Merge branch 'master' into develop

modules/mol/alg/pymod/wrap_mol_alg.cc

@@ -30,6 +30,7 @@
 #include <ost/mol/alg/consistency_checks.hh>
 #include <ost/mol/alg/pdbize.hh>
 #include <ost/mol/alg/contact_overlap.hh>
+#include <ost/mol/alg/construct_cbeta.hh>
 #include <ost/export_helper/pair_to_tuple_conv.hh>
 #include <ost/export_helper/vec_to_list_conv.hh>
 
@@ -295,6 +296,15 @@ void print_lddt_per_residue_stats_wrapper(list& scores, bool structural_checks,
  return mol::alg::PrintlDDTPerResidueStats(scores_vector, structural_checks, cutoffs_size);
 }
 
+geom::Vec3 cbeta_vectors(const geom::Vec3& n_pos, const geom::Vec3& ca_pos, 
+                         const geom::Vec3& c_pos, Real l) {
+  return mol::alg::CBetaPosition(n_pos, ca_pos, c_pos, l);
+}
+
+geom::Vec3 cbeta_residue(const ost::mol::ResidueHandle& r, Real l) {
+  return mol::alg::CBetaPosition(r, l);
+}
+  
 }
 
 
@@ -529,4 +539,10 @@ BOOST_PYTHON_MODULE(_ost_mol_alg)
   def("DRMSD",&mol::alg::DRMSD,(arg("view"),arg("distance_list"),
                                 arg("cap_distance")=5.0,arg("sequence_separation")=0));
 
+  def("CBetaPosition", &cbeta_vectors, (arg("n_pos"), arg("ca_pos"), 
+                                        arg("c_pos"), arg("l")=1.5));
+  def("CBetaPosition", &cbeta_residue, (arg("r"), arg("l") = 1.5));
+
+  def("ConstructCBetas", &mol::alg::ConstructCBetas, (arg("ent"), 
+                                                      arg("include_gly")=false));
 }

modules/seq/alg/src/data/BLOSUM100

+#  Matrix made by matblas from blosum100_3.iij
+#  * column uses minimum score
+#  BLOSUM Clustered Scoring Matrix in 1/3 Bit Units
+#  Blocks Database = /data/blocks_5.0/blocks.dat
+#  Cluster Percentage: >= 100
+#  Entropy =   1.4516, Expected =  -1.0948
+   A  R  N  D  C  Q  E  G  H  I  L  K  M  F  P  S  T  W  Y  V  B  Z  X  *
+A  8 -3 -4 -5 -2 -2 -3 -1 -4 -4 -4 -2 -3 -5 -2  1 -1 -6 -5 -2 -4 -2 -2 -10 
+R -3 10 -2 -5 -8  0 -2 -6 -1 -7 -6  3 -4 -6 -5 -3 -3 -7 -5 -6 -4 -1 -3 -10 
+N -4 -2 11  1 -5 -1 -2 -2  0 -7 -7 -1 -5 -7 -5  0 -1 -8 -5 -7  5 -2 -3 -10 
+D -5 -5  1 10 -8 -2  2 -4 -3 -8 -8 -3 -8 -8 -5 -2 -4 -10 -7 -8  6  0 -4 -10 
+C -2 -8 -5 -8 14 -7 -9 -7 -8 -3 -5 -8 -4 -4 -8 -3 -3 -7 -6 -3 -7 -8 -5 -10 
+Q -2  0 -1 -2 -7 11  2 -5  1 -6 -5  2 -2 -6 -4 -2 -3 -5 -4 -5 -2  5 -2 -10 
+E -3 -2 -2  2 -9  2 10 -6 -2 -7 -7  0 -5 -8 -4 -2 -3 -8 -7 -5  0  7 -3 -10 
+G -1 -6 -2 -4 -7 -5 -6  9 -6 -9 -8 -5 -7 -8 -6 -2 -5 -7 -8 -8 -3 -5 -4 -10 
+H -4 -1  0 -3 -8  1 -2 -6 13 -7 -6 -3 -5 -4 -5 -3 -4 -5  1 -7 -2 -1 -4 -10 
+I -4 -7 -7 -8 -3 -6 -7 -9 -7  8  2 -6  1 -2 -7 -5 -3 -6 -4  4 -8 -7 -3 -10 
+L -4 -6 -7 -8 -5 -5 -7 -8 -6  2  8 -6  3  0 -7 -6 -4 -5 -4  0 -8 -6 -3 -10 
+K -2  3 -1 -3 -8  2  0 -5 -3 -6 -6 10 -4 -6 -3 -2 -3 -8 -5 -5 -2  0 -3 -10 
+M -3 -4 -5 -8 -4 -2 -5 -7 -5  1  3 -4 12 -1 -5 -4 -2 -4 -5  0 -7 -4 -3 -10 
+F -5 -6 -7 -8 -4 -6 -8 -8 -4 -2  0 -6 -1 11 -7 -5 -5  0  4 -3 -7 -7 -4 -10 
+P -2 -5 -5 -5 -8 -4 -4 -6 -5 -7 -7 -3 -5 -7 12 -3 -4 -8 -7 -6 -5 -4 -4 -10 
+S  1 -3  0 -2 -3 -2 -2 -2 -3 -5 -6 -2 -4 -5 -3  9  2 -7 -5 -4 -1 -2 -2 -10 
+T -1 -3 -1 -4 -3 -3 -3 -5 -4 -3 -4 -3 -2 -5 -4  2  9 -7 -5 -1 -2 -3 -2 -10 
+W -6 -7 -8 -10 -7 -5 -8 -7 -5 -6 -5 -8 -4  0 -8 -7 -7 17  2 -5 -9 -7 -6 -10 
+Y -5 -5 -5 -7 -6 -4 -7 -8  1 -4 -4 -5 -5  4 -7 -5 -5  2 12 -5 -6 -6 -4 -10 
+V -2 -6 -7 -8 -3 -5 -5 -8 -7  4  0 -5  0 -3 -6 -4 -1 -5 -5  8 -7 -5 -3 -10 
+B -4 -4  5  6 -7 -2  0 -3 -2 -8 -8 -2 -7 -7 -5 -1 -2 -9 -6 -7  6  0 -4 -10 
+Z -2 -1 -2  0 -8  5  7 -5 -1 -7 -6  0 -4 -7 -4 -2 -3 -7 -6 -5  0  6 -2 -10 
+X -2 -3 -3 -4 -5 -2 -3 -4 -4 -3 -3 -3 -3 -4 -4 -2 -2 -6 -4 -3 -4 -2 -3 -10 
+* -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10  1 

modules/seq/alg/src/data/BLOSUM45

+#  Matrix made by matblas from blosum45.iij
+#  * column uses minimum score
+#  BLOSUM Clustered Scoring Matrix in 1/3 Bit Units
+#  Blocks Database = /data/blocks_5.0/blocks.dat
+#  Cluster Percentage: >= 45
+#  Entropy =   0.3795, Expected =  -0.2789
+   A  R  N  D  C  Q  E  G  H  I  L  K  M  F  P  S  T  W  Y  V  B  Z  X  *
+A  5 -2 -1 -2 -1 -1 -1  0 -2 -1 -1 -1 -1 -2 -1  1  0 -2 -2  0 -1 -1  0 -5 
+R -2  7  0 -1 -3  1  0 -2  0 -3 -2  3 -1 -2 -2 -1 -1 -2 -1 -2 -1  0 -1 -5 
+N -1  0  6  2 -2  0  0  0  1 -2 -3  0 -2 -2 -2  1  0 -4 -2 -3  4  0 -1 -5 
+D -2 -1  2  7 -3  0  2 -1  0 -4 -3  0 -3 -4 -1  0 -1 -4 -2 -3  5  1 -1 -5 
+C -1 -3 -2 -3 12 -3 -3 -3 -3 -3 -2 -3 -2 -2 -4 -1 -1 -5 -3 -1 -2 -3 -2 -5 
+Q -1  1  0  0 -3  6  2 -2  1 -2 -2  1  0 -4 -1  0 -1 -2 -1 -3  0  4 -1 -5 
+E -1  0  0  2 -3  2  6 -2  0 -3 -2  1 -2 -3  0  0 -1 -3 -2 -3  1  4 -1 -5 
+G  0 -2  0 -1 -3 -2 -2  7 -2 -4 -3 -2 -2 -3 -2  0 -2 -2 -3 -3 -1 -2 -1 -5 
+H -2  0  1  0 -3  1  0 -2 10 -3 -2 -1  0 -2 -2 -1 -2 -3  2 -3  0  0 -1 -5 
+I -1 -3 -2 -4 -3 -2 -3 -4 -3  5  2 -3  2  0 -2 -2 -1 -2  0  3 -3 -3 -1 -5 
+L -1 -2 -3 -3 -2 -2 -2 -3 -2  2  5 -3  2  1 -3 -3 -1 -2  0  1 -3 -2 -1 -5 
+K -1  3  0  0 -3  1  1 -2 -1 -3 -3  5 -1 -3 -1 -1 -1 -2 -1 -2  0  1 -1 -5 
+M -1 -1 -2 -3 -2  0 -2 -2  0  2  2 -1  6  0 -2 -2 -1 -2  0  1 -2 -1 -1 -5 
+F -2 -2 -2 -4 -2 -4 -3 -3 -2  0  1 -3  0  8 -3 -2 -1  1  3  0 -3 -3 -1 -5 
+P -1 -2 -2 -1 -4 -1  0 -2 -2 -2 -3 -1 -2 -3  9 -1 -1 -3 -3 -3 -2 -1 -1 -5 
+S  1 -1  1  0 -1  0  0  0 -1 -2 -3 -1 -2 -2 -1  4  2 -4 -2 -1  0  0  0 -5 
+T  0 -1  0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -1 -1  2  5 -3 -1  0  0 -1  0 -5 
+W -2 -2 -4 -4 -5 -2 -3 -2 -3 -2 -2 -2 -2  1 -3 -4 -3 15  3 -3 -4 -2 -2 -5 
+Y -2 -1 -2 -2 -3 -1 -2 -3  2  0  0 -1  0  3 -3 -2 -1  3  8 -1 -2 -2 -1 -5 
+V  0 -2 -3 -3 -1 -3 -3 -3 -3  3  1 -2  1  0 -3 -1  0 -3 -1  5 -3 -3 -1 -5 
+B -1 -1  4  5 -2  0  1 -1  0 -3 -3  0 -2 -3 -2  0  0 -4 -2 -3  4  2 -1 -5 
+Z -1  0  0  1 -3  4  4 -2  0 -3 -2  1 -1 -3 -1  0 -1 -2 -2 -3  2  4 -1 -5 
+X  0 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1  0  0 -2 -1 -1 -1 -1 -1 -5 
+* -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5  1 

modules/seq/alg/src/data/BLOSUM62

+#  Matrix made by matblas from blosum62.iij
+#  * column uses minimum score
+#  BLOSUM Clustered Scoring Matrix in 1/2 Bit Units
+#  Blocks Database = /data/blocks_5.0/blocks.dat
+#  Cluster Percentage: >= 62
+#  Entropy =   0.6979, Expected =  -0.5209
+   A  R  N  D  C  Q  E  G  H  I  L  K  M  F  P  S  T  W  Y  V  B  Z  X  *
+A  4 -1 -2 -2  0 -1 -1  0 -2 -1 -1 -1 -1 -2 -1  1  0 -3 -2  0 -2 -1  0 -4 
+R -1  5  0 -2 -3  1  0 -2  0 -3 -2  2 -1 -3 -2 -1 -1 -3 -2 -3 -1  0 -1 -4 
+N -2  0  6  1 -3  0  0  0  1 -3 -3  0 -2 -3 -2  1  0 -4 -2 -3  3  0 -1 -4 
+D -2 -2  1  6 -3  0  2 -1 -1 -3 -4 -1 -3 -3 -1  0 -1 -4 -3 -3  4  1 -1 -4 
+C  0 -3 -3 -3  9 -3 -4 -3 -3 -1 -1 -3 -1 -2 -3 -1 -1 -2 -2 -1 -3 -3 -2 -4 
+Q -1  1  0  0 -3  5  2 -2  0 -3 -2  1  0 -3 -1  0 -1 -2 -1 -2  0  3 -1 -4 
+E -1  0  0  2 -4  2  5 -2  0 -3 -3  1 -2 -3 -1  0 -1 -3 -2 -2  1  4 -1 -4 
+G  0 -2  0 -1 -3 -2 -2  6 -2 -4 -4 -2 -3 -3 -2  0 -2 -2 -3 -3 -1 -2 -1 -4 
+H -2  0  1 -1 -3  0  0 -2  8 -3 -3 -1 -2 -1 -2 -1 -2 -2  2 -3  0  0 -1 -4 
+I -1 -3 -3 -3 -1 -3 -3 -4 -3  4  2 -3  1  0 -3 -2 -1 -3 -1  3 -3 -3 -1 -4 
+L -1 -2 -3 -4 -1 -2 -3 -4 -3  2  4 -2  2  0 -3 -2 -1 -2 -1  1 -4 -3 -1 -4 
+K -1  2  0 -1 -3  1  1 -2 -1 -3 -2  5 -1 -3 -1  0 -1 -3 -2 -2  0  1 -1 -4 
+M -1 -1 -2 -3 -1  0 -2 -3 -2  1  2 -1  5  0 -2 -1 -1 -1 -1  1 -3 -1 -1 -4 
+F -2 -3 -3 -3 -2 -3 -3 -3 -1  0  0 -3  0  6 -4 -2 -2  1  3 -1 -3 -3 -1 -4 
+P -1 -2 -2 -1 -3 -1 -1 -2 -2 -3 -3 -1 -2 -4  7 -1 -1 -4 -3 -2 -2 -1 -2 -4 
+S  1 -1  1  0 -1  0  0  0 -1 -2 -2  0 -1 -2 -1  4  1 -3 -2 -2  0  0  0 -4 
+T  0 -1  0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1  1  5 -2 -2  0 -1 -1  0 -4 
+W -3 -3 -4 -4 -2 -2 -3 -2 -2 -3 -2 -3 -1  1 -4 -3 -2 11  2 -3 -4 -3 -2 -4 
+Y -2 -2 -2 -3 -2 -1 -2 -3  2 -1 -1 -2 -1  3 -3 -2 -2  2  7 -1 -3 -2 -1 -4 
+V  0 -3 -3 -3 -1 -2 -2 -3 -3  3  1 -2  1 -1 -2 -2  0 -3 -1  4 -3 -2 -1 -4 
+B -2 -1  3  4 -3  0  1 -1  0 -3 -4  0 -3 -3 -2  0 -1 -4 -3 -3  4  1 -1 -4 
+Z -1  0  0  1 -3  3  4 -2  0 -3 -3  1 -1 -3 -1  0 -1 -3 -2 -2  1  4 -1 -4 
+X  0 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -2  0  0 -2 -1 -1 -1 -1 -1 -4 
+* -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4  1 

modules/seq/alg/src/data/BLOSUM80

+#  Matrix made by matblas from blosum80_3.iij
+#  * column uses minimum score
+#  BLOSUM Clustered Scoring Matrix in 1/3 Bit Units
+#  Blocks Database = /data/blocks_5.0/blocks.dat
+#  Cluster Percentage: >= 80
+#  Entropy =   0.9868, Expected =  -0.7442
+   A  R  N  D  C  Q  E  G  H  I  L  K  M  F  P  S  T  W  Y  V  B  Z  X  *
+A  7 -3 -3 -3 -1 -2 -2  0 -3 -3 -3 -1 -2 -4 -1  2  0 -5 -4 -1 -3 -2 -1 -8 
+R -3  9 -1 -3 -6  1 -1 -4  0 -5 -4  3 -3 -5 -3 -2 -2 -5 -4 -4 -2  0 -2 -8 
+N -3 -1  9  2 -5  0 -1 -1  1 -6 -6  0 -4 -6 -4  1  0 -7 -4 -5  5 -1 -2 -8 
+D -3 -3  2 10 -7 -1  2 -3 -2 -7 -7 -2 -6 -6 -3 -1 -2 -8 -6 -6  6  1 -3 -8 
+C -1 -6 -5 -7 13 -5 -7 -6 -7 -2 -3 -6 -3 -4 -6 -2 -2 -5 -5 -2 -6 -7 -4 -8 
+Q -2  1  0 -1 -5  9  3 -4  1 -5 -4  2 -1 -5 -3 -1 -1 -4 -3 -4 -1  5 -2 -8 
+E -2 -1 -1  2 -7  3  8 -4  0 -6 -6  1 -4 -6 -2 -1 -2 -6 -5 -4  1  6 -2 -8 
+G  0 -4 -1 -3 -6 -4 -4  9 -4 -7 -7 -3 -5 -6 -5 -1 -3 -6 -6 -6 -2 -4 -3 -8 
+H -3  0  1 -2 -7  1  0 -4 12 -6 -5 -1 -4 -2 -4 -2 -3 -4  3 -5 -1  0 -2 -8 
+I -3 -5 -6 -7 -2 -5 -6 -7 -6  7  2 -5  2 -1 -5 -4 -2 -5 -3  4 -6 -6 -2 -8 
+L -3 -4 -6 -7 -3 -4 -6 -7 -5  2  6 -4  3  0 -5 -4 -3 -4 -2  1 -7 -5 -2 -8 
+K -1  3  0 -2 -6  2  1 -3 -1 -5 -4  8 -3 -5 -2 -1 -1 -6 -4 -4 -1  1 -2 -8 
+M -2 -3 -4 -6 -3 -1 -4 -5 -4  2  3 -3  9  0 -4 -3 -1 -3 -3  1 -5 -3 -2 -8 
+F -4 -5 -6 -6 -4 -5 -6 -6 -2 -1  0 -5  0 10 -6 -4 -4  0  4 -2 -6 -6 -3 -8 
+P -1 -3 -4 -3 -6 -3 -2 -5 -4 -5 -5 -2 -4 -6 12 -2 -3 -7 -6 -4 -4 -2 -3 -8 
+S  2 -2  1 -1 -2 -1 -1 -1 -2 -4 -4 -1 -3 -4 -2  7  2 -6 -3 -3  0 -1 -1 -8 
+T  0 -2  0 -2 -2 -1 -2 -3 -3 -2 -3 -1 -1 -4 -3  2  8 -5 -3  0 -1 -2 -1 -8 
+W -5 -5 -7 -8 -5 -4 -6 -6 -4 -5 -4 -6 -3  0 -7 -6 -5 16  3 -5 -8 -5 -5 -8 
+Y -4 -4 -4 -6 -5 -3 -5 -6  3 -3 -2 -4 -3  4 -6 -3 -3  3 11 -3 -5 -4 -3 -8 
+V -1 -4 -5 -6 -2 -4 -4 -6 -5  4  1 -4  1 -2 -4 -3  0 -5 -3  7 -6 -4 -2 -8 
+B -3 -2  5  6 -6 -1  1 -2 -1 -6 -7 -1 -5 -6 -4  0 -1 -8 -5 -6  6  0 -3 -8 
+Z -2  0 -1  1 -7  5  6 -4  0 -6 -5  1 -3 -6 -2 -1 -2 -5 -4 -4  0  6 -1 -8 
+X -1 -2 -2 -3 -4 -2 -2 -3 -2 -2 -2 -2 -2 -3 -3 -1 -1 -5 -3 -2 -3 -1 -2 -8 
+* -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8  1 

modules/seq/alg/src/data/generate_blosum_data.py

+# code generation for subst_weight_matrix.cc
+# loads BLOSUM substitution matrices from files provided by NCBI at:
+# ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/
+
+def Generate(filename, matrix_name):
+
+    with open(filename) as f:
+        data = f.readlines()
+
+    scores = dict()
+    olcs = None    
+    for line in data:
+        if line.startswith('#'):
+            continue
+        if olcs is None:
+            if " A " in line and " R " in line and " N " in line:
+                # very high likelihood that this line contains the olcs
+                olcs = line.strip().split()
+            continue
+        split_line = line.strip().split()
+        if split_line[0] in olcs:
+            olc = split_line[0]
+            for score_idx, score in enumerate(split_line[1:]):
+                scores[(olc, olcs[score_idx])] = score
+
+    ost_olcs = "ABCDEFGHIKLMNPQRSTVWXYZ"
+    print("short %s[23][23]={"%(matrix_name))
+    for a in ost_olcs:
+        score_string = "" 
+        for b in ost_olcs:
+            score = scores[(a,b)]
+            if len(score_string) == 0:
+                entry = [' ', ' ']
+            else:
+                entry = [',', ' ', ' ', ' ']
+            for i in range(len(score)):
+                entry[-1-i] = score[-1-i]
+            score_string += ''.join(entry)
+        print("  {%s},"%(score_string))
+    print("};")
+    print()
+
+Generate("BLOSUM45", "RAW_BLOSUM45_DATA")
+Generate("BLOSUM62", "RAW_BLOSUM62_DATA")
+Generate("BLOSUM80", "RAW_BLOSUM80_DATA")
+Generate("BLOSUM100", "RAW_BLOSUM100_DATA")
+

modules/seq/alg/src/subst_weight_matrix.cc

@@ -23,6 +23,9 @@
 
 namespace{
 
+// The data for the following matrices can be reproduced by running generate_blosum_data.py
+// in OST_SOURCE/modules/seq/alg/src/data
+
 short RAW_BLOSUM45_DATA[23][23]={
   { 5, -1, -1, -2, -1, -2,  0, -2, -1, -1, -1, -1, -1, -1, -1, -2,  1,  0,  0, -2,  0, -2, -1},
   {-1,  4, -2,  5,  1, -3, -1,  0, -3,  0, -3, -2,  4, -2,  0, -1,  0,  0, -3, -4, -1, -2,  2},
@@ -121,7 +124,7 @@ short RAW_BLOSUM100_DATA[23][23]={
   { 1, -1, -3, -2, -2, -5, -2, -3, -5, -2, -6, -4,  0, -3, -2, -3,  9,  2, -4, -7, -2, -5, -2},
   {-1, -2, -3, -4, -3, -5, -5, -4, -3, -3, -4, -2, -1, -4, -3, -3,  2,  9, -1, -7, -2, -5, -3},
   {-2, -7, -3, -8, -5, -3, -8, -7,  4, -5,  0,  0, -7, -6, -5, -6, -4, -1,  8, -5, -3, -5, -5},
-  {-6, -9, -7, 10, -8,  0, -7, -5, -6, -8, -5, -4, -8, -8, -5, -7, -7, -7, -5, 17, -6,  2, -7},
+  {-6, -9, -7,-10, -8,  0, -7, -5, -6, -8, -5, -4, -8, -8, -5, -7, -7, -7, -5, 17, -6,  2, -7},
   {-2, -4, -5, -4, -3, -4, -4, -4, -3, -3, -3, -3, -3, -4, -2, -3, -2, -2, -3, -6, -3, -4, -2},
   {-5, -6, -6, -7, -7,  4, -8,  1, -4, -5, -4, -5, -5, -7, -4, -5, -5, -5, -5,  2, -4, 12, -6},
   {-2,  0, -8,  0,  7, -7, -5, -1, -7,  0, -6, -4, -2, -4,  5, -1, -2, -3, -5, -7, -2, -6,  6},

scripts/bump-version.py

@@ -42,6 +42,6 @@ lines = open(vfile).readlines()
 for i, line in enumerate(lines):
   if line.startswith("From: registry.scicore.unibas.ch/schwede/openstructure:"):
     lines[i] = 'From: registry.scicore.unibas.ch/schwede/openstructure:'+\
-      '"%s"' % version_string
+      '%s' % version_string
     break
 open(vfile, "w").writelines(lines)

singularity/Singularity

 BootStrap: docker
-From: registry.scicore.unibas.ch/schwede/openstructure:"2.0.0"
+From: registry.scicore.unibas.ch/schwede/openstructure:2.0.0
 
 %post
 ##############################################################################