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| author | Bruce Smith <bruce@nanorex.com> | 2008-05-23 23:16:23 +0000 |
|---|---|---|
| committer | Bruce Smith <bruce@nanorex.com> | 2008-05-23 23:16:23 +0000 |
| commit | 96ad2a60a08082703657167d999e73854b04159f (patch) | |
| tree | a4836d9d4cf32f2c757c292dd2222a9bea443e31 | |
| parent | a012a977c731e985f0feb85e5d44359717c0bcb5 (diff) | |
| download | nanoengineer-96ad2a60a08082703657167d999e73854b04159f.tar.gz nanoengineer-96ad2a60a08082703657167d999e73854b04159f.zip | |
split _do_pam_conversions out of update_PAM_chunks
| -rw-r--r-- | cad/src/dna/updater/dna_updater_chunks.py | 206 |
1 files changed, 111 insertions, 95 deletions
diff --git a/cad/src/dna/updater/dna_updater_chunks.py b/cad/src/dna/updater/dna_updater_chunks.py index 3b4853817..44d9b48f9 100644 --- a/cad/src/dna/updater/dna_updater_chunks.py +++ b/cad/src/dna/updater/dna_updater_chunks.py @@ -201,106 +201,15 @@ def update_PAM_chunks( changed_atoms, homeless_markers): # and they will change it back to its prior value before returning default_pam = pref_dna_updater_convert_to_PAM3plus5() and MODEL_PAM3 or None - # None means "whatever you already are", i.e. do no conversion. + # None means "whatever you already are", i.e. do no conversion + # except whatever is requested by manual conversion operations. # There is not yet a way to say "display everything in PAM5". # We will probably need either that, or "convert selection to PAM5", # or both. As of 080401 we only have "convert one ladder to PAM5" (unfinished). - - number_converted = 0 # not counting failures - number_failed = 0 - - ladders_dict = _f_ladders_with_up_to_date_baseframes_at_ends - if ladders_dict: - print "***BUG: _f_ladders_with_up_to_date_baseframes_at_ends was found with leftover garbage; clearing it now" - ladders_dict.clear() - - locator = _f_atom_to_ladder_location_dict - if locator: - print "***BUG: _f_atom_to_ladder_location_dict was found with leftover garbage; clearing it now" - locator.clear() - - if 1: - # make errors more obvious, bugs less likely; - # also make it easy & reliable to locate all atoms in new ladders - # (this could surely be optimized, but simple & reliable is primary - # concern for now) - - for ladder in all_new_unmerged_ladders: - if not ladder.error: - ladder.clear_baseframe_data() - ladder._f_store_locator_data() - for ladder1 in ladder.strand_neighbor_ladders(): - ladder.clear_baseframe_data() - # no need to store locator data for these - pass - - for ladder in all_new_unmerged_ladders: - assert ladder.valid, "bug: new ladder %r not valid!" % self - wanted, succeeded = ladder._f_convert_pam_if_desired(default_pam) - # - this checks for ladder.error and won't succeed if set - # - this sets baseframe data if conversion succeeds, - # and stores ladder in ladders_dict, with value False - assert ladder.valid, "bug: _f_convert_pam_if_desired made %r invalid!" % ladder - didit = wanted and succeeded - failed = wanted and not succeeded - number_converted += not not didit - number_failed += not not failed - if didit: - assert ladders_dict.get(ladder, None) == False - if debug_flags.DEBUG_DNA_UPDATER_VERBOSE: - print "converted:", ladder.ladder_string() - continue - - if number_converted: -## for ladder in all_new_unmerged_ladders: -## ladders_dict[ladder] = None # TODO: refactor this -- see above comment - for ladder in all_new_unmerged_ladders: - if not ladder.error: - ladder._f_finish_converting_bridging_Pl_atoms() - # this assert not ladder.error - assert ladder.valid, "bug: _f_finish_converting_bridging_Pl_atoms made %r invalid!" % ladder - ladder.fix_bondpoint_positions_at_ends_of_rails() - # (don't pass ladders_dict, it's accessed as the global which - # is assigned to it above [080409 revision]) - # the ladders in ladders_dict are known to have valid baseframes - # (as we start this loop) or valid baseframes at the ends - # (as we continue this loop); - # this method needs to look at neighboring ladders - # (touching ladder at corners) and use end-baseframes from - # them; if it sees one not in the dict, it computes its - # baseframes (perhaps just at both ends as an optim) - # and also stores that ladder in the dict so this won't - # be done to it again. - continue - pass - ladders_dict.clear() - del ladders_dict - locator.clear() - del locator - _f_baseatom_wants_pam.clear() - - # Note: if ladders were converted, their chains are still ok, - # since those only store baseatoms (for strand and axis), - # and those transmuted and moved but didn't change identity. - # So the ladders also don't change identity, and remain valid - # unless they had conversion errors. If not valid, they are ok - # in those lists since this was already possible in other ways - # (I think). (All this needs test and review.) - # - # But lots of atoms got changed in lots of ways (transmute, move, - # rebond, create Pl, kill Pl). Ignore all that. - # (review: any changes to ignore if conversion wanted and failed?) - msg = "from converting %d ladders" % number_converted - if number_failed: - msg += " (%d desired conversions failed)" % number_failed - # msg is just for debug, nevermind calling fix_plurals + #### TODO: check default_pam and _f_baseatom_wants_pam to optim by not always calling this + _do_pam_conversions( default_pam, all_new_unmerged_ladders ) #bruce 080523 split this out - if number_converted: - ignore_new_changes(msg, changes_ok = True) - else: - ignore_new_changes(msg, changes_ok = False) - if _f_invalid_dna_ladders: #bruce 080413 print "\n*** likely bug: _f_invalid_dna_ladders is nonempty " \ @@ -489,6 +398,113 @@ def update_PAM_chunks( changed_atoms, homeless_markers): # == +def _do_pam_conversions( default_pam, all_new_unmerged_ladders): + """ + #doc + [private helper] + """ + #bruce 080523 split this out of its sole caller + # maybe: put it into its own module, or an existing one? + + number_converted = 0 # not counting failures + number_failed = 0 + + ladders_dict = _f_ladders_with_up_to_date_baseframes_at_ends + if ladders_dict: + print "***BUG: _f_ladders_with_up_to_date_baseframes_at_ends was found with leftover garbage; clearing it now" + ladders_dict.clear() + + locator = _f_atom_to_ladder_location_dict + if locator: + print "***BUG: _f_atom_to_ladder_location_dict was found with leftover garbage; clearing it now" + locator.clear() + + if 1: + # make errors more obvious, bugs less likely; + # also make it easy & reliable to locate all atoms in new ladders + # (this could surely be optimized, but simple & reliable is primary + # concern for now) + + for ladder in all_new_unmerged_ladders: + if not ladder.error: + ladder.clear_baseframe_data() + ladder._f_store_locator_data() + for ladder1 in ladder.strand_neighbor_ladders(): + ladder.clear_baseframe_data() + # no need to store locator data for these + pass + + for ladder in all_new_unmerged_ladders: + assert ladder.valid, "bug: new ladder %r not valid!" % self + wanted, succeeded = ladder._f_convert_pam_if_desired(default_pam) + # - this checks for ladder.error and won't succeed if set + # - this sets baseframe data if conversion succeeds, + # and stores ladder in ladders_dict, with value False + assert ladder.valid, "bug: _f_convert_pam_if_desired made %r invalid!" % ladder + didit = wanted and succeeded + failed = wanted and not succeeded + number_converted += not not didit + number_failed += not not failed + if didit: + assert ladders_dict.get(ladder, None) == False + if debug_flags.DEBUG_DNA_UPDATER_VERBOSE: + print "converted:", ladder.ladder_string() + continue + + if number_converted: +## for ladder in all_new_unmerged_ladders: +## ladders_dict[ladder] = None # TODO: refactor this -- see above comment + for ladder in all_new_unmerged_ladders: + if not ladder.error: + ladder._f_finish_converting_bridging_Pl_atoms() + # this assert not ladder.error + assert ladder.valid, "bug: _f_finish_converting_bridging_Pl_atoms made %r invalid!" % ladder + ladder.fix_bondpoint_positions_at_ends_of_rails() + # (don't pass ladders_dict, it's accessed as the global which + # is assigned to it above [080409 revision]) + # the ladders in ladders_dict are known to have valid baseframes + # (as we start this loop) or valid baseframes at the ends + # (as we continue this loop); + # this method needs to look at neighboring ladders + # (touching ladder at corners) and use end-baseframes from + # them; if it sees one not in the dict, it computes its + # baseframes (perhaps just at both ends as an optim) + # and also stores that ladder in the dict so this won't + # be done to it again. + continue + pass + ladders_dict.clear() + del ladders_dict + locator.clear() + del locator + _f_baseatom_wants_pam.clear() + + # Note: if ladders were converted, their chains are still ok, + # since those only store baseatoms (for strand and axis), + # and those transmuted and moved but didn't change identity. + # So the ladders also don't change identity, and remain valid + # unless they had conversion errors. If not valid, they are ok + # in those lists since this was already possible in other ways + # (I think). (All this needs test and review.) + # + # But lots of atoms got changed in lots of ways (transmute, move, + # rebond, create Pl, kill Pl). Ignore all that. + # (review: any changes to ignore if conversion wanted and failed?) + + msg = "from converting %d ladders" % number_converted + if number_failed: + msg += " (%d desired conversions failed)" % number_failed + # msg is just for debug, nevermind calling fix_plurals + + if number_converted: + ignore_new_changes(msg, changes_ok = True) + else: + ignore_new_changes(msg, changes_ok = False) + + return # from _do_pam_conversions + +# == + def _find_rail_of_atom( atom, ladder_to_rails_function): """ [private helper] |