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core
ramachandran.h
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//C Copyright (C) 2000-2006 Kevin Cowtan and University of York
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//L
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//L This library is free software and is distributed under the terms
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//L and conditions of version 2.1 of the GNU Lesser General Public
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//L Licence (LGPL) with the following additional clause:
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//L
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//L `You may also combine or link a "work that uses the Library" to
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//L produce a work containing portions of the Library, and distribute
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//L that work under terms of your choice, provided that you give
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//L prominent notice with each copy of the work that the specified
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//L version of the Library is used in it, and that you include or
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//L provide public access to the complete corresponding
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//L machine-readable source code for the Library including whatever
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//L changes were used in the work. (i.e. If you make changes to the
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//L Library you must distribute those, but you do not need to
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//L distribute source or object code to those portions of the work
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//L not covered by this licence.)'
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//L
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//L Note that this clause grants an additional right and does not impose
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//L any additional restriction, and so does not affect compatibility
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//L with the GNU General Public Licence (GPL). If you wish to negotiate
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//L other terms, please contact the maintainer.
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//L
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//L You can redistribute it and/or modify the library under the terms of
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//L the GNU Lesser General Public License as published by the Free Software
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//L Foundation; either version 2.1 of the License, or (at your option) any
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//L later version.
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//L
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//L This library is distributed in the hope that it will be useful, but
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//L WITHOUT ANY WARRANTY; without even the implied warranty of
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//L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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//L Lesser General Public License for more details.
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//L
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//L You should have received a copy of the CCP4 licence and/or GNU
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//L Lesser General Public License along with this library; if not, write
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//L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK.
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//L The GNU Lesser General Public can also be obtained by writing to the
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//L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston,
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//L MA 02111-1307 USA
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#ifndef CLIPPER_RAMACHANDRAN
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#define CLIPPER_RAMACHANDRAN
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#include "clipper_types.h"
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namespace
clipper {
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class
Prob_phi_2d
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{
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public
:
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void
init
(
const
int
& size );
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void
accumulate
(
const
ftype32 table[] );
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void
accumulate
(
const
ftype
& phi1,
const
ftype
& phi2,
ftype
wgt = 1.0 );
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void
normalise
();
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ftype
probability
(
const
ftype
& phi1,
const
ftype
& phi2 )
const
;
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String
format
()
const
;
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const
ftype
&
data
(
const
int
& i,
const
int
& j )
const
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{
return
data_[n*i+j]; }
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ftype
&
data
(
const
int
& i,
const
int
& j )
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{
return
data_[n*i+j]; }
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private
:
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int
n;
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std::vector<ftype> data_;
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};
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class
Ramachandran
:
private
Prob_phi_2d
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{
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public
:
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enum
TYPE
{ Gly, Pro, NonGlyPro, NonGly, All };
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Ramachandran
() {}
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Ramachandran
(
TYPE
type );
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void
init
(
TYPE
type );
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void
set_thresholds
(
ftype
prob_favored = 0.01,
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ftype
prob_allowed = 0.0005 );
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ftype
probability
(
const
ftype
& phi,
const
ftype
& psi )
const
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{
return
Prob_phi_2d::probability
( phi, psi ); }
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bool
favored
(
const
ftype
& phi,
const
ftype
& psi )
const
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{
return
(
probability
( phi, psi ) > p_favored ); }
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bool
allowed
(
const
ftype
& phi,
const
ftype
& psi )
const
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{
return
(
probability
( phi, psi ) > p_allowed ); }
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private
:
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ftype
p_favored, p_allowed;
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};
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}
// namespace clipper
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#endif
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