diff --git a/modules/mol/alg/pymod/chain_mapping.py b/modules/mol/alg/pymod/chain_mapping.py
index 25a19259a2de600490e74a89f292246ed15e76e3..fe3304d4193aceee0d6ea0b2c1dc2887b1dc4b28 100644
--- a/modules/mol/alg/pymod/chain_mapping.py
+++ b/modules/mol/alg/pymod/chain_mapping.py
@@ -820,9 +820,8 @@ class ChainMapper:
* **greedy_block**: try multiple seeds for greedy extension, i.e. try
all ref/mdl chain combinations within the respective chem groups and
- compute single chain lDDTs. The *block_blocks_per_chem_group* best
- scoring ones are extend by *block_seed_size* chains and the best
- scoring one is exhaustively extended.
+ extend them to *block_seed_size*. *block_blocks_per_chem_group*
+ for each chem group are selected for exhaustive extension.
Sets :attr:`MappingResult.opt_score` in case of no trivial one-to-one
mapping.
@@ -961,9 +960,8 @@ class ChainMapper:
* **greedy_block**: try multiple seeds for greedy extension, i.e. try
all ref/mdl chain combinations within the respective chem groups and
- compute single chain lDDTs. The *block_blocks_per_chem_group* best
- scoring ones are extend by *block_seed_size* chains and the block with
- with best QS score is exhaustively extended.
+ extend them to *block_seed_size*. *block_blocks_per_chem_group*
+ for each chem group are selected for exhaustive extension.
Sets :attr:`MappingResult.opt_score` in case of no trivial one-to-one
mapping.
@@ -1034,7 +1032,6 @@ class ChainMapper:
# cached => QSScore computation is fast here
opt_qsscore = the_greed.Score(mapping, check=False)
-
alns = dict()
for ref_group, mdl_group in zip(self.chem_groups, mapping):
for ref_ch, mdl_ch in zip(ref_group, mdl_group):
@@ -2540,30 +2537,32 @@ def _lDDTGreedyBlock(the_greed, seed_size, blocks_per_chem_group):
for ref_chains, mdl_chains in zip(ref_chem_groups, mdl_chem_groups):
if len(mdl_chains) == 0:
continue # nothing to map
-
- # Identify starting seeds for *blocks_per_chem_group* blocks
- seeds = list()
- for ref_ch in ref_chains:
- seeds += [(ref_ch, mdl_ch) for mdl_ch in mdl_chains]
- counts = [the_greed.SCCounts(s[0], s[1]) for s in seeds]
- tmp = [(a,b) for a,b in zip(counts, seeds)]
- tmp.sort(reverse=True)
- seeds = [item[1] for item in tmp[:blocks_per_chem_group]]
-
- # extend starting seeds to *seed_size* and retain best scoring block
- # for further extension
- best_lddt = 0.0
- best_mapping = None
- for s in seeds:
- seed = dict(mapping)
- seed.update({s[0]: s[1]})
- seed = the_greed.ExtendMapping(seed, max_ext = max_ext)
- seed_lddt = the_greed.lDDTFromFlatMap(seed)
- if seed_lddt > best_lddt:
- best_lddt = seed_lddt
- best_mapping = seed
- if best_mapping != None:
- starting_blocks.append(best_mapping)
+ ref_chains_copy = list(ref_chains)
+ for i in range(blocks_per_chem_group):
+ if len(ref_chains_copy) == 0:
+ break
+ seeds = list()
+ for ref_ch in ref_chains_copy:
+ seeds += [(ref_ch, mdl_ch) for mdl_ch in mdl_chains]
+ # extend starting seeds to *seed_size* and retain best scoring
+ # block for further extension
+ best_score = -1.0
+ best_mapping = None
+ best_seed = None
+ for s in seeds:
+ seed = dict(mapping)
+ seed.update({s[0]: s[1]})
+ seed = the_greed.ExtendMapping(seed, max_ext = max_ext)
+ seed_lddt = the_greed.lDDTFromFlatMap(seed)
+ if seed_lddt > best_score:
+ best_score = seed_lddt
+ best_mapping = seed
+ best_seed = s
+ if best_mapping != None:
+ starting_blocks.append(best_mapping)
+ if best_seed[0] in ref_chains_copy:
+ # remove that ref chain to enforce diversity
+ ref_chains_copy.remove(best_seed[0])
# fully expand initial starting blocks
best_lddt = 0.0
@@ -2963,31 +2962,32 @@ def _QSScoreGreedyBlock(the_greed, seed_size, blocks_per_chem_group):
for ref_chains, mdl_chains in zip(ref_chem_groups, mdl_chem_groups):
if len(mdl_chains) == 0:
continue # nothing to map
-
- # Identify starting seeds for *blocks_per_chem_group* blocks
- # thats done with lDDT
- seeds = list()
- for ref_ch in ref_chains:
- seeds += [(ref_ch, mdl_ch) for mdl_ch in mdl_chains]
- counts = [the_greed.SCCounts(s[0], s[1]) for s in seeds]
- tmp = [(a,b) for a,b in zip(counts, seeds)]
- tmp.sort(reverse=True)
- seeds = [item[1] for item in tmp[:blocks_per_chem_group]]
-
- # extend starting seeds to *seed_size* and retain best scoring block
- # for further extension
- best_score = -1.0
- best_mapping = None
- for s in seeds:
- seed = dict(mapping)
- seed.update({s[0]: s[1]})
- seed = the_greed.ExtendMapping(seed, max_ext = max_ext)
- score_result = the_greed.FromFlatMapping(seed)
- if score_result.QS_global > best_score:
- best_score = score_result.QS_global
- best_mapping = seed
- if best_mapping != None:
- starting_blocks.append(best_mapping)
+ ref_chains_copy = list(ref_chains)
+ for i in range(blocks_per_chem_group):
+ if len(ref_chains_copy) == 0:
+ break
+ seeds = list()
+ for ref_ch in ref_chains_copy:
+ seeds += [(ref_ch, mdl_ch) for mdl_ch in mdl_chains]
+ # extend starting seeds to *seed_size* and retain best scoring block
+ # for further extension
+ best_score = -1.0
+ best_mapping = None
+ best_seed = None
+ for s in seeds:
+ seed = dict(mapping)
+ seed.update({s[0]: s[1]})
+ seed = the_greed.ExtendMapping(seed, max_ext = max_ext)
+ score_result = the_greed.FromFlatMapping(seed)
+ if score_result.QS_global > best_score:
+ best_score = score_result.QS_global
+ best_mapping = seed
+ best_seed = s
+ if best_mapping != None:
+ starting_blocks.append(best_mapping)
+ if best_seed[0] in ref_chains_copy:
+ # remove selected ref chain to enforce diversity
+ ref_chains_copy.remove(best_seed[0])
# fully expand initial starting blocks
best_score = -1.0