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pdb-mode.el
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;; pdb-mode.el --- Major mode for editing Protein Data Bank files
;;; This file is not part of GNU Emacs.
;; Copyright (C) 1997 Charlie Bond, University of Sydney
;; 2000-2002 Charlie Bond, University of Dundee
;; 2000 David Love, CLRC Daresbury Laboratory (marked sections)
;; Author: C.S.Bond@dundee.ac.uk
;; X-URL: http://stein.bioch.dundee.ac.uk/~charlie/scripts/pdb-mode.el
;; Version: Major update Jan 2002
;; Keywords: data
;; This file is free software; you can redistribute it and/or modify
;; it under the terms of the GNU General Public License as published by
;; the Free Software Foundation; either version 2, or (at your option)
;; any later version.
;; This file is distributed in the hope that it will be useful,
;; but WITHOUT ANY WARRANTY; without even the implied warranty of
;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
;; GNU General Public License for more details.
;; You should have received a copy of the GNU General Public License
;; along with GNU Emacs; see the file COPYING. If not, write to
;; the Free Software Foundation, Inc., 59 Temple Place - Suite 330,
;; Boston, MA 02111-1307, USA.
;;{{{ Documentation
;;; Commentary:
;; PDB mode is set up to do a few useful things to PDB (protein databank
;; format) files.
;; Other programs (MOLEMAN and PDBSET etc) do all this and more, but not
;; within an editor.
;; To take benefit of the PDB mode, add the following
;; line to your .emacs (or get your sysadmin to
;; add it to the site-start.el) and visit a pdb file.
;; (load-file "/{path-to}/pdb-mode.el")
;; ;; Need (setq pdb-rasmol-name "\"c:/Program Files/Rasmol/rw32b2a.exe\"")
;; ;; or something similar for windows
;; (setq auto-mode-alist
;; (cons (cons "pdb$" 'pdb-mode)
;; auto-mode-alist ) )
;; (autoload 'pdb-mode "PDB")
;;; This package is known to work (insofar as it's tested) with XEmacs
;;; 20.4, XEmacs 21.1, Emacs 20.5 and Emacs 21.1.1
;;}}}
;;; Code:
(require 'easymenu)
(defvar pdb-mode nil
"This buffer specific variable tells if the pdb mode is active." )
(make-variable-buffer-local 'pdb-mode)
;; initialise menu and hooks
(defvar pdb-mode-map (make-sparse-keymap))
(defvar pdb-mode-hook nil "Mode hook for pdb-mode")
(defvar pdb-menu-hook nil "Menu hook for pdb-mode")
(defconst pdb-mode-menu-def
'("PDB"
("rna-tools ..."
["RNApuzzle ready" rna-puzzle-ready t]
)
("Select ..."
["Select chain" pdb-select-chain t]
["Select current chain" (pdb-select-chain "") t]
["Select current residue" pdb-select-residue t]
["Select zone of residues" pdb-select-zone t])
("Navigate"
["Jump to next residue" pdb-forward-residue t]
["Jump to previous residue" pdb-back-residue t]
["Jump to next chain" pdb-forward-chain t]
["Jump to previous chain" pdb-back-chain t])
("Change Values"
["Set alternate conformer" pdb-change-alternate t]
["Set B-factor" pdb-change-bfactor t]
["Set chain ID" pdb-change-chain t]
["Set atom name" pdb-change-name t]
["Set occupancy" pdb-change-occu t]
["Set residue number" pdb-change-residue t]
["Set SEGID" pdb-change-segid t]
["Set residue type" pdb-change-type t]
["Mutate residue(s)" pdb-change-mutate t]
["Convert frac->orth" pdb-change-frac2orth t]
["Convert orth->frac" pdb-change-orth2frac t]
)
("Increment Values"
["Add value to B-factor" pdb-increment-bfactor t]
["Change centroid" pdb-increment-centroid t]
["Add value to residue number" pdb-increment-residue t]
["Add vector to xyz (orthogonal)" pdb-increment-xyz t]
["Add vector to xyz (fractional)" pdb-increment-fractional t]
["Scale coordinates" pdb-scale-xyz t]
["Scale B-factors" pdb-scale-bfactor t]
["Rotate xyz by 3x3 matrix" pdb-increment-matrix t]
["Rotate xyz by Euler triplet" pdb-increment-euler t])
("Renumber"
["Consecutive atom numbers" pdb-renumber-atoms t]
["Consecutive water residue numbers" pdb-renumber-waters t])
("Tidy Up"
["Remove non-protein atoms" pdb-tidy-amino t]
["Convert ATOM -> HETATM" pdb-tidy-atom2hetatm t]
["Reduce to CA only" pdb-tidy-ca t]
["Remove hydrogens" pdb-tidy-dehydrogenate t]
["Convert HETATM -> ATOM" pdb-tidy-hetatm2atom t]
["Cut back to poly-ALA/GLY" pdb-tidy-polyalanine t]
["Remove all but ATOM/HETATM records" pdb-tidy-xyz t])
("New..."
["amino acid(s)" pdb-new-sequence t]
["DNA base(s)" pdb-new-dnaseq t]
["PDB entry" pdb-new-pdb t]
("HICUP compound"
["User defined..." pdb-new-hicup t]
["Selenomethionine" (pdb-new-hicup "mse") t]
("Nucleotide"
["ATP" (pdb-new-hicup "atp") t]
["ADP" (pdb-new-hicup "adp") t]
["AMP" (pdb-new-hicup "amp") t]
["CTP" (pdb-new-hicup "ctp") t]
["CDP" (pdb-new-hicup "cdp") t]
["CMP" (pdb-new-hicup "cmp") t]
["GTP" (pdb-new-hicup "gtp") t]
["GDP" (pdb-new-hicup "gdp") t]
["GMP" (pdb-new-hicup "gmp") t]
["NAD" (pdb-new-hicup "nad") t]
["NADP+" (pdb-new-hicup "nap") t]
["NADPH" (pdb-new-hicup "ndp") t]
["S-adenosylmethionine" (pdb-new-hicup "sam") t]
["FAD" (pdb-new-hicup "fad") t])
("Sugar"
["Glucose" (pdb-new-hicup "glc") t]
["Linear glucose" (pdb-new-hicup "glo") t]
["n-Glycosyl chain" (pdb-new-hicup "asf") t]
["NAG (N-acetyl glucosamine)" (pdb-new-hicup "nag") t]
["Fructose" (pdb-new-hicup "fru") t]
["Sucrose" (pdb-new-hicup "suc") t]
["Fucose" (pdb-new-hicup "fuc") t]
["Inositol hexaphosphate" (pdb-new-hicup "ihp") t])
("Small"
["Sodium" (pdb-new-hicup "na") t]
["Calcium" (pdb-new-hicup "ca") t]
["Magnesium" (pdb-new-hicup "mg") t]
["Zinc" (pdb-new-hicup "zn") t]
["Iron" (pdb-new-hicup "fe") t]
["Mercury" (pdb-new-hicup "hg") t]
["Chloride" (pdb-new-hicup "cl") t]
["Oxygen molecule" (pdb-new-hicup "o2") t]
["Ammonium (NH4+)" (pdb-new-hicup "nh4") t]
["Carbon dioxide" (pdb-new-hicup "co2") t]
["Acetate" (pdb-new-hicup "acy") t]
["Acetone" (pdb-new-hicup "acn") t]
["Sulfate (SO4)" (pdb-new-hicup "so4") t]
["Sulfite (SO3)" (pdb-new-hicup "so3") t]
["Azide" (pdb-new-hicup "azi") t]
["Phosphate" (pdb-new-hicup "po4") t]
["Nitrate" (pdb-new-hicup "no3") t]
["DMSO (dimethyl sulfoxide)" (pdb-new-hicup "dms") t]
["Urea" (pdb-new-hicup "ure") t])
("Organic"
["Citrate" (pdb-new-hicup "cit") t]
["Ascorbate" (pdb-new-hicup "asc") t]
["Salicylic acid" (pdb-new-hicup "sal") t]
["Tartaric acid" (pdb-new-hicup "tar") t]
["Benzoic acid" (pdb-new-hicup "box") t]
["Succinic acid" (pdb-new-hicup "sin") t]
["6-Amino hexanoic acid" (pdb-new-hicup "aha") t]
["2-Phenylethylamine" (pdb-new-hicup "pea") t]
["Beta-mercaptoethanol" (pdb-new-hicup "bme") t]
["DTT (1,4-dithiothreitol)" (pdb-new-hicup "dtt") t]
["Ethanol" (pdb-new-hicup "eoh") t]
["2-Propanol" (pdb-new-hicup "ipa") t]
["Ethanediol" (pdb-new-hicup "edo") t]
["MPD (2-methyl-2,4-pentanediol)" (pdb-new-hicup "mpd") t]
["Glycerol" (pdb-new-hicup "gol") t]
["Retinol" (pdb-new-hicup "rtl") t]
["Methylparaben" (pdb-new-hicup "mpb") t]
["Tylenol" (pdb-new-hicup "tyl") t]
["Camphor" (pdb-new-hicup "cam") t]
["Tris (tromethamine)" (pdb-new-hicup "trs") t])
("Miscellaneous"
["Aminopyridine" (pdb-new-hicup "4ap") t]
["Isoquinoline" (pdb-new-hicup "isq") t]
["AlF3" (pdb-new-hicup "af3") t]
["AlF4-" (pdb-new-hicup "alf") t]
["SC-58272 synthetic peptidic inhibitor" (pdb-new-hicup "mim") t]
["N1-carboxypiperazine" (pdb-new-hicup "bzp") t]
["4-(Acetylamino)-3-amino benzoic acid" (pdb-new-hicup "st3") t]
["Porphyrin Fe(III)" (pdb-new-hicup "por") t])
))
("Miscellaneous"
[" Open in PYMOL" pdb-view t]
[" Toggle Fontification" (font-lock-mode) :style toggle :selected font-lock-mode])))
;; initialise some variables
(eval-when-compile
(defvar pdb-start-user-region nil "PDB Mode: Used by some functions")
(defvar pdb-end-user-region nil "PDB Mode: Used by some functions")
(defvar pdb-rasmol-name "rasmol" "PDB Mode: Full path to rasmol executable (only necessary if typing rasmol in a shell doesn't work. In Windows \(setq pdb-rasmol-name \"c:/Program Files/Rasmol/rw32b2a.exe\"\) or something similar to .emacs for windows")
(defvar pdb-rasmol-filestamp nil "PDB Mode: Temporary filename for rasmol display. Of the form (concat (getenv \"PWD\") \"/#TMP-emacs-rasmol\" (number-to-string (elt (current-time) 1)) (number-to-string (emacs-pid)) \"#\")))")
(defvar pdb-amino-lookup nil "PDB Mode: Lookup table to convert single-letter to three-letter amino acid codes")
(defvar pdb-record-lookup nil "PDB Mode: Lookup table to access side-chain PDB coordinates for amino acids from their three-letter code.")
(defvar pdb-mode-syntax-table nil "Syntax table in use in set file mode buffers.")
(defvar pdb-font-lock-keywords nil "Table of set file font lock keywords."))
;; Default binding for pdb-rasmol-name
;; Need to add (setq pdb-rasmol-name "\"c:/Program Files/Rasmol/rw32b2a.exe\"")
;; or something similar to .emacs for windows
(unless (boundp 'pdb-rasmol-name)
(setq pdb-rasmol-name "pymol"))
;; Some necessary data
(setq pdb-amino-lookup '(("A" . "ALA") ("C" . "CYS") ("D" . "ASP") ("E" . "GLU") ("F" . "PHE") ("G" . "GLY") ("H" . "HIS") ("I" . "ILE") ("K" . "LYS") ("L" . "LEU") ("M" . "MET") ("N" . "ASN") ("P" . "PRO") ("Q" . "GLN") ("R" . "ARG") ("S" . "SER") ("T" . "THR") ("V" . "VAL") ("W" . "TRP") ("Y" . "TYR") ("dA" . "A ") ("dG" . "G ") ("dT" . "T ") ("dC" . "C ")))
(setq pdb-record-lookup '(("ALA" .
"ATOM 2 CB ALA A 1 -0.532 -0.774 -1.196 1.00 20.00 C\n")
("ARG" .
"ATOM 1 CB ARG A 1 -0.526 -0.779 -1.207 1.00 20.00 C
ATOM 1 CG ARG A 1 -2.041 -0.900 -1.254 1.00 20.00 C
ATOM 1 CD ARG A 1 -2.494 -1.684 -2.476 1.00 20.00 C
ATOM 1 NE ARG A 1 -3.946 -1.811 -2.537 1.00 20.00 N
ATOM 1 CZ ARG A 1 -4.600 -2.437 -3.509 1.00 20.00 C
ATOM 1 NH1 ARG A 1 -3.929 -3.023 -4.492 1.00 20.00 N
ATOM 1 NH2 ARG A 1 -5.923 -2.518 -3.476 1.00 20.00 N\n")
("ASN" .
"ATOM 1 CB ASN A 1 -0.526 -0.778 -1.208 1.00 20.00 C
ATOM 1 CG ASN A 1 -2.037 -0.888 -1.218 1.00 20.00 C
ATOM 1 OD1 ASN A 1 -2.638 -1.406 -0.276 1.00 20.00 O
ATOM 1 ND2 ASN A 1 -2.663 -0.345 -2.255 1.00 20.00 N\n")
("ASP" .
"ATOM 1 CB ASP A 1 -0.526 -0.779 -1.207 1.00 20.00 C
ATOM 1 CG ASP A 1 -2.039 -0.881 -1.221 1.00 20.00 C
ATOM 1 OD1 ASP A 1 -2.585 -1.504 -2.156 1.00 20.00 O
ATOM 1 OD2 ASP A 1 -2.680 -0.356 -0.287 1.00 20.00 O\n")
("CYS" .
"ATOM 1 CB CYS A 1 -0.526 -0.779 -1.207 1.00 20.00 C
ATOM 1 SG CYS A 1 -2.327 -0.928 -1.273 1.00 20.00 S\n")
("GLN" .
"ATOM 1 CB GLN A 1 -0.526 -0.778 -1.208 1.00 20.00 C
ATOM 1 CG GLN A 1 -2.039 -0.907 -1.254 1.00 20.00 C
ATOM 1 CD GLN A 1 -2.522 -1.683 -2.462 1.00 20.00 C
ATOM 1 OE1 GLN A 1 -2.803 -1.106 -3.513 1.00 20.00 O
ATOM 1 NE2 GLN A 1 -2.663 -2.995 -2.307 1.00 20.00 N\n")
("GLU" .
"ATOM 1 CB GLU A 1 -0.525 -0.778 -1.208 1.00 20.00 C
ATOM 1 CG GLU A 1 -2.039 -0.902 -1.255 1.00 20.00 C
ATOM 1 CD GLU A 1 -2.523 -1.677 -2.465 1.00 20.00 C
ATOM 1 OE1 GLU A 1 -2.792 -1.045 -3.508 1.00 20.00 O
ATOM 1 OE2 GLU A 1 -2.679 -2.911 -2.359 1.00 20.00 O\n")
("GLY" .
"")
("HIS" .
"ATOM 1 CB HIS A 1 -0.525 -0.779 -1.208 1.00 20.00 C
ATOM 1 CG HIS A 1 -2.017 -0.903 -1.245 1.00 20.00 C
ATOM 1 ND1 HIS A 1 -2.826 0.022 -1.867 1.00 20.00 N
ATOM 1 CE1 HIS A 1 -4.089 -0.341 -1.737 1.00 20.00 C
ATOM 1 NE2 HIS A 1 -4.129 -1.468 -1.049 1.00 20.00 N
ATOM 1 CD2 HIS A 1 -2.846 -1.841 -0.728 1.00 20.00 C\n")
("ILE" .
"ATOM 1 CB ILE A 1 -0.504 -0.800 -1.215 1.00 20.00 C
ATOM 1 CG1 ILE A 1 -2.032 -0.886 -1.201 1.00 20.00 C
ATOM 1 CG2 ILE A 1 0.111 -2.191 -1.229 1.00 20.00 C
ATOM 1 CD1 ILE A 1 -2.612 -1.659 -2.365 1.00 20.00 C\n")
("LEU" .
"ATOM 1 CB LEU A 1 -0.525 -0.777 -1.209 1.00 20.00 C
ATOM 1 CG LEU A 1 -2.045 -0.935 -1.304 1.00 20.00 C
ATOM 1 CD1 LEU A 1 -2.727 0.424 -1.304 1.00 20.00 C
ATOM 1 CD2 LEU A 1 -2.425 -1.730 -2.544 1.00 20.00 C\n")
("LYS" .
"ATOM 1 CB LYS A 1 -0.526 -0.781 -1.206 1.00 20.00 C
ATOM 1 CG LYS A 1 -2.041 -0.890 -1.262 1.00 20.00 C
ATOM 1 CD LYS A 1 -2.494 -1.671 -2.486 1.00 20.00 C
ATOM 1 CE LYS A 1 -4.008 -1.792 -2.534 1.00 20.00 C
ATOM 1 NZ LYS A 1 -4.466 -2.556 -3.727 1.00 20.00 N\n")
("MET" .
"ATOM 1 CB MET A 1 -0.525 -0.780 -1.206 1.00 20.00 C
ATOM 1 CG MET A 1 -2.039 -0.908 -1.252 1.00 20.00 C
ATOM 1 SD MET A 1 -2.617 -1.831 -2.688 1.00 20.00 S
ATOM 1 CE MET A 1 -4.389 -1.785 -2.430 1.00 20.00 C
ATOM 1 SE MET A 1 -2.652 -1.887 -2.776 1.00 20.00 S
ATOM 1 CE2 MET A 1 -4.533 -1.839 -2.502 1.00 20.00 C\n")
("PHE" .
"ATOM 1 CB PHE A 1 -0.525 -0.779 -1.208 1.00 20.00 C
ATOM 1 CG PHE A 1 -2.023 -0.890 -1.253 1.00 20.00 C
ATOM 1 CD1 PHE A 1 -2.784 0.081 -1.880 1.00 20.00 C
ATOM 1 CE1 PHE A 1 -4.161 -0.024 -1.934 1.00 20.00 C
ATOM 1 CZ PHE A 1 -4.794 -1.087 -1.322 1.00 20.00 C
ATOM 1 CE2 PHE A 1 -4.048 -2.050 -0.672 1.00 20.00 C
ATOM 1 CD2 PHE A 1 -2.672 -1.940 -0.624 1.00 20.00 C\n")
("PRO" .
"ATOM 1 CB PRO A 1 -0.525 -0.582 -1.313 1.00 20.00 C
ATOM 1 CG PRO A 1 -1.785 0.165 -1.573 1.00 20.00 C
ATOM 1 CD PRO A 1 -1.548 1.557 -1.063 1.00 20.00 C\n")
("SER" .
"ATOM 1 CB SER A 1 -0.526 -0.778 -1.207 1.00 20.00 C
ATOM 1 OG SER A 1 -0.146 -0.155 -2.421 1.00 20.00 O\n")
("THR" .
"ATOM 1 CB THR A 1 -0.504 -0.800 -1.216 1.00 20.00 C
ATOM 1 OG1 THR A 1 -0.087 -0.151 -2.424 1.00 20.00 O
ATOM 1 CG2 THR A 1 -2.021 -0.899 -1.197 1.00 20.00 C\n")
("TRP" .
"ATOM 1 CB TRP A 1 -0.525 -0.777 -1.208 1.00 20.00 C
ATOM 1 CG TRP A 1 -2.019 -0.894 -1.243 1.00 20.00 C
ATOM 1 CD1 TRP A 1 -2.895 -0.028 -1.831 1.00 20.00 C
ATOM 1 NE1 TRP A 1 -4.184 -0.464 -1.649 1.00 20.00 N
ATOM 1 CE2 TRP A 1 -4.161 -1.635 -0.937 1.00 20.00 C
ATOM 1 CZ2 TRP A 1 -5.210 -2.445 -0.505 1.00 20.00 C
ATOM 1 CH2 TRP A 1 -4.888 -3.567 0.205 1.00 20.00 C
ATOM 1 CZ3 TRP A 1 -3.556 -3.890 0.499 1.00 20.00 C
ATOM 1 CE3 TRP A 1 -2.514 -3.089 0.069 1.00 20.00 C
ATOM 1 CD2 TRP A 1 -2.814 -1.925 -0.646 1.00 20.00 C\n")
("TYR" .
"ATOM 1 CB TYR A 1 -0.525 -0.779 -1.207 1.00 20.00 C
ATOM 1 CG TYR A 1 -2.033 -0.894 -1.254 1.00 20.00 C
ATOM 1 CD1 TYR A 1 -2.799 0.051 -1.923 1.00 20.00 C
ATOM 1 CE1 TYR A 1 -4.177 -0.052 -1.971 1.00 20.00 C
ATOM 1 CZ TYR A 1 -4.802 -1.121 -1.366 1.00 20.00 C
ATOM 1 CE2 TYR A 1 -4.061 -2.087 -0.720 1.00 20.00 C
ATOM 1 CD2 TYR A 1 -2.684 -1.975 -0.676 1.00 20.00 C
ATOM 1 OH TYR A 1 -6.173 -1.228 -1.413 1.00 20.00 O\n")
("VAL" .
"ATOM 1 CB VAL A 1 -0.504 -0.802 -1.214 1.00 20.00 C
ATOM 1 CG1 VAL A 1 0.110 -2.194 -1.227 1.00 20.00 C
ATOM 1 CG2 VAL A 1 -2.023 -0.883 -1.206 1.00 20.00 C\n")
("A " .
"ATOM 1 N9 A A 1 0.213 0.660 1.287 1.00 20.00
ATOM 2 C4 A A 1 0.250 2.016 1.509 1.00 20.00
ATOM 3 N3 A A 1 0.016 2.995 0.619 1.00 20.00
ATOM 4 C2 A A 1 0.142 4.189 1.194 1.00 20.00
ATOM 5 N1 A A 1 0.451 4.493 2.459 1.00 20.00
ATOM 6 C6 A A 1 0.681 3.485 3.329 1.00 20.00
ATOM 7 N6 A A 1 0.990 3.787 4.592 1.00 20.00
ATOM 8 C5 A A 1 0.579 2.170 2.844 1.00 20.00
ATOM 9 N7 A A 1 0.747 0.934 3.454 1.00 20.00
ATOM 10 C8 A A 1 0.520 0.074 2.491 1.00 20.00\n")
("C " .
"ATOM 1 N1 C A 1 0.212 0.668 1.294 1.00 20.00
ATOM 2 C6 C A 1 0.193 -0.043 2.462 1.00 20.00
ATOM 3 C2 C A 1 0.374 2.055 1.315 1.00 20.00
ATOM 4 O2 C A 1 0.388 2.673 0.240 1.00 20.00
ATOM 5 N3 C A 1 0.511 2.687 2.504 1.00 20.00
ATOM 6 C4 C A 1 0.491 1.984 3.638 1.00 20.00
ATOM 7 N4 C A 1 0.631 2.649 4.788 1.00 20.00
ATOM 8 C5 C A 1 0.328 0.569 3.645 1.00 20.00\n")
("G " .
"ATOM 1 N9 G A 1 0.214 0.659 1.283 1.00 20.00
ATOM 2 C4 G A 1 0.254 2.014 1.509 1.00 20.00
ATOM 3 N3 G A 1 0.034 2.979 0.591 1.00 20.00
ATOM 4 C2 G A 1 0.142 4.190 1.110 1.00 20.00
ATOM 5 N2 G A 1 -0.047 5.269 0.336 1.00 20.00
ATOM 6 N1 G A 1 0.444 4.437 2.427 1.00 20.00
ATOM 7 C6 G A 1 0.676 3.459 3.389 1.00 20.00
ATOM 8 O6 G A 1 0.941 3.789 4.552 1.00 20.00
ATOM 9 C5 G A 1 0.562 2.154 2.846 1.00 20.00
ATOM 10 N7 G A 1 0.712 0.912 3.448 1.00 20.00
ATOM 11 C8 G A 1 0.498 0.057 2.485 1.00 20.00\n")
("T " .
"ATOM 1 N1 T A 1 0.214 0.668 1.296 1.00 20.00
ATOM 2 C6 T A 1 0.171 -0.052 2.470 1.00 20.00
ATOM 3 C2 T A 1 0.374 2.035 1.303 1.00 20.00
ATOM 4 O2 T A 1 0.416 2.705 0.284 1.00 20.00
ATOM 5 N3 T A 1 0.483 2.592 2.553 1.00 20.00
ATOM 6 C4 T A 1 0.449 1.933 3.767 1.00 20.00
ATOM 7 O4 T A 1 0.560 2.568 4.812 1.00 20.00
ATOM 8 C5 T A 1 0.279 0.500 3.685 1.00 20.00
ATOM 9 C5A T A 1 0.231 -0.299 4.949 1.00 20.00\n")
("U " .
"ATOM 5 N1 U A 1 0.212 0.676 1.281 1.00 20.00
ATOM 6 C6 U A 1 0.195 -0.023 2.466 1.00 20.00
ATOM 7 C2 U A 1 0.370 2.048 1.265 1.00 20.00
ATOM 8 O2 U A 1 0.390 2.698 0.235 1.00 20.00
ATOM 9 N3 U A 1 0.505 2.629 2.502 1.00 20.00
ATOM 11 C4 U A 1 0.497 1.990 3.725 1.00 20.00
ATOM 12 O4 U A 1 0.629 2.653 4.755 1.00 20.00
ATOM 13 C5 U A 1 0.329 0.571 3.657 1.00 20.00\n")
))
;; Set up font lock
(setq pdb-mode-syntax-table (make-syntax-table (standard-syntax-table)))
(make-face 'pdb-key1-face)
(set-face-background 'pdb-key1-face "dim gray")
(make-face 'pdb-comment-face)
(set-face-foreground 'pdb-comment-face "dark gray")
(if (string-match "GNU" (emacs-version))
(progn
(setq pdb-font-lock-keywords
(list
'("\\(^ATOM..\\|HETATM\\).....\\(.\\)....\\(.\\)...\\(.\\).\\(....\\)............\\(........\\)........\\(......\\)......\\(......\\)" (1 'pdb-key1-face) (2 'pdb-key1-face) (3 'pdb-key1-face) (4 'pdb-key1-face) (5 'pdb-key1-face) (6 'pdb-key1-face) (7 'pdb-key1-face) (8 'pdb-key1-face nil t))
'("\\(^\\([B-G]\\|[I-Z]\\|AU\\|HE[AL]\\).*$\\)" 1 'pdb-comment-face t))))
)
(if (string-match "XEmacs" (emacs-version))
(progn
(setq pdb-font-lock-keywords
(list
'("^\\(^ATOM..\\|HETATM\\).\\{74\\}\\(.\\{2\\}\\)" 2 pdb-key1-face t)
'("^\\(^ATOM..\\|HETATM\\).\\{70\\}\\(.\\{2\\}\\)" 2 pdb-key1-face t)
'("^\\(^ATOM..\\|HETATM\\).\\{60\\}\\(.\\{6\\}\\)" 2 pdb-key1-face t)
'("^\\(^ATOM..\\|HETATM\\).\\{48\\}\\(.\\{6\\}\\)" 2 pdb-key1-face t)
'("^\\(^ATOM..\\|HETATM\\).\\{32\\}\\(.\\{8\\}\\)" 2 pdb-key1-face t)
'("^\\(^ATOM..\\|HETATM\\).\\{16\\}\\(.\\{4\\}\\)" 2 pdb-key1-face t)
'("^\\(^ATOM..\\|HETATM\\).\\{14\\}\\(.\\{1\\}\\)" 2 pdb-key1-face t)
'("^\\(^ATOM..\\|HETATM\\).\\{10\\}\\(.\\{1\\}\\)" 2 pdb-key1-face t)
'("^\\(^ATOM..\\|HETATM\\).\\{5\\}\\(.\\{1\\}\\)" 2 pdb-key1-face t)
'("\\(^ATOM..\\|HETATM\\)" 1 pdb-key1-face t)
'("\\(^\\([B-G]\\|[I-Z]\\|AU\\|HE[AL]\\).*$\\)" 1 pdb-comment-face t)))
(add-hook 'pdb-mode-hook (function
(lambda()
(setq font-lock-mode-disable-list
(cons 'pdb-mode font-lock-mode-disable-list)))))))
;;Final blast of commands on startup
(add-hook 'pdb-mode-hook (function
(lambda()
;; If CRYST1 card is present, set pdb-cell-local as a list of 6 numbers
;; Spacegroup will be picked up too if present.
(save-excursion
(goto-char (point-min))
(if (re-search-forward "^CRYST1" nil t)
(let ((str (buffer-substring (+ (point-at-bol) 7) (+ (point-at-bol) 55))))
(string-match "[0-9].*[0-9]" str)
(let ((str (split-string (match-string 0 str))))
(setq pdb-cell-local (list (string-to-number (elt str 0)) (string-to-number (elt str 1)) (string-to-number (elt str 2)) (string-to-number (elt str 3)) (string-to-number (elt str 4)) (string-to-number (elt str 5)))))
(setq pdb-spacegroup-local (buffer-substring (+ (point-at-bol) 55) (+ (point-at-bol) 64)))
(if (eq (elt pdb-orth2frac-local 0) 0)
(progn
(pdb-sub-orth2frac)
(pdb-sub-frac2orth)))))))))
;; PDB-MODE
(defun pdb-mode ()
"PDB mode is set up to do a few useful things to PDB (protein databank
format) files.
Other programs (MOLEMAN and PDBSET etc) do all this and more, but not
within an editor.
pdb-mode commands can be accessed from the menu bar PDB or from the minibuffer
(M-x pdb SPACE gives you a list of commands).
Some mouse/key bindings aid PDB file navigation:
C-middlemouse selects residue where button clicked.
C-pageup and C-pagedown jump to the previous/next residue.
C-M-pageup and C-M-pagedown jump to the previous/next chain."
(interactive)
;; Set up mode stuff
(kill-all-local-variables)
(setq mode-name "PDB")
(setq major-mode 'pdb-mode)
(setq kill-whole-line t)
;; Set up menu stuff
(use-local-map pdb-mode-map)
(easy-menu-define pdb-mode-menu pdb-mode-map "Emacs menu for PDB mode"
pdb-mode-menu-def)
;; Need this for Xemacs
(easy-menu-add pdb-mode-menu)
;; Customise tabbing to match PDB definition - David Love
(set (make-local-variable 'indent-line-function) #'tab-to-tab-stop)
(set (make-local-variable 'tab-stop-list)
'(;; ATOM
6 ; serial no.
11 ; Chemical symbol
14 ; Remoteness indicator
15 ; Branch designator
16 ; Alternate location indicator
17 ; Residue name
20 ; Reserved
21 ; Chain identifier
22 ; Residue sequence number
26 ; Code for inserting residue
27 ; Reserved
30 ; X
38 ; Y
46 ; Z
54 ; Pdb-Occupancy
60 ; Isotropic B-factor
66 ; Reserved
72 ; Segment identifier
76 ; Element symbol
78 ; Charge on atom
80
))
;; Redefine some keys for easy navigation
(local-set-key '[(control tab)] 'move-to-tab-stop)
(local-set-key '[(control next)] 'pdb-forward-residue)
(local-set-key '[(control prior)] 'pdb-back-residue)
(local-set-key '[(control meta next)] 'pdb-forward-chain)
(local-set-key '[(control meta prior)] 'pdb-back-chain)
;; Setup unit cell data - used for fractional coordinates
(set (make-local-variable 'pdb-cell-local) (make-list 6 0))
(set (make-local-variable 'pdb-spacegroup-local) "")
(set (make-local-variable 'pdb-orth2frac-local) (make-list 9 0))
(set (make-local-variable 'pdb-frac2orth-local) (make-list 9 0))
;; Some things are handled differently in GNU- and X-emacs
(if (string-match "XEmacs" (emacs-version))
(progn (redraw-modeline)
(setq zmacs-region-stays t )
;; Bind C-mouse2 to select clicked residue
(define-key pdb-mode-map [(control button2)] 'pdb-sub-mouse-cmouse2)
;; Bind C-Mmouse2 to select clicked chain
(define-key pdb-mode-map [(control meta button2)] 'pdb-sub-mouse-cmmouse2)
;; Setup Popup menu
(if (boundp 'mode-popup-menu)
(setq mode-popup-menu
(cons (concat mode-name " Mode Commands") pdb-mode-menu)))))
(if (string-match "GNU Emacs" (emacs-version))
(progn
;; Get font-lock to work
(make-local-variable 'font-lock-defaults)
(setq font-lock-defaults '(pdb-font-lock-keywords nil nil ((?_ . "w"))))
;; Bind C-mouse2 to select clicked residue
(define-key pdb-mode-map [(control down-mouse-2)] 'pdb-sub-mouse-cmouse2)
;; Bind C-mmouse2 to select clicked chain
(define-key pdb-mode-map [(control meta down-mouse-2)] 'pdb-sub-mouse-cmmouse2)
;; Some aliases
(defalias 'point-at-bol 'line-beginning-position)
(defalias 'point-at-eol 'line-end-position)
(defun activate-region ()
(exchange-point-and-mark)
(exchange-point-and-mark))))
;; Individual Functions:
;; SELECT...
(defun pdb-select-chain (pdb-test-string)
"PDB mode: Select current chain\n"
(interactive "sWhich chain ?(1 char. RET signifies current chain):")
(if (= 0 (length pdb-test-string))
(progn
(goto-char (point-at-bol))
(re-search-forward "^\\(ATOM \\|HETATM\\|ANISOU\\)" nil t)
(setq pdb-test-string (buffer-substring (+ (point-at-bol) 21) (+ (point-at-bol) 22)))))
(pdb-sub-selectlocal (concat "..............." pdb-test-string)))
(defun pdb-select-residue ( )
"PDB mode: Select current residue"
(interactive "")
(let ((str (concat "..........." (buffer-substring (+ (point-at-bol) 17) (+ (point-at-bol) 26)))))
(pdb-sub-selectlocal str)))
(defun pdb-select-zone (pdb-test-string)
"PDB mode: Select zone"
(interactive "sEnter zone ([Chain][Res1] [Chain][Res2]):")
(let (
(vec (split-string pdb-test-string))
(start-chain " ")
(end-chain " ")
(start-number 0)
(end-number 0)
(str ""))
;; Input is a 2 element array - need to grok chain and numbers from it
(if (string-match "^[A-Z]" (elt vec 0))
(setq start-chain (match-string 0 (elt vec 0))))
(if (string-match "^[A-Z]" (elt vec 1))
(setq pdb-end-chain (match-string 0 (elt vec 1))))
(string-match "[-0-9]*$" (elt vec 0))
(setq start-number (match-string 0 (elt vec 0)))
(string-match "[-0-9]*$" (elt vec 1))
(setq pdb-end-number (match-string 0 (elt vec 1)))
;; Find the ends
(goto-char (point-min))
(setq str (concat "^\\(ATOM \\|HETATM\\)..............." start-chain (format "%4d" (string-to-number start-number))))
(re-search-forward str nil (point) nil)
(setq pdb-start-user-region (point-at-bol))
(setq str (concat "^\\(ATOM \\|HETATM\\)..............." pdb-end-chain (format "%4d" (string-to-number pdb-end-number))))
(goto-char (point-max))
(re-search-backward str nil (point) nil))
(setq pdb-end-user-region (+ (point-at-eol) 1))
(pdb-sub-markregion))
;; NAVIGATE
(defun pdb-forward-residue ( )
"PDB mode: Jump to start of next residue"
(interactive "")
(let ((str (concat "..... ....." (buffer-substring (+ (point-at-bol) 17) (+ (point-at-bol) 26)))))
(re-search-forward "^\\(ATOM \\|HETATM\\)" nil t)
(goto-char (point-at-bol))
;; elisp has no not (regexp) search, so this is complicated
(while (progn
(re-search-forward "^\\(ATOM \\|HETATM\\)" (point-max) (point) nil)
(cond ((not (looking-at str))
(progn
(goto-char (point-at-bol)))
nil)
(t)))))
(goto-char (point-at-bol))
(activate-region)
)
(defun pdb-forward-chain ( )
"PDB mode: Jump to start of next chain"
(interactive "")
(let ((str (concat "..............." (buffer-substring (+ (point-at-bol) 21) (+ (point-at-bol) 22)))))
(re-search-forward "^\\(ATOM \\|HETATM\\)" nil t)
(goto-char (point-at-bol))
(while (progn
(re-search-forward "^\\(ATOM \\|HETATM\\)" (point-max) (point) nil)
(cond ((not (looking-at str))
(progn
;; roll back to previous matching residue
(goto-char (point-at-bol)))
nil)
(t)))))
(setq pdb-end-user-region (point-at-bol))
;; mark out region
(goto-char pdb-end-user-region)
(activate-region))
(defun pdb-back-residue ( )
"PDB mode: Jump to start of current/previous residue"
(interactive "")
(re-search-backward "^\\(ATOM \\|HETATM\\)" nil t )
(let ((str (concat "................." (buffer-substring (+ (point-at-bol) 17) (+ (point-at-bol) 26)))))
(while (and
(re-search-backward "^\\(ATOM \\|HETATM\\)" nil t )
(looking-at str)))
(if (not (looking-at str)) (re-search-forward "^\\(ATOM \\|HETATM\\)" nil t 2)))
(setq pdb-end-user-region (point-at-bol))
(goto-char pdb-end-user-region)
(activate-region))
(defun pdb-back-chain ( )
"PDB mode: Jump to start of current/previous chain"
(interactive "")
(re-search-backward "^\\(ATOM \\|HETATM\\)" nil t )
(let ((str (concat "....................." (buffer-substring (+ (point-at-bol) 21) (+ (point-at-bol) 22)))))
(while (and
(re-search-backward "^\\(ATOM \\|HETATM\\)" nil t )
(looking-at str)))
(if (not (looking-at str)) (re-search-forward "^\\(ATOM \\|HETATM\\)" nil t 2)))
(setq pdb-end-user-region (point-at-bol))
(goto-char pdb-end-user-region)
(activate-region))
;; CHANGE VALUES
(defun pdb-change-bfactor (b e pdb-test-number)
"PDB mode: Change selected B-factors to requested value"
(interactive "r\nnRequested B-factor (max 999.99): ")
(if (> pdb-test-number 999.99) (error "ERROR[PDB]: Number too big"))
(if ( < pdb-test-number 0) (setq pdb-test-number 20 ))
(setq pdb-test-number (format "%6.2f" pdb-test-number))
(pdb-sub-defineregion b e)
(pdb-sub-change pdb-test-number 60 6)
(pdb-sub-markregion))
(defun pdb-change-occu (b e pdb-test-number)
"PDB mode: Change occupancy to requested value"
(interactive "r\nnRequested occupancy: ")
(if (> pdb-test-number 99.99) (error "ERROR[PDB]: Number too big"))
(if (> pdb-test-number 1) (print "WARNING: Occupancy greater than 1.00" t))
(if (< pdb-test-number 0) (setq pdb-test-number "0.00" ))
(setq pdb-test-number (format "%5.2f" pdb-test-number))
(pdb-sub-defineregion b e)
(pdb-sub-change pdb-test-number 55 5)
(pdb-sub-markregion))
(defun pdb-change-alternate (b e pdb-test-string)
"PDB mode: Change alternate conformation ID of selected atoms"
(interactive "r \ns:Alternate ID: ")
(if (= (length pdb-test-string) 0)
(error "ERROR[PDB]: One character please - try again"))
(setq pdb-test-string (upcase (substring pdb-test-string 0 1)))
(pdb-sub-defineregion b e)
(pdb-sub-change pdb-test-string 16 1)
(pdb-sub-markregion))
(defun pdb-change-chain (b e pdb-test-string)
"PDB mode: Change chain ID of selected atoms"
(interactive "r \nsChain ID: ")
(if (= (length pdb-test-string) 0)
(error "ERROR[PDB]: One character please - try again"))
(setq pdb-test-string (upcase (substring pdb-test-string 0 1)))
(pdb-sub-defineregion b e)
(pdb-sub-change pdb-test-string 21 1)
(pdb-sub-markregion))
(defun pdb-change-name (b e pdb-test-string)
"PDB mode: Change selected atom names"
(interactive "r \nsAtom Name (4 chars, space first if not metal): ")
(if (/= (length pdb-test-string) 4)
(error "ERROR[PDB]: 4 characters please. Space first if not a metal"))
(setq pdb-test-string (upcase pdb-test-string))
(pdb-sub-defineregion b e)
(pdb-sub-change pdb-test-string 12 4)
(pdb-sub-markregion))
(defun pdb-change-residue (b e pdb-test-number)
"PDB mode: Change residue number to given value"
(interactive "r \nnNew residue number:")
(setq pdb-test-number (format "%4d" pdb-test-number))
(pdb-sub-defineregion b e )
(pdb-sub-change pdb-test-number 22 4)
(pdb-sub-markregion))
(defun pdb-change-segid (b e pdb-test-string)
"PDB mode: Add SEGID to selected atoms"
(interactive "r \nsSEGID: ")
(if ( = (length pdb-test-string) 0)
(setq pdb-test-string (buffer-substring (+ (point-at-bol) 21) (+ (point-at-bol) 22))))
(setq pdb-test-string (upcase pdb-test-string))
(setq pdb-test-string (format "%-4s" pdb-test-string))
(pdb-sub-defineregion b e )
(pdb-sub-change pdb-test-string 72 4)
(pdb-sub-markregion))
(defun pdb-change-type (b e pdb-test-string)
"PDB mode: Change residue type of selected atoms"
(interactive "r \nsNew Residue type: ")
(if (< (length pdb-test-string) 3)
(error "ERROR[PDB]: Three characters please - try again"))
(setq pdb-test-string (upcase (substring pdb-test-string 0 3)))
(pdb-sub-defineregion b e)
(pdb-sub-change pdb-test-string 17 3)
(pdb-sub-markregion))
;; INCREMENT VALUES
(defun pdb-increment-bfactor (b e pdb-test-string)
"PDB mode: Increment B-factor by given value"
(interactive "r \nsNumber to add to B-factor:")
(pdb-sub-defineregion b e)
(while (< (point) pdb-end-user-region)
(re-search-forward "^\\(ATOM\\|HETATM\\)" pdb-end-user-region 1 nil)
(cond ((< (point) pdb-end-user-region)
(pdb-sub-pad)
(let (( str (buffer-substring (+ (point-at-bol) 60) (+ (point-at-bol) 66))))
(setq str (+ (eval (string-to-number str)) (eval (string-to-number pdb-test-string))))
(pdb-sub-change2 (format "%6.2f" str) 60 6)))))
(pdb-sub-markregion))
(defun pdb-scale-bfactor (b e pdb-test-string)
"PDB mode: Scale B-factor by given value"
(interactive "r \nsNumber to scale B-factor by:")
(pdb-sub-defineregion b e)
(while (< (point) pdb-end-user-region)
(re-search-forward "^\\(ATOM\\|HETATM\\)" pdb-end-user-region 1 nil)
(cond ((< (point) pdb-end-user-region)
(pdb-sub-pad)
(let (( str (buffer-substring (+ (point-at-bol) 60) (+ (point-at-bol) 66))))
(setq str (* (eval (string-to-number str)) (eval (string-to-number pdb-test-string))))
(pdb-sub-change2 (format "%6.2f" str) 60 6)))))
(pdb-sub-markregion))
(defun pdb-increment-residue (b e pdb-test-string)
"PDB mode: Increment residue number by given value"
(interactive "r \nsNumber to increase residue number by:")
(pdb-sub-defineregion b e)
(while (< (point) pdb-end-user-region)
(re-search-forward "^\\(ATOM\\|HETATM\\|ANISOU\\|TER \\)" pdb-end-user-region 1 nil)
(cond ((< (point) pdb-end-user-region)
(pdb-sub-pad)
(let ((str (buffer-substring (+ (point-at-bol) 22) (+ (point-at-bol) 26))))
(let ((str (+ (eval (string-to-number str)) (eval (string-to-number pdb-test-string)))))
(pdb-sub-change2 (format "%4d" str) 22 4))))))
(pdb-sub-markregion))
(defun pdb-increment-fractional (b e pdb-test-string)
"PDB mode: Translate selected atoms by given fractional vector"
(interactive "r \nsGive fractional vector (3 numbers, space delimited):")
(pdb-sub-defineregion b e)
(pdb-change-orth2frac pdb-start-user-region pdb-end-user-region )
(let* ((vec (split-string pdb-test-string))
(xadd (string-to-number (elt vec 0)))
(yadd (string-to-number (elt vec 1)))
(zadd (string-to-number (elt vec 2))))
(pdb-increment-xyz pdb-start-user-region pdb-end-user-region (format "%f %f %f" xadd yadd zadd)))
(pdb-change-frac2orth pdb-start-user-region pdb-end-user-region)
(pdb-sub-markregion))
(defun pdb-scale-xyz (b e sf)
"PDB mode: Scale coordinates by given factor.\nIf one number is given, x,y and z are scaled by this number.\n If 3 numbers given, they apply to x,y and z independently."
(interactive "r \nsScale factor (1 number or 3 numbers:")
(pdb-sub-defineregion b e)
(let* ((sf (concat sf " " sf " " sf))
(vec (split-string sf))
(xadd (string-to-number (elt vec 0)))
(yadd (string-to-number (elt vec 1)))
(zadd (string-to-number (elt vec 2))))
(while (and (progn
(re-search-forward "^\\(ATOM\\|HETATM\\)" pdb-end-user-region 1 nil))
(not (progn
(pdb-sub-pad)
(let ((xyz (list (string-to-number (buffer-substring (+ (point-at-bol) 30) (+ (point-at-bol) 38))) (string-to-number (buffer-substring (+ (point-at-bol) 38) (+ (point-at-bol) 46))) (string-to-number (buffer-substring (+ (point-at-bol) 46) (+ (point-at-bol) 54))))))
(pdb-sub-change2 (format "%8.3f%8.3f%8.3f" (* xadd (elt xyz 0)) (* yadd (elt xyz 1)) (* zadd (elt xyz 2))) 30 24))))))
(pdb-sub-markregion)))
(defun pdb-increment-xyz (b e pdb-test-string)
"PDB mode: Translate selected atoms by given vector"
(interactive "r \nsGive vector (3 numbers, space delimited):")
(let* ((li (split-string pdb-test-string))
(xadd (string-to-number (elt li 0)))
(yadd (string-to-number (elt li 1)))
(zadd (string-to-number (elt li 2))))
(pdb-sub-defineregion b e)
(while (and (progn
(re-search-forward "^\\(ATOM\\|HETATM\\)" pdb-end-user-region 1 nil))
(not (progn
(pdb-sub-pad)
(let ((str (list (string-to-number (buffer-substring (+ (point-at-bol) 30) (+ (point-at-bol) 38))) (string-to-number (buffer-substring (+ (point-at-bol) 38) (+ (point-at-bol) 46))) (string-to-number (buffer-substring (+ (point-at-bol) 46) (+ (point-at-bol) 54))))))
(pdb-sub-change2 (format "%8.3f%8.3f%8.3f" (+ (elt str 0) xadd) (+ (elt str 1) yadd) (+ (elt str 2) zadd)) 30 24)))))))
(pdb-sub-markregion))
(defun pdb-change-frac2orth (b e)
"PDB mode: Change fractional to orthogonal coordinates"
(interactive "r")
(pdb-sub-defineregion b e)
(if (eq (elt pdb-cell-local 1) 0)
(call-interactively 'pdb-data-cell))
(while (< (point) pdb-end-user-region)
(re-search-forward "^\\(ATOM\\|HETATM\\)" pdb-end-user-region 1 nil)
(cond ((< (point) pdb-end-user-region)
(pdb-sub-pad)
(let* ((frac (list (string-to-number (buffer-substring (+ (point-at-bol) 30) (+ (point-at-bol) 38))) (string-to-number (buffer-substring (+ (point-at-bol) 38) (+ (point-at-bol) 46))) (string-to-number (buffer-substring (+ (point-at-bol) 46) (+ (point-at-bol) 54)))))
(newx (+ (* (elt pdb-frac2orth-local 0) (elt frac 0)) (* (elt pdb-frac2orth-local 1) (elt frac 1)) (* (elt pdb-frac2orth-local 2) (elt frac 2))))
(newy (+ (* (elt pdb-frac2orth-local 4) (elt frac 1)) (* (elt pdb-frac2orth-local 5) (elt frac 2))))
(newz (* (elt pdb-frac2orth-local 8) (elt frac 2))))
(pdb-sub-change2 (format "%8.3f%8.3f%8.3f" newx newy newz) 30 24)))))
(pdb-sub-markregion))
(defun pdb-change-orth2frac (b e)
"PDB mode: Change orthogonal to fractional coordinates"
(interactive "r")
(pdb-sub-defineregion b e)
(if (eq (elt pdb-cell-local 1) 0)
(call-interactively 'pdb-data-cell))
(while (< (point) pdb-end-user-region)
(re-search-forward "^\\(ATOM\\|HETATM\\)" pdb-end-user-region 1 nil)
(cond ((< (point) pdb-end-user-region)
(pdb-sub-pad)
(let* ((orth (list (string-to-number (buffer-substring (+ (point-at-bol) 30) (+ (point-at-bol) 38))) (string-to-number (buffer-substring (+ (point-at-bol) 38) (+ (point-at-bol) 46))) (string-to-number (buffer-substring (+ (point-at-bol) 46) (+ (point-at-bol) 54)))))
(newx (+ (* (elt pdb-orth2frac-local 0) (elt orth 0)) (* (elt pdb-orth2frac-local 1) (elt orth 1)) (* (elt pdb-orth2frac-local 2) (elt orth 2))))
(newy (+ (* (elt pdb-orth2frac-local 4) (elt orth 1)) (* (elt pdb-orth2frac-local 5) (elt orth 2))))
(newz (* (elt pdb-orth2frac-local 8) (elt orth 2)))
)
(pdb-sub-change2 (format "%8.3f%8.3f%8.3f" newx newy newz) 30 24)))))
(pdb-sub-markregion))
(defun pdb-increment-matrix (b e rm)
"PDB mode: Rotate selected atoms by given 3x3 matrix"
(interactive "r \nsGive matrix (9 numbers, space delimited):")
(let* ((rm (split-string rm))
(rm (list (string-to-number (elt rm 0)) (string-to-number (elt rm 1)) (string-to-number (elt rm 2)) (string-to-number (elt rm 3)) (string-to-number (elt rm 4)) (string-to-number (elt rm 5)) (string-to-number (elt rm 6)) (string-to-number (elt rm 7)) (string-to-number (elt rm 8)))))
(pdb-sub-defineregion b e)
(while (< (point) pdb-end-user-region)
(re-search-forward "^\\(ATOM\\|HETATM\\)" pdb-end-user-region 1 nil)
(cond ((< (point) pdb-end-user-region)
(pdb-sub-pad)
(let* ((xyz (list (string-to-number (buffer-substring (+ (point-at-bol) 30) (+ (point-at-bol) 38))) (string-to-number (buffer-substring (+ (point-at-bol) 38) (+ (point-at-bol) 46))) (string-to-number (buffer-substring (+ (point-at-bol) 46) (+ (point-at-bol) 54)))))
(nx (+ (* (nth 0 rm) (nth 0 xyz)) (* (nth 1 rm ) (nth 1 xyz)) (* (nth 2 rm ) (nth 2 xyz))))
(ny (+ (* (nth 3 rm) (nth 0 xyz)) (* (nth 4 rm ) (nth 1 xyz)) (* (nth 5 rm ) (nth 2 xyz))))
(nz (+ (* (nth 6 rm) (nth 0 xyz)) (* (nth 7 rm ) (nth 1 xyz)) (* (nth 8 rm ) (nth 2 xyz)))))
(pdb-sub-change2 (format "%8.3f%8.3f%8.3f" nx ny nz) 30 24)
)))))
(pdb-sub-markregion))
(defun pdb-increment-euler (b e pdb-test-string)
"PDB mode: Rotate selected atoms by given euler triplet"
(interactive "r \nsGive eulers (3 numbers, space delimited):")
(pdb-sub-defineregion b e)
(let* ((pdb-test-vector (split-string pdb-test-string))
(rad (/ 3.141593 180))
(al (* rad (string-to-number (elt pdb-test-vector 0))))
(be (* rad (string-to-number (elt pdb-test-vector 1))))
(ga (* rad (string-to-number (elt pdb-test-vector 2))))
(rm (list
(- (* (cos al) (cos be) (cos ga)) (* (sin al) (sin ga)))
(- (* -1 (cos al) (cos be) (sin ga)) (* (sin al) (cos ga)))
(* (cos al) (sin be))
(+ (* (sin al) (cos be) (cos ga)) (* (cos al) (sin ga)))
(- (* (cos al) (cos ga)) (* (sin al) (cos be) (sin ga)))
(* (sin al) (sin be))
(* -1 (sin be) (cos ga))
(* (sin be) (sin ga))
(cos be)
)))
(message (format "Matrix: %f %f %f %f %f %f %f %f %f" (elt rm 0) (elt rm 1) (elt rm 2) (elt rm 3) (elt rm 4) (elt rm 5) (elt rm 6) (elt rm 7) (elt rm 8)))
(pdb-increment-matrix b e (format "%f %f %f %f %f %f %f %f %f" (elt rm 0) (elt rm 1) (elt rm 2) (elt rm 3) (elt rm 4) (elt rm 5) (elt rm 6) (elt rm 7) (elt rm 8))))
(pdb-sub-markregion))
(defun pdb-increment-centroid (b e pdb-test-string)
"PDB mode: Translate selected atoms by given vector"
(interactive "r \nsGive vector (3 numbers, space delimited):")
(let* ((inc (split-string pdb-test-string))
(inc (list (string-to-number (elt inc 0)) (string-to-number (elt inc 1)) (string-to-number (elt inc 2))))
(vec (make-list 3 0))
(cnt 0)
(xyz (make-list 3 0))
(str ""))
;; first pass to calculate average
(pdb-sub-defineregion b e)
(while (< (point) pdb-end-user-region)
(re-search-forward "^\\(ATOM\\|HETATM\\)" pdb-end-user-region 1 nil)
(cond ((< (point) pdb-end-user-region)
;; get current xyz
(setq xyz (list (string-to-number (buffer-substring (+ (point-at-bol) 30) (+ (point-at-bol) 38))) (string-to-number (buffer-substring (+ (point-at-bol) 38) (+ (point-at-bol) 46))) (string-to-number (buffer-substring (+ (point-at-bol) 46) (+ (point-at-bol) 54)))))
;; add current xyz to running total (vec)
(setq vec (vector (+ (elt xyz 0) (elt vec 0)) (+ (elt xyz 1) (elt vec 1)) (+ (elt xyz 2) (elt vec 2))))
;; keep count of atoms
(setq cnt (+ cnt 1)))))
;; calculate average xyz and store in pdb-test-vec
(setq vec (vector (/ (elt vec 0) cnt)(/ (elt vec 1) cnt)(/ (elt vec 2) cnt)))
(message (format "Old centroid: %8.3f %8.3f %8.3f" (elt vec 0) (elt vec 1) (elt vec 2)))
;; second pass to adjust numbers
(goto-char pdb-start-user-region)
(while (< (point) pdb-end-user-region)
(re-search-forward "^\\(ATOM\\|HETATM\\)" pdb-end-user-region 1 nil)
(cond ((< (point) pdb-end-user-region)
(pdb-sub-pad)
(setq str (list (string-to-number (buffer-substring (+ (point-at-bol) 30) (+ (point-at-bol) 38))) (string-to-number (buffer-substring (+ (point-at-bol) 38) (+ (point-at-bol) 46))) (string-to-number (buffer-substring (+ (point-at-bol) 46) (+ (point-at-bol) 54)))))
(pdb-sub-change2 (format "%8.3f%8.3f%8.3f" (- (elt str 0) (- (elt vec 0) (elt inc 0))) (- (elt str 1) (- (elt vec 1) (elt inc 1))) (- (elt str 2) (- (elt vec 2) (elt inc 2)))) 30 24))))
(pdb-sub-markregion)))
;; RENUMBER
(defun pdb-renumber-atoms (b e pdb-start-number)
"PDB mode: Renumber selected atoms consecutively"
(interactive "r \nnRenumber atoms, starting at?:")
(if ( = pdb-start-number 0) (setq pdb-start-number 1))
(pdb-sub-defineregion b e)
(let ((i (- pdb-start-number 1)))
(while (< (point) pdb-end-user-region)
(re-search-forward "^\\(ATOM\\|HETATM\\|TER \\|ANISOU\\)" pdb-end-user-region 1 nil)
(unless (string= (buffer-substring (point-at-bol) (+ 6 (point-at-bol))) "ANISOU")
(setq i (+ 1 i)))
(cond ((< (point) pdb-end-user-region)
(goto-char (+ (point-at-bol) 11))
(delete-backward-char 5)
(insert (format "%5s" (int-to-string i))))))
(pdb-sub-markregion)))
(defun pdb-renumber-waters (b e pdb-start-number)
"PDB mode: Renumber selected waters consecutively"
(interactive "r \nnRenumber waters, starting at?:")
(if ( = pdb-start-number 0) (setq pdb-start-number 1))
(pdb-sub-defineregion b e)
(let ((i (- pdb-start-number 1)))
(while (< (point) pdb-end-user-region)
(re-search-forward "^\\(ATOM\\|HETATM\\|TER \\|ANISOU\\)" pdb-end-user-region 1 nil)
(if (string-match (buffer-substring (point-at-bol) (+ 6 (point-at-bol))) "\\(ATOM \\|HETATM\\)")
(setq i (+ 1 i)))
(cond ((< (point) pdb-end-user-region)
(goto-char (+ (point-at-bol) 26))
(delete-backward-char 4)
(insert (format "%4s" (int-to-string i))))))
(pdb-sub-markregion)))
;;TIDY UP
(defun pdb-tidy-atom2hetatm (b e)
"PDB mode: Replace selected ATOMs with HETATM"
(interactive "r")
(pdb-sub-defineregion b e)
(goto-char pdb-start-user-region)
(while (and (progn
(re-search-forward "^ATOM" pdb-end-user-region 1 nil))
(not (progn
(beginning-of-line)
(delete-char 6)
(insert "HETATM")))))
(pdb-sub-markregion))
(defun pdb-tidy-hetatm2atom (b e)
"PDB mode: Replace selected HETATMS with ATOM"
(interactive "r")
(pdb-sub-defineregion b e)
(goto-char pdb-start-user-region)
(while (and (progn
(re-search-forward "^HETATM" pdb-end-user-region 1 nil))
(not (progn
(beginning-of-line)
(delete-char 6)
(insert "ATOM ")))))
(pdb-sub-markregion))
(defun pdb-tidy-ca ( b e )
"PDB mode: Reduce to CAs only"
(interactive "r" )
(pdb-sub-defineregion b e)
(while (< (point) pdb-end-user-region)
(re-search-forward "^." pdb-end-user-region pdb-end-user-region nil)
(if (and (< (point) pdb-end-user-region) (not (looking-at "TOM ..... CA" )))
(progn
(beginning-of-line)
(setq pdb-end-user-region (- pdb-end-user-region (+ 1 (- (point-at-eol) (point-at-bol)))))
(kill-line))))
(pdb-sub-markregion))
(defun pdb-tidy-dehydrogenate (b e )
"PDB mode: Remove hydrogen atoms"
(interactive "r" )
(pdb-sub-defineregion b e)
(while (< (point) e)
(re-search-forward "^\\(ATOM \\|HETATM\\)..... .?H.*$" e 1 nil)
(if (< (point) e)
(progn
(beginning-of-line)