Code cleanup: added tests for amino acids and updated doc. for structure comparisons.

modules/conop/tests/CMakeLists.txt

 set(OST_CONOP_UNIT_TESTS
+  test_amino_acids.cc
   test_heuristic_conop.cc
   tests.cc
   test_rule_based_conop.cc 

modules/conop/tests/test_amino_acids.cc

+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2016 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+//------------------------------------------------------------------------------
+
+/*
+  Author: Gerardo Tauriello
+ */
+
+#define BOOST_TEST_DYN_LINK
+#include <boost/test/unit_test.hpp>
+#include <boost/test/auto_unit_test.hpp>
+
+#include <ost/conop/amino_acids.hh>
+
+using namespace ost;
+using namespace ost::conop;
+
+BOOST_AUTO_TEST_SUITE(conop);
+
+BOOST_AUTO_TEST_CASE(test_amino_acid_to_residue_name) {
+  BOOST_CHECK_EQUAL(AminoAcidToResidueName(ALA), "ALA");
+  BOOST_CHECK_EQUAL(AminoAcidToResidueName(ARG), "ARG");
+  BOOST_CHECK_EQUAL(AminoAcidToResidueName(ASN), "ASN");
+  BOOST_CHECK_EQUAL(AminoAcidToResidueName(ASP), "ASP");
+  BOOST_CHECK_EQUAL(AminoAcidToResidueName(CYS), "CYS");
+  BOOST_CHECK_EQUAL(AminoAcidToResidueName(GLU), "GLU");
+  BOOST_CHECK_EQUAL(AminoAcidToResidueName(GLN), "GLN");
+  BOOST_CHECK_EQUAL(AminoAcidToResidueName(GLY), "GLY");
+  BOOST_CHECK_EQUAL(AminoAcidToResidueName(HIS), "HIS");
+  BOOST_CHECK_EQUAL(AminoAcidToResidueName(ILE), "ILE");
+  BOOST_CHECK_EQUAL(AminoAcidToResidueName(LEU), "LEU");
+  BOOST_CHECK_EQUAL(AminoAcidToResidueName(LYS), "LYS");
+  BOOST_CHECK_EQUAL(AminoAcidToResidueName(MET), "MET");
+  BOOST_CHECK_EQUAL(AminoAcidToResidueName(PHE), "PHE");
+  BOOST_CHECK_EQUAL(AminoAcidToResidueName(PRO), "PRO");
+  BOOST_CHECK_EQUAL(AminoAcidToResidueName(SER), "SER");
+  BOOST_CHECK_EQUAL(AminoAcidToResidueName(THR), "THR");
+  BOOST_CHECK_EQUAL(AminoAcidToResidueName(TRP), "TRP");
+  BOOST_CHECK_EQUAL(AminoAcidToResidueName(TYR), "TYR");
+  BOOST_CHECK_EQUAL(AminoAcidToResidueName(VAL), "VAL");
+  BOOST_CHECK_EQUAL(AminoAcidToResidueName(XXX), "UNK");
+}
+
+BOOST_AUTO_TEST_CASE(test_one_letter_code_to_residue_name) {
+  BOOST_CHECK_EQUAL(OneLetterCodeToResidueName('A'), "ALA");
+  BOOST_CHECK_EQUAL(OneLetterCodeToResidueName('R'), "ARG");
+  BOOST_CHECK_EQUAL(OneLetterCodeToResidueName('N'), "ASN");
+  BOOST_CHECK_EQUAL(OneLetterCodeToResidueName('D'), "ASP");
+  BOOST_CHECK_EQUAL(OneLetterCodeToResidueName('C'), "CYS");
+  BOOST_CHECK_EQUAL(OneLetterCodeToResidueName('E'), "GLU");
+  BOOST_CHECK_EQUAL(OneLetterCodeToResidueName('Q'), "GLN");
+  BOOST_CHECK_EQUAL(OneLetterCodeToResidueName('G'), "GLY");
+  BOOST_CHECK_EQUAL(OneLetterCodeToResidueName('H'), "HIS");
+  BOOST_CHECK_EQUAL(OneLetterCodeToResidueName('I'), "ILE");
+  BOOST_CHECK_EQUAL(OneLetterCodeToResidueName('L'), "LEU");
+  BOOST_CHECK_EQUAL(OneLetterCodeToResidueName('K'), "LYS");
+  BOOST_CHECK_EQUAL(OneLetterCodeToResidueName('M'), "MET");
+  BOOST_CHECK_EQUAL(OneLetterCodeToResidueName('F'), "PHE");
+  BOOST_CHECK_EQUAL(OneLetterCodeToResidueName('P'), "PRO");
+  BOOST_CHECK_EQUAL(OneLetterCodeToResidueName('S'), "SER");
+  BOOST_CHECK_EQUAL(OneLetterCodeToResidueName('T'), "THR");
+  BOOST_CHECK_EQUAL(OneLetterCodeToResidueName('W'), "TRP");
+  BOOST_CHECK_EQUAL(OneLetterCodeToResidueName('Y'), "TYR");
+  BOOST_CHECK_EQUAL(OneLetterCodeToResidueName('V'), "VAL");
+  // should also wiork if not uppercase!
+  BOOST_CHECK_EQUAL(OneLetterCodeToResidueName('a'), "ALA");
+  BOOST_CHECK_EQUAL(OneLetterCodeToResidueName('r'), "ARG");
+  BOOST_CHECK_EQUAL(OneLetterCodeToResidueName('n'), "ASN");
+  BOOST_CHECK_EQUAL(OneLetterCodeToResidueName('d'), "ASP");
+  BOOST_CHECK_EQUAL(OneLetterCodeToResidueName('c'), "CYS");
+  BOOST_CHECK_EQUAL(OneLetterCodeToResidueName('e'), "GLU");
+  BOOST_CHECK_EQUAL(OneLetterCodeToResidueName('q'), "GLN");
+  BOOST_CHECK_EQUAL(OneLetterCodeToResidueName('g'), "GLY");
+  BOOST_CHECK_EQUAL(OneLetterCodeToResidueName('h'), "HIS");
+  BOOST_CHECK_EQUAL(OneLetterCodeToResidueName('i'), "ILE");
+  BOOST_CHECK_EQUAL(OneLetterCodeToResidueName('l'), "LEU");
+  BOOST_CHECK_EQUAL(OneLetterCodeToResidueName('k'), "LYS");
+  BOOST_CHECK_EQUAL(OneLetterCodeToResidueName('m'), "MET");
+  BOOST_CHECK_EQUAL(OneLetterCodeToResidueName('f'), "PHE");
+  BOOST_CHECK_EQUAL(OneLetterCodeToResidueName('p'), "PRO");
+  BOOST_CHECK_EQUAL(OneLetterCodeToResidueName('s'), "SER");
+  BOOST_CHECK_EQUAL(OneLetterCodeToResidueName('t'), "THR");
+  BOOST_CHECK_EQUAL(OneLetterCodeToResidueName('w'), "TRP");
+  BOOST_CHECK_EQUAL(OneLetterCodeToResidueName('y'), "TYR");
+  BOOST_CHECK_EQUAL(OneLetterCodeToResidueName('v'), "VAL");
+  // unknown ones
+  BOOST_CHECK_EQUAL(OneLetterCodeToResidueName('B'), "UNK");
+  BOOST_CHECK_EQUAL(OneLetterCodeToResidueName('O'), "UNK");
+  BOOST_CHECK_EQUAL(OneLetterCodeToResidueName('Z'), "UNK");
+}
+
+BOOST_AUTO_TEST_CASE(test_one_letter_code_to_amino_acid) {
+  BOOST_CHECK_EQUAL(OneLetterCodeToAminoAcid('A'), ALA);
+  BOOST_CHECK_EQUAL(OneLetterCodeToAminoAcid('R'), ARG);
+  BOOST_CHECK_EQUAL(OneLetterCodeToAminoAcid('N'), ASN);
+  BOOST_CHECK_EQUAL(OneLetterCodeToAminoAcid('D'), ASP);
+  BOOST_CHECK_EQUAL(OneLetterCodeToAminoAcid('C'), CYS);
+  BOOST_CHECK_EQUAL(OneLetterCodeToAminoAcid('E'), GLU);
+  BOOST_CHECK_EQUAL(OneLetterCodeToAminoAcid('Q'), GLN);
+  BOOST_CHECK_EQUAL(OneLetterCodeToAminoAcid('G'), GLY);
+  BOOST_CHECK_EQUAL(OneLetterCodeToAminoAcid('H'), HIS);
+  BOOST_CHECK_EQUAL(OneLetterCodeToAminoAcid('I'), ILE);
+  BOOST_CHECK_EQUAL(OneLetterCodeToAminoAcid('L'), LEU);
+  BOOST_CHECK_EQUAL(OneLetterCodeToAminoAcid('K'), LYS);
+  BOOST_CHECK_EQUAL(OneLetterCodeToAminoAcid('M'), MET);
+  BOOST_CHECK_EQUAL(OneLetterCodeToAminoAcid('F'), PHE);
+  BOOST_CHECK_EQUAL(OneLetterCodeToAminoAcid('P'), PRO);
+  BOOST_CHECK_EQUAL(OneLetterCodeToAminoAcid('S'), SER);
+  BOOST_CHECK_EQUAL(OneLetterCodeToAminoAcid('T'), THR);
+  BOOST_CHECK_EQUAL(OneLetterCodeToAminoAcid('W'), TRP);
+  BOOST_CHECK_EQUAL(OneLetterCodeToAminoAcid('Y'), TYR);
+  BOOST_CHECK_EQUAL(OneLetterCodeToAminoAcid('V'), VAL);
+  // should also wiork if not uppercase!
+  BOOST_CHECK_EQUAL(OneLetterCodeToAminoAcid('a'), ALA);
+  BOOST_CHECK_EQUAL(OneLetterCodeToAminoAcid('r'), ARG);
+  BOOST_CHECK_EQUAL(OneLetterCodeToAminoAcid('n'), ASN);
+  BOOST_CHECK_EQUAL(OneLetterCodeToAminoAcid('d'), ASP);
+  BOOST_CHECK_EQUAL(OneLetterCodeToAminoAcid('c'), CYS);
+  BOOST_CHECK_EQUAL(OneLetterCodeToAminoAcid('e'), GLU);
+  BOOST_CHECK_EQUAL(OneLetterCodeToAminoAcid('q'), GLN);
+  BOOST_CHECK_EQUAL(OneLetterCodeToAminoAcid('g'), GLY);
+  BOOST_CHECK_EQUAL(OneLetterCodeToAminoAcid('h'), HIS);
+  BOOST_CHECK_EQUAL(OneLetterCodeToAminoAcid('i'), ILE);
+  BOOST_CHECK_EQUAL(OneLetterCodeToAminoAcid('l'), LEU);
+  BOOST_CHECK_EQUAL(OneLetterCodeToAminoAcid('k'), LYS);
+  BOOST_CHECK_EQUAL(OneLetterCodeToAminoAcid('m'), MET);
+  BOOST_CHECK_EQUAL(OneLetterCodeToAminoAcid('f'), PHE);
+  BOOST_CHECK_EQUAL(OneLetterCodeToAminoAcid('p'), PRO);
+  BOOST_CHECK_EQUAL(OneLetterCodeToAminoAcid('s'), SER);
+  BOOST_CHECK_EQUAL(OneLetterCodeToAminoAcid('t'), THR);
+  BOOST_CHECK_EQUAL(OneLetterCodeToAminoAcid('w'), TRP);
+  BOOST_CHECK_EQUAL(OneLetterCodeToAminoAcid('y'), TYR);
+  BOOST_CHECK_EQUAL(OneLetterCodeToAminoAcid('v'), VAL);
+  // unknown ones
+  BOOST_CHECK_EQUAL(OneLetterCodeToAminoAcid('B'), XXX);
+  BOOST_CHECK_EQUAL(OneLetterCodeToAminoAcid('O'), XXX);
+  BOOST_CHECK_EQUAL(OneLetterCodeToAminoAcid('Z'), XXX);
+}
+
+BOOST_AUTO_TEST_CASE(test_residue_name_to_one_letter_code) {
+  BOOST_CHECK_EQUAL(ResidueNameToOneLetterCode("ALA"), 'A');
+  BOOST_CHECK_EQUAL(ResidueNameToOneLetterCode("ARG"), 'R');
+  BOOST_CHECK_EQUAL(ResidueNameToOneLetterCode("ASN"), 'N');
+  BOOST_CHECK_EQUAL(ResidueNameToOneLetterCode("ASP"), 'D');
+  BOOST_CHECK_EQUAL(ResidueNameToOneLetterCode("CYS"), 'C');
+  BOOST_CHECK_EQUAL(ResidueNameToOneLetterCode("GLU"), 'E');
+  BOOST_CHECK_EQUAL(ResidueNameToOneLetterCode("GLN"), 'Q');
+  BOOST_CHECK_EQUAL(ResidueNameToOneLetterCode("GLY"), 'G');
+  BOOST_CHECK_EQUAL(ResidueNameToOneLetterCode("HIS"), 'H');
+  BOOST_CHECK_EQUAL(ResidueNameToOneLetterCode("ILE"), 'I');
+  BOOST_CHECK_EQUAL(ResidueNameToOneLetterCode("LEU"), 'L');
+  BOOST_CHECK_EQUAL(ResidueNameToOneLetterCode("LYS"), 'K');
+  BOOST_CHECK_EQUAL(ResidueNameToOneLetterCode("MET"), 'M');
+  BOOST_CHECK_EQUAL(ResidueNameToOneLetterCode("PHE"), 'F');
+  BOOST_CHECK_EQUAL(ResidueNameToOneLetterCode("PRO"), 'P');
+  BOOST_CHECK_EQUAL(ResidueNameToOneLetterCode("SER"), 'S');
+  BOOST_CHECK_EQUAL(ResidueNameToOneLetterCode("THR"), 'T');
+  BOOST_CHECK_EQUAL(ResidueNameToOneLetterCode("TRP"), 'W');
+  BOOST_CHECK_EQUAL(ResidueNameToOneLetterCode("TYR"), 'Y');
+  BOOST_CHECK_EQUAL(ResidueNameToOneLetterCode("VAL"), 'V');
+  // should also wiork if not uppercase!
+  BOOST_CHECK_EQUAL(ResidueNameToOneLetterCode("Ala"), 'A');
+  BOOST_CHECK_EQUAL(ResidueNameToOneLetterCode("Arg"), 'R');
+  BOOST_CHECK_EQUAL(ResidueNameToOneLetterCode("Asn"), 'N');
+  BOOST_CHECK_EQUAL(ResidueNameToOneLetterCode("Asp"), 'D');
+  BOOST_CHECK_EQUAL(ResidueNameToOneLetterCode("Cys"), 'C');
+  BOOST_CHECK_EQUAL(ResidueNameToOneLetterCode("Glu"), 'E');
+  BOOST_CHECK_EQUAL(ResidueNameToOneLetterCode("Gln"), 'Q');
+  BOOST_CHECK_EQUAL(ResidueNameToOneLetterCode("Gly"), 'G');
+  BOOST_CHECK_EQUAL(ResidueNameToOneLetterCode("His"), 'H');
+  BOOST_CHECK_EQUAL(ResidueNameToOneLetterCode("Ile"), 'I');
+  BOOST_CHECK_EQUAL(ResidueNameToOneLetterCode("Leu"), 'L');
+  BOOST_CHECK_EQUAL(ResidueNameToOneLetterCode("Lys"), 'K');
+  BOOST_CHECK_EQUAL(ResidueNameToOneLetterCode("Met"), 'M');
+  BOOST_CHECK_EQUAL(ResidueNameToOneLetterCode("Phe"), 'F');
+  BOOST_CHECK_EQUAL(ResidueNameToOneLetterCode("Pro"), 'P');
+  BOOST_CHECK_EQUAL(ResidueNameToOneLetterCode("Ser"), 'S');
+  BOOST_CHECK_EQUAL(ResidueNameToOneLetterCode("Thr"), 'T');
+  BOOST_CHECK_EQUAL(ResidueNameToOneLetterCode("Trp"), 'W');
+  BOOST_CHECK_EQUAL(ResidueNameToOneLetterCode("Tyr"), 'Y');
+  BOOST_CHECK_EQUAL(ResidueNameToOneLetterCode("Val"), 'V');
+  // unknown ones
+  BOOST_CHECK_EQUAL(ResidueNameToOneLetterCode("MUH"), 'X');
+  BOOST_CHECK_EQUAL(ResidueNameToOneLetterCode("FOO"), 'X');
+  BOOST_CHECK_EQUAL(ResidueNameToOneLetterCode("BAR"), 'X');
+}
+
+BOOST_AUTO_TEST_CASE(test_residue_name_to_amino_acid) {
+  BOOST_CHECK_EQUAL(ResidueNameToAminoAcid("ALA"), ALA);
+  BOOST_CHECK_EQUAL(ResidueNameToAminoAcid("ARG"), ARG);
+  BOOST_CHECK_EQUAL(ResidueNameToAminoAcid("ASN"), ASN);
+  BOOST_CHECK_EQUAL(ResidueNameToAminoAcid("ASP"), ASP);
+  BOOST_CHECK_EQUAL(ResidueNameToAminoAcid("CYS"), CYS);
+  BOOST_CHECK_EQUAL(ResidueNameToAminoAcid("GLU"), GLU);
+  BOOST_CHECK_EQUAL(ResidueNameToAminoAcid("GLN"), GLN);
+  BOOST_CHECK_EQUAL(ResidueNameToAminoAcid("GLY"), GLY);
+  BOOST_CHECK_EQUAL(ResidueNameToAminoAcid("HIS"), HIS);
+  BOOST_CHECK_EQUAL(ResidueNameToAminoAcid("ILE"), ILE);
+  BOOST_CHECK_EQUAL(ResidueNameToAminoAcid("LEU"), LEU);
+  BOOST_CHECK_EQUAL(ResidueNameToAminoAcid("LYS"), LYS);
+  BOOST_CHECK_EQUAL(ResidueNameToAminoAcid("MET"), MET);
+  BOOST_CHECK_EQUAL(ResidueNameToAminoAcid("PHE"), PHE);
+  BOOST_CHECK_EQUAL(ResidueNameToAminoAcid("PRO"), PRO);
+  BOOST_CHECK_EQUAL(ResidueNameToAminoAcid("SER"), SER);
+  BOOST_CHECK_EQUAL(ResidueNameToAminoAcid("THR"), THR);
+  BOOST_CHECK_EQUAL(ResidueNameToAminoAcid("TRP"), TRP);
+  BOOST_CHECK_EQUAL(ResidueNameToAminoAcid("TYR"), TYR);
+  BOOST_CHECK_EQUAL(ResidueNameToAminoAcid("VAL"), VAL);
+  // should also wiork if not uppercase!
+  BOOST_CHECK_EQUAL(ResidueNameToAminoAcid("Ala"), ALA);
+  BOOST_CHECK_EQUAL(ResidueNameToAminoAcid("Arg"), ARG);
+  BOOST_CHECK_EQUAL(ResidueNameToAminoAcid("Asn"), ASN);
+  BOOST_CHECK_EQUAL(ResidueNameToAminoAcid("Asp"), ASP);
+  BOOST_CHECK_EQUAL(ResidueNameToAminoAcid("Cys"), CYS);
+  BOOST_CHECK_EQUAL(ResidueNameToAminoAcid("Glu"), GLU);
+  BOOST_CHECK_EQUAL(ResidueNameToAminoAcid("Gln"), GLN);
+  BOOST_CHECK_EQUAL(ResidueNameToAminoAcid("Gly"), GLY);
+  BOOST_CHECK_EQUAL(ResidueNameToAminoAcid("His"), HIS);
+  BOOST_CHECK_EQUAL(ResidueNameToAminoAcid("Ile"), ILE);
+  BOOST_CHECK_EQUAL(ResidueNameToAminoAcid("Leu"), LEU);
+  BOOST_CHECK_EQUAL(ResidueNameToAminoAcid("Lys"), LYS);
+  BOOST_CHECK_EQUAL(ResidueNameToAminoAcid("Met"), MET);
+  BOOST_CHECK_EQUAL(ResidueNameToAminoAcid("Phe"), PHE);
+  BOOST_CHECK_EQUAL(ResidueNameToAminoAcid("Pro"), PRO);
+  BOOST_CHECK_EQUAL(ResidueNameToAminoAcid("Ser"), SER);
+  BOOST_CHECK_EQUAL(ResidueNameToAminoAcid("Thr"), THR);
+  BOOST_CHECK_EQUAL(ResidueNameToAminoAcid("Trp"), TRP);
+  BOOST_CHECK_EQUAL(ResidueNameToAminoAcid("Tyr"), TYR);
+  BOOST_CHECK_EQUAL(ResidueNameToAminoAcid("Val"), VAL);
+  // unknown ones
+  BOOST_CHECK_EQUAL(ResidueNameToAminoAcid("MUH"), XXX);
+  BOOST_CHECK_EQUAL(ResidueNameToAminoAcid("FOO"), XXX);
+  BOOST_CHECK_EQUAL(ResidueNameToAminoAcid("BAR"), XXX);
+}
+
+BOOST_AUTO_TEST_SUITE_END();

modules/io/pymod/__init__.py

@@ -300,7 +300,7 @@ def LoadMMCIF(filename, restrict_chains="", fault_tolerant=None, calpha_only=Non
 
   if remote:
     from ost.io.remote import RemoteGet
-    tmp_file =RemoteGet(filename, from_repo='cif')
+    tmp_file = RemoteGet(filename, from_repo='cif')
     filename = tmp_file.name
   
   try:

modules/seq/alg/doc/seqalg.rst

@@ -298,6 +298,11 @@ corresponding to interacting residues.
 Get and analyze distance matrices from alignments
 --------------------------------------------------------------------------------
 
+Given a multiple sequence alignment between a reference sequence (first sequence
+in alignment) and a list of structures (remaining sequences in alignment with an
+attached view to the structure), this set of functions can be used to analyze
+differences between the structures.
+
 **Example:**
 
 .. code-block:: python
@@ -308,10 +313,12 @@ Get and analyze distance matrices from alignments
   # clip alignment to only have parts with at least 3 sequences (incl. ref.)
   # -> aln will be cut and clip_start is 1st column of aln that was kept
   clip_start = seq.alg.ClipAlignment(aln, 3)
+  
   # get variance measure and distance to mean for each residue pair
   d_map = seq.alg.CreateDistanceMap(aln)
   var_map = seq.alg.CreateVarianceMap(d_map)
   dist_to_mean = seq.alg.CreateDist2Mean(d_map)
+
   # report min. and max. variances
   print "MIN-MAX:", var_map.Min(), "-", var_map.Max()
   # get data and json-strings for further processing