable_doctest:4,entiti:[4,1],perfect:4,output_vari:4,funni:8,fix:[4,0],selenium:6,structuralgaplist:6,relev:8,carri:[4,0],drawback:4,onc:4,bin:4,python_doc_url:4,therefor:4,easier:1,linkcheck:[8,4],them:4,good:4,"return":[0,1,6],thei:[8,4,1],python:[0,1,2,3,4,5,6,7,8,9,10],dai:0,exot:4,"break":4,framework:4,conquer:4,clash_bb_scor:1,instead:[8,0,4],front:[8,0,4],now:[4,6],minimalist:6,cmake_cxx_flags_releas:4,libexec_stage_path:4,name:[4,0],rmsd:1,anyth:[8,4],drop:4,separ:4,easili:4,achiev:4,each:4,debug:4,found:4,went:4,complet:[4,6],side:4,mean:[8,0,4],compil:4,everyth:4,monolith:4,parwis:6,cmake_module_path:4,test_sidechain:4,idea:[4,3],realli:[8,0,4],runtest:4,"static":4,"2b1":8,our:4,extract:4,special:[8,4],out:[8,4],variabl:[8,4],shown:4,goe:[8,4],promod3_unittest:4,crucial:4,content:[4,5,10],reader:4,print:[8,6],got:8,exec_program:4,merg:4,dive:4,integr:4,runtimeerror:[1,6],differ:[8,4],free:4,standard:[],test_someth:4,reason:4,base:[0,6],ask:4,org:4,basi:4,could:[4,6],insert:[1,6],keep:4,turn:[4,0],clash_sc_scor:1,place:4,think:4,first:[4,3],oper:4,softwar:4,major:4,suffix:0,obviou:4,prevent:4,feel:4,sidechains_pymod:4,number:[1,6],yourself:[8,4],restrict:4,date:4,alreadi:4,done:4,least:[8,4],blank:4,stabl:4,miss:[0,1,6],exit_statu:0,given:[0,1],level:[8,4],script:[8,0,4],top:[8,4],perfectli:4,mkdir:4,system:[8,4,3],messag:[4,0],stack:4,attach:6,stori:4,master:4,too:4,termin:0,scheme:4,"final":[4,6],store:[4,1,6],includ:[4,0,3],shell:[8,0],option:[8,0,4],tool:0,copi:[4,6],restrict_chain:6,openstructur:[0,1,2,3,4,5,6,7,8,9,10],part:4,pars:0,boost_include_dir:4,mostli:4,rst:4,off:[4,6],exactli:8,than:4,kind:4,grep:8,target:[8,4],whenev:4,provid:[8,4],seamlessli:4,tree:4,unrecognis:0,project:4,nevertheless:4,reus:6,str:[0,6],were:4,posit:[0,1],toward:4,initi:3,builder:8,pre:4,python_binari:4,sometim:4,mind:4,argument:[],packag:4,manner:4,have:[8,4,1,6],"__main__":4,need:[8,0,4],fasta:6,tidi:4,cmake_current_source_dir:4,optimis:4,rmsdto:1,imagin:4,probabl:[8,4],built:4,advic:4,inform:6,diverg:4,self:4,dedic:[8,4],also:[8,0,4,6],exampl:[8,4,6],take:[4,6],which:[8,4,6,7],thoroughli:4,noth:4,singl:[4,6],"_opt":4,sure:4,distribut:4,clash:1,track:0,forg:4,compress:0,strict:4,wno:4,fragment:1,eigen3_found:4,hotfix:4,"class":[4,9,1,6,7],charg:4,renam:3,bug:4,url:4,doc:[8,4],later:4,cover:[4,0,7],doe:[4,0,6],ext:0,declar:4,clean:[8,4],latest:8,review:4,came:4,cmakelist:[8,4],show:4,test_suite_your_module_run:4,dbg:4,attachview:6,bring:4,permiss:4,cmake_support:4,fine:4,anywai:4,help:[8,4],involv:4,access:1,onli:[4,0,6],locat:8,explain:4,configur:[8,4],solut:4,figur:4,should:[4,0],header_stage_path:4,suppos:[4,1],templat:6,folder:4,move:4,hit:4,unus:4,variou:8,get:[8,4],watch:4,soon:4,cannot:4,loadpdb:6,increas:1,toolbox:4,requir:[8,4,1],setup_compiler_flag:4,add_changelog_to_doc:4,candit:1,enabl:0,coord:1,"default":[8,4],common:[4,0],contain:[8,0,4,6,9],python_root:8,where:4,remov:8,view:4,set:[8,0,1,4,6],project_nam:4,seq:4,allatom_scor:1,frame:4,ost_include_dir:4,see:4,temporarili:4,mandatori:4,result:[8,4,6],arg:4,testcas:4,close:4,sport:4,servic:4,subject:4,awar:4,statu:4,detect:0,extend:4,someth:4,version_great:4,enumer:4,label:4,state:[8,4],score:1,subdir:4,simplest:4,"import":[8,0,4,6],awai:4,paramet:[0,1,6],approach:4,attribut:4,accord:4,parent:6,sole:4,cmake_cxx_compiler_vers:4,test_your_modul:4,recent:4,solv:4,come:[4,0],addit:[4,0],fail:[4,1],extens:[0,1],howev:1,disable_doctest:[8,4],promod3_version_patch:4,tutori:4,grain:4,fno:4,modif:6,whole:[4,6],pdb:[0,6],comment:4,sidechains_rst:4,"1ake":6,point:[8,4,1],cxx:4,overview:4,unittest:4,argumentpars:0,pop:4,walk:4,residu:[1,6],header:[8,4],featur:4,littl:4,test_submodule1:4,assum:4,torsion:1,quit:4,template_structur:6,creat:[8,4],coupl:4,rebuild:[8,4],three:4,been:4,sinc:[8,0,4],compon:4,trigger:4,besid:8,treat:[4,6],basic:[8,4,6],txt:[8,4],ost_root:[8,4],popul:[8,4],seq_alg:4,tini:4,quickli:4,life:[4,1],convert:6,ani:4,coordin:[],togeth:4,els:4,fileexist:0,educ:4,those:[8,4],"case":4,cmake_c_compiler_vers:4,uncertain:4,look:[4,0],raw:[],testfileexistsfals:4,disable_disable_linkcheck:4,straight:4,properti:4,commerci:4,formatt:4,invok:[8,4],boost_root:8,abov:4,error:0,dost_root:[8,4],loop:[],pack:1,methionin:6,real:4,smng:3,helper:1,readi:8,sidechain:[4,1,6],henc:4,non:4,itself:4,clutter:4,conf:[8,4],protein:[9,6],vanish:4,calpha_onli:6,"__init__":4,reviv:4,develop:[],fedora:4,etc:4,suggest:4,belong:4,savepdb:6,files_to_be_remov:4,"while":[4,0],member:[4,6],binari:4,complex:4,advis:4,admir:4,document:3,start:[],conflict:4,higher:8,http:4,cmakecach:8,optim:[8,4],bienchen:4,make_directori:4,hand:8,driven:4,moment:4,rais:[1,6],disable_linkcheck:[8,4],user:[],kic:4,respons:4,tradition:0,expand:4,codetest:4,task:4,conop:4,pymod:4,find_packag:4,macro:4,markup:4,well:[8,4,1,6],without:[4,0,6],command:[],branchnam:4,thi:[0,1,6,7,8,9,4],endif:4,gzip:0,model:7,academ:4,spend:4,piec:4,usual:[8,4],add_doc_sourc:4,clash_scor:1,just:[8,4],entri:4,elabor:4,reduced_scor:1,obtain:6,reserv:0,touch:4,rest:[0,1,2,3,4,5,6,7,8,9,10],web:[8,4],loopcandid:1,lapack:[8,4],restructuredtext:[0,1,2,3,4,5,6,7,8,9,10],makefil:[8,4],except:4,param:1,add:[4,1],eigen3:4,densiti:1,input:0,subsequ:6,match:[4,6],opt:0,around:4,format:4,handl:6,specimen:0,term:4,source2:4,source1:4,know:8,background:8,mol:4,bit:[8,4],you:[8,0,4],mod:4,eigen3_include_dir:[8,4],loss:4,like:[8,4,6],success:[0,1],incred:6,manual:[8,4],html:[8,4,3],test_:4,test_awesome_featur:4,"boolean":0,either:[4,6],output:[4,0],hook:4,page:[8,5,4],www:4,right:[8,4],often:[4,0],acknowledg:4,some:[8,0,4],begin:4,resolv:4,intern:4,proper:4,librari:4,qmean:[8,4],thu:0,smallish:[8,4],lead:0,avoid:4,definit:4,subclass:4,exit:0,select:6,recognis:4,devot:7,condit:4,amino:6,core:0,plu:4,cmake_source_dir:4,backbon:[1,6],step:4,promot:4,repositori:[4,3],"__name__":4,add_subdirectori:4,intervent:4,mmcif:0,stage:[],trustworthi:4,src:4,about:[4,6],rare:4,most:[4,0,6],materi:4,manag:4,coars:4,commit:4,mol_alg:4,disabl:4,qmean_root:[8,4],"float":1,automat:[4,0],due:[1,6],promod3_version_str:4,empti:4,cmake_cxx_flag:4,strip:6,announc:4,your:[],per:[4,7],git:3,log:4,wai:[8,4],pictur:4,qmean_include_dir:4,support:[4,0],renumb:6,custom:4,avail:[8,4],lost:4,sortbycorrel:1,much:[4,6],interfac:4,author:4,lot:[4,0],suit:4,forward:4,parse_arg:0,unfortun:4,"function":0,headach:4,unexpect:8,enough:4,tupl:0,buildrawmodel:6,somethingtest:4,back:4,link:[8,4],atom:[1,6],don:[8,4],line:[],inlin:4,"true":[4,0,1,6],setup_stag:4,pull:[8,4],tripl:0,immedi:4,consist:4,possibl:[4,6],whether:0,type:[0,1,6],insertinto:1,displai:0,below:4,otherwis:4,problem:4,similar:8,eigenvector:4,testutil:4,gather:[4,7],evalu:4,"int":0,certain:8,utilis:[4,0],fellow:4,incomplet:6,exist:[4,0,1],file:[],dqmean_root:[8,4],deuterium:6,check:[8,0,4],fill:4,echo:4,again:[8,4],calpha:6,when:[4,6],detail:[4,6],other:[8,4,6],bool:[0,1],seem:4,test:[],cmake_compiler_is_gnucxx:4,phosphoserin:6,nice:4,correl:1,bb_list:1,toentiti:1,additional_make_clean_fil:4,extern:4,determin:0,rawmodelingresult:6,sequenc:[9,1,6],cmake_build_typ:4,cmake_minimum_requir:4,briefli:4,eigenvalu:4,consid:4,gap:[1,6],homolog:7,doptim:4,fatal_error:4,stai:4,reduc:1,peptid:[1,6],algorithm:[4,6],project_binary_dir:4,directori:[],descript:4,pseudo:6,rule:4,ignor:6,time:[4,6],push:4},objtypes:{"0":"py:module","1":"py:function","2":"py:method","3":"py:attribute","4":"py:class"},objnames:{"0":["py","module","Python module"],"1":["py","function","Python function"],"2":["py","method","Python method"],"3":["py","attribute","Python attribute"],"4":["py","class","Python class"]},filenames:["core/argcheck","meld/loop","users","changelog","contributing","index","meld/rawmodel","core/index","buildsystem","meld/index","developers"],titles:["<tt class=\"docutils literal\"><span class=\"pre\">argcheck</span></tt> - Standard tests for command line arguments","Loop Modeling","Documentation For Users","Changelog","Contributing","Welcome to ProMod3’s documentation!","Raw Coordinate Modeling","<tt class=\"docutils literal\"><span class=\"pre\">core</span></tt> - ProMod3 core functionality","Building ProMod3","<tt class=\"docutils literal\"><span class=\"pre\">meld</span></tt> - Coordinate modeling","Documentation For Developes"],objects:{"promod3.core.argcheck":{FileExtension:[0,1,1,""],FileExists:[0,1,1,""]},"sm.meld.LoopCandidate":{correl:[1,3,1,""],clash_score:[1,3,1,""],allatom_score:[1,3,1,""],score:[1,3,1,""],reduced_score:[1,3,1,""],torsion_score:[1,3,1,""],InsertInto:[1,2,1,""],gap:[1,3,1,""],clash_sc_score:[1,3,1,""],ToEntity:[1,2,1,""],clash_bb_score:[1,3,1,""],coords:[1,3,1,""],packing_score:[1,3,1,""],RmsdTo:[1,2,1,""]},"sm.meld":{LoopCandidate:[1,4,1,""],LoopCandidates:[1,4,1,""],BuildRawModel:[6,1,1,""],RawModelingResult:[6,4,1,""]},"sm.meld.RawModelingResult":{model:[6,3,1,""],gaps:[6,3,1,""]},"sm.meld.LoopCandidates":{SortByScore:[1,2,1,""],model:[1,3,1,""],SortByCorrel:[1,2,1,""],Add:[1,2,1,""]},promod3:{core:[7,0,0,"-"],meld:[9,0,0,"-"]}},titleterms:{own:4,modul:4,argument:0,indic:5,raw:6,api:[1,6],file:0,tabl:5,run:8,your:4,unit:4,git:4,develop:10,welcom:5,how:4,parti:4,make:8,write:4,start:4,build:8,branch:4,test:[4,0],document:[4,5,10,2],promod3:[8,5,7],meld:9,"function":7,core:7,argcheck:0,contribut:4,standard:0,coordin:[9,6],user:2,releas:3,cmake:[8,4],line:0,chang:3,stage:4,third:4,changelog:3,directori:4,introduct:[0,6],structur:4,issu:4,command:0,model:[9,1,6],licens:4,loop:1,depend:8}}) \ No newline at end of file