Well, jet-lag enables me to tinker with this script further. Now it does fitting, refinement, scoring and
sorting - not what you asked for, but it might be useful.
Paul.
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(define (mutate-poly-ala seq pdb-file-name ch-id)
(let ((imol (read-pdb pdb-file-name))) ;; or whatever
(let* ((residues (residues-in-chain imol ch-id))
(n-residues (length residues))
(resno-start (residue-spec->res-no (car residues)))
(resno-end (residue-spec->res-no (car (reverse residues))))
(n-trials (- (string-length seq) n-residues)))
(map (lambda (i-trial)
(let ((file-name (string-append "trial-" (number->string
i-trial) ".pdb"))
(mol-name (string-append "trial-" (number->string
i-trial)))
(imol-copy (copy-molecule imol))
(frag-seq (substring seq i-trial (+ i-trial
n-residues)))
(score 0)
(alt-loc "")
(ins-code ""))
(mutate-chain imol-copy ch-id frag-seq)
(for-each (lambda (res-no)
(let ((s (auto-fit-best-rotamer res-no
alt-loc ins-code ch-id imol-copy (imol-refinement-map) 1 0.5)))
(set! score (+ score s))))
(number-list resno-start resno-end))
(with-auto-accept (chain-refine imol-copy ch-id))
(set-molecule-name imol-copy mol-name)
(write-pdb-file imol-copy file-name)
(let ((c (map-to-model-correlation imol-copy residues '()
2 (imol-refinement-map))))
(list mol-name c))))
(range n-trials)))))
(let ((seq "DVSGTVCLSALPPEATDTLNLIASDGPFPYSQD") ;; or whatever
(pdb-file-name "poly-ala-frag.pdb")
(ch-id "A"))
(let ((scores (mutate-poly-ala seq pdb-file-name ch-id)))
(let ((sorted (sort scores (lambda (e1 e2) (> (cadr e1) (cadr e2))))))
(for-each (lambda (i) (format #t "sorted list: ~s~%" i)) sorted))))
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