From 578b745dfe5fa86c430ffc5970466c8cdfa1d793 Mon Sep 17 00:00:00 2001 From: Danny Yoo Date: Tue, 21 Feb 2012 18:04:51 -0500 Subject: [PATCH] adding nucleic2 test --- js-assembler/runtime-src/runtime.js | 2 +- tests/more-tests/nucleic2.expected | 1 + tests/more-tests/nucleic2.rkt | 3511 +++++++++++++++++++++++++++ tests/run-more-tests.rkt | 1 + 4 files changed, 3514 insertions(+), 1 deletion(-) create mode 100644 tests/more-tests/nucleic2.expected create mode 100644 tests/more-tests/nucleic2.rkt diff --git a/js-assembler/runtime-src/runtime.js b/js-assembler/runtime-src/runtime.js index 2acae92..e7798da 100644 --- a/js-assembler/runtime-src/runtime.js +++ b/js-assembler/runtime-src/runtime.js @@ -944,7 +944,6 @@ }; var checkedGreaterThan = function(M, x, y) { - var i; // fast path optimization: binop comparison on fixnums if (arguments.length === 3) { if (typeof(x) === 'number' && typeof(y) === 'number') { @@ -955,6 +954,7 @@ }; var checkedGreaterThanSlowPath = function(M, args) { + var i; if (! isNumber(args[0])) { raiseArgumentTypeError(M, '>', 'number', 0, args[0]); } diff --git a/tests/more-tests/nucleic2.expected b/tests/more-tests/nucleic2.expected new file mode 100644 index 0000000..488d235 --- /dev/null +++ b/tests/more-tests/nucleic2.expected @@ -0,0 +1 @@ +33.797594890762696 diff --git a/tests/more-tests/nucleic2.rkt b/tests/more-tests/nucleic2.rkt new file mode 100644 index 0000000..97152c7 --- /dev/null +++ b/tests/more-tests/nucleic2.rkt @@ -0,0 +1,3511 @@ +#lang planet dyoo/whalesong/base +(require (for-syntax racket/base)) + +; File: "nucleic2.scm" +; +; Author: Marc Feeley (feeley@iro.umontreal.ca) +; Last modification by Feeley: June 6, 1994. +; Modified for R5RS Scheme by William D Clinger: 22 October 1996. +; Last modification by Clinger: 19 March 1999. +; +; This program is a modified version of the program described in +; +; M. Feeley, M. Turcotte, G. Lapalme. Using Multilisp for Solving +; Constraint Satisfaction Problems: an Application to Nucleic Acid 3D +; Structure Determination. Lisp and Symbolic Computation 7(2/3), +; 231-246, 1994. +; +; The differences between this program and the original are described in +; +; P.H. Hartel, M. Feeley, et al. Benchmarking Implementations of +; Functional Languages with "Pseudoknot", a Float-Intensive Benchmark. +; Journal of Functional Programming 6(4), 621-655, 1996. + +; This procedure uses Marc Feeley's run-benchmark procedure to time +; the benchmark. + +; PORTABILITY. +; +; This program should run in any R5RS-conforming implementation of Scheme. +; To run this program in an implementation that does not support the R5RS +; macro system, however, you will have to place a single quotation mark (') +; on the following line and also modify the "SYSTEM DEPENDENT CODE" below. + +; ********** R5RS Scheme + +(begin + +(define-syntax FLOAT+ (syntax-rules () ((FLOAT+ x ...) (+ x ...)))) +(define-syntax FLOAT- (syntax-rules () ((FLOAT- x ...) (- x ...)))) +(define-syntax FLOAT* (syntax-rules () ((FLOAT* x ...) (* x ...)))) +(define-syntax FLOAT/ (syntax-rules () ((FLOAT/ x ...) (/ x ...)))) +(define-syntax FLOAT= (syntax-rules () ((FLOAT= x y) (= x y)))) +(define-syntax FLOAT< (syntax-rules () ((FLOAT< x y) (< x y)))) +(define-syntax FLOAT<= (syntax-rules () ((FLOAT<= x y) (<= x y)))) +(define-syntax FLOAT> (syntax-rules () ((FLOAT> x y) (> x y)))) +(define-syntax FLOAT>= (syntax-rules () ((FLOAT>= x y) (>= x y)))) +(define-syntax FLOATsin (syntax-rules () ((FLOATsin x) (sin x)))) +(define-syntax FLOATcos (syntax-rules () ((FLOATcos x) (cos x)))) +(define-syntax FLOATatan (syntax-rules () ((FLOATatan x) (atan x)))) +(define-syntax FLOATsqrt (syntax-rules () ((FLOATsqrt x) (sqrt x)))) + +(define-syntax FUTURE (syntax-rules () ((FUTURE x) x))) +(define-syntax TOUCH (syntax-rules () ((TOUCH x) x))) + +(define-syntax define-structure + (syntax-rules () + ((define-structure #f + name make make-constant (select1 ...) (set1 ...)) + (begin (define-syntax make + (syntax-rules () + ((make select1 ...) + (vector select1 ...)))) + (define-syntax make-constant + (syntax-rules () + ; The vectors that are passed to make-constant aren't quoted. + ((make-constant . args) + (constant-maker make . args)))) + (define-selectors (select1 ...) + (0 1 2 3 4 5 6 7 8 9 + 10 11 12 13 14 15 16 17 18 19 + 20 21 22 23 24 25 26 27 28 29 + 30 31 32 33 34 35 36 37 38 39 + 40 41 42 43 44 45 46 47 48 49)) + (define-setters (set1 ...) + (0 1 2 3 4 5 6 7 8 9 + 10 11 12 13 14 15 16 17 18 19 + 20 21 22 23 24 25 26 27 28 29 + 30 31 32 33 34 35 36 37 38 39 + 40 41 42 43 44 45 46 47 48 49)))) + ((define-structure pred? + name make make-constant (select1 ...) (set1 ...)) + (begin (define-syntax pred? + (syntax-rules () + ((pred? v) + (and (vector? v) (eq? (vector-ref v 0) 'name))))) + (define-syntax make + (syntax-rules () + ((make select1 ...) + (vector 'name select1 ...)))) + (define-syntax make-constant + (syntax-rules () + ; The vectors that are passed to make-constant aren't quoted. + ((make-constant . args) + (constant-maker make . args)))) + (define-selectors (select1 ...) + (1 2 3 4 5 6 7 8 9 + 10 11 12 13 14 15 16 17 18 19 + 20 21 22 23 24 25 26 27 28 29 + 30 31 32 33 34 35 36 37 38 39 + 40 41 42 43 44 45 46 47 48 49)) + (define-setters (set1 ...) + (1 2 3 4 5 6 7 8 9 + 10 11 12 13 14 15 16 17 18 19 + 20 21 22 23 24 25 26 27 28 29 + 30 31 32 33 34 35 36 37 38 39 + 40 41 42 43 44 45 46 47 48 49)))))) +(define-syntax constant-maker + (syntax-rules () + ; The quotation marks are added here. + ((constant-maker make arg ...) + (make 'arg ...)))) +(define-syntax define-selectors + (syntax-rules () + ((define-selectors (select) (i i1 ...)) + (define-syntax select + (syntax-rules () + ((select v) (vector-ref v i))))) + ((define-selectors (select select1 ...) (i i1 ...)) + (begin (define-syntax select + (syntax-rules () + ((select v) (vector-ref v i)))) + (define-selectors (select1 ...) (i1 ...)))))) +(define-syntax define-setters + (syntax-rules () + ((define-setters (set) (i i1 ...)) + (define-syntax set + (syntax-rules () + ((set v x) (vector-set! v i x))))) + ((define-setters (set set1 ...) (i i1 ...)) + (begin (define-syntax set + (syntax-rules () + ((set v x) (vector-set! v i x)))) + (define-setters (set1 ...) (i1 ...)))))) + +(define-structure #f pt + make-pt make-constant-pt + (pt-x pt-y pt-z) + (pt-x-set! pt-y-set! pt-z-set!)) + +(define-structure #f tfo + make-tfo make-constant-tfo + (tfo-a tfo-b tfo-c tfo-d tfo-e tfo-f tfo-g tfo-h tfo-i tfo-tx tfo-ty tfo-tz) + (tfo-a-set! tfo-b-set! tfo-c-set! tfo-d-set! tfo-e-set! tfo-f-set! + tfo-g-set! tfo-h-set! tfo-i-set! tfo-tx-set! tfo-ty-set! tfo-tz-set!)) + +(define-structure nuc? nuc + make-nuc make-constant-nuc + (nuc-dgf-base-tfo ; defines the standard position for wc and wc-dumas + nuc-P-O3*-275-tfo ; defines the standard position for the connect function + nuc-P-O3*-180-tfo + nuc-P-O3*-60-tfo + nuc-P nuc-O1P nuc-O2P nuc-O5* nuc-C5* + nuc-H5* nuc-H5** + nuc-C4* nuc-H4* nuc-O4* nuc-C1* nuc-H1* + nuc-C2* nuc-H2** + nuc-O2* nuc-H2* nuc-C3* nuc-H3* nuc-O3* + nuc-N1 nuc-N3 nuc-C2 nuc-C4 nuc-C5 nuc-C6) + (nuc-dgf-base-tfo-set! + nuc-P-O3*-275-tfo-set! + nuc-P-O3*-180-tfo-set! + nuc-P-O3*-60-tfo-set! + nuc-P-set! nuc-O1P-set! nuc-O2P-set! nuc-O5*-set! nuc-C5*-set! + nuc-H5*-set! nuc-H5**-set! + nuc-C4*-set! nuc-H4*-set! nuc-O4*-set! nuc-C1*-set! nuc-H1*-set! + nuc-C2*-set! nuc-H2**-set! + nuc-O2*-set! nuc-H2*-set! nuc-C3*-set! nuc-H3*-set! nuc-O3*-set! + nuc-N1-set! nuc-N3-set! nuc-C2-set! nuc-C4-set! nuc-C5-set! nuc-C6-set!)) + +(define-structure rA? rA + make-rA make-constant-rA + (rA-dgf-base-tfo ; defines the standard position for wc and wc-dumas + rA-P-O3*-275-tfo ; defines the standard position for the connect function + rA-P-O3*-180-tfo + rA-P-O3*-60-tfo + rA-P rA-O1P rA-O2P rA-O5* rA-C5* + rA-H5* rA-H5** + rA-C4* rA-H4* rA-O4* rA-C1* rA-H1* + rA-C2* rA-H2** + rA-O2* rA-H2* rA-C3* rA-H3* rA-O3* + rA-N1 rA-N3 rA-C2 rA-C4 rA-C5 rA-C6 + rA-N6 rA-N7 rA-N9 rA-C8 + rA-H2 rA-H61 rA-H62 rA-H8) + (rA-dgf-base-tfo-set! + rA-P-O3*-275-tfo-set! + rA-P-O3*-180-tfo-set! + rA-P-O3*-60-tfo-set! + rA-P-set! rA-O1P-set! rA-O2P-set! rA-O5*-set! rA-C5*-set! + rA-H5*-set! rA-H5**-set! + rA-C4*-set! rA-H4*-set! rA-O4*-set! rA-C1*-set! rA-H1*-set! + rA-C2*-set! rA-H2**-set! + rA-O2*-set! rA-H2*-set! rA-C3*-set! rA-H3*-set! rA-O3*-set! + rA-N1-set! rA-N3-set! rA-C2-set! rA-C4-set! rA-C5-set! rA-C6-set! + rA-N6-set! rA-N7-set! rA-N9-set! rA-C8-set! + rA-H2-set! rA-H61-set! rA-H62-set! rA-H8-set!)) + +(define-structure rC? rC + make-rC make-constant-rC + (rC-dgf-base-tfo ; defines the standard position for wc and wc-dumas + rC-P-O3*-275-tfo ; defines the standard position for the connect function + rC-P-O3*-180-tfo + rC-P-O3*-60-tfo + rC-P rC-O1P rC-O2P rC-O5* rC-C5* + rC-H5* rC-H5** + rC-C4* rC-H4* rC-O4* rC-C1* rC-H1* + rC-C2* rC-H2** + rC-O2* rC-H2* rC-C3* rC-H3* rC-O3* + rC-N1 rC-N3 rC-C2 rC-C4 rC-C5 rC-C6 + rC-N4 rC-O2 rC-H41 rC-H42 rC-H5 rC-H6) + (rC-dgf-base-tfo-set! + rC-P-O3*-275-tfo-set! + rC-P-O3*-180-tfo-set! + rC-P-O3*-60-tfo-set! + rC-P-set! rC-O1P-set! rC-O2P-set! rC-O5*-set! rC-C5*-set! + rC-H5*-set! rC-H5**-set! + rC-C4*-set! rC-H4*-set! rC-O4*-set! rC-C1*-set! rC-H1*-set! + rC-C2*-set! rC-H2**-set! + rC-O2*-set! rC-H2*-set! rC-C3*-set! rC-H3*-set! rC-O3*-set! + rC-N1-set! rC-N3-set! rC-C2-set! rC-C4-set! rC-C5-set! rC-C6-set! + rC-N4-set! rC-O2-set! rC-H41-set! rC-H42-set! rC-H5-set! rC-H6-set!)) + +(define-structure rG? rG + make-rG make-constant-rG + (rG-dgf-base-tfo ; defines the standard position for wc and wc-dumas + rG-P-O3*-275-tfo ; defines the standard position for the connect function + rG-P-O3*-180-tfo + rG-P-O3*-60-tfo + rG-P rG-O1P rG-O2P rG-O5* rG-C5* + rG-H5* rG-H5** + rG-C4* rG-H4* rG-O4* rG-C1* rG-H1* + rG-C2* rG-H2** + rG-O2* rG-H2* rG-C3* rG-H3* rG-O3* + rG-N1 rG-N3 rG-C2 rG-C4 rG-C5 rG-C6 + rG-N2 rG-N7 rG-N9 rG-C8 rG-O6 + rG-H1 rG-H21 rG-H22 rG-H8) + (rG-dgf-base-tfo-set! + rG-P-O3*-275-tfo-set! + rG-P-O3*-180-tfo-set! + rG-P-O3*-60-tfo-set! + rG-P-set! rG-O1P-set! rG-O2P-set! rG-O5*-set! rG-C5*-set! + rG-H5*-set! rG-H5**-set! + rG-C4*-set! rG-H4*-set! rG-O4*-set! rG-C1*-set! rG-H1*-set! + rG-C2*-set! rG-H2**-set! + rG-O2*-set! rG-H2*-set! rG-C3*-set! rG-H3*-set! rG-O3*-set! + rG-N1-set! rG-N3-set! rG-C2-set! rG-C4-set! rG-C5-set! rG-C6-set! + rG-N2-set! rG-N7-set! rG-N9-set! rG-C8-set! rG-O6-set! + rG-H1-set! rG-H21-set! rG-H22-set! rG-H8-set!)) + +(define-structure rU? rU + make-rU make-constant-rU + (rU-dgf-base-tfo ; defines the standard position for wc and wc-dumas + rU-P-O3*-275-tfo ; defines the standard position for the connect function + rU-P-O3*-180-tfo + rU-P-O3*-60-tfo + rU-P rU-O1P rU-O2P rU-O5* rU-C5* + rU-H5* rU-H5** + rU-C4* rU-H4* rU-O4* rU-C1* rU-H1* + rU-C2* rU-H2** + rU-O2* rU-H2* rU-C3* rU-H3* rU-O3* + rU-N1 rU-N3 rU-C2 rU-C4 rU-C5 rU-C6 + rU-O2 rU-O4 rU-H3 rU-H5 rU-H6) + (rU-dgf-base-tfo-set! + rU-P-O3*-275-tfo-set! + rU-P-O3*-180-tfo-set! + rU-P-O3*-60-tfo-set! + rU-P-set! rU-O1P-set! rU-O2P-set! rU-O5*-set! rU-C5*-set! + rU-H5*-set! rU-H5**-set! + rU-C4*-set! rU-H4*-set! rU-O4*-set! rU-C1*-set! rU-H1*-set! + rU-C2*-set! rU-H2**-set! + rU-O2*-set! rU-H2*-set! rU-C3*-set! rU-H3*-set! rU-O3*-set! + rU-N1-set! rU-N3-set! rU-C2-set! rU-C4-set! rU-C5-set! rU-C6-set! + rU-O2-set! rU-O4-set! rU-H3-set! rU-H5-set! rU-H6-set!)) + +(define-structure #f var + make-var make-constant-var + (var-id var-tfo var-nuc) + (var-id-set! var-tfo-set! var-nuc-set!)) + +; Comment out the next three syntax definitions if you want +; lazy computation. + +(define-syntax mk-var + (syntax-rules () + ((mk-var i tfo nuc) + (make-var i tfo nuc)))) + +(define-syntax absolute-pos + (syntax-rules () + ((absolute-pos var p) + (tfo-apply (var-tfo var) p)))) + +(define-syntax lazy-computation-of + (syntax-rules () + ((lazy-computation-of expr) + expr))) + +; Uncomment the next three syntax definitions if you want +; lazy computation. + +; (define-syntax mk-var +; (syntax-rules () +; ((mk-var i tfo nuc) +; (make-var i tfo (make-relative-nuc tfo nuc))))) +; +; (define-syntax absolute-pos +; (syntax-rules () +; ((absolute-pos var p) +; (force p)))) +; +; (define-syntax lazy-computation-of +; (syntax-rules () +; ((lazy-computation-of expr) +; (delay expr)))) + +(define-syntax atom-pos + (syntax-rules () + ((atom-pos atom var) + (let ((v var)) + (absolute-pos v (atom (var-nuc v))))))) + +) + +; -- MATH UTILITIES ----------------------------------------------------------- + +(define constant-pi 3.14159265358979323846) +(define constant-minus-pi -3.14159265358979323846) +(define constant-pi/2 1.57079632679489661923) +(define constant-minus-pi/2 -1.57079632679489661923) + +(define (math-atan2 y x) + (cond ((FLOAT> x 0.0) + (FLOATatan (FLOAT/ y x))) + ((FLOAT< y 0.0) + (if (FLOAT= x 0.0) + constant-minus-pi/2 + (FLOAT+ (FLOATatan (FLOAT/ y x)) constant-minus-pi))) + (else + (if (FLOAT= x 0.0) + constant-pi/2 + (FLOAT+ (FLOATatan (FLOAT/ y x)) constant-pi))))) + +; -- POINTS ------------------------------------------------------------------- + +(define (pt-sub p1 p2) + (make-pt (FLOAT- (pt-x p1) (pt-x p2)) + (FLOAT- (pt-y p1) (pt-y p2)) + (FLOAT- (pt-z p1) (pt-z p2)))) + +(define (pt-dist p1 p2) + (let ((dx (FLOAT- (pt-x p1) (pt-x p2))) + (dy (FLOAT- (pt-y p1) (pt-y p2))) + (dz (FLOAT- (pt-z p1) (pt-z p2)))) + (FLOATsqrt (FLOAT+ (FLOAT* dx dx) (FLOAT* dy dy) (FLOAT* dz dz))))) + +(define (pt-phi p) + (let* ((x (pt-x p)) + (y (pt-y p)) + (z (pt-z p)) + (b (math-atan2 x z))) + (math-atan2 (FLOAT+ (FLOAT* (FLOATcos b) z) (FLOAT* (FLOATsin b) x)) y))) + +(define (pt-theta p) + (math-atan2 (pt-x p) (pt-z p))) + +; -- COORDINATE TRANSFORMATIONS ----------------------------------------------- + +; The notation for the transformations follows "Paul, R.P. (1981) Robot +; Manipulators. MIT Press." with the exception that our transformation +; matrices don't have the perspective terms and are the transpose of +; Paul's one. See also "M\"antyl\"a, M. (1985) An Introduction to +; Solid Modeling, Computer Science Press" Appendix A. +; +; The components of a transformation matrix are named like this: +; +; a b c +; d e f +; g h i +; tx ty tz +; +; The components tx, ty, and tz are the translation vector. + +(define tfo-id ; the identity transformation matrix + '#(1.0 0.0 0.0 + 0.0 1.0 0.0 + 0.0 0.0 1.0 + 0.0 0.0 0.0)) + +; The function "tfo-apply" multiplies a transformation matrix, tfo, by a +; point vector, p. The result is a new point. + +(define (tfo-apply tfo p) + (let ((x (pt-x p)) + (y (pt-y p)) + (z (pt-z p))) + (make-pt + (FLOAT+ (FLOAT* x (tfo-a tfo)) + (FLOAT* y (tfo-d tfo)) + (FLOAT* z (tfo-g tfo)) + (tfo-tx tfo)) + (FLOAT+ (FLOAT* x (tfo-b tfo)) + (FLOAT* y (tfo-e tfo)) + (FLOAT* z (tfo-h tfo)) + (tfo-ty tfo)) + (FLOAT+ (FLOAT* x (tfo-c tfo)) + (FLOAT* y (tfo-f tfo)) + (FLOAT* z (tfo-i tfo)) + (tfo-tz tfo))))) + +; The function "tfo-combine" multiplies two transformation matrices A and B. +; The result is a new matrix which cumulates the transformations described +; by A and B. + +(define (tfo-combine A B) + (make-tfo + (FLOAT+ (FLOAT* (tfo-a A) (tfo-a B)) + (FLOAT* (tfo-b A) (tfo-d B)) + (FLOAT* (tfo-c A) (tfo-g B))) + (FLOAT+ (FLOAT* (tfo-a A) (tfo-b B)) + (FLOAT* (tfo-b A) (tfo-e B)) + (FLOAT* (tfo-c A) (tfo-h B))) + (FLOAT+ (FLOAT* (tfo-a A) (tfo-c B)) + (FLOAT* (tfo-b A) (tfo-f B)) + (FLOAT* (tfo-c A) (tfo-i B))) + (FLOAT+ (FLOAT* (tfo-d A) (tfo-a B)) + (FLOAT* (tfo-e A) (tfo-d B)) + (FLOAT* (tfo-f A) (tfo-g B))) + (FLOAT+ (FLOAT* (tfo-d A) (tfo-b B)) + (FLOAT* (tfo-e A) (tfo-e B)) + (FLOAT* (tfo-f A) (tfo-h B))) + (FLOAT+ (FLOAT* (tfo-d A) (tfo-c B)) + (FLOAT* (tfo-e A) (tfo-f B)) + (FLOAT* (tfo-f A) (tfo-i B))) + (FLOAT+ (FLOAT* (tfo-g A) (tfo-a B)) + (FLOAT* (tfo-h A) (tfo-d B)) + (FLOAT* (tfo-i A) (tfo-g B))) + (FLOAT+ (FLOAT* (tfo-g A) (tfo-b B)) + (FLOAT* (tfo-h A) (tfo-e B)) + (FLOAT* (tfo-i A) (tfo-h B))) + (FLOAT+ (FLOAT* (tfo-g A) (tfo-c B)) + (FLOAT* (tfo-h A) (tfo-f B)) + (FLOAT* (tfo-i A) (tfo-i B))) + (FLOAT+ (FLOAT* (tfo-tx A) (tfo-a B)) + (FLOAT* (tfo-ty A) (tfo-d B)) + (FLOAT* (tfo-tz A) (tfo-g B)) + (tfo-tx B)) + (FLOAT+ (FLOAT* (tfo-tx A) (tfo-b B)) + (FLOAT* (tfo-ty A) (tfo-e B)) + (FLOAT* (tfo-tz A) (tfo-h B)) + (tfo-ty B)) + (FLOAT+ (FLOAT* (tfo-tx A) (tfo-c B)) + (FLOAT* (tfo-ty A) (tfo-f B)) + (FLOAT* (tfo-tz A) (tfo-i B)) + (tfo-tz B)))) + +; The function "tfo-inv-ortho" computes the inverse of a homogeneous +; transformation matrix. + +(define (tfo-inv-ortho tfo) + (let* ((tx (tfo-tx tfo)) + (ty (tfo-ty tfo)) + (tz (tfo-tz tfo))) + (make-tfo + (tfo-a tfo) (tfo-d tfo) (tfo-g tfo) + (tfo-b tfo) (tfo-e tfo) (tfo-h tfo) + (tfo-c tfo) (tfo-f tfo) (tfo-i tfo) + (FLOAT- (FLOAT+ (FLOAT* (tfo-a tfo) tx) + (FLOAT* (tfo-b tfo) ty) + (FLOAT* (tfo-c tfo) tz))) + (FLOAT- (FLOAT+ (FLOAT* (tfo-d tfo) tx) + (FLOAT* (tfo-e tfo) ty) + (FLOAT* (tfo-f tfo) tz))) + (FLOAT- (FLOAT+ (FLOAT* (tfo-g tfo) tx) + (FLOAT* (tfo-h tfo) ty) + (FLOAT* (tfo-i tfo) tz)))))) + +; Given three points p1, p2, and p3, the function "tfo-align" computes +; a transformation matrix such that point p1 gets mapped to (0,0,0), p2 gets +; mapped to the Y axis and p3 gets mapped to the YZ plane. + +(define (tfo-align p1 p2 p3) + (let* ((x1 (pt-x p1)) (y1 (pt-y p1)) (z1 (pt-z p1)) + (x3 (pt-x p3)) (y3 (pt-y p3)) (z3 (pt-z p3)) + (x31 (FLOAT- x3 x1)) (y31 (FLOAT- y3 y1)) (z31 (FLOAT- z3 z1)) + (rotpY (pt-sub p2 p1)) + (Phi (pt-phi rotpY)) + (Theta (pt-theta rotpY)) + (sinP (FLOATsin Phi)) + (sinT (FLOATsin Theta)) + (cosP (FLOATcos Phi)) + (cosT (FLOATcos Theta)) + (sinPsinT (FLOAT* sinP sinT)) + (sinPcosT (FLOAT* sinP cosT)) + (cosPsinT (FLOAT* cosP sinT)) + (cosPcosT (FLOAT* cosP cosT)) + (rotpZ + (make-pt + (FLOAT- (FLOAT* cosT x31) + (FLOAT* sinT z31)) + (FLOAT+ (FLOAT* sinPsinT x31) + (FLOAT* cosP y31) + (FLOAT* sinPcosT z31)) + (FLOAT+ (FLOAT* cosPsinT x31) + (FLOAT- (FLOAT* sinP y31)) + (FLOAT* cosPcosT z31)))) + (Rho (pt-theta rotpZ)) + (cosR (FLOATcos Rho)) + (sinR (FLOATsin Rho)) + (x (FLOAT+ (FLOAT- (FLOAT* x1 cosT)) + (FLOAT* z1 sinT))) + (y (FLOAT- (FLOAT- (FLOAT- (FLOAT* x1 sinPsinT)) + (FLOAT* y1 cosP)) + (FLOAT* z1 sinPcosT))) + (z (FLOAT- (FLOAT+ (FLOAT- (FLOAT* x1 cosPsinT)) + (FLOAT* y1 sinP)) + (FLOAT* z1 cosPcosT)))) + (make-tfo + (FLOAT- (FLOAT* cosT cosR) (FLOAT* cosPsinT sinR)) + sinPsinT + (FLOAT+ (FLOAT* cosT sinR) (FLOAT* cosPsinT cosR)) + (FLOAT* sinP sinR) + cosP + (FLOAT- (FLOAT* sinP cosR)) + (FLOAT- (FLOAT- (FLOAT* sinT cosR)) (FLOAT* cosPcosT sinR)) + sinPcosT + (FLOAT+ (FLOAT- (FLOAT* sinT sinR)) (FLOAT* cosPcosT cosR)) + (FLOAT- (FLOAT* x cosR) (FLOAT* z sinR)) + y + (FLOAT+ (FLOAT* x sinR) (FLOAT* z cosR))))) + +; -- NUCLEIC ACID CONFORMATIONS DATA BASE ------------------------------------- + +; Numbering of atoms follows the paper: +; +; IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN) +; (1983) Abbreviations and Symbols for the Description of +; Conformations of Polynucleotide Chains. Eur. J. Biochem 131, +; 9-15. +; +; In the atom names, we have used "*" instead of "'". + +; Define part common to all 4 nucleotide types. + +; Define remaining atoms for each nucleotide type. + +; Database of nucleotide conformations: + +(define rA + (make-constant-rA + #( -0.0018 -0.8207 0.5714 ; dgf-base-tfo + 0.2679 -0.5509 -0.7904 + 0.9634 0.1517 0.2209 + 0.0073 8.4030 0.6232) + #( -0.8143 -0.5091 -0.2788 ; P-O3*-275-tfo + -0.0433 -0.4257 0.9038 + -0.5788 0.7480 0.3246 + 1.5227 6.9114 -7.0765) + #( 0.3822 -0.7477 0.5430 ; P-O3*-180-tfo + 0.4552 0.6637 0.5935 + -0.8042 0.0203 0.5941 + -6.9472 -4.1186 -5.9108) + #( 0.5640 0.8007 -0.2022 ; P-O3*-60-tfo + -0.8247 0.5587 -0.0878 + 0.0426 0.2162 0.9754 + 6.2694 -7.0540 3.3316) + #( 2.8930 8.5380 -3.3280) ; P + #( 1.6980 7.6960 -3.5570) ; O1P + #( 3.2260 9.5010 -4.4020) ; O2P + #( 4.1590 7.6040 -3.0340) ; O5* + #( 5.4550 8.2120 -2.8810) ; C5* + #( 5.4546 8.8508 -1.9978) ; H5* + #( 5.7588 8.6625 -3.8259) ; H5** + #( 6.4970 7.1480 -2.5980) ; C4* + #( 7.4896 7.5919 -2.5214) ; H4* + #( 6.1630 6.4860 -1.3440) ; O4* + #( 6.5400 5.1200 -1.4190) ; C1* + #( 7.2763 4.9681 -0.6297) ; H1* + #( 7.1940 4.8830 -2.7770) ; C2* + #( 6.8667 3.9183 -3.1647) ; H2** + #( 8.5860 5.0910 -2.6140) ; O2* + #( 8.9510 4.7626 -1.7890) ; H2* + #( 6.5720 6.0040 -3.6090) ; C3* + #( 5.5636 5.7066 -3.8966) ; H3* + #( 7.3801 6.3562 -4.7350) ; O3* + #( 4.7150 0.4910 -0.1360) ; N1 + #( 6.3490 2.1730 -0.6020) ; N3 + #( 5.9530 0.9650 -0.2670) ; C2 + #( 5.2900 2.9790 -0.8260) ; C4 + #( 3.9720 2.6390 -0.7330) ; C5 + #( 3.6770 1.3160 -0.3660) ; C6 + #( 2.4280 0.8450 -0.2360) ; N6 + #( 3.1660 3.7290 -1.0360) ; N7 + #( 5.3170 4.2990 -1.1930) ; N9 + #( 4.0100 4.6780 -1.2990) ; C8 + #( 6.6890 0.1903 -0.0518) ; H2 + #( 1.6470 1.4460 -0.4040) ; H61 + #( 2.2780 -0.1080 -0.0280) ; H62 + #( 3.4421 5.5744 -1.5482) ; H8 + )) + +(define rA01 + (make-constant-rA + #( -0.0043 -0.8175 0.5759 ; dgf-base-tfo + 0.2617 -0.5567 -0.7884 + 0.9651 0.1473 0.2164 + 0.0359 8.3929 0.5532) + #( -0.8143 -0.5091 -0.2788 ; P-O3*-275-tfo + -0.0433 -0.4257 0.9038 + -0.5788 0.7480 0.3246 + 1.5227 6.9114 -7.0765) + #( 0.3822 -0.7477 0.5430 ; P-O3*-180-tfo + 0.4552 0.6637 0.5935 + -0.8042 0.0203 0.5941 + -6.9472 -4.1186 -5.9108) + #( 0.5640 0.8007 -0.2022 ; P-O3*-60-tfo + -0.8247 0.5587 -0.0878 + 0.0426 0.2162 0.9754 + 6.2694 -7.0540 3.3316) + #( 2.8930 8.5380 -3.3280) ; P + #( 1.6980 7.6960 -3.5570) ; O1P + #( 3.2260 9.5010 -4.4020) ; O2P + #( 4.1590 7.6040 -3.0340) ; O5* + #( 5.4352 8.2183 -2.7757) ; C5* + #( 5.3830 8.7883 -1.8481) ; H5* + #( 5.7729 8.7436 -3.6691) ; H5** + #( 6.4830 7.1518 -2.5252) ; C4* + #( 7.4749 7.5972 -2.4482) ; H4* + #( 6.1626 6.4620 -1.2827) ; O4* + #( 6.5431 5.0992 -1.3905) ; C1* + #( 7.2871 4.9328 -0.6114) ; H1* + #( 7.1852 4.8935 -2.7592) ; C2* + #( 6.8573 3.9363 -3.1645) ; H2** + #( 8.5780 5.1025 -2.6046) ; O2* + #( 8.9516 4.7577 -1.7902) ; H2* + #( 6.5522 6.0300 -3.5612) ; C3* + #( 5.5420 5.7356 -3.8459) ; H3* + #( 7.3487 6.4089 -4.6867) ; O3* + #( 4.7442 0.4514 -0.1390) ; N1 + #( 6.3687 2.1459 -0.5926) ; N3 + #( 5.9795 0.9335 -0.2657) ; C2 + #( 5.3052 2.9471 -0.8125) ; C4 + #( 3.9891 2.5987 -0.7230) ; C5 + #( 3.7016 1.2717 -0.3647) ; C6 + #( 2.4553 0.7925 -0.2390) ; N6 + #( 3.1770 3.6859 -1.0198) ; N7 + #( 5.3247 4.2695 -1.1710) ; N9 + #( 4.0156 4.6415 -1.2759) ; C8 + #( 6.7198 0.1618 -0.0547) ; H2 + #( 1.6709 1.3900 -0.4039) ; H61 + #( 2.3107 -0.1627 -0.0373) ; H62 + #( 3.4426 5.5361 -1.5199) ; H8 + )) + +(define rA02 + (make-constant-rA + #( 0.5566 0.0449 0.8296 ; dgf-base-tfo + 0.5125 0.7673 -0.3854 + -0.6538 0.6397 0.4041 + -9.1161 -3.7679 -2.9968) + #( -0.8143 -0.5091 -0.2788 ; P-O3*-275-tfo + -0.0433 -0.4257 0.9038 + -0.5788 0.7480 0.3246 + 1.5227 6.9114 -7.0765) + #( 0.3822 -0.7477 0.5430 ; P-O3*-180-tfo + 0.4552 0.6637 0.5935 + -0.8042 0.0203 0.5941 + -6.9472 -4.1186 -5.9108) + #( 0.5640 0.8007 -0.2022 ; P-O3*-60-tfo + -0.8247 0.5587 -0.0878 + 0.0426 0.2162 0.9754 + 6.2694 -7.0540 3.3316) + #( 2.8930 8.5380 -3.3280) ; P + #( 1.6980 7.6960 -3.5570) ; O1P + #( 3.2260 9.5010 -4.4020) ; O2P + #( 4.1590 7.6040 -3.0340) ; O5* + #( 4.5778 6.6594 -4.0364) ; C5* + #( 4.9220 7.1963 -4.9204) ; H5* + #( 3.7996 5.9091 -4.1764) ; H5** + #( 5.7873 5.8869 -3.5482) ; C4* + #( 6.0405 5.0875 -4.2446) ; H4* + #( 6.9135 6.8036 -3.4310) ; O4* + #( 7.7293 6.4084 -2.3392) ; C1* + #( 8.7078 6.1815 -2.7624) ; H1* + #( 7.1305 5.1418 -1.7347) ; C2* + #( 7.2040 5.1982 -0.6486) ; H2** + #( 7.7417 4.0392 -2.3813) ; O2* + #( 8.6785 4.1443 -2.5630) ; H2* + #( 5.6666 5.2728 -2.1536) ; C3* + #( 5.1747 5.9805 -1.4863) ; H3* + #( 4.9997 4.0086 -2.1973) ; O3* + #( 10.3245 8.5459 1.5467) ; N1 + #( 9.8051 6.9432 -0.1497) ; N3 + #( 10.5175 7.4328 0.8408) ; C2 + #( 8.7523 7.7422 -0.4228) ; C4 + #( 8.4257 8.9060 0.2099) ; C5 + #( 9.2665 9.3242 1.2540) ; C6 + #( 9.0664 10.4462 1.9610) ; N6 + #( 7.2750 9.4537 -0.3428) ; N7 + #( 7.7962 7.5519 -1.3859) ; N9 + #( 6.9479 8.6157 -1.2771) ; C8 + #( 11.4063 6.9047 1.1859) ; H2 + #( 8.2845 11.0341 1.7552) ; H61 + #( 9.6584 10.6647 2.7198) ; H62 + #( 6.0430 8.9853 -1.7594) ; H8 + )) + +(define rA03 + (make-constant-rA + #( -0.5021 0.0731 0.8617 ; dgf-base-tfo + -0.8112 0.3054 -0.4986 + -0.2996 -0.9494 -0.0940 + 6.4273 -5.1944 -3.7807) + #( -0.8143 -0.5091 -0.2788 ; P-O3*-275-tfo + -0.0433 -0.4257 0.9038 + -0.5788 0.7480 0.3246 + 1.5227 6.9114 -7.0765) + #( 0.3822 -0.7477 0.5430 ; P-O3*-180-tfo + 0.4552 0.6637 0.5935 + -0.8042 0.0203 0.5941 + -6.9472 -4.1186 -5.9108) + #( 0.5640 0.8007 -0.2022 ; P-O3*-60-tfo + -0.8247 0.5587 -0.0878 + 0.0426 0.2162 0.9754 + 6.2694 -7.0540 3.3316) + #( 2.8930 8.5380 -3.3280) ; P + #( 1.6980 7.6960 -3.5570) ; O1P + #( 3.2260 9.5010 -4.4020) ; O2P + #( 4.1590 7.6040 -3.0340) ; O5* + #( 4.1214 6.7116 -1.9049) ; C5* + #( 3.3465 5.9610 -2.0607) ; H5* + #( 4.0789 7.2928 -0.9837) ; H5** + #( 5.4170 5.9293 -1.8186) ; C4* + #( 5.4506 5.3400 -0.9023) ; H4* + #( 5.5067 5.0417 -2.9703) ; O4* + #( 6.8650 4.9152 -3.3612) ; C1* + #( 7.1090 3.8577 -3.2603) ; H1* + #( 7.7152 5.7282 -2.3894) ; C2* + #( 8.5029 6.2356 -2.9463) ; H2** + #( 8.1036 4.8568 -1.3419) ; O2* + #( 8.3270 3.9651 -1.6184) ; H2* + #( 6.7003 6.7565 -1.8911) ; C3* + #( 6.5898 7.5329 -2.6482) ; H3* + #( 7.0505 7.2878 -0.6105) ; O3* + #( 9.6740 4.7656 -7.6614) ; N1 + #( 9.0739 4.3013 -5.3941) ; N3 + #( 9.8416 4.2192 -6.4581) ; C2 + #( 7.9885 5.0632 -5.6446) ; C4 + #( 7.6822 5.6856 -6.8194) ; C5 + #( 8.5831 5.5215 -7.8840) ; C6 + #( 8.4084 6.0747 -9.0933) ; N6 + #( 6.4857 6.3816 -6.7035) ; N7 + #( 6.9740 5.3703 -4.7760) ; N9 + #( 6.1133 6.1613 -5.4808) ; C8 + #( 10.7627 3.6375 -6.4220) ; H2 + #( 7.6031 6.6390 -9.2733) ; H61 + #( 9.1004 5.9708 -9.7893) ; H62 + #( 5.1705 6.6830 -5.3167) ; H8 + )) + +(define rA04 + (make-constant-rA + #( -0.5426 -0.8175 0.1929 ; dgf-base-tfo + 0.8304 -0.5567 -0.0237 + 0.1267 0.1473 0.9809 + -0.5075 8.3929 0.2229) + #( -0.8143 -0.5091 -0.2788 ; P-O3*-275-tfo + -0.0433 -0.4257 0.9038 + -0.5788 0.7480 0.3246 + 1.5227 6.9114 -7.0765) + #( 0.3822 -0.7477 0.5430 ; P-O3*-180-tfo + 0.4552 0.6637 0.5935 + -0.8042 0.0203 0.5941 + -6.9472 -4.1186 -5.9108) + #( 0.5640 0.8007 -0.2022 ; P-O3*-60-tfo + -0.8247 0.5587 -0.0878 + 0.0426 0.2162 0.9754 + 6.2694 -7.0540 3.3316) + #( 2.8930 8.5380 -3.3280) ; P + #( 1.6980 7.6960 -3.5570) ; O1P + #( 3.2260 9.5010 -4.4020) ; O2P + #( 4.1590 7.6040 -3.0340) ; O5* + #( 5.4352 8.2183 -2.7757) ; C5* + #( 5.3830 8.7883 -1.8481) ; H5* + #( 5.7729 8.7436 -3.6691) ; H5** + #( 6.4830 7.1518 -2.5252) ; C4* + #( 7.4749 7.5972 -2.4482) ; H4* + #( 6.1626 6.4620 -1.2827) ; O4* + #( 6.5431 5.0992 -1.3905) ; C1* + #( 7.2871 4.9328 -0.6114) ; H1* + #( 7.1852 4.8935 -2.7592) ; C2* + #( 6.8573 3.9363 -3.1645) ; H2** + #( 8.5780 5.1025 -2.6046) ; O2* + #( 8.9516 4.7577 -1.7902) ; H2* + #( 6.5522 6.0300 -3.5612) ; C3* + #( 5.5420 5.7356 -3.8459) ; H3* + #( 7.3487 6.4089 -4.6867) ; O3* + #( 3.6343 2.6680 2.0783) ; N1 + #( 5.4505 3.9805 1.2446) ; N3 + #( 4.7540 3.3816 2.1851) ; C2 + #( 4.8805 3.7951 0.0354) ; C4 + #( 3.7416 3.0925 -0.2305) ; C5 + #( 3.0873 2.4980 0.8606) ; C6 + #( 1.9600 1.7805 0.7462) ; N6 + #( 3.4605 3.1184 -1.5906) ; N7 + #( 5.3247 4.2695 -1.1710) ; N9 + #( 4.4244 3.8244 -2.0953) ; C8 + #( 5.0814 3.4352 3.2234) ; H2 + #( 1.5423 1.6454 -0.1520) ; H61 + #( 1.5716 1.3398 1.5392) ; H62 + #( 4.2675 3.8876 -3.1721) ; H8 + )) + +(define rA05 + (make-constant-rA + #( -0.5891 0.0449 0.8068 ; dgf-base-tfo + 0.5375 0.7673 0.3498 + -0.6034 0.6397 -0.4762 + -0.3019 -3.7679 -9.5913) + #( -0.8143 -0.5091 -0.2788 ; P-O3*-275-tfo + -0.0433 -0.4257 0.9038 + -0.5788 0.7480 0.3246 + 1.5227 6.9114 -7.0765) + #( 0.3822 -0.7477 0.5430 ; P-O3*-180-tfo + 0.4552 0.6637 0.5935 + -0.8042 0.0203 0.5941 + -6.9472 -4.1186 -5.9108) + #( 0.5640 0.8007 -0.2022 ; P-O3*-60-tfo + -0.8247 0.5587 -0.0878 + 0.0426 0.2162 0.9754 + 6.2694 -7.0540 3.3316) + #( 2.8930 8.5380 -3.3280) ; P + #( 1.6980 7.6960 -3.5570) ; O1P + #( 3.2260 9.5010 -4.4020) ; O2P + #( 4.1590 7.6040 -3.0340) ; O5* + #( 4.5778 6.6594 -4.0364) ; C5* + #( 4.9220 7.1963 -4.9204) ; H5* + #( 3.7996 5.9091 -4.1764) ; H5** + #( 5.7873 5.8869 -3.5482) ; C4* + #( 6.0405 5.0875 -4.2446) ; H4* + #( 6.9135 6.8036 -3.4310) ; O4* + #( 7.7293 6.4084 -2.3392) ; C1* + #( 8.7078 6.1815 -2.7624) ; H1* + #( 7.1305 5.1418 -1.7347) ; C2* + #( 7.2040 5.1982 -0.6486) ; H2** + #( 7.7417 4.0392 -2.3813) ; O2* + #( 8.6785 4.1443 -2.5630) ; H2* + #( 5.6666 5.2728 -2.1536) ; C3* + #( 5.1747 5.9805 -1.4863) ; H3* + #( 4.9997 4.0086 -2.1973) ; O3* + #( 10.2594 10.6774 -1.0056) ; N1 + #( 9.7528 8.7080 -2.2631) ; N3 + #( 10.4471 9.7876 -1.9791) ; C2 + #( 8.7271 8.5575 -1.3991) ; C4 + #( 8.4100 9.3803 -0.3580) ; C5 + #( 9.2294 10.5030 -0.1574) ; C6 + #( 9.0349 11.3951 0.8250) ; N6 + #( 7.2891 8.9068 0.3121) ; N7 + #( 7.7962 7.5519 -1.3859) ; N9 + #( 6.9702 7.8292 -0.3353) ; C8 + #( 11.3132 10.0537 -2.5851) ; H2 + #( 8.2741 11.2784 1.4629) ; H61 + #( 9.6733 12.1368 0.9529) ; H62 + #( 6.0888 7.3990 0.1403) ; H8 + )) + +(define rA06 + (make-constant-rA + #( -0.9815 0.0731 -0.1772 ; dgf-base-tfo + 0.1912 0.3054 -0.9328 + -0.0141 -0.9494 -0.3137 + 5.7506 -5.1944 4.7470) + #( -0.8143 -0.5091 -0.2788 ; P-O3*-275-tfo + -0.0433 -0.4257 0.9038 + -0.5788 0.7480 0.3246 + 1.5227 6.9114 -7.0765) + #( 0.3822 -0.7477 0.5430 ; P-O3*-180-tfo + 0.4552 0.6637 0.5935 + -0.8042 0.0203 0.5941 + -6.9472 -4.1186 -5.9108) + #( 0.5640 0.8007 -0.2022 ; P-O3*-60-tfo + -0.8247 0.5587 -0.0878 + 0.0426 0.2162 0.9754 + 6.2694 -7.0540 3.3316) + #( 2.8930 8.5380 -3.3280) ; P + #( 1.6980 7.6960 -3.5570) ; O1P + #( 3.2260 9.5010 -4.4020) ; O2P + #( 4.1590 7.6040 -3.0340) ; O5* + #( 4.1214 6.7116 -1.9049) ; C5* + #( 3.3465 5.9610 -2.0607) ; H5* + #( 4.0789 7.2928 -0.9837) ; H5** + #( 5.4170 5.9293 -1.8186) ; C4* + #( 5.4506 5.3400 -0.9023) ; H4* + #( 5.5067 5.0417 -2.9703) ; O4* + #( 6.8650 4.9152 -3.3612) ; C1* + #( 7.1090 3.8577 -3.2603) ; H1* + #( 7.7152 5.7282 -2.3894) ; C2* + #( 8.5029 6.2356 -2.9463) ; H2** + #( 8.1036 4.8568 -1.3419) ; O2* + #( 8.3270 3.9651 -1.6184) ; H2* + #( 6.7003 6.7565 -1.8911) ; C3* + #( 6.5898 7.5329 -2.6482) ; H3* + #( 7.0505 7.2878 -0.6105) ; O3* + #( 6.6624 3.5061 -8.2986) ; N1 + #( 6.5810 3.2570 -5.9221) ; N3 + #( 6.5151 2.8263 -7.1625) ; C2 + #( 6.8364 4.5817 -5.8882) ; C4 + #( 7.0116 5.4064 -6.9609) ; C5 + #( 6.9173 4.8260 -8.2361) ; C6 + #( 7.0668 5.5163 -9.3763) ; N6 + #( 7.2573 6.7070 -6.5394) ; N7 + #( 6.9740 5.3703 -4.7760) ; N9 + #( 7.2238 6.6275 -5.2453) ; C8 + #( 6.3146 1.7741 -7.3641) ; H2 + #( 7.2568 6.4972 -9.3456) ; H61 + #( 7.0437 5.0478 -10.2446) ; H62 + #( 7.4108 7.6227 -4.8418) ; H8 + )) + +(define rA07 + (make-constant-rA + #( 0.2379 0.1310 -0.9624 ; dgf-base-tfo + -0.5876 -0.7696 -0.2499 + -0.7734 0.6249 -0.1061 + 30.9870 -26.9344 42.6416) + #( 0.7529 0.1548 0.6397 ; P-O3*-275-tfo + 0.2952 -0.9481 -0.1180 + 0.5882 0.2777 -0.7595 + -58.8919 -11.3095 6.0866) + #( -0.0239 0.9667 -0.2546 ; P-O3*-180-tfo + 0.9731 -0.0359 -0.2275 + -0.2290 -0.2532 -0.9399 + 3.5401 -29.7913 52.2796) + #( -0.8912 -0.4531 0.0242 ; P-O3*-60-tfo + -0.1183 0.1805 -0.9764 + 0.4380 -0.8730 -0.2145 + 19.9023 54.8054 15.2799) + #( 41.8210 8.3880 43.5890) ; P + #( 42.5400 8.0450 44.8330) ; O1P + #( 42.2470 9.6920 42.9910) ; O2P + #( 40.2550 8.2030 43.7340) ; O5* + #( 39.3505 8.4697 42.6565) ; C5* + #( 39.1377 7.5433 42.1230) ; H5* + #( 39.7203 9.3119 42.0717) ; H5** + #( 38.0405 8.9195 43.2869) ; C4* + #( 37.3687 9.3036 42.5193) ; H4* + #( 37.4319 7.8146 43.9387) ; O4* + #( 37.1959 8.1354 45.3237) ; C1* + #( 36.1788 8.5202 45.3970) ; H1* + #( 38.1721 9.2328 45.6504) ; C2* + #( 39.1555 8.7939 45.8188) ; H2** + #( 37.7862 10.0617 46.7013) ; O2* + #( 37.3087 9.6229 47.4092) ; H2* + #( 38.1844 10.0268 44.3367) ; C3* + #( 39.1578 10.5054 44.2289) ; H3* + #( 37.0547 10.9127 44.3441) ; O3* + #( 34.8811 4.2072 47.5784) ; N1 + #( 35.1084 6.1336 46.1818) ; N3 + #( 34.4108 5.1360 46.7207) ; C2 + #( 36.3908 6.1224 46.6053) ; C4 + #( 36.9819 5.2334 47.4697) ; C5 + #( 36.1786 4.1985 48.0035) ; C6 + #( 36.6103 3.2749 48.8452) ; N6 + #( 38.3236 5.5522 47.6595) ; N7 + #( 37.3887 7.0024 46.2437) ; N9 + #( 38.5055 6.6096 46.9057) ; C8 + #( 33.3553 5.0152 46.4771) ; H2 + #( 37.5730 3.2804 49.1507) ; H61 + #( 35.9775 2.5638 49.1828) ; H62 + #( 39.5461 6.9184 47.0041) ; H8 + )) + +(define rA08 + (make-constant-rA + #( 0.1084 -0.0895 -0.9901 ; dgf-base-tfo + 0.9789 -0.1638 0.1220 + -0.1731 -0.9824 0.0698 + -2.9039 47.2655 33.0094) + #( 0.7529 0.1548 0.6397 ; P-O3*-275-tfo + 0.2952 -0.9481 -0.1180 + 0.5882 0.2777 -0.7595 + -58.8919 -11.3095 6.0866) + #( -0.0239 0.9667 -0.2546 ; P-O3*-180-tfo + 0.9731 -0.0359 -0.2275 + -0.2290 -0.2532 -0.9399 + 3.5401 -29.7913 52.2796) + #( -0.8912 -0.4531 0.0242 ; P-O3*-60-tfo + -0.1183 0.1805 -0.9764 + 0.4380 -0.8730 -0.2145 + 19.9023 54.8054 15.2799) + #( 41.8210 8.3880 43.5890) ; P + #( 42.5400 8.0450 44.8330) ; O1P + #( 42.2470 9.6920 42.9910) ; O2P + #( 40.2550 8.2030 43.7340) ; O5* + #( 39.4850 8.9301 44.6977) ; C5* + #( 39.0638 9.8199 44.2296) ; H5* + #( 40.0757 9.0713 45.6029) ; H5** + #( 38.3102 8.0414 45.0789) ; C4* + #( 37.7842 8.4637 45.9351) ; H4* + #( 37.4200 7.9453 43.9769) ; O4* + #( 37.2249 6.5609 43.6273) ; C1* + #( 36.3360 6.2168 44.1561) ; H1* + #( 38.4347 5.8414 44.1590) ; C2* + #( 39.2688 5.9974 43.4749) ; H2** + #( 38.2344 4.4907 44.4348) ; O2* + #( 37.6374 4.0386 43.8341) ; H2* + #( 38.6926 6.6079 45.4637) ; C3* + #( 39.7585 6.5640 45.6877) ; H3* + #( 37.8238 6.0705 46.4723) ; O3* + #( 33.9162 6.2598 39.7758) ; N1 + #( 34.6709 6.5759 42.0215) ; N3 + #( 33.7257 6.5186 41.0858) ; C2 + #( 35.8935 6.3324 41.5018) ; C4 + #( 36.2105 6.0601 40.1932) ; C5 + #( 35.1538 6.0151 39.2537) ; C6 + #( 35.3088 5.7642 37.9649) ; N6 + #( 37.5818 5.8677 40.0507) ; N7 + #( 37.0932 6.3197 42.1810) ; N9 + #( 38.0509 6.0354 41.2635) ; C8 + #( 32.6830 6.6898 41.3532) ; H2 + #( 36.2305 5.5855 37.5925) ; H61 + #( 34.5056 5.7512 37.3528) ; H62 + #( 39.1318 5.8993 41.2285) ; H8 + )) + +(define rA09 + (make-constant-rA + #( 0.8467 0.4166 -0.3311 ; dgf-base-tfo + -0.3962 0.9089 0.1303 + 0.3552 0.0209 0.9346 + -42.7319 -26.6223 -29.8163) + #( 0.7529 0.1548 0.6397 ; P-O3*-275-tfo + 0.2952 -0.9481 -0.1180 + 0.5882 0.2777 -0.7595 + -58.8919 -11.3095 6.0866) + #( -0.0239 0.9667 -0.2546 ; P-O3*-180-tfo + 0.9731 -0.0359 -0.2275 + -0.2290 -0.2532 -0.9399 + 3.5401 -29.7913 52.2796) + #( -0.8912 -0.4531 0.0242 ; P-O3*-60-tfo + -0.1183 0.1805 -0.9764 + 0.4380 -0.8730 -0.2145 + 19.9023 54.8054 15.2799) + #( 41.8210 8.3880 43.5890) ; P + #( 42.5400 8.0450 44.8330) ; O1P + #( 42.2470 9.6920 42.9910) ; O2P + #( 40.2550 8.2030 43.7340) ; O5* + #( 39.3505 8.4697 42.6565) ; C5* + #( 39.1377 7.5433 42.1230) ; H5* + #( 39.7203 9.3119 42.0717) ; H5** + #( 38.0405 8.9195 43.2869) ; C4* + #( 37.6479 8.1347 43.9335) ; H4* + #( 38.2691 10.0933 44.0524) ; O4* + #( 37.3999 11.1488 43.5973) ; C1* + #( 36.5061 11.1221 44.2206) ; H1* + #( 37.0364 10.7838 42.1836) ; C2* + #( 37.8636 11.0489 41.5252) ; H2** + #( 35.8275 11.3133 41.7379) ; O2* + #( 35.6214 12.1896 42.0714) ; H2* + #( 36.9316 9.2556 42.2837) ; C3* + #( 37.1778 8.8260 41.3127) ; H3* + #( 35.6285 8.9334 42.7926) ; O3* + #( 38.1482 15.2833 46.4641) ; N1 + #( 37.3641 13.0968 45.9007) ; N3 + #( 37.5032 14.1288 46.7300) ; C2 + #( 37.9570 13.3377 44.7113) ; C4 + #( 38.6397 14.4660 44.3267) ; C5 + #( 38.7473 15.5229 45.2609) ; C6 + #( 39.3720 16.6649 45.0297) ; N6 + #( 39.1079 14.3351 43.0223) ; N7 + #( 38.0132 12.4868 43.6280) ; N9 + #( 38.7058 13.1402 42.6620) ; C8 + #( 37.0731 14.0857 47.7306) ; H2 + #( 39.8113 16.8281 44.1350) ; H61 + #( 39.4100 17.3741 45.7478) ; H62 + #( 39.0412 12.9660 41.6397) ; H8 + )) + +(define rA10 + (make-constant-rA + #( 0.7063 0.6317 -0.3196 ; dgf-base-tfo + -0.0403 -0.4149 -0.9090 + -0.7068 0.6549 -0.2676 + 6.4402 -52.1496 30.8246) + #( 0.7529 0.1548 0.6397 ; P-O3*-275-tfo + 0.2952 -0.9481 -0.1180 + 0.5882 0.2777 -0.7595 + -58.8919 -11.3095 6.0866) + #( -0.0239 0.9667 -0.2546 ; P-O3*-180-tfo + 0.9731 -0.0359 -0.2275 + -0.2290 -0.2532 -0.9399 + 3.5401 -29.7913 52.2796) + #( -0.8912 -0.4531 0.0242 ; P-O3*-60-tfo + -0.1183 0.1805 -0.9764 + 0.4380 -0.8730 -0.2145 + 19.9023 54.8054 15.2799) + #( 41.8210 8.3880 43.5890) ; P + #( 42.5400 8.0450 44.8330) ; O1P + #( 42.2470 9.6920 42.9910) ; O2P + #( 40.2550 8.2030 43.7340) ; O5* + #( 39.4850 8.9301 44.6977) ; C5* + #( 39.0638 9.8199 44.2296) ; H5* + #( 40.0757 9.0713 45.6029) ; H5** + #( 38.3102 8.0414 45.0789) ; C4* + #( 37.7099 7.8166 44.1973) ; H4* + #( 38.8012 6.8321 45.6380) ; O4* + #( 38.2431 6.6413 46.9529) ; C1* + #( 37.3505 6.0262 46.8385) ; H1* + #( 37.8484 8.0156 47.4214) ; C2* + #( 38.7381 8.5406 47.7690) ; H2** + #( 36.8286 8.0368 48.3701) ; O2* + #( 36.8392 7.3063 48.9929) ; H2* + #( 37.3576 8.6512 46.1132) ; C3* + #( 37.5207 9.7275 46.1671) ; H3* + #( 35.9985 8.2392 45.9032) ; O3* + #( 39.9117 2.2278 48.8527) ; N1 + #( 38.6207 3.6941 47.4757) ; N3 + #( 38.9872 2.4888 47.9057) ; C2 + #( 39.2961 4.6720 48.1174) ; C4 + #( 40.2546 4.5307 49.0912) ; C5 + #( 40.5932 3.2189 49.4985) ; C6 + #( 41.4938 2.9317 50.4229) ; N6 + #( 40.7195 5.7755 49.5060) ; N7 + #( 39.1730 6.0305 47.9170) ; N9 + #( 40.0413 6.6250 48.7728) ; C8 + #( 38.5257 1.5960 47.4838) ; H2 + #( 41.9907 3.6753 50.8921) ; H61 + #( 41.6848 1.9687 50.6599) ; H62 + #( 40.3571 7.6321 49.0452) ; H8 + )) + +(define rAs + (list rA01 rA02 rA03 rA04 rA05 rA06 rA07 rA08 rA09 rA10)) + +(define rC + (make-constant-rC + #( -0.0359 -0.8071 0.5894 ; dgf-base-tfo + -0.2669 0.5761 0.7726 + -0.9631 -0.1296 -0.2361 + 0.1584 8.3434 0.5434) + #( -0.8313 -0.4738 -0.2906 ; P-O3*-275-tfo + 0.0649 0.4366 -0.8973 + 0.5521 -0.7648 -0.3322 + 1.6833 6.8060 -7.0011) + #( 0.3445 -0.7630 0.5470 ; P-O3*-180-tfo + -0.4628 -0.6450 -0.6082 + 0.8168 -0.0436 -0.5753 + -6.8179 -3.9778 -5.9887) + #( 0.5855 0.7931 -0.1682 ; P-O3*-60-tfo + 0.8103 -0.5790 0.0906 + -0.0255 -0.1894 -0.9816 + 6.1203 -7.1051 3.1984) + #( 2.6760 -8.4960 3.2880) ; P + #( 1.4950 -7.6230 3.4770) ; O1P + #( 2.9490 -9.4640 4.3740) ; O2P + #( 3.9730 -7.5950 3.0340) ; O5* + #( 5.2430 -8.2420 2.8260) ; C5* + #( 5.1974 -8.8497 1.9223) ; H5* + #( 5.5548 -8.7348 3.7469) ; H5** + #( 6.3140 -7.2060 2.5510) ; C4* + #( 7.2954 -7.6762 2.4898) ; H4* + #( 6.0140 -6.5420 1.2890) ; O4* + #( 6.4190 -5.1840 1.3620) ; C1* + #( 7.1608 -5.0495 0.5747) ; H1* + #( 7.0760 -4.9560 2.7270) ; C2* + #( 6.7770 -3.9803 3.1099) ; H2** + #( 8.4500 -5.1930 2.5810) ; O2* + #( 8.8309 -4.8755 1.7590) ; H2* + #( 6.4060 -6.0590 3.5580) ; C3* + #( 5.4021 -5.7313 3.8281) ; H3* + #( 7.1570 -6.4240 4.7070) ; O3* + #( 5.2170 -4.3260 1.1690) ; N1 + #( 4.2960 -2.2560 0.6290) ; N3 + #( 5.4330 -3.0200 0.7990) ; C2 + #( 2.9930 -2.6780 0.7940) ; C4 + #( 2.8670 -4.0630 1.1830) ; C5 + #( 3.9570 -4.8300 1.3550) ; C6 + #( 2.0187 -1.8047 0.5874) ; N4 + #( 6.5470 -2.5560 0.6290) ; O2 + #( 1.0684 -2.1236 0.7109) ; H41 + #( 2.2344 -0.8560 0.3162) ; H42 + #( 1.8797 -4.4972 1.3404) ; H5 + #( 3.8479 -5.8742 1.6480) ; H6 + )) + +(define rC01 + (make-constant-rC + #( -0.0137 -0.8012 0.5983 ; dgf-base-tfo + -0.2523 0.5817 0.7733 + -0.9675 -0.1404 -0.2101 + 0.2031 8.3874 0.4228) + #( -0.8313 -0.4738 -0.2906 ; P-O3*-275-tfo + 0.0649 0.4366 -0.8973 + 0.5521 -0.7648 -0.3322 + 1.6833 6.8060 -7.0011) + #( 0.3445 -0.7630 0.5470 ; P-O3*-180-tfo + -0.4628 -0.6450 -0.6082 + 0.8168 -0.0436 -0.5753 + -6.8179 -3.9778 -5.9887) + #( 0.5855 0.7931 -0.1682 ; P-O3*-60-tfo + 0.8103 -0.5790 0.0906 + -0.0255 -0.1894 -0.9816 + 6.1203 -7.1051 3.1984) + #( 2.6760 -8.4960 3.2880) ; P + #( 1.4950 -7.6230 3.4770) ; O1P + #( 2.9490 -9.4640 4.3740) ; O2P + #( 3.9730 -7.5950 3.0340) ; O5* + #( 5.2416 -8.2422 2.8181) ; C5* + #( 5.2050 -8.8128 1.8901) ; H5* + #( 5.5368 -8.7738 3.7227) ; H5** + #( 6.3232 -7.2037 2.6002) ; C4* + #( 7.3048 -7.6757 2.5577) ; H4* + #( 6.0635 -6.5092 1.3456) ; O4* + #( 6.4697 -5.1547 1.4629) ; C1* + #( 7.2354 -5.0043 0.7018) ; H1* + #( 7.0856 -4.9610 2.8521) ; C2* + #( 6.7777 -3.9935 3.2487) ; H2** + #( 8.4627 -5.1992 2.7423) ; O2* + #( 8.8693 -4.8638 1.9399) ; H2* + #( 6.3877 -6.0809 3.6362) ; C3* + #( 5.3770 -5.7562 3.8834) ; H3* + #( 7.1024 -6.4754 4.7985) ; O3* + #( 5.2764 -4.2883 1.2538) ; N1 + #( 4.3777 -2.2062 0.7229) ; N3 + #( 5.5069 -2.9779 0.9088) ; C2 + #( 3.0693 -2.6246 0.8500) ; C4 + #( 2.9279 -4.0146 1.2149) ; C5 + #( 4.0101 -4.7892 1.4017) ; C6 + #( 2.1040 -1.7437 0.6331) ; N4 + #( 6.6267 -2.5166 0.7728) ; O2 + #( 1.1496 -2.0600 0.7287) ; H41 + #( 2.3303 -0.7921 0.3815) ; H42 + #( 1.9353 -4.4465 1.3419) ; H5 + #( 3.8895 -5.8371 1.6762) ; H6 + )) + +(define rC02 + (make-constant-rC + #( 0.5141 0.0246 0.8574 ; dgf-base-tfo + -0.5547 -0.7529 0.3542 + 0.6542 -0.6577 -0.3734 + -9.1111 -3.4598 -3.2939) + #( -0.8313 -0.4738 -0.2906 ; P-O3*-275-tfo + 0.0649 0.4366 -0.8973 + 0.5521 -0.7648 -0.3322 + 1.6833 6.8060 -7.0011) + #( 0.3445 -0.7630 0.5470 ; P-O3*-180-tfo + -0.4628 -0.6450 -0.6082 + 0.8168 -0.0436 -0.5753 + -6.8179 -3.9778 -5.9887) + #( 0.5855 0.7931 -0.1682 ; P-O3*-60-tfo + 0.8103 -0.5790 0.0906 + -0.0255 -0.1894 -0.9816 + 6.1203 -7.1051 3.1984) + #( 2.6760 -8.4960 3.2880) ; P + #( 1.4950 -7.6230 3.4770) ; O1P + #( 2.9490 -9.4640 4.3740) ; O2P + #( 3.9730 -7.5950 3.0340) ; O5* + #( 4.3825 -6.6585 4.0489) ; C5* + #( 4.6841 -7.2019 4.9443) ; H5* + #( 3.6189 -5.8889 4.1625) ; H5** + #( 5.6255 -5.9175 3.5998) ; C4* + #( 5.8732 -5.1228 4.3034) ; H4* + #( 6.7337 -6.8605 3.5222) ; O4* + #( 7.5932 -6.4923 2.4548) ; C1* + #( 8.5661 -6.2983 2.9064) ; H1* + #( 7.0527 -5.2012 1.8322) ; C2* + #( 7.1627 -5.2525 0.7490) ; H2** + #( 7.6666 -4.1249 2.4880) ; O2* + #( 8.5944 -4.2543 2.6981) ; H2* + #( 5.5661 -5.3029 2.2009) ; C3* + #( 5.0841 -6.0018 1.5172) ; H3* + #( 4.9062 -4.0452 2.2042) ; O3* + #( 7.6298 -7.6136 1.4752) ; N1 + #( 8.6945 -8.7046 -0.2857) ; N3 + #( 8.6943 -7.6514 0.6066) ; C2 + #( 7.7426 -9.6987 -0.3801) ; C4 + #( 6.6642 -9.5742 0.5722) ; C5 + #( 6.6391 -8.5592 1.4526) ; C6 + #( 7.9033 -10.6371 -1.3010) ; N4 + #( 9.5840 -6.8186 0.6136) ; O2 + #( 7.2009 -11.3604 -1.3619) ; H41 + #( 8.7058 -10.6168 -1.9140) ; H42 + #( 5.8585 -10.3083 0.5822) ; H5 + #( 5.8197 -8.4773 2.1667) ; H6 + )) + +(define rC03 + (make-constant-rC + #( -0.4993 0.0476 0.8651 ; dgf-base-tfo + 0.8078 -0.3353 0.4847 + 0.3132 0.9409 0.1290 + 6.2989 -5.2303 -3.8577) + #( -0.8313 -0.4738 -0.2906 ; P-O3*-275-tfo + 0.0649 0.4366 -0.8973 + 0.5521 -0.7648 -0.3322 + 1.6833 6.8060 -7.0011) + #( 0.3445 -0.7630 0.5470 ; P-O3*-180-tfo + -0.4628 -0.6450 -0.6082 + 0.8168 -0.0436 -0.5753 + -6.8179 -3.9778 -5.9887) + #( 0.5855 0.7931 -0.1682 ; P-O3*-60-tfo + 0.8103 -0.5790 0.0906 + -0.0255 -0.1894 -0.9816 + 6.1203 -7.1051 3.1984) + #( 2.6760 -8.4960 3.2880) ; P + #( 1.4950 -7.6230 3.4770) ; O1P + #( 2.9490 -9.4640 4.3740) ; O2P + #( 3.9730 -7.5950 3.0340) ; O5* + #( 3.9938 -6.7042 1.9023) ; C5* + #( 3.2332 -5.9343 2.0319) ; H5* + #( 3.9666 -7.2863 0.9812) ; H5** + #( 5.3098 -5.9546 1.8564) ; C4* + #( 5.3863 -5.3702 0.9395) ; H4* + #( 5.3851 -5.0642 3.0076) ; O4* + #( 6.7315 -4.9724 3.4462) ; C1* + #( 7.0033 -3.9202 3.3619) ; H1* + #( 7.5997 -5.8018 2.4948) ; C2* + #( 8.3627 -6.3254 3.0707) ; H2** + #( 8.0410 -4.9501 1.4724) ; O2* + #( 8.2781 -4.0644 1.7570) ; H2* + #( 6.5701 -6.8129 1.9714) ; C3* + #( 6.4186 -7.5809 2.7299) ; H3* + #( 6.9357 -7.3841 0.7235) ; O3* + #( 6.8024 -5.4718 4.8475) ; N1 + #( 7.9218 -5.5700 6.8877) ; N3 + #( 7.8908 -5.0886 5.5944) ; C2 + #( 6.9789 -6.3827 7.4823) ; C4 + #( 5.8742 -6.7319 6.6202) ; C5 + #( 5.8182 -6.2769 5.3570) ; C6 + #( 7.1702 -6.7511 8.7402) ; N4 + #( 8.7747 -4.3728 5.1568) ; O2 + #( 6.4741 -7.3461 9.1662) ; H41 + #( 7.9889 -6.4396 9.2429) ; H42 + #( 5.0736 -7.3713 6.9922) ; H5 + #( 4.9784 -6.5473 4.7170) ; H6 + )) + +(define rC04 + (make-constant-rC + #( -0.5669 -0.8012 0.1918 ; dgf-base-tfo + -0.8129 0.5817 0.0273 + -0.1334 -0.1404 -0.9811 + -0.3279 8.3874 0.3355) + #( -0.8313 -0.4738 -0.2906 ; P-O3*-275-tfo + 0.0649 0.4366 -0.8973 + 0.5521 -0.7648 -0.3322 + 1.6833 6.8060 -7.0011) + #( 0.3445 -0.7630 0.5470 ; P-O3*-180-tfo + -0.4628 -0.6450 -0.6082 + 0.8168 -0.0436 -0.5753 + -6.8179 -3.9778 -5.9887) + #( 0.5855 0.7931 -0.1682 ; P-O3*-60-tfo + 0.8103 -0.5790 0.0906 + -0.0255 -0.1894 -0.9816 + 6.1203 -7.1051 3.1984) + #( 2.6760 -8.4960 3.2880) ; P + #( 1.4950 -7.6230 3.4770) ; O1P + #( 2.9490 -9.4640 4.3740) ; O2P + #( 3.9730 -7.5950 3.0340) ; O5* + #( 5.2416 -8.2422 2.8181) ; C5* + #( 5.2050 -8.8128 1.8901) ; H5* + #( 5.5368 -8.7738 3.7227) ; H5** + #( 6.3232 -7.2037 2.6002) ; C4* + #( 7.3048 -7.6757 2.5577) ; H4* + #( 6.0635 -6.5092 1.3456) ; O4* + #( 6.4697 -5.1547 1.4629) ; C1* + #( 7.2354 -5.0043 0.7018) ; H1* + #( 7.0856 -4.9610 2.8521) ; C2* + #( 6.7777 -3.9935 3.2487) ; H2** + #( 8.4627 -5.1992 2.7423) ; O2* + #( 8.8693 -4.8638 1.9399) ; H2* + #( 6.3877 -6.0809 3.6362) ; C3* + #( 5.3770 -5.7562 3.8834) ; H3* + #( 7.1024 -6.4754 4.7985) ; O3* + #( 5.2764 -4.2883 1.2538) ; N1 + #( 3.8961 -3.0896 -0.1893) ; N3 + #( 5.0095 -3.8907 -0.0346) ; C2 + #( 3.0480 -2.6632 0.8116) ; C4 + #( 3.4093 -3.1310 2.1292) ; C5 + #( 4.4878 -3.9124 2.3088) ; C6 + #( 2.0216 -1.8941 0.4804) ; N4 + #( 5.7005 -4.2164 -0.9842) ; O2 + #( 1.4067 -1.5873 1.2205) ; H41 + #( 1.8721 -1.6319 -0.4835) ; H42 + #( 2.8048 -2.8507 2.9918) ; H5 + #( 4.7491 -4.2593 3.3085) ; H6 + )) + +(define rC05 + (make-constant-rC + #( -0.6298 0.0246 0.7763 ; dgf-base-tfo + -0.5226 -0.7529 -0.4001 + 0.5746 -0.6577 0.4870 + -0.0208 -3.4598 -9.6882) + #( -0.8313 -0.4738 -0.2906 ; P-O3*-275-tfo + 0.0649 0.4366 -0.8973 + 0.5521 -0.7648 -0.3322 + 1.6833 6.8060 -7.0011) + #( 0.3445 -0.7630 0.5470 ; P-O3*-180-tfo + -0.4628 -0.6450 -0.6082 + 0.8168 -0.0436 -0.5753 + -6.8179 -3.9778 -5.9887) + #( 0.5855 0.7931 -0.1682 ; P-O3*-60-tfo + 0.8103 -0.5790 0.0906 + -0.0255 -0.1894 -0.9816 + 6.1203 -7.1051 3.1984) + #( 2.6760 -8.4960 3.2880) ; P + #( 1.4950 -7.6230 3.4770) ; O1P + #( 2.9490 -9.4640 4.3740) ; O2P + #( 3.9730 -7.5950 3.0340) ; O5* + #( 4.3825 -6.6585 4.0489) ; C5* + #( 4.6841 -7.2019 4.9443) ; H5* + #( 3.6189 -5.8889 4.1625) ; H5** + #( 5.6255 -5.9175 3.5998) ; C4* + #( 5.8732 -5.1228 4.3034) ; H4* + #( 6.7337 -6.8605 3.5222) ; O4* + #( 7.5932 -6.4923 2.4548) ; C1* + #( 8.5661 -6.2983 2.9064) ; H1* + #( 7.0527 -5.2012 1.8322) ; C2* + #( 7.1627 -5.2525 0.7490) ; H2** + #( 7.6666 -4.1249 2.4880) ; O2* + #( 8.5944 -4.2543 2.6981) ; H2* + #( 5.5661 -5.3029 2.2009) ; C3* + #( 5.0841 -6.0018 1.5172) ; H3* + #( 4.9062 -4.0452 2.2042) ; O3* + #( 7.6298 -7.6136 1.4752) ; N1 + #( 8.5977 -9.5977 0.7329) ; N3 + #( 8.5951 -8.5745 1.6594) ; C2 + #( 7.7372 -9.7371 -0.3364) ; C4 + #( 6.7596 -8.6801 -0.4476) ; C5 + #( 6.7338 -7.6721 0.4408) ; C6 + #( 7.8849 -10.7881 -1.1289) ; N4 + #( 9.3993 -8.5377 2.5743) ; O2 + #( 7.2499 -10.8809 -1.9088) ; H41 + #( 8.6122 -11.4649 -0.9468) ; H42 + #( 6.0317 -8.6941 -1.2588) ; H5 + #( 5.9901 -6.8809 0.3459) ; H6 + )) + +(define rC06 + (make-constant-rC + #( -0.9837 0.0476 -0.1733 ; dgf-base-tfo + -0.1792 -0.3353 0.9249 + -0.0141 0.9409 0.3384 + 5.7793 -5.2303 4.5997) + #( -0.8313 -0.4738 -0.2906 ; P-O3*-275-tfo + 0.0649 0.4366 -0.8973 + 0.5521 -0.7648 -0.3322 + 1.6833 6.8060 -7.0011) + #( 0.3445 -0.7630 0.5470 ; P-O3*-180-tfo + -0.4628 -0.6450 -0.6082 + 0.8168 -0.0436 -0.5753 + -6.8179 -3.9778 -5.9887) + #( 0.5855 0.7931 -0.1682 ; P-O3*-60-tfo + 0.8103 -0.5790 0.0906 + -0.0255 -0.1894 -0.9816 + 6.1203 -7.1051 3.1984) + #( 2.6760 -8.4960 3.2880) ; P + #( 1.4950 -7.6230 3.4770) ; O1P + #( 2.9490 -9.4640 4.3740) ; O2P + #( 3.9730 -7.5950 3.0340) ; O5* + #( 3.9938 -6.7042 1.9023) ; C5* + #( 3.2332 -5.9343 2.0319) ; H5* + #( 3.9666 -7.2863 0.9812) ; H5** + #( 5.3098 -5.9546 1.8564) ; C4* + #( 5.3863 -5.3702 0.9395) ; H4* + #( 5.3851 -5.0642 3.0076) ; O4* + #( 6.7315 -4.9724 3.4462) ; C1* + #( 7.0033 -3.9202 3.3619) ; H1* + #( 7.5997 -5.8018 2.4948) ; C2* + #( 8.3627 -6.3254 3.0707) ; H2** + #( 8.0410 -4.9501 1.4724) ; O2* + #( 8.2781 -4.0644 1.7570) ; H2* + #( 6.5701 -6.8129 1.9714) ; C3* + #( 6.4186 -7.5809 2.7299) ; H3* + #( 6.9357 -7.3841 0.7235) ; O3* + #( 6.8024 -5.4718 4.8475) ; N1 + #( 6.6920 -5.0495 7.1354) ; N3 + #( 6.6201 -4.5500 5.8506) ; C2 + #( 6.9254 -6.3614 7.4926) ; C4 + #( 7.1046 -7.2543 6.3718) ; C5 + #( 7.0391 -6.7951 5.1106) ; C6 + #( 6.9614 -6.6648 8.7815) ; N4 + #( 6.4083 -3.3696 5.6340) ; O2 + #( 7.1329 -7.6280 9.0324) ; H41 + #( 6.8204 -5.9469 9.4777) ; H42 + #( 7.2954 -8.3135 6.5440) ; H5 + #( 7.1753 -7.4798 4.2735) ; H6 + )) + +(define rC07 + (make-constant-rC + #( 0.0033 0.2720 -0.9623 ; dgf-base-tfo + 0.3013 -0.9179 -0.2584 + -0.9535 -0.2891 -0.0850 + 43.0403 13.7233 34.5710) + #( 0.9187 0.2887 0.2694 ; P-O3*-275-tfo + 0.0302 -0.7316 0.6811 + 0.3938 -0.6176 -0.6808 + -48.4330 26.3254 13.6383) + #( -0.1504 0.7744 -0.6145 ; P-O3*-180-tfo + 0.7581 0.4893 0.4311 + 0.6345 -0.4010 -0.6607 + -31.9784 -13.4285 44.9650) + #( -0.6236 -0.7810 -0.0337 ; P-O3*-60-tfo + -0.6890 0.5694 -0.4484 + 0.3694 -0.2564 -0.8932 + 12.1105 30.8774 46.0946) + #( 33.3400 11.0980 46.1750) ; P + #( 34.5130 10.2320 46.4660) ; O1P + #( 33.4130 12.3960 46.9340) ; O2P + #( 31.9810 10.3390 46.4820) ; O5* + #( 30.8152 11.1619 46.2003) ; C5* + #( 30.4519 10.9454 45.1957) ; H5* + #( 31.0379 12.2016 46.4400) ; H5** + #( 29.7081 10.7448 47.1428) ; C4* + #( 28.8710 11.4416 47.0982) ; H4* + #( 29.2550 9.4394 46.8162) ; O4* + #( 29.3907 8.5625 47.9460) ; C1* + #( 28.4416 8.5669 48.4819) ; H1* + #( 30.4468 9.2031 48.7952) ; C2* + #( 31.4222 8.9651 48.3709) ; H2** + #( 30.3701 8.9157 50.1624) ; O2* + #( 30.0652 8.0304 50.3740) ; H2* + #( 30.1622 10.6879 48.6120) ; C3* + #( 31.0952 11.2399 48.7254) ; H3* + #( 29.1076 11.1535 49.4702) ; O3* + #( 29.7883 7.2209 47.5235) ; N1 + #( 29.1825 5.0438 46.8275) ; N3 + #( 28.8008 6.2912 47.2263) ; C2 + #( 30.4888 4.6890 46.7186) ; C4 + #( 31.5034 5.6405 47.0249) ; C5 + #( 31.1091 6.8691 47.4156) ; C6 + #( 30.8109 3.4584 46.3336) ; N4 + #( 27.6171 6.5989 47.3189) ; O2 + #( 31.7923 3.2301 46.2638) ; H41 + #( 30.0880 2.7857 46.1215) ; H42 + #( 32.5542 5.3634 46.9395) ; H5 + #( 31.8523 7.6279 47.6603) ; H6 + )) + +(define rC08 + (make-constant-rC + #( 0.0797 -0.6026 -0.7941 ; dgf-base-tfo + 0.7939 0.5201 -0.3150 + 0.6028 -0.6054 0.5198 + -36.8341 41.5293 1.6628) + #( 0.9187 0.2887 0.2694 ; P-O3*-275-tfo + 0.0302 -0.7316 0.6811 + 0.3938 -0.6176 -0.6808 + -48.4330 26.3254 13.6383) + #( -0.1504 0.7744 -0.6145 ; P-O3*-180-tfo + 0.7581 0.4893 0.4311 + 0.6345 -0.4010 -0.6607 + -31.9784 -13.4285 44.9650) + #( -0.6236 -0.7810 -0.0337 ; P-O3*-60-tfo + -0.6890 0.5694 -0.4484 + 0.3694 -0.2564 -0.8932 + 12.1105 30.8774 46.0946) + #( 33.3400 11.0980 46.1750) ; P + #( 34.5130 10.2320 46.4660) ; O1P + #( 33.4130 12.3960 46.9340) ; O2P + #( 31.9810 10.3390 46.4820) ; O5* + #( 31.8779 9.9369 47.8760) ; C5* + #( 31.3239 10.6931 48.4322) ; H5* + #( 32.8647 9.6624 48.2489) ; H5** + #( 31.0429 8.6773 47.9401) ; C4* + #( 31.0779 8.2331 48.9349) ; H4* + #( 29.6956 8.9669 47.5983) ; O4* + #( 29.2784 8.1700 46.4782) ; C1* + #( 28.8006 7.2731 46.8722) ; H1* + #( 30.5544 7.7940 45.7875) ; C2* + #( 30.8837 8.6410 45.1856) ; H2** + #( 30.5100 6.6007 45.0582) ; O2* + #( 29.6694 6.4168 44.6326) ; H2* + #( 31.5146 7.5954 46.9527) ; C3* + #( 32.5255 7.8261 46.6166) ; H3* + #( 31.3876 6.2951 47.5516) ; O3* + #( 28.3976 8.9302 45.5933) ; N1 + #( 26.2155 9.6135 44.9910) ; N3 + #( 27.0281 8.8961 45.8192) ; C2 + #( 26.7044 10.3489 43.9595) ; C4 + #( 28.1088 10.3837 43.7247) ; C5 + #( 28.8978 9.6708 44.5535) ; C6 + #( 25.8715 11.0249 43.1749) ; N4 + #( 26.5733 8.2371 46.7484) ; O2 + #( 26.2707 11.5609 42.4177) ; H41 + #( 24.8760 10.9939 43.3427) ; H42 + #( 28.5089 10.9722 42.8990) ; H5 + #( 29.9782 9.6687 44.4097) ; H6 + )) + +(define rC09 + (make-constant-rC + #( 0.8727 0.4760 -0.1091 ; dgf-base-tfo + -0.4188 0.6148 -0.6682 + -0.2510 0.6289 0.7359 + -8.1687 -52.0761 -25.0726) + #( 0.9187 0.2887 0.2694 ; P-O3*-275-tfo + 0.0302 -0.7316 0.6811 + 0.3938 -0.6176 -0.6808 + -48.4330 26.3254 13.6383) + #( -0.1504 0.7744 -0.6145 ; P-O3*-180-tfo + 0.7581 0.4893 0.4311 + 0.6345 -0.4010 -0.6607 + -31.9784 -13.4285 44.9650) + #( -0.6236 -0.7810 -0.0337 ; P-O3*-60-tfo + -0.6890 0.5694 -0.4484 + 0.3694 -0.2564 -0.8932 + 12.1105 30.8774 46.0946) + #( 33.3400 11.0980 46.1750) ; P + #( 34.5130 10.2320 46.4660) ; O1P + #( 33.4130 12.3960 46.9340) ; O2P + #( 31.9810 10.3390 46.4820) ; O5* + #( 30.8152 11.1619 46.2003) ; C5* + #( 30.4519 10.9454 45.1957) ; H5* + #( 31.0379 12.2016 46.4400) ; H5** + #( 29.7081 10.7448 47.1428) ; C4* + #( 29.4506 9.6945 47.0059) ; H4* + #( 30.1045 10.9634 48.4885) ; O4* + #( 29.1794 11.8418 49.1490) ; C1* + #( 28.4388 11.2210 49.6533) ; H1* + #( 28.5211 12.6008 48.0367) ; C2* + #( 29.1947 13.3949 47.7147) ; H2** + #( 27.2316 13.0683 48.3134) ; O2* + #( 27.0851 13.3391 49.2227) ; H2* + #( 28.4131 11.5507 46.9391) ; C3* + #( 28.4451 12.0512 45.9713) ; H3* + #( 27.2707 10.6955 47.1097) ; O3* + #( 29.8751 12.7405 50.0682) ; N1 + #( 30.7172 13.1841 52.2328) ; N3 + #( 30.0617 12.3404 51.3847) ; C2 + #( 31.1834 14.3941 51.8297) ; C4 + #( 30.9913 14.8074 50.4803) ; C5 + #( 30.3434 13.9610 49.6548) ; C6 + #( 31.8090 15.1847 52.6957) ; N4 + #( 29.6470 11.2494 51.7616) ; O2 + #( 32.1422 16.0774 52.3606) ; H41 + #( 31.9392 14.8893 53.6527) ; H42 + #( 31.3632 15.7771 50.1491) ; H5 + #( 30.1742 14.2374 48.6141) ; H6 + )) + +(define rC10 + (make-constant-rC + #( 0.1549 0.8710 -0.4663 ; dgf-base-tfo + 0.6768 -0.4374 -0.5921 + -0.7197 -0.2239 -0.6572 + 25.2447 -14.1920 50.3201) + #( 0.9187 0.2887 0.2694 ; P-O3*-275-tfo + 0.0302 -0.7316 0.6811 + 0.3938 -0.6176 -0.6808 + -48.4330 26.3254 13.6383) + #( -0.1504 0.7744 -0.6145 ; P-O3*-180-tfo + 0.7581 0.4893 0.4311 + 0.6345 -0.4010 -0.6607 + -31.9784 -13.4285 44.9650) + #( -0.6236 -0.7810 -0.0337 ; P-O3*-60-tfo + -0.6890 0.5694 -0.4484 + 0.3694 -0.2564 -0.8932 + 12.1105 30.8774 46.0946) + #( 33.3400 11.0980 46.1750) ; P + #( 34.5130 10.2320 46.4660) ; O1P + #( 33.4130 12.3960 46.9340) ; O2P + #( 31.9810 10.3390 46.4820) ; O5* + #( 31.8779 9.9369 47.8760) ; C5* + #( 31.3239 10.6931 48.4322) ; H5* + #( 32.8647 9.6624 48.2489) ; H5** + #( 31.0429 8.6773 47.9401) ; C4* + #( 30.0440 8.8473 47.5383) ; H4* + #( 31.6749 7.6351 47.2119) ; O4* + #( 31.9159 6.5022 48.0616) ; C1* + #( 31.0691 5.8243 47.9544) ; H1* + #( 31.9300 7.0685 49.4493) ; C2* + #( 32.9024 7.5288 49.6245) ; H2** + #( 31.5672 6.1750 50.4632) ; O2* + #( 31.8416 5.2663 50.3200) ; H2* + #( 30.8618 8.1514 49.3749) ; C3* + #( 31.1122 8.9396 50.0850) ; H3* + #( 29.5351 7.6245 49.5409) ; O3* + #( 33.1890 5.8629 47.7343) ; N1 + #( 34.4004 4.2636 46.4828) ; N3 + #( 33.2062 4.8497 46.7851) ; C2 + #( 35.5600 4.6374 47.0822) ; C4 + #( 35.5444 5.6751 48.0577) ; C5 + #( 34.3565 6.2450 48.3432) ; C6 + #( 36.6977 4.0305 46.7598) ; N4 + #( 32.1661 4.5034 46.2348) ; O2 + #( 37.5405 4.3347 47.2259) ; H41 + #( 36.7033 3.2923 46.0706) ; H42 + #( 36.4713 5.9811 48.5428) ; H5 + #( 34.2986 7.0426 49.0839) ; H6 + )) + +(define rCs + (list rC01 rC02 rC03 rC04 rC05 rC06 rC07 rC08 rC09 rC10)) + +(define rG + (make-constant-rG + #( -0.0018 -0.8207 0.5714 ; dgf-base-tfo + 0.2679 -0.5509 -0.7904 + 0.9634 0.1517 0.2209 + 0.0073 8.4030 0.6232) + #( -0.8143 -0.5091 -0.2788 ; P-O3*-275-tfo + -0.0433 -0.4257 0.9038 + -0.5788 0.7480 0.3246 + 1.5227 6.9114 -7.0765) + #( 0.3822 -0.7477 0.5430 ; P-O3*-180-tfo + 0.4552 0.6637 0.5935 + -0.8042 0.0203 0.5941 + -6.9472 -4.1186 -5.9108) + #( 0.5640 0.8007 -0.2022 ; P-O3*-60-tfo + -0.8247 0.5587 -0.0878 + 0.0426 0.2162 0.9754 + 6.2694 -7.0540 3.3316) + #( 2.8930 8.5380 -3.3280) ; P + #( 1.6980 7.6960 -3.5570) ; O1P + #( 3.2260 9.5010 -4.4020) ; O2P + #( 4.1590 7.6040 -3.0340) ; O5* + #( 5.4550 8.2120 -2.8810) ; C5* + #( 5.4546 8.8508 -1.9978) ; H5* + #( 5.7588 8.6625 -3.8259) ; H5** + #( 6.4970 7.1480 -2.5980) ; C4* + #( 7.4896 7.5919 -2.5214) ; H4* + #( 6.1630 6.4860 -1.3440) ; O4* + #( 6.5400 5.1200 -1.4190) ; C1* + #( 7.2763 4.9681 -0.6297) ; H1* + #( 7.1940 4.8830 -2.7770) ; C2* + #( 6.8667 3.9183 -3.1647) ; H2** + #( 8.5860 5.0910 -2.6140) ; O2* + #( 8.9510 4.7626 -1.7890) ; H2* + #( 6.5720 6.0040 -3.6090) ; C3* + #( 5.5636 5.7066 -3.8966) ; H3* + #( 7.3801 6.3562 -4.7350) ; O3* + #( 4.7150 0.4910 -0.1360) ; N1 + #( 6.3490 2.1730 -0.6020) ; N3 + #( 5.9530 0.9650 -0.2670) ; C2 + #( 5.2900 2.9790 -0.8260) ; C4 + #( 3.9720 2.6390 -0.7330) ; C5 + #( 3.6770 1.3160 -0.3660) ; C6 + #( 6.8426 0.0056 -0.0019) ; N2 + #( 3.1660 3.7290 -1.0360) ; N7 + #( 5.3170 4.2990 -1.1930) ; N9 + #( 4.0100 4.6780 -1.2990) ; C8 + #( 2.4280 0.8450 -0.2360) ; O6 + #( 4.6151 -0.4677 0.1305) ; H1 + #( 6.6463 -0.9463 0.2729) ; H21 + #( 7.8170 0.2642 -0.0640) ; H22 + #( 3.4421 5.5744 -1.5482) ; H8 + )) + +(define rG01 + (make-constant-rG + #( -0.0043 -0.8175 0.5759 ; dgf-base-tfo + 0.2617 -0.5567 -0.7884 + 0.9651 0.1473 0.2164 + 0.0359 8.3929 0.5532) + #( -0.8143 -0.5091 -0.2788 ; P-O3*-275-tfo + -0.0433 -0.4257 0.9038 + -0.5788 0.7480 0.3246 + 1.5227 6.9114 -7.0765) + #( 0.3822 -0.7477 0.5430 ; P-O3*-180-tfo + 0.4552 0.6637 0.5935 + -0.8042 0.0203 0.5941 + -6.9472 -4.1186 -5.9108) + #( 0.5640 0.8007 -0.2022 ; P-O3*-60-tfo + -0.8247 0.5587 -0.0878 + 0.0426 0.2162 0.9754 + 6.2694 -7.0540 3.3316) + #( 2.8930 8.5380 -3.3280) ; P + #( 1.6980 7.6960 -3.5570) ; O1P + #( 3.2260 9.5010 -4.4020) ; O2P + #( 4.1590 7.6040 -3.0340) ; O5* + #( 5.4352 8.2183 -2.7757) ; C5* + #( 5.3830 8.7883 -1.8481) ; H5* + #( 5.7729 8.7436 -3.6691) ; H5** + #( 6.4830 7.1518 -2.5252) ; C4* + #( 7.4749 7.5972 -2.4482) ; H4* + #( 6.1626 6.4620 -1.2827) ; O4* + #( 6.5431 5.0992 -1.3905) ; C1* + #( 7.2871 4.9328 -0.6114) ; H1* + #( 7.1852 4.8935 -2.7592) ; C2* + #( 6.8573 3.9363 -3.1645) ; H2** + #( 8.5780 5.1025 -2.6046) ; O2* + #( 8.9516 4.7577 -1.7902) ; H2* + #( 6.5522 6.0300 -3.5612) ; C3* + #( 5.5420 5.7356 -3.8459) ; H3* + #( 7.3487 6.4089 -4.6867) ; O3* + #( 4.7442 0.4514 -0.1390) ; N1 + #( 6.3687 2.1459 -0.5926) ; N3 + #( 5.9795 0.9335 -0.2657) ; C2 + #( 5.3052 2.9471 -0.8125) ; C4 + #( 3.9891 2.5987 -0.7230) ; C5 + #( 3.7016 1.2717 -0.3647) ; C6 + #( 6.8745 -0.0224 -0.0058) ; N2 + #( 3.1770 3.6859 -1.0198) ; N7 + #( 5.3247 4.2695 -1.1710) ; N9 + #( 4.0156 4.6415 -1.2759) ; C8 + #( 2.4553 0.7925 -0.2390) ; O6 + #( 4.6497 -0.5095 0.1212) ; H1 + #( 6.6836 -0.9771 0.2627) ; H21 + #( 7.8474 0.2424 -0.0653) ; H22 + #( 3.4426 5.5361 -1.5199) ; H8 + )) + +(define rG02 + (make-constant-rG + #( 0.5566 0.0449 0.8296 ; dgf-base-tfo + 0.5125 0.7673 -0.3854 + -0.6538 0.6397 0.4041 + -9.1161 -3.7679 -2.9968) + #( -0.8143 -0.5091 -0.2788 ; P-O3*-275-tfo + -0.0433 -0.4257 0.9038 + -0.5788 0.7480 0.3246 + 1.5227 6.9114 -7.0765) + #( 0.3822 -0.7477 0.5430 ; P-O3*-180-tfo + 0.4552 0.6637 0.5935 + -0.8042 0.0203 0.5941 + -6.9472 -4.1186 -5.9108) + #( 0.5640 0.8007 -0.2022 ; P-O3*-60-tfo + -0.8247 0.5587 -0.0878 + 0.0426 0.2162 0.9754 + 6.2694 -7.0540 3.3316) + #( 2.8930 8.5380 -3.3280) ; P + #( 1.6980 7.6960 -3.5570) ; O1P + #( 3.2260 9.5010 -4.4020) ; O2P + #( 4.1590 7.6040 -3.0340) ; O5* + #( 4.5778 6.6594 -4.0364) ; C5* + #( 4.9220 7.1963 -4.9204) ; H5* + #( 3.7996 5.9091 -4.1764) ; H5** + #( 5.7873 5.8869 -3.5482) ; C4* + #( 6.0405 5.0875 -4.2446) ; H4* + #( 6.9135 6.8036 -3.4310) ; O4* + #( 7.7293 6.4084 -2.3392) ; C1* + #( 8.7078 6.1815 -2.7624) ; H1* + #( 7.1305 5.1418 -1.7347) ; C2* + #( 7.2040 5.1982 -0.6486) ; H2** + #( 7.7417 4.0392 -2.3813) ; O2* + #( 8.6785 4.1443 -2.5630) ; H2* + #( 5.6666 5.2728 -2.1536) ; C3* + #( 5.1747 5.9805 -1.4863) ; H3* + #( 4.9997 4.0086 -2.1973) ; O3* + #( 10.3245 8.5459 1.5467) ; N1 + #( 9.8051 6.9432 -0.1497) ; N3 + #( 10.5175 7.4328 0.8408) ; C2 + #( 8.7523 7.7422 -0.4228) ; C4 + #( 8.4257 8.9060 0.2099) ; C5 + #( 9.2665 9.3242 1.2540) ; C6 + #( 11.6077 6.7966 1.2752) ; N2 + #( 7.2750 9.4537 -0.3428) ; N7 + #( 7.7962 7.5519 -1.3859) ; N9 + #( 6.9479 8.6157 -1.2771) ; C8 + #( 9.0664 10.4462 1.9610) ; O6 + #( 10.9838 8.7524 2.2697) ; H1 + #( 12.2274 7.0896 2.0170) ; H21 + #( 11.8502 5.9398 0.7984) ; H22 + #( 6.0430 8.9853 -1.7594) ; H8 + )) + +(define rG03 + (make-constant-rG + #( -0.5021 0.0731 0.8617 ; dgf-base-tfo + -0.8112 0.3054 -0.4986 + -0.2996 -0.9494 -0.0940 + 6.4273 -5.1944 -3.7807) + #( -0.8143 -0.5091 -0.2788 ; P-O3*-275-tfo + -0.0433 -0.4257 0.9038 + -0.5788 0.7480 0.3246 + 1.5227 6.9114 -7.0765) + #( 0.3822 -0.7477 0.5430 ; P-O3*-180-tfo + 0.4552 0.6637 0.5935 + -0.8042 0.0203 0.5941 + -6.9472 -4.1186 -5.9108) + #( 0.5640 0.8007 -0.2022 ; P-O3*-60-tfo + -0.8247 0.5587 -0.0878 + 0.0426 0.2162 0.9754 + 6.2694 -7.0540 3.3316) + #( 2.8930 8.5380 -3.3280) ; P + #( 1.6980 7.6960 -3.5570) ; O1P + #( 3.2260 9.5010 -4.4020) ; O2P + #( 4.1590 7.6040 -3.0340) ; O5* + #( 4.1214 6.7116 -1.9049) ; C5* + #( 3.3465 5.9610 -2.0607) ; H5* + #( 4.0789 7.2928 -0.9837) ; H5** + #( 5.4170 5.9293 -1.8186) ; C4* + #( 5.4506 5.3400 -0.9023) ; H4* + #( 5.5067 5.0417 -2.9703) ; O4* + #( 6.8650 4.9152 -3.3612) ; C1* + #( 7.1090 3.8577 -3.2603) ; H1* + #( 7.7152 5.7282 -2.3894) ; C2* + #( 8.5029 6.2356 -2.9463) ; H2** + #( 8.1036 4.8568 -1.3419) ; O2* + #( 8.3270 3.9651 -1.6184) ; H2* + #( 6.7003 6.7565 -1.8911) ; C3* + #( 6.5898 7.5329 -2.6482) ; H3* + #( 7.0505 7.2878 -0.6105) ; O3* + #( 9.6740 4.7656 -7.6614) ; N1 + #( 9.0739 4.3013 -5.3941) ; N3 + #( 9.8416 4.2192 -6.4581) ; C2 + #( 7.9885 5.0632 -5.6446) ; C4 + #( 7.6822 5.6856 -6.8194) ; C5 + #( 8.5831 5.5215 -7.8840) ; C6 + #( 10.9733 3.5117 -6.4286) ; N2 + #( 6.4857 6.3816 -6.7035) ; N7 + #( 6.9740 5.3703 -4.7760) ; N9 + #( 6.1133 6.1613 -5.4808) ; C8 + #( 8.4084 6.0747 -9.0933) ; O6 + #( 10.3759 4.5855 -8.3504) ; H1 + #( 11.6254 3.3761 -7.1879) ; H21 + #( 11.1917 3.0460 -5.5593) ; H22 + #( 5.1705 6.6830 -5.3167) ; H8 + )) + +(define rG04 + (make-constant-rG + #( -0.5426 -0.8175 0.1929 ; dgf-base-tfo + 0.8304 -0.5567 -0.0237 + 0.1267 0.1473 0.9809 + -0.5075 8.3929 0.2229) + #( -0.8143 -0.5091 -0.2788 ; P-O3*-275-tfo + -0.0433 -0.4257 0.9038 + -0.5788 0.7480 0.3246 + 1.5227 6.9114 -7.0765) + #( 0.3822 -0.7477 0.5430 ; P-O3*-180-tfo + 0.4552 0.6637 0.5935 + -0.8042 0.0203 0.5941 + -6.9472 -4.1186 -5.9108) + #( 0.5640 0.8007 -0.2022 ; P-O3*-60-tfo + -0.8247 0.5587 -0.0878 + 0.0426 0.2162 0.9754 + 6.2694 -7.0540 3.3316) + #( 2.8930 8.5380 -3.3280) ; P + #( 1.6980 7.6960 -3.5570) ; O1P + #( 3.2260 9.5010 -4.4020) ; O2P + #( 4.1590 7.6040 -3.0340) ; O5* + #( 5.4352 8.2183 -2.7757) ; C5* + #( 5.3830 8.7883 -1.8481) ; H5* + #( 5.7729 8.7436 -3.6691) ; H5** + #( 6.4830 7.1518 -2.5252) ; C4* + #( 7.4749 7.5972 -2.4482) ; H4* + #( 6.1626 6.4620 -1.2827) ; O4* + #( 6.5431 5.0992 -1.3905) ; C1* + #( 7.2871 4.9328 -0.6114) ; H1* + #( 7.1852 4.8935 -2.7592) ; C2* + #( 6.8573 3.9363 -3.1645) ; H2** + #( 8.5780 5.1025 -2.6046) ; O2* + #( 8.9516 4.7577 -1.7902) ; H2* + #( 6.5522 6.0300 -3.5612) ; C3* + #( 5.5420 5.7356 -3.8459) ; H3* + #( 7.3487 6.4089 -4.6867) ; O3* + #( 3.6343 2.6680 2.0783) ; N1 + #( 5.4505 3.9805 1.2446) ; N3 + #( 4.7540 3.3816 2.1851) ; C2 + #( 4.8805 3.7951 0.0354) ; C4 + #( 3.7416 3.0925 -0.2305) ; C5 + #( 3.0873 2.4980 0.8606) ; C6 + #( 5.1433 3.4373 3.4609) ; N2 + #( 3.4605 3.1184 -1.5906) ; N7 + #( 5.3247 4.2695 -1.1710) ; N9 + #( 4.4244 3.8244 -2.0953) ; C8 + #( 1.9600 1.7805 0.7462) ; O6 + #( 3.2489 2.2879 2.9191) ; H1 + #( 4.6785 3.0243 4.2568) ; H21 + #( 5.9823 3.9654 3.6539) ; H22 + #( 4.2675 3.8876 -3.1721) ; H8 + )) + +(define rG05 + (make-constant-rG + #( -0.5891 0.0449 0.8068 ; dgf-base-tfo + 0.5375 0.7673 0.3498 + -0.6034 0.6397 -0.4762 + -0.3019 -3.7679 -9.5913) + #( -0.8143 -0.5091 -0.2788 ; P-O3*-275-tfo + -0.0433 -0.4257 0.9038 + -0.5788 0.7480 0.3246 + 1.5227 6.9114 -7.0765) + #( 0.3822 -0.7477 0.5430 ; P-O3*-180-tfo + 0.4552 0.6637 0.5935 + -0.8042 0.0203 0.5941 + -6.9472 -4.1186 -5.9108) + #( 0.5640 0.8007 -0.2022 ; P-O3*-60-tfo + -0.8247 0.5587 -0.0878 + 0.0426 0.2162 0.9754 + 6.2694 -7.0540 3.3316) + #( 2.8930 8.5380 -3.3280) ; P + #( 1.6980 7.6960 -3.5570) ; O1P + #( 3.2260 9.5010 -4.4020) ; O2P + #( 4.1590 7.6040 -3.0340) ; O5* + #( 4.5778 6.6594 -4.0364) ; C5* + #( 4.9220 7.1963 -4.9204) ; H5* + #( 3.7996 5.9091 -4.1764) ; H5** + #( 5.7873 5.8869 -3.5482) ; C4* + #( 6.0405 5.0875 -4.2446) ; H4* + #( 6.9135 6.8036 -3.4310) ; O4* + #( 7.7293 6.4084 -2.3392) ; C1* + #( 8.7078 6.1815 -2.7624) ; H1* + #( 7.1305 5.1418 -1.7347) ; C2* + #( 7.2040 5.1982 -0.6486) ; H2** + #( 7.7417 4.0392 -2.3813) ; O2* + #( 8.6785 4.1443 -2.5630) ; H2* + #( 5.6666 5.2728 -2.1536) ; C3* + #( 5.1747 5.9805 -1.4863) ; H3* + #( 4.9997 4.0086 -2.1973) ; O3* + #( 10.2594 10.6774 -1.0056) ; N1 + #( 9.7528 8.7080 -2.2631) ; N3 + #( 10.4471 9.7876 -1.9791) ; C2 + #( 8.7271 8.5575 -1.3991) ; C4 + #( 8.4100 9.3803 -0.3580) ; C5 + #( 9.2294 10.5030 -0.1574) ; C6 + #( 11.5110 10.1256 -2.7114) ; N2 + #( 7.2891 8.9068 0.3121) ; N7 + #( 7.7962 7.5519 -1.3859) ; N9 + #( 6.9702 7.8292 -0.3353) ; C8 + #( 9.0349 11.3951 0.8250) ; O6 + #( 10.9013 11.4422 -0.9512) ; H1 + #( 12.1031 10.9341 -2.5861) ; H21 + #( 11.7369 9.5180 -3.4859) ; H22 + #( 6.0888 7.3990 0.1403) ; H8 + )) + +(define rG06 + (make-constant-rG + #( -0.9815 0.0731 -0.1772 ; dgf-base-tfo + 0.1912 0.3054 -0.9328 + -0.0141 -0.9494 -0.3137 + 5.7506 -5.1944 4.7470) + #( -0.8143 -0.5091 -0.2788 ; P-O3*-275-tfo + -0.0433 -0.4257 0.9038 + -0.5788 0.7480 0.3246 + 1.5227 6.9114 -7.0765) + #( 0.3822 -0.7477 0.5430 ; P-O3*-180-tfo + 0.4552 0.6637 0.5935 + -0.8042 0.0203 0.5941 + -6.9472 -4.1186 -5.9108) + #( 0.5640 0.8007 -0.2022 ; P-O3*-60-tfo + -0.8247 0.5587 -0.0878 + 0.0426 0.2162 0.9754 + 6.2694 -7.0540 3.3316) + #( 2.8930 8.5380 -3.3280) ; P + #( 1.6980 7.6960 -3.5570) ; O1P + #( 3.2260 9.5010 -4.4020) ; O2P + #( 4.1590 7.6040 -3.0340) ; O5* + #( 4.1214 6.7116 -1.9049) ; C5* + #( 3.3465 5.9610 -2.0607) ; H5* + #( 4.0789 7.2928 -0.9837) ; H5** + #( 5.4170 5.9293 -1.8186) ; C4* + #( 5.4506 5.3400 -0.9023) ; H4* + #( 5.5067 5.0417 -2.9703) ; O4* + #( 6.8650 4.9152 -3.3612) ; C1* + #( 7.1090 3.8577 -3.2603) ; H1* + #( 7.7152 5.7282 -2.3894) ; C2* + #( 8.5029 6.2356 -2.9463) ; H2** + #( 8.1036 4.8568 -1.3419) ; O2* + #( 8.3270 3.9651 -1.6184) ; H2* + #( 6.7003 6.7565 -1.8911) ; C3* + #( 6.5898 7.5329 -2.6482) ; H3* + #( 7.0505 7.2878 -0.6105) ; O3* + #( 6.6624 3.5061 -8.2986) ; N1 + #( 6.5810 3.2570 -5.9221) ; N3 + #( 6.5151 2.8263 -7.1625) ; C2 + #( 6.8364 4.5817 -5.8882) ; C4 + #( 7.0116 5.4064 -6.9609) ; C5 + #( 6.9173 4.8260 -8.2361) ; C6 + #( 6.2717 1.5402 -7.4250) ; N2 + #( 7.2573 6.7070 -6.5394) ; N7 + #( 6.9740 5.3703 -4.7760) ; N9 + #( 7.2238 6.6275 -5.2453) ; C8 + #( 7.0668 5.5163 -9.3763) ; O6 + #( 6.5754 2.9964 -9.1545) ; H1 + #( 6.1908 1.1105 -8.3354) ; H21 + #( 6.1346 0.9352 -6.6280) ; H22 + #( 7.4108 7.6227 -4.8418) ; H8 + )) + +(define rG07 + (make-constant-rG + #( 0.0894 -0.6059 0.7905 ; dgf-base-tfo + -0.6810 0.5420 0.4924 + -0.7268 -0.5824 -0.3642 + 34.1424 45.9610 -11.8600) + #( -0.8644 -0.4956 -0.0851 ; P-O3*-275-tfo + -0.0427 0.2409 -0.9696 + 0.5010 -0.8345 -0.2294 + 4.0167 54.5377 12.4779) + #( 0.3706 -0.6167 0.6945 ; P-O3*-180-tfo + -0.2867 -0.7872 -0.5460 + 0.8834 0.0032 -0.4686 + -52.9020 18.6313 -0.6709) + #( 0.4155 0.9025 -0.1137 ; P-O3*-60-tfo + 0.9040 -0.4236 -0.0582 + -0.1007 -0.0786 -0.9918 + -7.6624 -25.2080 49.5181) + #( 31.3810 0.1400 47.5810) ; P + #( 29.9860 0.6630 47.6290) ; O1P + #( 31.7210 -0.6460 48.8090) ; O2P + #( 32.4940 1.2540 47.2740) ; O5* + #( 33.8709 0.7918 47.2113) ; C5* + #( 34.1386 0.5870 46.1747) ; H5* + #( 34.0186 -0.0095 47.9353) ; H5** + #( 34.7297 1.9687 47.6685) ; C4* + #( 35.7723 1.6845 47.8113) ; H4* + #( 34.6455 2.9768 46.6660) ; O4* + #( 34.1690 4.1829 47.2627) ; C1* + #( 35.0437 4.7633 47.5560) ; H1* + #( 33.4145 3.7532 48.4954) ; C2* + #( 32.4340 3.3797 48.2001) ; H2** + #( 33.3209 4.6953 49.5217) ; O2* + #( 33.2374 5.6059 49.2295) ; H2* + #( 34.2724 2.5970 48.9773) ; C3* + #( 33.6373 1.8935 49.5157) ; H3* + #( 35.3453 3.1884 49.7285) ; O3* + #( 34.0511 7.8930 43.7791) ; N1 + #( 34.9937 6.3369 45.3199) ; N3 + #( 35.0882 7.3126 44.4200) ; C2 + #( 33.7190 5.9650 45.5374) ; C4 + #( 32.5845 6.4770 44.9458) ; C5 + #( 32.7430 7.5179 43.9914) ; C6 + #( 36.3030 7.7827 44.1036) ; N2 + #( 31.4499 5.8335 45.4368) ; N7 + #( 33.2760 4.9817 46.4043) ; N9 + #( 31.9235 4.9639 46.2934) ; C8 + #( 31.8602 8.1000 43.3695) ; O6 + #( 34.2623 8.6223 43.1283) ; H1 + #( 36.5188 8.5081 43.4347) ; H21 + #( 37.0888 7.3524 44.5699) ; H22 + #( 31.0815 4.4201 46.7218) ; H8 + )) + +(define rG08 + (make-constant-rG + #( 0.2224 0.6335 0.7411 ; dgf-base-tfo + -0.3644 -0.6510 0.6659 + 0.9043 -0.4181 0.0861 + -47.6824 -0.5823 -31.7554) + #( -0.8644 -0.4956 -0.0851 ; P-O3*-275-tfo + -0.0427 0.2409 -0.9696 + 0.5010 -0.8345 -0.2294 + 4.0167 54.5377 12.4779) + #( 0.3706 -0.6167 0.6945 ; P-O3*-180-tfo + -0.2867 -0.7872 -0.5460 + 0.8834 0.0032 -0.4686 + -52.9020 18.6313 -0.6709) + #( 0.4155 0.9025 -0.1137 ; P-O3*-60-tfo + 0.9040 -0.4236 -0.0582 + -0.1007 -0.0786 -0.9918 + -7.6624 -25.2080 49.5181) + #( 31.3810 0.1400 47.5810) ; P + #( 29.9860 0.6630 47.6290) ; O1P + #( 31.7210 -0.6460 48.8090) ; O2P + #( 32.4940 1.2540 47.2740) ; O5* + #( 32.5924 2.3488 48.2255) ; C5* + #( 33.3674 2.1246 48.9584) ; H5* + #( 31.5994 2.5917 48.6037) ; H5** + #( 33.0722 3.5577 47.4258) ; C4* + #( 33.0310 4.4778 48.0089) ; H4* + #( 34.4173 3.3055 47.0316) ; O4* + #( 34.5056 3.3910 45.6094) ; C1* + #( 34.7881 4.4152 45.3663) ; H1* + #( 33.1122 3.1198 45.1010) ; C2* + #( 32.9230 2.0469 45.1369) ; H2** + #( 32.7946 3.6590 43.8529) ; O2* + #( 33.5170 3.6707 43.2207) ; H2* + #( 32.2730 3.8173 46.1566) ; C3* + #( 31.3094 3.3123 46.2244) ; H3* + #( 32.2391 5.2039 45.7807) ; O3* + #( 39.3337 2.7157 44.1441) ; N1 + #( 37.4430 3.8242 45.0824) ; N3 + #( 38.7276 3.7646 44.7403) ; C2 + #( 36.7791 2.6963 44.7704) ; C4 + #( 37.2860 1.5653 44.1678) ; C5 + #( 38.6647 1.5552 43.8235) ; C6 + #( 39.5123 4.8216 44.9936) ; N2 + #( 36.2829 0.6110 44.0078) ; N7 + #( 35.4394 2.4314 44.9931) ; N9 + #( 35.2180 1.1815 44.5128) ; C8 + #( 39.2907 0.6514 43.2796) ; O6 + #( 40.3076 2.8048 43.9352) ; H1 + #( 40.4994 4.9066 44.7977) ; H21 + #( 39.0738 5.6108 45.4464) ; H22 + #( 34.3856 0.4842 44.4185) ; H8 + )) + +(define rG09 + (make-constant-rG + #( -0.9699 -0.1688 -0.1753 ; dgf-base-tfo + -0.1050 -0.3598 0.9271 + -0.2196 0.9176 0.3312 + 45.6217 -38.9484 -12.3208) + #( -0.8644 -0.4956 -0.0851 ; P-O3*-275-tfo + -0.0427 0.2409 -0.9696 + 0.5010 -0.8345 -0.2294 + 4.0167 54.5377 12.4779) + #( 0.3706 -0.6167 0.6945 ; P-O3*-180-tfo + -0.2867 -0.7872 -0.5460 + 0.8834 0.0032 -0.4686 + -52.9020 18.6313 -0.6709) + #( 0.4155 0.9025 -0.1137 ; P-O3*-60-tfo + 0.9040 -0.4236 -0.0582 + -0.1007 -0.0786 -0.9918 + -7.6624 -25.2080 49.5181) + #( 31.3810 0.1400 47.5810) ; P + #( 29.9860 0.6630 47.6290) ; O1P + #( 31.7210 -0.6460 48.8090) ; O2P + #( 32.4940 1.2540 47.2740) ; O5* + #( 33.8709 0.7918 47.2113) ; C5* + #( 34.1386 0.5870 46.1747) ; H5* + #( 34.0186 -0.0095 47.9353) ; H5** + #( 34.7297 1.9687 47.6685) ; C4* + #( 34.5880 2.8482 47.0404) ; H4* + #( 34.3575 2.2770 49.0081) ; O4* + #( 35.5157 2.1993 49.8389) ; C1* + #( 35.9424 3.2010 49.8893) ; H1* + #( 36.4701 1.2820 49.1169) ; C2* + #( 36.1545 0.2498 49.2683) ; H2** + #( 37.8262 1.4547 49.4008) ; O2* + #( 38.0227 1.6945 50.3094) ; H2* + #( 36.2242 1.6797 47.6725) ; C3* + #( 36.4297 0.8197 47.0351) ; H3* + #( 37.0289 2.8480 47.4426) ; O3* + #( 34.3005 3.5042 54.6070) ; N1 + #( 34.7693 3.7936 52.2874) ; N3 + #( 34.4484 4.2541 53.4939) ; C2 + #( 34.9354 2.4584 52.2785) ; C4 + #( 34.8092 1.5915 53.3422) ; C5 + #( 34.4646 2.1367 54.6085) ; C6 + #( 34.2514 5.5708 53.6503) ; N2 + #( 35.0641 0.2835 52.9337) ; N7 + #( 35.2669 1.6690 51.1915) ; N9 + #( 35.3288 0.3954 51.6563) ; C8 + #( 34.3151 1.5317 55.6650) ; O6 + #( 34.0623 3.9797 55.4539) ; H1 + #( 33.9950 6.0502 54.5016) ; H21 + #( 34.3512 6.1432 52.8242) ; H22 + #( 35.5414 -0.6006 51.2679) ; H8 + )) + +(define rG10 + (make-constant-rG + #( -0.0980 -0.9723 0.2122 ; dgf-base-tfo + -0.9731 0.1383 0.1841 + -0.2083 -0.1885 -0.9597 + 17.8469 38.8265 37.0475) + #( -0.8644 -0.4956 -0.0851 ; P-O3*-275-tfo + -0.0427 0.2409 -0.9696 + 0.5010 -0.8345 -0.2294 + 4.0167 54.5377 12.4779) + #( 0.3706 -0.6167 0.6945 ; P-O3*-180-tfo + -0.2867 -0.7872 -0.5460 + 0.8834 0.0032 -0.4686 + -52.9020 18.6313 -0.6709) + #( 0.4155 0.9025 -0.1137 ; P-O3*-60-tfo + 0.9040 -0.4236 -0.0582 + -0.1007 -0.0786 -0.9918 + -7.6624 -25.2080 49.5181) + #( 31.3810 0.1400 47.5810) ; P + #( 29.9860 0.6630 47.6290) ; O1P + #( 31.7210 -0.6460 48.8090) ; O2P + #( 32.4940 1.2540 47.2740) ; O5* + #( 32.5924 2.3488 48.2255) ; C5* + #( 33.3674 2.1246 48.9584) ; H5* + #( 31.5994 2.5917 48.6037) ; H5** + #( 33.0722 3.5577 47.4258) ; C4* + #( 34.0333 3.3761 46.9447) ; H4* + #( 32.0890 3.8338 46.4332) ; O4* + #( 31.6377 5.1787 46.5914) ; C1* + #( 32.2499 5.8016 45.9392) ; H1* + #( 31.9167 5.5319 48.0305) ; C2* + #( 31.1507 5.0820 48.6621) ; H2** + #( 32.0865 6.8890 48.3114) ; O2* + #( 31.5363 7.4819 47.7942) ; H2* + #( 33.2398 4.8224 48.2563) ; C3* + #( 33.3166 4.5570 49.3108) ; H3* + #( 34.2528 5.7056 47.7476) ; O3* + #( 28.2782 6.3049 42.9364) ; N1 + #( 30.4001 5.8547 43.9258) ; N3 + #( 29.6195 6.1568 42.8913) ; C2 + #( 29.7005 5.7006 45.0649) ; C4 + #( 28.3383 5.8221 45.2343) ; C5 + #( 27.5519 6.1461 44.0958) ; C6 + #( 30.1838 6.3385 41.6890) ; N2 + #( 27.9936 5.5926 46.5651) ; N7 + #( 30.2046 5.3825 46.3136) ; N9 + #( 29.1371 5.3398 47.1506) ; C8 + #( 26.3361 6.3024 44.0495) ; O6 + #( 27.8122 6.5394 42.0833) ; H1 + #( 29.7125 6.5595 40.8235) ; H21 + #( 31.1859 6.2231 41.6389) ; H22 + #( 28.9406 5.1504 48.2059) ; H8 + )) + +(define rGs + (list rG01 rG02 rG03 rG04 rG05 rG06 rG07 rG08 rG09 rG10)) + +(define rU + (make-constant-rU + #( -0.0359 -0.8071 0.5894 ; dgf-base-tfo + -0.2669 0.5761 0.7726 + -0.9631 -0.1296 -0.2361 + 0.1584 8.3434 0.5434) + #( -0.8313 -0.4738 -0.2906 ; P-O3*-275-tfo + 0.0649 0.4366 -0.8973 + 0.5521 -0.7648 -0.3322 + 1.6833 6.8060 -7.0011) + #( 0.3445 -0.7630 0.5470 ; P-O3*-180-tfo + -0.4628 -0.6450 -0.6082 + 0.8168 -0.0436 -0.5753 + -6.8179 -3.9778 -5.9887) + #( 0.5855 0.7931 -0.1682 ; P-O3*-60-tfo + 0.8103 -0.5790 0.0906 + -0.0255 -0.1894 -0.9816 + 6.1203 -7.1051 3.1984) + #( 2.6760 -8.4960 3.2880) ; P + #( 1.4950 -7.6230 3.4770) ; O1P + #( 2.9490 -9.4640 4.3740) ; O2P + #( 3.9730 -7.5950 3.0340) ; O5* + #( 5.2430 -8.2420 2.8260) ; C5* + #( 5.1974 -8.8497 1.9223) ; H5* + #( 5.5548 -8.7348 3.7469) ; H5** + #( 6.3140 -7.2060 2.5510) ; C4* + #( 7.2954 -7.6762 2.4898) ; H4* + #( 6.0140 -6.5420 1.2890) ; O4* + #( 6.4190 -5.1840 1.3620) ; C1* + #( 7.1608 -5.0495 0.5747) ; H1* + #( 7.0760 -4.9560 2.7270) ; C2* + #( 6.7770 -3.9803 3.1099) ; H2** + #( 8.4500 -5.1930 2.5810) ; O2* + #( 8.8309 -4.8755 1.7590) ; H2* + #( 6.4060 -6.0590 3.5580) ; C3* + #( 5.4021 -5.7313 3.8281) ; H3* + #( 7.1570 -6.4240 4.7070) ; O3* + #( 5.2170 -4.3260 1.1690) ; N1 + #( 4.2960 -2.2560 0.6290) ; N3 + #( 5.4330 -3.0200 0.7990) ; C2 + #( 2.9930 -2.6780 0.7940) ; C4 + #( 2.8670 -4.0630 1.1830) ; C5 + #( 3.9570 -4.8300 1.3550) ; C6 + #( 6.5470 -2.5560 0.6290) ; O2 + #( 2.0540 -1.9000 0.6130) ; O4 + #( 4.4300 -1.3020 0.3600) ; H3 + #( 1.9590 -4.4570 1.3250) ; H5 + #( 3.8460 -5.7860 1.6240) ; H6 + )) + +(define rU01 + (make-constant-rU + #( -0.0137 -0.8012 0.5983 ; dgf-base-tfo + -0.2523 0.5817 0.7733 + -0.9675 -0.1404 -0.2101 + 0.2031 8.3874 0.4228) + #( -0.8313 -0.4738 -0.2906 ; P-O3*-275-tfo + 0.0649 0.4366 -0.8973 + 0.5521 -0.7648 -0.3322 + 1.6833 6.8060 -7.0011) + #( 0.3445 -0.7630 0.5470 ; P-O3*-180-tfo + -0.4628 -0.6450 -0.6082 + 0.8168 -0.0436 -0.5753 + -6.8179 -3.9778 -5.9887) + #( 0.5855 0.7931 -0.1682 ; P-O3*-60-tfo + 0.8103 -0.5790 0.0906 + -0.0255 -0.1894 -0.9816 + 6.1203 -7.1051 3.1984) + #( 2.6760 -8.4960 3.2880) ; P + #( 1.4950 -7.6230 3.4770) ; O1P + #( 2.9490 -9.4640 4.3740) ; O2P + #( 3.9730 -7.5950 3.0340) ; O5* + #( 5.2416 -8.2422 2.8181) ; C5* + #( 5.2050 -8.8128 1.8901) ; H5* + #( 5.5368 -8.7738 3.7227) ; H5** + #( 6.3232 -7.2037 2.6002) ; C4* + #( 7.3048 -7.6757 2.5577) ; H4* + #( 6.0635 -6.5092 1.3456) ; O4* + #( 6.4697 -5.1547 1.4629) ; C1* + #( 7.2354 -5.0043 0.7018) ; H1* + #( 7.0856 -4.9610 2.8521) ; C2* + #( 6.7777 -3.9935 3.2487) ; H2** + #( 8.4627 -5.1992 2.7423) ; O2* + #( 8.8693 -4.8638 1.9399) ; H2* + #( 6.3877 -6.0809 3.6362) ; C3* + #( 5.3770 -5.7562 3.8834) ; H3* + #( 7.1024 -6.4754 4.7985) ; O3* + #( 5.2764 -4.2883 1.2538) ; N1 + #( 4.3777 -2.2062 0.7229) ; N3 + #( 5.5069 -2.9779 0.9088) ; C2 + #( 3.0693 -2.6246 0.8500) ; C4 + #( 2.9279 -4.0146 1.2149) ; C5 + #( 4.0101 -4.7892 1.4017) ; C6 + #( 6.6267 -2.5166 0.7728) ; O2 + #( 2.1383 -1.8396 0.6581) ; O4 + #( 4.5223 -1.2489 0.4716) ; H3 + #( 2.0151 -4.4065 1.3290) ; H5 + #( 3.8886 -5.7486 1.6535) ; H6 + )) + +(define rU02 + (make-constant-rU + #( 0.5141 0.0246 0.8574 ; dgf-base-tfo + -0.5547 -0.7529 0.3542 + 0.6542 -0.6577 -0.3734 + -9.1111 -3.4598 -3.2939) + #( -0.8313 -0.4738 -0.2906 ; P-O3*-275-tfo + 0.0649 0.4366 -0.8973 + 0.5521 -0.7648 -0.3322 + 1.6833 6.8060 -7.0011) + #( 0.3445 -0.7630 0.5470 ; P-O3*-180-tfo + -0.4628 -0.6450 -0.6082 + 0.8168 -0.0436 -0.5753 + -6.8179 -3.9778 -5.9887) + #( 0.5855 0.7931 -0.1682 ; P-O3*-60-tfo + 0.8103 -0.5790 0.0906 + -0.0255 -0.1894 -0.9816 + 6.1203 -7.1051 3.1984) + #( 2.6760 -8.4960 3.2880) ; P + #( 1.4950 -7.6230 3.4770) ; O1P + #( 2.9490 -9.4640 4.3740) ; O2P + #( 3.9730 -7.5950 3.0340) ; O5* + #( 4.3825 -6.6585 4.0489) ; C5* + #( 4.6841 -7.2019 4.9443) ; H5* + #( 3.6189 -5.8889 4.1625) ; H5** + #( 5.6255 -5.9175 3.5998) ; C4* + #( 5.8732 -5.1228 4.3034) ; H4* + #( 6.7337 -6.8605 3.5222) ; O4* + #( 7.5932 -6.4923 2.4548) ; C1* + #( 8.5661 -6.2983 2.9064) ; H1* + #( 7.0527 -5.2012 1.8322) ; C2* + #( 7.1627 -5.2525 0.7490) ; H2** + #( 7.6666 -4.1249 2.4880) ; O2* + #( 8.5944 -4.2543 2.6981) ; H2* + #( 5.5661 -5.3029 2.2009) ; C3* + #( 5.0841 -6.0018 1.5172) ; H3* + #( 4.9062 -4.0452 2.2042) ; O3* + #( 7.6298 -7.6136 1.4752) ; N1 + #( 8.6945 -8.7046 -0.2857) ; N3 + #( 8.6943 -7.6514 0.6066) ; C2 + #( 7.7426 -9.6987 -0.3801) ; C4 + #( 6.6642 -9.5742 0.5722) ; C5 + #( 6.6391 -8.5592 1.4526) ; C6 + #( 9.5840 -6.8186 0.6136) ; O2 + #( 7.8505 -10.5925 -1.2223) ; O4 + #( 9.4601 -8.7514 -0.9277) ; H3 + #( 5.9281 -10.2509 0.5782) ; H5 + #( 5.8831 -8.4931 2.1028) ; H6 + )) + +(define rU03 + (make-constant-rU + #( -0.4993 0.0476 0.8651 ; dgf-base-tfo + 0.8078 -0.3353 0.4847 + 0.3132 0.9409 0.1290 + 6.2989 -5.2303 -3.8577) + #( -0.8313 -0.4738 -0.2906 ; P-O3*-275-tfo + 0.0649 0.4366 -0.8973 + 0.5521 -0.7648 -0.3322 + 1.6833 6.8060 -7.0011) + #( 0.3445 -0.7630 0.5470 ; P-O3*-180-tfo + -0.4628 -0.6450 -0.6082 + 0.8168 -0.0436 -0.5753 + -6.8179 -3.9778 -5.9887) + #( 0.5855 0.7931 -0.1682 ; P-O3*-60-tfo + 0.8103 -0.5790 0.0906 + -0.0255 -0.1894 -0.9816 + 6.1203 -7.1051 3.1984) + #( 2.6760 -8.4960 3.2880) ; P + #( 1.4950 -7.6230 3.4770) ; O1P + #( 2.9490 -9.4640 4.3740) ; O2P + #( 3.9730 -7.5950 3.0340) ; O5* + #( 3.9938 -6.7042 1.9023) ; C5* + #( 3.2332 -5.9343 2.0319) ; H5* + #( 3.9666 -7.2863 0.9812) ; H5** + #( 5.3098 -5.9546 1.8564) ; C4* + #( 5.3863 -5.3702 0.9395) ; H4* + #( 5.3851 -5.0642 3.0076) ; O4* + #( 6.7315 -4.9724 3.4462) ; C1* + #( 7.0033 -3.9202 3.3619) ; H1* + #( 7.5997 -5.8018 2.4948) ; C2* + #( 8.3627 -6.3254 3.0707) ; H2** + #( 8.0410 -4.9501 1.4724) ; O2* + #( 8.2781 -4.0644 1.7570) ; H2* + #( 6.5701 -6.8129 1.9714) ; C3* + #( 6.4186 -7.5809 2.7299) ; H3* + #( 6.9357 -7.3841 0.7235) ; O3* + #( 6.8024 -5.4718 4.8475) ; N1 + #( 7.9218 -5.5700 6.8877) ; N3 + #( 7.8908 -5.0886 5.5944) ; C2 + #( 6.9789 -6.3827 7.4823) ; C4 + #( 5.8742 -6.7319 6.6202) ; C5 + #( 5.8182 -6.2769 5.3570) ; C6 + #( 8.7747 -4.3728 5.1568) ; O2 + #( 7.1154 -6.7509 8.6509) ; O4 + #( 8.7055 -5.3037 7.4491) ; H3 + #( 5.1416 -7.3178 6.9665) ; H5 + #( 5.0441 -6.5310 4.7784) ; H6 + )) + +(define rU04 + (make-constant-rU + #( -0.5669 -0.8012 0.1918 ; dgf-base-tfo + -0.8129 0.5817 0.0273 + -0.1334 -0.1404 -0.9811 + -0.3279 8.3874 0.3355) + #( -0.8313 -0.4738 -0.2906 ; P-O3*-275-tfo + 0.0649 0.4366 -0.8973 + 0.5521 -0.7648 -0.3322 + 1.6833 6.8060 -7.0011) + #( 0.3445 -0.7630 0.5470 ; P-O3*-180-tfo + -0.4628 -0.6450 -0.6082 + 0.8168 -0.0436 -0.5753 + -6.8179 -3.9778 -5.9887) + #( 0.5855 0.7931 -0.1682 ; P-O3*-60-tfo + 0.8103 -0.5790 0.0906 + -0.0255 -0.1894 -0.9816 + 6.1203 -7.1051 3.1984) + #( 2.6760 -8.4960 3.2880) ; P + #( 1.4950 -7.6230 3.4770) ; O1P + #( 2.9490 -9.4640 4.3740) ; O2P + #( 3.9730 -7.5950 3.0340) ; O5* + #( 5.2416 -8.2422 2.8181) ; C5* + #( 5.2050 -8.8128 1.8901) ; H5* + #( 5.5368 -8.7738 3.7227) ; H5** + #( 6.3232 -7.2037 2.6002) ; C4* + #( 7.3048 -7.6757 2.5577) ; H4* + #( 6.0635 -6.5092 1.3456) ; O4* + #( 6.4697 -5.1547 1.4629) ; C1* + #( 7.2354 -5.0043 0.7018) ; H1* + #( 7.0856 -4.9610 2.8521) ; C2* + #( 6.7777 -3.9935 3.2487) ; H2** + #( 8.4627 -5.1992 2.7423) ; O2* + #( 8.8693 -4.8638 1.9399) ; H2* + #( 6.3877 -6.0809 3.6362) ; C3* + #( 5.3770 -5.7562 3.8834) ; H3* + #( 7.1024 -6.4754 4.7985) ; O3* + #( 5.2764 -4.2883 1.2538) ; N1 + #( 3.8961 -3.0896 -0.1893) ; N3 + #( 5.0095 -3.8907 -0.0346) ; C2 + #( 3.0480 -2.6632 0.8116) ; C4 + #( 3.4093 -3.1310 2.1292) ; C5 + #( 4.4878 -3.9124 2.3088) ; C6 + #( 5.7005 -4.2164 -0.9842) ; O2 + #( 2.0800 -1.9458 0.5503) ; O4 + #( 3.6834 -2.7882 -1.1190) ; H3 + #( 2.8508 -2.8721 2.9172) ; H5 + #( 4.7188 -4.2247 3.2295) ; H6 + )) + +(define rU05 + (make-constant-rU + #( -0.6298 0.0246 0.7763 ; dgf-base-tfo + -0.5226 -0.7529 -0.4001 + 0.5746 -0.6577 0.4870 + -0.0208 -3.4598 -9.6882) + #( -0.8313 -0.4738 -0.2906 ; P-O3*-275-tfo + 0.0649 0.4366 -0.8973 + 0.5521 -0.7648 -0.3322 + 1.6833 6.8060 -7.0011) + #( 0.3445 -0.7630 0.5470 ; P-O3*-180-tfo + -0.4628 -0.6450 -0.6082 + 0.8168 -0.0436 -0.5753 + -6.8179 -3.9778 -5.9887) + #( 0.5855 0.7931 -0.1682 ; P-O3*-60-tfo + 0.8103 -0.5790 0.0906 + -0.0255 -0.1894 -0.9816 + 6.1203 -7.1051 3.1984) + #( 2.6760 -8.4960 3.2880) ; P + #( 1.4950 -7.6230 3.4770) ; O1P + #( 2.9490 -9.4640 4.3740) ; O2P + #( 3.9730 -7.5950 3.0340) ; O5* + #( 4.3825 -6.6585 4.0489) ; C5* + #( 4.6841 -7.2019 4.9443) ; H5* + #( 3.6189 -5.8889 4.1625) ; H5** + #( 5.6255 -5.9175 3.5998) ; C4* + #( 5.8732 -5.1228 4.3034) ; H4* + #( 6.7337 -6.8605 3.5222) ; O4* + #( 7.5932 -6.4923 2.4548) ; C1* + #( 8.5661 -6.2983 2.9064) ; H1* + #( 7.0527 -5.2012 1.8322) ; C2* + #( 7.1627 -5.2525 0.7490) ; H2** + #( 7.6666 -4.1249 2.4880) ; O2* + #( 8.5944 -4.2543 2.6981) ; H2* + #( 5.5661 -5.3029 2.2009) ; C3* + #( 5.0841 -6.0018 1.5172) ; H3* + #( 4.9062 -4.0452 2.2042) ; O3* + #( 7.6298 -7.6136 1.4752) ; N1 + #( 8.5977 -9.5977 0.7329) ; N3 + #( 8.5951 -8.5745 1.6594) ; C2 + #( 7.7372 -9.7371 -0.3364) ; C4 + #( 6.7596 -8.6801 -0.4476) ; C5 + #( 6.7338 -7.6721 0.4408) ; C6 + #( 9.3993 -8.5377 2.5743) ; O2 + #( 7.8374 -10.6990 -1.1008) ; O4 + #( 9.2924 -10.3081 0.8477) ; H3 + #( 6.0932 -8.6982 -1.1929) ; H5 + #( 6.0481 -6.9515 0.3446) ; H6 + )) + +(define rU06 + (make-constant-rU + #( -0.9837 0.0476 -0.1733 ; dgf-base-tfo + -0.1792 -0.3353 0.9249 + -0.0141 0.9409 0.3384 + 5.7793 -5.2303 4.5997) + #( -0.8313 -0.4738 -0.2906 ; P-O3*-275-tfo + 0.0649 0.4366 -0.8973 + 0.5521 -0.7648 -0.3322 + 1.6833 6.8060 -7.0011) + #( 0.3445 -0.7630 0.5470 ; P-O3*-180-tfo + -0.4628 -0.6450 -0.6082 + 0.8168 -0.0436 -0.5753 + -6.8179 -3.9778 -5.9887) + #( 0.5855 0.7931 -0.1682 ; P-O3*-60-tfo + 0.8103 -0.5790 0.0906 + -0.0255 -0.1894 -0.9816 + 6.1203 -7.1051 3.1984) + #( 2.6760 -8.4960 3.2880) ; P + #( 1.4950 -7.6230 3.4770) ; O1P + #( 2.9490 -9.4640 4.3740) ; O2P + #( 3.9730 -7.5950 3.0340) ; O5* + #( 3.9938 -6.7042 1.9023) ; C5* + #( 3.2332 -5.9343 2.0319) ; H5* + #( 3.9666 -7.2863 0.9812) ; H5** + #( 5.3098 -5.9546 1.8564) ; C4* + #( 5.3863 -5.3702 0.9395) ; H4* + #( 5.3851 -5.0642 3.0076) ; O4* + #( 6.7315 -4.9724 3.4462) ; C1* + #( 7.0033 -3.9202 3.3619) ; H1* + #( 7.5997 -5.8018 2.4948) ; C2* + #( 8.3627 -6.3254 3.0707) ; H2** + #( 8.0410 -4.9501 1.4724) ; O2* + #( 8.2781 -4.0644 1.7570) ; H2* + #( 6.5701 -6.8129 1.9714) ; C3* + #( 6.4186 -7.5809 2.7299) ; H3* + #( 6.9357 -7.3841 0.7235) ; O3* + #( 6.8024 -5.4718 4.8475) ; N1 + #( 6.6920 -5.0495 7.1354) ; N3 + #( 6.6201 -4.5500 5.8506) ; C2 + #( 6.9254 -6.3614 7.4926) ; C4 + #( 7.1046 -7.2543 6.3718) ; C5 + #( 7.0391 -6.7951 5.1106) ; C6 + #( 6.4083 -3.3696 5.6340) ; O2 + #( 6.9679 -6.6901 8.6800) ; O4 + #( 6.5626 -4.3957 7.8812) ; H3 + #( 7.2781 -8.2254 6.5350) ; H5 + #( 7.1657 -7.4312 4.3503) ; H6 + )) + +(define rU07 + (make-constant-rU + #( -0.9434 0.3172 0.0971 ; dgf-base-tfo + 0.2294 0.4125 0.8816 + 0.2396 0.8539 -0.4619 + 8.3625 -52.7147 1.3745) + #( 0.2765 -0.1121 -0.9545 ; P-O3*-275-tfo + -0.8297 0.4733 -0.2959 + 0.4850 0.8737 0.0379 + -14.7774 -45.2464 21.9088) + #( 0.1063 -0.6334 -0.7665 ; P-O3*-180-tfo + -0.5932 -0.6591 0.4624 + -0.7980 0.4055 -0.4458 + 43.7634 4.3296 28.4890) + #( 0.7136 -0.5032 -0.4873 ; P-O3*-60-tfo + 0.6803 0.3317 0.6536 + -0.1673 -0.7979 0.5791 + -17.1858 41.4390 -27.0751) + #( 21.3880 15.0780 45.5770) ; P + #( 21.9980 14.5500 46.8210) ; O1P + #( 21.1450 14.0270 44.5420) ; O2P + #( 22.1250 16.3600 44.9460) ; O5* + #( 21.5037 16.8594 43.7323) ; C5* + #( 20.8147 17.6663 43.9823) ; H5* + #( 21.1086 16.0230 43.1557) ; H5** + #( 22.5654 17.4874 42.8616) ; C4* + #( 22.1584 17.7243 41.8785) ; H4* + #( 23.0557 18.6826 43.4751) ; O4* + #( 24.4788 18.6151 43.6455) ; C1* + #( 24.9355 19.0840 42.7739) ; H1* + #( 24.7958 17.1427 43.6474) ; C2* + #( 24.5652 16.7400 44.6336) ; H2** + #( 26.1041 16.8773 43.2455) ; O2* + #( 26.7516 17.5328 43.5149) ; H2* + #( 23.8109 16.5979 42.6377) ; C3* + #( 23.5756 15.5686 42.9084) ; H3* + #( 24.2890 16.7447 41.2729) ; O3* + #( 24.9420 19.2174 44.8923) ; N1 + #( 25.2655 20.5636 44.8883) ; N3 + #( 25.1663 21.2219 43.8561) ; C2 + #( 25.6911 21.1219 46.0494) ; C4 + #( 25.8051 20.4068 47.2048) ; C5 + #( 26.2093 20.9962 48.2534) ; C6 + #( 25.4692 19.0221 47.2053) ; O2 + #( 25.0502 18.4827 46.0370) ; O4 + #( 25.9599 22.1772 46.0966) ; H3 + #( 25.5545 18.4409 48.1234) ; H5 + #( 24.7854 17.4265 45.9883) ; H6 + )) + +(define rU08 + (make-constant-rU + #( -0.0080 -0.7928 0.6094 ; dgf-base-tfo + -0.7512 0.4071 0.5197 + -0.6601 -0.4536 -0.5988 + 44.1482 30.7036 2.1088) + #( 0.2765 -0.1121 -0.9545 ; P-O3*-275-tfo + -0.8297 0.4733 -0.2959 + 0.4850 0.8737 0.0379 + -14.7774 -45.2464 21.9088) + #( 0.1063 -0.6334 -0.7665 ; P-O3*-180-tfo + -0.5932 -0.6591 0.4624 + -0.7980 0.4055 -0.4458 + 43.7634 4.3296 28.4890) + #( 0.7136 -0.5032 -0.4873 ; P-O3*-60-tfo + 0.6803 0.3317 0.6536 + -0.1673 -0.7979 0.5791 + -17.1858 41.4390 -27.0751) + #( 21.3880 15.0780 45.5770) ; P + #( 21.9980 14.5500 46.8210) ; O1P + #( 21.1450 14.0270 44.5420) ; O2P + #( 22.1250 16.3600 44.9460) ; O5* + #( 23.5096 16.1227 44.5783) ; C5* + #( 23.5649 15.8588 43.5222) ; H5* + #( 23.9621 15.4341 45.2919) ; H5** + #( 24.2805 17.4138 44.7151) ; C4* + #( 25.3492 17.2309 44.6030) ; H4* + #( 23.8497 18.3471 43.7208) ; O4* + #( 23.4090 19.5681 44.3321) ; C1* + #( 24.2595 20.2496 44.3524) ; H1* + #( 23.0418 19.1813 45.7407) ; C2* + #( 22.0532 18.7224 45.7273) ; H2** + #( 23.1307 20.2521 46.6291) ; O2* + #( 22.8888 21.1051 46.2611) ; H2* + #( 24.0799 18.1326 46.0700) ; C3* + #( 23.6490 17.4370 46.7900) ; H3* + #( 25.3329 18.7227 46.5109) ; O3* + #( 22.2515 20.1624 43.6698) ; N1 + #( 22.4760 21.0609 42.6406) ; N3 + #( 23.6229 21.3462 42.3061) ; C2 + #( 21.3986 21.6081 42.0236) ; C4 + #( 20.1189 21.3012 42.3804) ; C5 + #( 19.1599 21.8516 41.7578) ; C6 + #( 19.8919 20.3745 43.4387) ; O2 + #( 20.9790 19.8423 44.0440) ; O4 + #( 21.5235 22.3222 41.2097) ; H3 + #( 18.8732 20.1200 43.7312) ; H5 + #( 20.8545 19.1313 44.8608) ; H6 + )) + +(define rU09 + (make-constant-rU + #( -0.0317 0.1374 0.9900 ; dgf-base-tfo + -0.3422 -0.9321 0.1184 + 0.9391 -0.3351 0.0765 + -32.1929 25.8198 -28.5088) + #( 0.2765 -0.1121 -0.9545 ; P-O3*-275-tfo + -0.8297 0.4733 -0.2959 + 0.4850 0.8737 0.0379 + -14.7774 -45.2464 21.9088) + #( 0.1063 -0.6334 -0.7665 ; P-O3*-180-tfo + -0.5932 -0.6591 0.4624 + -0.7980 0.4055 -0.4458 + 43.7634 4.3296 28.4890) + #( 0.7136 -0.5032 -0.4873 ; P-O3*-60-tfo + 0.6803 0.3317 0.6536 + -0.1673 -0.7979 0.5791 + -17.1858 41.4390 -27.0751) + #( 21.3880 15.0780 45.5770) ; P + #( 21.9980 14.5500 46.8210) ; O1P + #( 21.1450 14.0270 44.5420) ; O2P + #( 22.1250 16.3600 44.9460) ; O5* + #( 21.5037 16.8594 43.7323) ; C5* + #( 20.8147 17.6663 43.9823) ; H5* + #( 21.1086 16.0230 43.1557) ; H5** + #( 22.5654 17.4874 42.8616) ; C4* + #( 23.0565 18.3036 43.3915) ; H4* + #( 23.5375 16.5054 42.4925) ; O4* + #( 23.6574 16.4257 41.0649) ; C1* + #( 24.4701 17.0882 40.7671) ; H1* + #( 22.3525 16.9643 40.5396) ; C2* + #( 21.5993 16.1799 40.6133) ; H2** + #( 22.4693 17.4849 39.2515) ; O2* + #( 23.0899 17.0235 38.6827) ; H2* + #( 22.0341 18.0633 41.5279) ; C3* + #( 20.9509 18.1709 41.5846) ; H3* + #( 22.7249 19.3020 41.2100) ; O3* + #( 23.8580 15.0648 40.5757) ; N1 + #( 25.1556 14.5982 40.4523) ; N3 + #( 26.1047 15.3210 40.7448) ; C2 + #( 25.3391 13.3315 40.0020) ; C4 + #( 24.2974 12.5148 39.6749) ; C5 + #( 24.5450 11.3410 39.2610) ; C6 + #( 22.9633 12.9979 39.8053) ; O2 + #( 22.8009 14.2648 40.2524) ; O4 + #( 26.3414 12.9194 39.8855) ; H3 + #( 22.1227 12.3533 39.5486) ; H5 + #( 21.7989 14.6788 40.3650) ; H6 + )) + +(define rU10 + (make-constant-rU + #( -0.9674 0.1021 -0.2318 ; dgf-base-tfo + -0.2514 -0.2766 0.9275 + 0.0306 0.9555 0.2933 + 27.8571 -42.1305 -24.4563) + #( 0.2765 -0.1121 -0.9545 ; P-O3*-275-tfo + -0.8297 0.4733 -0.2959 + 0.4850 0.8737 0.0379 + -14.7774 -45.2464 21.9088) + #( 0.1063 -0.6334 -0.7665 ; P-O3*-180-tfo + -0.5932 -0.6591 0.4624 + -0.7980 0.4055 -0.4458 + 43.7634 4.3296 28.4890) + #( 0.7136 -0.5032 -0.4873 ; P-O3*-60-tfo + 0.6803 0.3317 0.6536 + -0.1673 -0.7979 0.5791 + -17.1858 41.4390 -27.0751) + #( 21.3880 15.0780 45.5770) ; P + #( 21.9980 14.5500 46.8210) ; O1P + #( 21.1450 14.0270 44.5420) ; O2P + #( 22.1250 16.3600 44.9460) ; O5* + #( 23.5096 16.1227 44.5783) ; C5* + #( 23.5649 15.8588 43.5222) ; H5* + #( 23.9621 15.4341 45.2919) ; H5** + #( 24.2805 17.4138 44.7151) ; C4* + #( 23.8509 18.1819 44.0720) ; H4* + #( 24.2506 17.8583 46.0741) ; O4* + #( 25.5830 18.0320 46.5775) ; C1* + #( 25.8569 19.0761 46.4256) ; H1* + #( 26.4410 17.1555 45.7033) ; C2* + #( 26.3459 16.1253 46.0462) ; H2** + #( 27.7649 17.5888 45.6478) ; O2* + #( 28.1004 17.9719 46.4616) ; H2* + #( 25.7796 17.2997 44.3513) ; C3* + #( 25.9478 16.3824 43.7871) ; H3* + #( 26.2154 18.4984 43.6541) ; O3* + #( 25.7321 17.6281 47.9726) ; N1 + #( 25.5136 18.5779 48.9560) ; N3 + #( 25.2079 19.7276 48.6503) ; C2 + #( 25.6482 18.1987 50.2518) ; C4 + #( 25.9847 16.9266 50.6092) ; C5 + #( 26.0918 16.6439 51.8416) ; C6 + #( 26.2067 15.9515 49.5943) ; O2 + #( 26.0713 16.3497 48.3080) ; O4 + #( 25.4890 18.9105 51.0618) ; H3 + #( 26.4742 14.9310 49.8682) ; H5 + #( 26.2346 15.6394 47.4975) ; H6 + )) + +(define rUs + (list rU01 rU02 rU03 rU04 rU05 rU06 rU07 rU08 rU09 rU10)) + +(define rG* + (make-constant-rG + #( -0.2067 -0.0264 0.9780 ; dgf-base-tfo + 0.9770 -0.0586 0.2049 + 0.0519 0.9979 0.0379 + 1.0331 -46.8078 -36.4742) + #( -0.8644 -0.4956 -0.0851 ; P-O3*-275-tfo + -0.0427 0.2409 -0.9696 + 0.5010 -0.8345 -0.2294 + 4.0167 54.5377 12.4779) + #( 0.3706 -0.6167 0.6945 ; P-O3*-180-tfo + -0.2867 -0.7872 -0.5460 + 0.8834 0.0032 -0.4686 + -52.9020 18.6313 -0.6709) + #( 0.4155 0.9025 -0.1137 ; P-O3*-60-tfo + 0.9040 -0.4236 -0.0582 + -0.1007 -0.0786 -0.9918 + -7.6624 -25.2080 49.5181) + #( 31.3810 0.1400 47.5810) ; P + #( 29.9860 0.6630 47.6290) ; O1P + #( 31.7210 -0.6460 48.8090) ; O2P + #( 32.4940 1.2540 47.2740) ; O5* + #( 32.1610 2.2370 46.2560) ; C5* + #( 31.2986 2.8190 46.5812) ; H5* + #( 32.0980 1.7468 45.2845) ; H5** + #( 33.3476 3.1959 46.1947) ; C4* + #( 33.2668 3.8958 45.3630) ; H4* + #( 33.3799 3.9183 47.4216) ; O4* + #( 34.6515 3.7222 48.0398) ; C1* + #( 35.2947 4.5412 47.7180) ; H1* + #( 35.1756 2.4228 47.4827) ; C2* + #( 34.6778 1.5937 47.9856) ; H2** + #( 36.5631 2.2672 47.4798) ; O2* + #( 37.0163 2.6579 48.2305) ; H2* + #( 34.6953 2.5043 46.0448) ; C3* + #( 34.5444 1.4917 45.6706) ; H3* + #( 35.6679 3.3009 45.3487) ; O3* + #( 37.4804 4.0914 52.2559) ; N1 + #( 36.9670 4.1312 49.9281) ; N3 + #( 37.8045 4.2519 50.9550) ; C2 + #( 35.7171 3.8264 50.3222) ; C4 + #( 35.2668 3.6420 51.6115) ; C5 + #( 36.2037 3.7829 52.6706) ; C6 + #( 39.0869 4.5552 50.7092) ; N2 + #( 33.9075 3.3338 51.6102) ; N7 + #( 34.6126 3.6358 49.5108) ; N9 + #( 33.5805 3.3442 50.3425) ; C8 + #( 35.9958 3.6512 53.8724) ; O6 + #( 38.2106 4.2053 52.9295) ; H1 + #( 39.8218 4.6863 51.3896) ; H21 + #( 39.3420 4.6857 49.7407) ; H22 + #( 32.5194 3.1070 50.2664) ; H8 + )) + +(define rU* + (make-constant-rU + #( -0.0109 0.5907 0.8068 ; dgf-base-tfo + 0.2217 -0.7853 0.5780 + 0.9751 0.1852 -0.1224 + -1.4225 -11.0956 -2.5217) + #( -0.8313 -0.4738 -0.2906 ; P-O3*-275-tfo + 0.0649 0.4366 -0.8973 + 0.5521 -0.7648 -0.3322 + 1.6833 6.8060 -7.0011) + #( 0.3445 -0.7630 0.5470 ; P-O3*-180-tfo + -0.4628 -0.6450 -0.6082 + 0.8168 -0.0436 -0.5753 + -6.8179 -3.9778 -5.9887) + #( 0.5855 0.7931 -0.1682 ; P-O3*-60-tfo + 0.8103 -0.5790 0.0906 + -0.0255 -0.1894 -0.9816 + 6.1203 -7.1051 3.1984) + #( 2.6760 -8.4960 3.2880) ; P + #( 1.4950 -7.6230 3.4770) ; O1P + #( 2.9490 -9.4640 4.3740) ; O2P + #( 3.9730 -7.5950 3.0340) ; O5* + #( 5.2430 -8.2420 2.8260) ; C5* + #( 5.1974 -8.8497 1.9223) ; H5* + #( 5.5548 -8.7348 3.7469) ; H5** + #( 6.3140 -7.2060 2.5510) ; C4* + #( 5.8744 -6.2116 2.4731) ; H4* + #( 7.2798 -7.2260 3.6420) ; O4* + #( 8.5733 -6.9410 3.1329) ; C1* + #( 8.9047 -6.0374 3.6446) ; H1* + #( 8.4429 -6.6596 1.6327) ; C2* + #( 9.2880 -7.1071 1.1096) ; H2** + #( 8.2502 -5.2799 1.4754) ; O2* + #( 8.7676 -4.7284 2.0667) ; H2* + #( 7.1642 -7.4416 1.3021) ; C3* + #( 7.4125 -8.5002 1.2260) ; H3* + #( 6.5160 -6.9772 0.1267) ; O3* + #( 9.4531 -8.1107 3.4087) ; N1 + #( 11.5931 -9.0015 3.6357) ; N3 + #( 10.8101 -7.8950 3.3748) ; C2 + #( 11.1439 -10.2744 3.9206) ; C4 + #( 9.7056 -10.4026 3.9332) ; C5 + #( 8.9192 -9.3419 3.6833) ; C6 + #( 11.3013 -6.8063 3.1326) ; O2 + #( 11.9431 -11.1876 4.1375) ; O4 + #( 12.5840 -8.8673 3.6158) ; H3 + #( 9.2891 -11.2898 4.1313) ; H5 + #( 7.9263 -9.4537 3.6977) ; H6 + )) + + + +; -- PARTIAL INSTANTIATIONS --------------------------------------------------- + +(define (get-var id lst) + (let ((v (car lst))) + (if (= id (var-id v)) + v + (get-var id (cdr lst))))) + +(define (make-relative-nuc tfo n) + (cond ((rA? n) + (make-rA + (nuc-dgf-base-tfo n) + (nuc-P-O3*-275-tfo n) + (nuc-P-O3*-180-tfo n) + (nuc-P-O3*-60-tfo n) + (lazy-computation-of (tfo-apply tfo (nuc-P n))) + (lazy-computation-of (tfo-apply tfo (nuc-O1P n))) + (lazy-computation-of (tfo-apply tfo (nuc-O2P n))) + (lazy-computation-of (tfo-apply tfo (nuc-O5* n))) + (lazy-computation-of (tfo-apply tfo (nuc-C5* n))) + (lazy-computation-of (tfo-apply tfo (nuc-H5* n))) + (lazy-computation-of (tfo-apply tfo (nuc-H5** n))) + (lazy-computation-of (tfo-apply tfo (nuc-C4* n))) + (lazy-computation-of (tfo-apply tfo (nuc-H4* n))) + (lazy-computation-of (tfo-apply tfo (nuc-O4* n))) + (lazy-computation-of (tfo-apply tfo (nuc-C1* n))) + (lazy-computation-of (tfo-apply tfo (nuc-H1* n))) + (lazy-computation-of (tfo-apply tfo (nuc-C2* n))) + (lazy-computation-of (tfo-apply tfo (nuc-H2** n))) + (lazy-computation-of (tfo-apply tfo (nuc-O2* n))) + (lazy-computation-of (tfo-apply tfo (nuc-H2* n))) + (lazy-computation-of (tfo-apply tfo (nuc-C3* n))) + (lazy-computation-of (tfo-apply tfo (nuc-H3* n))) + (lazy-computation-of (tfo-apply tfo (nuc-O3* n))) + (lazy-computation-of (tfo-apply tfo (nuc-N1 n))) + (lazy-computation-of (tfo-apply tfo (nuc-N3 n))) + (lazy-computation-of (tfo-apply tfo (nuc-C2 n))) + (lazy-computation-of (tfo-apply tfo (nuc-C4 n))) + (lazy-computation-of (tfo-apply tfo (nuc-C5 n))) + (lazy-computation-of (tfo-apply tfo (nuc-C6 n))) + (lazy-computation-of (tfo-apply tfo (rA-N6 n))) + (lazy-computation-of (tfo-apply tfo (rA-N7 n))) + (lazy-computation-of (tfo-apply tfo (rA-N9 n))) + (lazy-computation-of (tfo-apply tfo (rA-C8 n))) + (lazy-computation-of (tfo-apply tfo (rA-H2 n))) + (lazy-computation-of (tfo-apply tfo (rA-H61 n))) + (lazy-computation-of (tfo-apply tfo (rA-H62 n))) + (lazy-computation-of (tfo-apply tfo (rA-H8 n))))) + ((rC? n) + (make-rC + (nuc-dgf-base-tfo n) + (nuc-P-O3*-275-tfo n) + (nuc-P-O3*-180-tfo n) + (nuc-P-O3*-60-tfo n) + (lazy-computation-of (tfo-apply tfo (nuc-P n))) + (lazy-computation-of (tfo-apply tfo (nuc-O1P n))) + (lazy-computation-of (tfo-apply tfo (nuc-O2P n))) + (lazy-computation-of (tfo-apply tfo (nuc-O5* n))) + (lazy-computation-of (tfo-apply tfo (nuc-C5* n))) + (lazy-computation-of (tfo-apply tfo (nuc-H5* n))) + (lazy-computation-of (tfo-apply tfo (nuc-H5** n))) + (lazy-computation-of (tfo-apply tfo (nuc-C4* n))) + (lazy-computation-of (tfo-apply tfo (nuc-H4* n))) + (lazy-computation-of (tfo-apply tfo (nuc-O4* n))) + (lazy-computation-of (tfo-apply tfo (nuc-C1* n))) + (lazy-computation-of (tfo-apply tfo (nuc-H1* n))) + (lazy-computation-of (tfo-apply tfo (nuc-C2* n))) + (lazy-computation-of (tfo-apply tfo (nuc-H2** n))) + (lazy-computation-of (tfo-apply tfo (nuc-O2* n))) + (lazy-computation-of (tfo-apply tfo (nuc-H2* n))) + (lazy-computation-of (tfo-apply tfo (nuc-C3* n))) + (lazy-computation-of (tfo-apply tfo (nuc-H3* n))) + (lazy-computation-of (tfo-apply tfo (nuc-O3* n))) + (lazy-computation-of (tfo-apply tfo (nuc-N1 n))) + (lazy-computation-of (tfo-apply tfo (nuc-N3 n))) + (lazy-computation-of (tfo-apply tfo (nuc-C2 n))) + (lazy-computation-of (tfo-apply tfo (nuc-C4 n))) + (lazy-computation-of (tfo-apply tfo (nuc-C5 n))) + (lazy-computation-of (tfo-apply tfo (nuc-C6 n))) + (lazy-computation-of (tfo-apply tfo (rC-N4 n))) + (lazy-computation-of (tfo-apply tfo (rC-O2 n))) + (lazy-computation-of (tfo-apply tfo (rC-H41 n))) + (lazy-computation-of (tfo-apply tfo (rC-H42 n))) + (lazy-computation-of (tfo-apply tfo (rC-H5 n))) + (lazy-computation-of (tfo-apply tfo (rC-H6 n))))) + ((rG? n) + (make-rG + (nuc-dgf-base-tfo n) + (nuc-P-O3*-275-tfo n) + (nuc-P-O3*-180-tfo n) + (nuc-P-O3*-60-tfo n) + (lazy-computation-of (tfo-apply tfo (nuc-P n))) + (lazy-computation-of (tfo-apply tfo (nuc-O1P n))) + (lazy-computation-of (tfo-apply tfo (nuc-O2P n))) + (lazy-computation-of (tfo-apply tfo (nuc-O5* n))) + (lazy-computation-of (tfo-apply tfo (nuc-C5* n))) + (lazy-computation-of (tfo-apply tfo (nuc-H5* n))) + (lazy-computation-of (tfo-apply tfo (nuc-H5** n))) + (lazy-computation-of (tfo-apply tfo (nuc-C4* n))) + (lazy-computation-of (tfo-apply tfo (nuc-H4* n))) + (lazy-computation-of (tfo-apply tfo (nuc-O4* n))) + (lazy-computation-of (tfo-apply tfo (nuc-C1* n))) + (lazy-computation-of (tfo-apply tfo (nuc-H1* n))) + (lazy-computation-of (tfo-apply tfo (nuc-C2* n))) + (lazy-computation-of (tfo-apply tfo (nuc-H2** n))) + (lazy-computation-of (tfo-apply tfo (nuc-O2* n))) + (lazy-computation-of (tfo-apply tfo (nuc-H2* n))) + (lazy-computation-of (tfo-apply tfo (nuc-C3* n))) + (lazy-computation-of (tfo-apply tfo (nuc-H3* n))) + (lazy-computation-of (tfo-apply tfo (nuc-O3* n))) + (lazy-computation-of (tfo-apply tfo (nuc-N1 n))) + (lazy-computation-of (tfo-apply tfo (nuc-N3 n))) + (lazy-computation-of (tfo-apply tfo (nuc-C2 n))) + (lazy-computation-of (tfo-apply tfo (nuc-C4 n))) + (lazy-computation-of (tfo-apply tfo (nuc-C5 n))) + (lazy-computation-of (tfo-apply tfo (nuc-C6 n))) + (lazy-computation-of (tfo-apply tfo (rG-N2 n))) + (lazy-computation-of (tfo-apply tfo (rG-N7 n))) + (lazy-computation-of (tfo-apply tfo (rG-N9 n))) + (lazy-computation-of (tfo-apply tfo (rG-C8 n))) + (lazy-computation-of (tfo-apply tfo (rG-O6 n))) + (lazy-computation-of (tfo-apply tfo (rG-H1 n))) + (lazy-computation-of (tfo-apply tfo (rG-H21 n))) + (lazy-computation-of (tfo-apply tfo (rG-H22 n))) + (lazy-computation-of (tfo-apply tfo (rG-H8 n))))) + (else + (make-rU + (nuc-dgf-base-tfo n) + (nuc-P-O3*-275-tfo n) + (nuc-P-O3*-180-tfo n) + (nuc-P-O3*-60-tfo n) + (lazy-computation-of (tfo-apply tfo (nuc-P n))) + (lazy-computation-of (tfo-apply tfo (nuc-O1P n))) + (lazy-computation-of (tfo-apply tfo (nuc-O2P n))) + (lazy-computation-of (tfo-apply tfo (nuc-O5* n))) + (lazy-computation-of (tfo-apply tfo (nuc-C5* n))) + (lazy-computation-of (tfo-apply tfo (nuc-H5* n))) + (lazy-computation-of (tfo-apply tfo (nuc-H5** n))) + (lazy-computation-of (tfo-apply tfo (nuc-C4* n))) + (lazy-computation-of (tfo-apply tfo (nuc-H4* n))) + (lazy-computation-of (tfo-apply tfo (nuc-O4* n))) + (lazy-computation-of (tfo-apply tfo (nuc-C1* n))) + (lazy-computation-of (tfo-apply tfo (nuc-H1* n))) + (lazy-computation-of (tfo-apply tfo (nuc-C2* n))) + (lazy-computation-of (tfo-apply tfo (nuc-H2** n))) + (lazy-computation-of (tfo-apply tfo (nuc-O2* n))) + (lazy-computation-of (tfo-apply tfo (nuc-H2* n))) + (lazy-computation-of (tfo-apply tfo (nuc-C3* n))) + (lazy-computation-of (tfo-apply tfo (nuc-H3* n))) + (lazy-computation-of (tfo-apply tfo (nuc-O3* n))) + (lazy-computation-of (tfo-apply tfo (nuc-N1 n))) + (lazy-computation-of (tfo-apply tfo (nuc-N3 n))) + (lazy-computation-of (tfo-apply tfo (nuc-C2 n))) + (lazy-computation-of (tfo-apply tfo (nuc-C4 n))) + (lazy-computation-of (tfo-apply tfo (nuc-C5 n))) + (lazy-computation-of (tfo-apply tfo (nuc-C6 n))) + (lazy-computation-of (tfo-apply tfo (rU-O2 n))) + (lazy-computation-of (tfo-apply tfo (rU-O4 n))) + (lazy-computation-of (tfo-apply tfo (rU-H3 n))) + (lazy-computation-of (tfo-apply tfo (rU-H5 n))) + (lazy-computation-of (tfo-apply tfo (rU-H6 n))))))) + +; -- SEARCH ------------------------------------------------------------------- + +; Sequential backtracking algorithm + +(define (search partial-inst domains constraint?) + (if (null? domains) + (list partial-inst) + (let ((remaining-domains (cdr domains))) + + (define (try-assignments lst) + (if (null? lst) + '() + (let ((var (car lst))) + (if (constraint? var partial-inst) + (let* ((subsols1 + (search + (cons var partial-inst) + remaining-domains + constraint?)) + (subsols2 + (try-assignments (cdr lst)))) + (append subsols1 subsols2)) + (try-assignments (cdr lst)))))) + + (try-assignments ((car domains) partial-inst))))) + +; -- DOMAINS ------------------------------------------------------------------ + +; Primary structure: strand A CUGCCACGUCUG, strand B CAGACGUGGCAG +; +; Secondary structure: strand A CUGCCACGUCUG +; |||||||||||| +; GACGGUGCAGAC strand B +; +; Tertiary structure: +; +; 5' end of strand A C1----G12 3' end of strand B +; U2-------A11 +; G3-------C10 +; C4-----G9 +; C5---G8 +; A6 +; G6-C7 +; C5----G8 +; A4-------U9 +; G3--------C10 +; A2-------U11 +; 5' end of strand B C1----G12 3' end of strand A +; +; "helix", "stacked" and "connected" describe the spatial relationship +; between two consecutive nucleotides. E.g. the nucleotides C1 and U2 +; from the strand A. +; +; "wc" (stands for Watson-Crick and is a type of base-pairing), +; and "wc-dumas" describe the spatial relationship between +; nucleotides from two chains that are growing in opposite directions. +; E.g. the nucleotides C1 from strand A and G12 from strand B. + +; Dynamic Domains + +; Given, +; "ref" a nucleotide which is already positioned, +; "nuc" the nucleotide to be placed, +; and "tfo" a transformation matrix which expresses the desired +; relationship between "ref" and "nuc", +; the function "dgf-base" computes the transformation matrix that +; places the nucleotide "nuc" in the given relationship to "ref". + +(define (dgf-base tfo ref nuc) + (let* ((ref-nuc (var-nuc ref)) + (align + (tfo-inv-ortho + (cond ((rA? ref-nuc) + (tfo-align (atom-pos nuc-C1* ref) + (atom-pos rA-N9 ref) + (atom-pos nuc-C4 ref))) + ((rC? ref-nuc) + (tfo-align (atom-pos nuc-C1* ref) + (atom-pos nuc-N1 ref) + (atom-pos nuc-C2 ref))) + ((rG? ref-nuc) + (tfo-align (atom-pos nuc-C1* ref) + (atom-pos rG-N9 ref) + (atom-pos nuc-C4 ref))) + (else + (tfo-align (atom-pos nuc-C1* ref) + (atom-pos nuc-N1 ref) + (atom-pos nuc-C2 ref))))))) + (tfo-combine (nuc-dgf-base-tfo nuc) + (tfo-combine tfo align)))) + +; Placement of first nucleotide. + +(define (reference nuc i) + (lambda (partial-inst) + (list (mk-var i tfo-id nuc)))) + +; The transformation matrix for wc is from: +; +; Chandrasekaran R. et al (1989) A Re-Examination of the Crystal +; Structure of A-DNA Using Fiber Diffraction Data. J. Biomol. +; Struct. & Dynamics 6(6):1189-1202. + +(define wc-tfo + '#(-1.0000 0.0028 -0.0019 + 0.0028 0.3468 -0.9379 + -0.0019 -0.9379 -0.3468 + -0.0080 6.0730 8.7208)) + +(define (wc nuc i j) + (lambda (partial-inst) + (let* ((ref (get-var j partial-inst)) + (tfo (dgf-base wc-tfo ref nuc))) + (list (mk-var i tfo nuc))))) + +(define wc-Dumas-tfo + '#(-0.9737 -0.1834 0.1352 + -0.1779 0.2417 -0.9539 + 0.1422 -0.9529 -0.2679 + 0.4837 6.2649 8.0285)) + +(define (wc-Dumas nuc i j) + (lambda (partial-inst) + (let* ((ref (get-var j partial-inst)) + (tfo (dgf-base wc-Dumas-tfo ref nuc))) + (list (mk-var i tfo nuc))))) + +(define helix5*-tfo + '#( 0.9886 -0.0961 0.1156 + 0.1424 0.8452 -0.5152 + -0.0482 0.5258 0.8492 + -3.8737 0.5480 3.8024)) + +(define (helix5* nuc i j) + (lambda (partial-inst) + (let* ((ref (get-var j partial-inst)) + (tfo (dgf-base helix5*-tfo ref nuc))) + (list (mk-var i tfo nuc))))) + +(define helix3*-tfo + '#( 0.9886 0.1424 -0.0482 + -0.0961 0.8452 0.5258 + 0.1156 -0.5152 0.8492 + 3.4426 2.0474 -3.7042)) + +(define (helix3* nuc i j) + (lambda (partial-inst) + (let* ((ref (get-var j partial-inst)) + (tfo (dgf-base helix3*-tfo ref nuc))) + (list (mk-var i tfo nuc))))) + +(define G37-A38-tfo + '#( 0.9991 0.0164 -0.0387 + -0.0375 0.7616 -0.6470 + 0.0189 0.6478 0.7615 + -3.3018 0.9975 2.5585)) + +(define (G37-A38 nuc i j) + (lambda (partial-inst) + (let* ((ref (get-var j partial-inst)) + (tfo (dgf-base G37-A38-tfo ref nuc))) + (mk-var i tfo nuc)))) + +(define (stacked5* nuc i j) + (lambda (partial-inst) + (cons ((G37-A38 nuc i j) partial-inst) + ((helix5* nuc i j) partial-inst)))) + +(define A38-G37-tfo + '#( 0.9991 -0.0375 0.0189 + 0.0164 0.7616 0.6478 + -0.0387 -0.6470 0.7615 + 3.3819 0.7718 -2.5321)) + +(define (A38-G37 nuc i j) + (lambda (partial-inst) + (let* ((ref (get-var j partial-inst)) + (tfo (dgf-base A38-G37-tfo ref nuc))) + (mk-var i tfo nuc)))) + +(define (stacked3* nuc i j) + (lambda (partial-inst) + (cons ((A38-G37 nuc i j) partial-inst) + ((helix3* nuc i j) partial-inst)))) + +(define (P-O3* nucs i j) + (lambda (partial-inst) + (let* ((ref (get-var j partial-inst)) + (align + (tfo-inv-ortho + (tfo-align (atom-pos nuc-O3* ref) + (atom-pos nuc-C3* ref) + (atom-pos nuc-C4* ref))))) + (let loop ((lst nucs) (domains '())) + (if (null? lst) + domains + (let ((nuc (car lst))) + (let ((tfo-60 (tfo-combine (nuc-P-O3*-60-tfo nuc) align)) + (tfo-180 (tfo-combine (nuc-P-O3*-180-tfo nuc) align)) + (tfo-275 (tfo-combine (nuc-P-O3*-275-tfo nuc) align))) + (loop (cdr lst) + (cons (mk-var i tfo-60 nuc) + (cons (mk-var i tfo-180 nuc) + (cons (mk-var i tfo-275 nuc) domains))))))))))) + +; -- PROBLEM STATEMENT -------------------------------------------------------- + +; Define anticodon problem -- Science 253:1255 Figure 3a, 3b and 3c + +(define anticodon-domains + (list + (reference rC 27 ) + (helix5* rC 28 27) + (helix5* rA 29 28) + (helix5* rG 30 29) + (helix5* rA 31 30) + (wc rU 39 31) + (helix5* rC 40 39) + (helix5* rU 41 40) + (helix5* rG 42 41) + (helix5* rG 43 42) + (stacked3* rA 38 39) + (stacked3* rG 37 38) + (stacked3* rA 36 37) + (stacked3* rA 35 36) + (stacked3* rG 34 35);<-. Distance + (P-O3* rCs 32 31); | Constraint + (P-O3* rUs 33 32);<-' 3.0 Angstroms + )) + +; Anticodon constraint + +(define (anticodon-constraint? v partial-inst) + (if (= (var-id v) 33) + (let ((p (atom-pos nuc-P (get-var 34 partial-inst))) ; P in nucleotide 34 + (o3* (atom-pos nuc-O3* v))) ; O3' in nucl. 33 + (FLOAT<= (pt-dist p o3*) 3.0)) ; check distance + #t)) + +(define (anticodon) + (search '() anticodon-domains anticodon-constraint?)) + +; Define pseudoknot problem -- Science 253:1255 Figure 4a and 4b + +(define pseudoknot-domains + (list + (reference rA 23 ) + (wc-Dumas rU 8 23) + (helix3* rG 22 23) + (wc-Dumas rC 9 22) + (helix3* rG 21 22) + (wc-Dumas rC 10 21) + (helix3* rC 20 21) + (wc-Dumas rG 11 20) + (helix3* rU* 19 20);<-. + (wc-Dumas rA 12 19); | Distance +; ; | Constraint +; Helix 1 ; | 4.0 Angstroms + (helix3* rC 3 19); | + (wc-Dumas rG 13 3); | + (helix3* rC 2 3); | + (wc-Dumas rG 14 2); | + (helix3* rC 1 2); | + (wc-Dumas rG* 15 1); | +; ; | +; L2 LOOP ; | + (P-O3* rUs 16 15); | + (P-O3* rCs 17 16); | + (P-O3* rAs 18 17);<-' +; +; L1 LOOP + (helix3* rU 7 8);<-. + (P-O3* rCs 4 3); | Constraint + (stacked5* rU 5 4); | 4.5 Angstroms + (stacked5* rC 6 5);<-' + )) + +; Pseudoknot constraint + +(define (pseudoknot-constraint? v partial-inst) + (case (var-id v) + ((18) + (let ((p (atom-pos nuc-P (get-var 19 partial-inst))) + (o3* (atom-pos nuc-O3* v))) + (FLOAT<= (pt-dist p o3*) 4.0))) + ((6) + (let ((p (atom-pos nuc-P (get-var 7 partial-inst))) + (o3* (atom-pos nuc-O3* v))) + (FLOAT<= (pt-dist p o3*) 4.5))) + (else + #t))) + +(define (pseudoknot) + (search '() pseudoknot-domains pseudoknot-constraint?)) + +; -- TESTING ----------------------------------------------------------------- + +(define (list-of-atoms n) + (append (list-of-common-atoms n) + (list-of-specific-atoms n))) + +(define (list-of-common-atoms n) + (list + (nuc-P n) + (nuc-O1P n) + (nuc-O2P n) + (nuc-O5* n) + (nuc-C5* n) + (nuc-H5* n) + (nuc-H5** n) + (nuc-C4* n) + (nuc-H4* n) + (nuc-O4* n) + (nuc-C1* n) + (nuc-H1* n) + (nuc-C2* n) + (nuc-H2** n) + (nuc-O2* n) + (nuc-H2* n) + (nuc-C3* n) + (nuc-H3* n) + (nuc-O3* n) + (nuc-N1 n) + (nuc-N3 n) + (nuc-C2 n) + (nuc-C4 n) + (nuc-C5 n) + (nuc-C6 n))) + +(define (list-of-specific-atoms n) + (cond ((rA? n) + (list + (rA-N6 n) + (rA-N7 n) + (rA-N9 n) + (rA-C8 n) + (rA-H2 n) + (rA-H61 n) + (rA-H62 n) + (rA-H8 n))) + ((rC? n) + (list + (rC-N4 n) + (rC-O2 n) + (rC-H41 n) + (rC-H42 n) + (rC-H5 n) + (rC-H6 n))) + ((rG? n) + (list + (rG-N2 n) + (rG-N7 n) + (rG-N9 n) + (rG-C8 n) + (rG-O6 n) + (rG-H1 n) + (rG-H21 n) + (rG-H22 n) + (rG-H8 n))) + (else + (list + (rU-O2 n) + (rU-O4 n) + (rU-H3 n) + (rU-H5 n) + (rU-H6 n))))) + +(define (var-most-distant-atom v) + + (define (distance pos) + (let ((abs-pos (absolute-pos v pos))) + (let ((x (pt-x abs-pos)) (y (pt-y abs-pos)) (z (pt-z abs-pos))) + (FLOATsqrt (FLOAT+ (FLOAT* x x) (FLOAT* y y) (FLOAT* z z)))))) + + (maximum (map distance (list-of-atoms (var-nuc v))))) + +(define (sol-most-distant-atom s) + (maximum (map var-most-distant-atom s))) + +(define (most-distant-atom sols) + (maximum (map sol-most-distant-atom sols))) + +(define (maximum lst) + (let loop ((m (car lst)) (l (cdr lst))) + (if (null? l) + m + (let ((x (car l))) + (loop (if (FLOAT> x m) x m) (cdr l)))))) + +(define (check) + (length (pseudoknot))) + +(define (run) + (most-distant-atom (pseudoknot))) + +; To run program, evaluate: (run) + +(run) diff --git a/tests/run-more-tests.rkt b/tests/run-more-tests.rkt index 86bce69..7eae8b2 100644 --- a/tests/run-more-tests.rkt +++ b/tests/run-more-tests.rkt @@ -49,3 +49,4 @@ (test "more-tests/graphs.rkt") (test "more-tests/scheme-whalesong.rkt") (test "more-tests/nestedloop.rkt") +(test "more-tests/nucleic2.rkt")