[Cctbx-cvs] cctbx/cctbx/maptbx __init__.py,1.4,1.5

[Ralf W. Grosse-K. <rw...@us...>]

Update of /cvsroot/cctbx/cctbx/cctbx/maptbx
In directory sc8-pr-cvs4.sourceforge.net:/tmp/cvs-serv22937/cctbx/maptbx

Modified Files:
	__init__.py 
Log Message:
crystal.site_cluster_analysis integrated into maptbx.peak_cluster_analysis; new site_cluster_analysis.discard_last(), insert_fixed_site_frac(), distinction between min_cross_distance and min_self_distance

Index: __init__.py
===================================================================
RCS file: /cvsroot/cctbx/cctbx/cctbx/maptbx/__init__.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** __init__.py	12 Aug 2005 08:55:01 -0000	1.4
--- __init__.py	3 Jun 2006 03:54:04 -0000	1.5
***************
*** 11,15 ****
  from scitbx.python_utils import dicts
  from libtbx import adopt_init_args
! import sys
  
  def value_at_closest_grid_point(map, x_frac):
--- 11,18 ----
  from scitbx.python_utils import dicts
  from libtbx import adopt_init_args
! import sys, os
! 
! debug_peak_cluster_analysis = os.environ.get(
!   "CCTBX_MAPTBX_DEBUG_PEAK_CLUSTER_ANALYSIS", "")
  
  def value_at_closest_grid_point(map, x_frac):
***************
*** 279,282 ****
--- 282,299 ----
      else:
        self._is_processed = None
+     if (   effective_resolution is not None
+         or debug_peak_cluster_analysis == "use_old"):
+       self._site_cluster_analysis = None
+       self.next = self.next_with_effective_resolution
+       self.all = self.all_with_effective_resolution
+     else:
+       self._site_cluster_analysis = \
+         self._special_position_settings.site_cluster_analysis(
+           min_cross_distance=self._min_cross_distance,
+           min_self_distance
+             =self._special_position_settings.min_distance_sym_equiv(),
+           general_positions_only=self._general_positions_only)
+       self.next = self.next_site_cluster_analysis
+       self.all = self.all_site_cluster_analysis
      self._peak_list_indices = flex.size_t()
      self._peak_list_index = 0
***************
*** 309,312 ****
--- 326,332 ----
      return self._max_clusters
  
+   def site_cluster_analysis(self):
+     return self._site_cluster_analysis
+ 
    def peak_list_indices(self):
      return self._peak_list_indices
***************
*** 327,330 ****
--- 347,352 ----
  
    def append_fixed_site(self, site, height=0):
+     if (self._site_cluster_analysis is not None):
+       self._site_cluster_analysis.insert_fixed_site_frac(original_site=site)
      self._fixed_site_indices.append(self._sites.size())
      self._sites.append(site)
***************
*** 332,336 ****
      self._peak_list_indices.append(self._peak_list.size())
  
!   def next(self):
      while 1:
        peak_list_index = self._peak_list_index
--- 354,397 ----
      self._peak_list_indices.append(self._peak_list.size())
  
!   def discard_last(self):
!     assert self._peak_list_indices.size() > 0
!     if (self._site_cluster_analysis is not None):
!       self._site_cluster_analysis.discard_last()
!     self._peak_list_indices.pop_back()
!     self._sites.pop_back()
!     self._heights.pop_back()
! 
!   def next_site_cluster_analysis(self):
!     while 1:
!       peak_list_index = self._peak_list_index
!       if (peak_list_index >= self._peak_list.size()): return None
!       self._peak_list_index += 1
!       site_symmetry = self._special_position_settings.site_symmetry(
!         site=self._peak_list.sites()[peak_list_index])
!       site = site_symmetry.exact_site()
!       if (not self._site_cluster_analysis.process_site_frac(
!                 original_site=site,
!                 site_symmetry_ops=site_symmetry)): continue
!       height = self._peak_list.heights()[peak_list_index]
!       self._peak_list_indices.append(peak_list_index)
!       self._sites.append(site)
!       self._heights.append(height)
!       return cluster_site_info(
!         peak_list_index=peak_list_index,
!         grid_index=self._peak_list.grid_indices(peak_list_index),
!         grid_height=self._peak_list.grid_heights()[peak_list_index],
!         site=site,
!         height=height)
! 
!   def all_site_cluster_analysis(self, max_clusters=None):
!     if (max_clusters is None):
!       max_clusters = self._max_clusters
!     assert max_clusters is not None
!     while 1:
!       if (self._sites.size() >= max_clusters): break
!       if (self.next_site_cluster_analysis() is None): break
!     return self
! 
!   def next_with_effective_resolution(self):
      while 1:
        peak_list_index = self._peak_list_index
***************
*** 351,354 ****
--- 412,421 ----
        equiv_sites = sgtbx.sym_equiv_sites(site_symmetry)
        keep = True
+       if (self._sites.size() > 50):
+         import warnings
+         warnings.warn(
+           message="This function should not be used for"
+                   " processing a large number of peaks.",
+           category=RuntimeWarning)
        for s in self._sites:
          dist = sgtbx.min_sym_equiv_distance_info(equiv_sites, s).dist()
***************
*** 402,406 ****
      return frac(sum_w_sites / sum_w), height
  
!   def all(self, max_clusters=None):
      if (max_clusters is None):
        max_clusters = self._max_clusters
--- 469,473 ----
      return frac(sum_w_sites / sum_w), height
  
!   def all_with_effective_resolution(self, max_clusters=None):
      if (max_clusters is None):
        max_clusters = self._max_clusters
***************
*** 408,417 ****
      while 1:
        if (self._sites.size() >= max_clusters): break
!       if (self.next() is None): break
      return self
- 
-   def discard_last(self):
-     assert self._peak_list_indices.size() > 0
-     self._peak_list_indices.pop_back()
-     self._sites.pop_back()
-     self._heights.pop_back()
--- 475,478 ----
      while 1:
        if (self._sites.size() >= max_clusters): break
!       if (self.next_with_effective_resolution() is None): break
      return self