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import numbers
# coot-lsq.py
# Copyright 2005, 2006 by Bernhard Lohkamp
# Copyright 2005, 2006 by Paul Emsley, The University of York
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3 of the License, or (at
# your option) any later version.
# This program 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
# General Public License for more details.
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 51 Franklin Street, Fifth Floor,
# Boston, MA 02110-1301, USA
# Internal type conversion for LSQ fitting. Return a number
# according to the symbod match_type_in
#
def lsq_match_type_symbol(match_type_in):
import operator
if (isinstance(match_type_in, numbers.Number)):
match_type_in = match_type_in
else:
if (match_type_in in ["CA","ca","Ca"]):
match_type_in = 2
elif (match_type_in in ["Main","main","mainchain","Mainchain"]):
match_type_in = 1
elif (match_type_in in ["ALL","all","All"]):
match_type_in = 0
else:
match_type_in = -1 # unknown
return match_type_in
#BL says, I guess I could make that more elegant...
#we use 0, 1 ,2 for ca, main, all (as it is in c++ code and not Paul's guile script)!!
# Create matchers, 7 elements:
# [ref_start_resno, ref_end_resno, ref_chain_id, imol_ref,
# mov_start_resno, mov_end_resno, mov_chain_id, imol_mov,
# match_type]
#
def set_match_element(m):
# m should be a list!!!!
# something like:
# match1 = [40,50,"A",40,50,"B","all"]
if (len(m)==7):
match_type=lsq_match_type_symbol(m[6])
coot.add_lsq_match(m[0],m[1],m[2],m[3],m[4],m[5],match_type)
else:
print("Wrong number of elements in match (was",len(m)," should be 7)")
# The scripting interface to LSQ matching. Pass molecule numbers for
# the reference (imol_ref) and moving (imol_moving) molecules and a
# match list. The match list format is described in the manual.
#
def lsq_match(imol_ref,imol_moving,match_list):
coot.clear_lsq_matches()
set_match_element(match_list)
apply_lsq_matches(imol_ref,imol_moving)
# Simple interface to LSQ fitting. More often than not this is what
# you will want, I imagine,
# e.g. simple_lsq_match(940, 950, "A", 0, 940, 950, "A", 1, "main")
#
def simple_lsq_match (ref_start_resno, ref_end_resno, ref_chain_id, imol_ref, mov_start_resno, mov_end_resno, mov_chain_id, imol_mov, match_type):
internal_match_type=lsq_match_type_symbol(match_type)
coot.clear_lsq_matches()
coot.add_lsq_match(ref_start_resno,ref_end_resno,ref_chain_id,
mov_start_resno,mov_end_resno,mov_chain_id,
internal_match_type)
apply_lsq_matches(imol_ref,imol_mov)
# examples:
# simple_lsq_match(940,950,"A",0,940,950,"A",1,"main")
#
# or another one:
#match1 = [40,50,"A",40,50,"B","all"]
#match2 = [45,55,"A",45,55,"B","main"]
#clear_lsq_matches()
#set_match_element(match1)
#set_match_element(match2)
#lsq_match(0,1,match1)
#
# BL says: still dont know exactly why we want that (2nd example) and what
# we should do with that! Or I havent understood and translated guile code
# wrong and screwed up!
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