Scripts/loadsave.rb

   1 # coding: utf-8
   2 #
   3 #  loadsave.rb
   4 #
   5 #  Created by Toshi Nagata.
   6 #  Copyright 2008 Toshi Nagata. All rights reserved.
   7 #
   8 # This program is free software; you can redistribute it and/or modify
   9 # it under the terms of the GNU General Public License as published by
  10 # the Free Software Foundation version 2 of the License.
  11 #
  12 # This program is distributed in the hope that it will be useful,
  13 # but WITHOUT ANY WARRANTY; without even the implied warranty of
  14 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  15 # GNU General Public License for more details.
  16
  17 require "scanf.rb"
  18
  19 class Molecule
  20
  21   def loadcrd(filename)
  22     if natoms == 0
  23       raise MolbyError, "cannot load crd; the molecule is empty"
  24     end
  25         fp = open(filename, "rb")
  26     count = 0
  27         frame = 0
  28         coords = (0...natoms).collect { Vector3D[0, 0, 0] }
  29     periodic = (self.box && self.box[4].any? { |n| n != 0 })
  30         show_progress_panel("Loading AMBER crd file...")
  31 #    puts "sframe = #{sframe}, pos = #{fp.pos}"
  32     while line = fp.gets
  33       line.chomp!
  34           values = line.scan(/......../)
  35           if fp.lineno == 1
  36             #  The first line should be skipped. However, if this line seems to contain
  37                 #  coordinates, then try reading them
  38                 if values.size != 10 && (values.size > 10 || values.size != natoms * 3)
  39                   next  #  Wrong number of coordinates
  40                 end
  41                 if values.each { |v| Float(v) rescue break } == nil
  42                   #  The line contains non-number
  43                   next
  44             end
  45                 puts "Loadcrd: The title line seems to be missing"
  46           end
  47       if count + values.size > natoms * 3
  48         raise MolbyError, sprintf("crd format error - too many values at line %d in file %s; number of atoms = %d, current frame = %d", fp.lineno, fp.path, natoms, frame)
  49       end
  50           values.each { |v|
  51             coords[count / 3][count % 3] = Float(v)
  52             count += 1
  53           }
  54       if count == natoms * 3
  55             #  End of frame
  56                 if frame == 0 && atoms.all? { |ap| ap.r.x == 0.0 && ap.r.y == 0.0 && ap.r.z == 0.0 }
  57                         #  Do not create a new frame
  58                         atoms.each_with_index { |ap, i| ap.r = coords[i] }
  59                 else
  60                         create_frame([coords])
  61                 end
  62                 if periodic
  63                   #  Should have box information
  64                   line = fp.gets
  65                   if line == nil || (values = line.chomp.scan(/......../)).length != 3
  66                     #  Periodic but no cell information
  67                         puts "Loadcrd: the molecule has a periodic cell but the crd file does not contain cell info"
  68                         periodic = false
  69                         redo
  70               end
  71                   self.cell = [Float(values[0]), Float(values[1]), Float(values[2]), 90, 90, 90]
  72                 end
  73         count = 0
  74         frame += 1
  75                 if frame % 5 == 0
  76                   set_progress_message("Loading AMBER crd file...\n(#{frame} frames completed)")
  77                 end
  78       end
  79     end
  80         fp.close
  81         if (count > 0)
  82           raise MolbyError, sprintf("crd format error - file ended in the middle of frame %d", frame)
  83         end
  84         hide_progress_panel
  85         if frame > 0
  86           self.frame = self.nframes - 1
  87           return true
  88         else
  89           return false
  90         end
  91   end
  92
  93   def savecrd(filename)
  94     if natoms == 0
  95       raise MolbyError, "cannot save crd; the molecule is empty"
  96     end
  97     fp = open(filename, "wb")
  98         show_progress_panel("Saving AMBER crd file...")
  99         fp.printf("TITLE: %d atoms\n", natoms)
 100         cframe = self.frame
 101         nframes = self.nframes
 102         j = 0
 103         self.update_enabled = false
 104         begin
 105                 (0...nframes).each { |i|
 106                   select_frame(i)
 107                   j = 0
 108                   while (j < natoms * 3)
 109                         w = atoms[j / 3].r[j % 3]
 110                         fp.printf(" %7.3f", w)
 111                         fp.print("\n") if (j % 10 == 9 || j == natoms * 3 - 1)
 112                         j += 1
 113                   end
 114                   if i % 5 == 0
 115                         set_progress_message("Saving AMBER crd file...\n(#{i} frames completed)")
 116                   end
 117                 }
 118         ensure
 119                 self.update_enabled = true
 120         end
 121         select_frame(cframe)
 122         fp.close
 123         hide_progress_panel
 124         true
 125   end
 126
 127   alias :loadmdcrd :loadcrd
 128   alias :savemdcrd :savecrd
 129
 130   def sub_load_gamess_log_basis_set(lines, lineno)
 131     ln = 0
 132         while (line = lines[ln])
 133                 ln += 1
 134                 break if line =~ /SHELL\s+TYPE\s+PRIMITIVE/
 135         end
 136         ln += 1
 137         i = -1
 138         nprims = 0
 139         sym = -10  #  undefined
 140         ncomps = 0
 141         clear_basis_set
 142         while (line = lines[ln])
 143                 ln += 1
 144                 break if line =~ /TOTAL NUMBER OF BASIS SET/
 145                 if line =~ /^\s*$/
 146                   #  End of one shell
 147                   add_gaussian_orbital_shell(i, sym, nprims)
 148                   nprims = 0
 149                   sym = -10
 150                   next
 151                 end
 152                 a = line.split
 153                 if a.length == 1
 154                   i += 1
 155                   ln += 1  #  Skip the blank line
 156                   next
 157                 elsif a.length == 5 || a.length == 6
 158                   if sym == -10
 159                         case a[1]
 160                         when "S"
 161                           sym = 0; n = 1
 162                         when "P"
 163                           sym = 1; n = 3
 164                         when "L"
 165                           sym = -1; n = 4
 166                         when "D"
 167                           sym = 2; n = 6
 168                         when "F"
 169                           sym = 3; n = 10
 170                         when "G"
 171                           sym = 4; n = 15
 172                         else
 173                           raise MolbyError, "Unknown gaussian shell type at line #{lineno + ln}"
 174                         end
 175                         ncomps += n
 176                   end
 177                   if (a.length == 5 && sym == -1) || (a.length == 6 && sym != -1)
 178                         raise MolbyError, "Wrong format in gaussian shell information at line #{lineno + ln}"
 179                   end
 180                   exp = Float(a[3])
 181                   c = Float(a[4])
 182                   csp = Float(a[5] || 0.0)
 183                   add_gaussian_primitive_coefficients(exp, c, csp)
 184                   nprims += 1
 185                 else
 186                   raise MolbyError, "Error in reading basis set information at line #{lineno + ln}"
 187                 end
 188         end
 189         return ncomps
 190   end
 191
 192   def sub_load_gamess_log_mo_coefficients(lines, lineno, ncomps)
 193     ln = 0
 194         idx = 0
 195         alpha = true
 196         while (line = lines[ln]) != nil
 197                 ln += 1
 198                 if line =~ /BETA SET/
 199                         alpha = false
 200                         next
 201                 end
 202                 if line =~ /------------/ || line =~ /EIGENVECTORS/ || line =~ /\*\*\*\* (ALPHA|BETA) SET/
 203                         next
 204                 end
 205                 next unless line =~ /^\s*\d/
 206                 mo_labels = line.split       #  MO numbers (1-based)
 207                 mo_energies = lines[ln].split
 208                 mo_symmetries = lines[ln + 1].split
 209         #       puts "mo #{mo_labels.inspect}"
 210                 ln += 2
 211                 mo = mo_labels.map { [] }    #  array of *independent* empty arrays
 212                 while (line = lines[ln]) != nil
 213                         ln += 1
 214                         break unless line =~ /^\s*\d/
 215                         5.times { |i|
 216                           s = line[15 + 11 * i, 11].chomp
 217                           break if s =~ /^\s*$/
 218                           mo[i].push(Float(s)) rescue print "line = #{line}, s = #{s}"
 219                         # line[15..-1].split.each_with_index { |s, i|
 220                         #       mo[i].push(Float(s))
 221                         }
 222                 end
 223                 mo.each_with_index { |m, i|
 224                         idx = Integer(mo_labels[i])
 225                         set_mo_coefficients(idx + (alpha ? 0 : ncomps), Float(mo_energies[i]), m)
 226                 #       if mo_labels[i] % 8 == 1
 227                 #               puts "set_mo_coefficients #{idx}, #{mo_energies[i]}, [#{m[0]}, ..., #{m[-1]}]"
 228                 #       end
 229                 }
 230 #               if line =~ /^\s*$/
 231 #                       next
 232 #               else
 233 #                       break
 234 #               end
 235         end
 236   end
 237
 238   def sub_load_gamess_log(fp)
 239
 240     if natoms == 0
 241                 new_unit = true
 242         else
 243                 new_unit = false
 244     end
 245         self.update_enabled = false
 246         mes = "Loading GAMESS log file"
 247         show_progress_panel(mes)
 248         energy = nil
 249         ne_alpha = ne_beta = 0   #  number of electrons
 250         rflag = nil  #  0, UHF; 1, RHF; 2, ROHF
 251         mo_count = 0
 252         search_mode = 0   #  0, no search; 1, optimize; 2, irc
 253         ncomps = 0   #  Number of AO terms per one MO (sum of the number of components over all shells)
 254         alpha_beta = nil   #  Flag to read alpha/beta MO appropriately
 255         nsearch = 0  #  Search number for optimization
 256         begin
 257         #       if nframes > 0
 258         #               create_frame
 259         #               frame = nframes - 1
 260         #       end
 261                 n = 0
 262                 while 1
 263                         line = fp.gets
 264                         if line == nil
 265                                 break
 266                         end
 267                         line.chomp!
 268                         if line =~ /ATOM\s+ATOMIC\s+COORDINATES/ || line =~ /COORDINATES OF ALL ATOMS ARE/ || line =~ /COORDINATES \(IN ANGSTROM\) FOR \$DATA GROUP ARE/
 269                                 set_progress_message(mes + "\nReading atomic coordinates...")
 270                                 if line =~ /ATOMIC/
 271                                   first_line = true
 272                                 #  if !new_unit
 273                                 #    next   #  Skip initial atomic coordinates unless loading into an empty molecule
 274                                 #  end
 275                                   line = fp.gets  #  Skip one line
 276                                 else
 277                                   first_line = false
 278                                   nsearch += 1
 279                                   if line =~ /COORDINATES OF ALL ATOMS ARE/
 280                                     line = fp.gets  #  Skip one line
 281                               end
 282                                 end
 283                                 n = 0
 284                                 coords = []
 285                                 names = []
 286                                 while (line = fp.gets) != nil
 287                                         break if line =~ /^\s*$/ || line =~ /END OF ONE/ || line =~ /\$END/
 288                                         next if line =~ /-----/
 289                                         name, charge, x, y, z = line.split
 290                                         v = Vector3D[x, y, z]
 291                                         coords.push(v * (first_line ? 0.529177 : 1.0))  #  Bohr to angstrom
 292                                         names.push([name, charge])
 293                                 end
 294                                 if new_unit
 295                                         #  Build a new molecule
 296                                         names.each_index { |i|
 297                                                 ap = add_atom(names[i][0])
 298                                                 ap.atomic_number = names[i][1].to_i
 299                                                 ap.atom_type = ap.element
 300                                                 ap.r = coords[i]
 301                                         }
 302                                         #  Find bonds
 303                                         guess_bonds
 304                                 #       atoms.each { |ap|
 305                                 #               j = ap.index
 306                                 #               (j + 1 ... natoms).each { |k|
 307                                 #                       if calc_bond(j, k) < 1.7
 308                                 #                               create_bond(j, k)
 309                                 #                       end
 310                                 #               }
 311                                 #       }
 312                                         new_unit = false
 313                                 #       create_frame
 314                                 else
 315                                     dont_create = false
 316                                         if (search_mode == 1 && nsearch == 1) || first_line
 317                                                 #  The input coordinate and the first frame for geometry search
 318                                                 #  can have the same coordinate as the last frame; if this is the case, then
 319                                                 #  do not create the new frame
 320                                                 select_frame(nframes - 1)
 321                                                 dont_create = true
 322                                                 each_atom { |ap|
 323                                                   if (ap.r - coords[ap.index]).length2 > 1e-8
 324                                                     dont_create = false
 325                                                         break
 326                                                   end
 327                                                 }
 328                                         end
 329                                         if !dont_create
 330                                                 create_frame([coords])  #  Should not be (coords)
 331                                         end
 332                                 end
 333                                 set_property("energy", energy) if energy
 334                         elsif line =~ /BEGINNING GEOMETRY SEARCH POINT/
 335                                 energy = nil   #  New search has begun, so clear the energy
 336                                 search_mode = 1
 337                         elsif line =~ /CONSTRAINED OPTIMIZATION POINT/
 338                                 energy = nil   #  New search has begun, so clear the energy
 339                                 search_mode = 2
 340                         elsif line =~ /FINAL .* ENERGY IS *([-.0-9]+) AFTER/
 341                                 if search_mode != 2
 342                                         energy = $1.to_f
 343                                         set_property("energy", energy)
 344                                 end
 345                         elsif line =~ /TOTAL ENERGY += +([-.0-9]+)/
 346                                 energy = $1.to_f
 347                         elsif false && line =~ /EQUILIBRIUM GEOMETRY LOCATED/i
 348                                 set_progress_message(mes + "\nReading optimized coordinates...")
 349                                 fp.gets; fp.gets; fp.gets
 350                                 n = 0
 351                                 while (line = fp.gets) != nil
 352                                         break if line =~ /^\s*$/
 353                                         line.chomp
 354                                         atom, an, x, y, z = line.split
 355                                         ap = atoms[n]
 356                                         ap.r = Vector3D[x, y, z]
 357                                         n += 1
 358                                         break if n >= natoms
 359                                 end
 360                         #       if ne_alpha > 0 && ne_beta > 0
 361                         #               #  Allocate basis set record again, to update the atomic coordinates
 362                         #               allocate_basis_set_record(rflag, ne_alpha, ne_beta)
 363                         #       end
 364                         elsif line =~ /ATOMIC BASIS SET/
 365                                 lines = []
 366                                 lineno = fp.lineno
 367                                 while (line = fp.gets)
 368                                         break if line =~ /TOTAL NUMBER OF BASIS SET/
 369                                         line.chomp!
 370                                         lines.push(line)
 371                                 end
 372                                 ncomps = sub_load_gamess_log_basis_set(lines, lineno)
 373                         elsif line =~ /NUMBER OF OCCUPIED ORBITALS/
 374                                 line =~ /=\s*(\d+)/
 375                                 n = Integer($1)
 376                                 if line =~ /ALPHA/
 377                                         ne_alpha = n
 378                                 else
 379                                         ne_beta = n
 380                                 end
 381                         elsif line =~ /SCFTYP=(\w+)/
 382                                 scftyp = $1
 383                                 if ne_alpha > 0 || ne_beta > 0
 384                                         rflag = 0
 385                                         case scftyp
 386                                         when "RHF"
 387                                                 rflag = 1
 388                                         when "ROHF"
 389                                                 rflag = 2
 390                                         end
 391                                 end
 392                         elsif line =~ /(ALPHA|BETA)\s*SET/
 393                                 alpha_beta = $1
 394                         elsif line =~ /^\s*(EIGENVECTORS|MOLECULAR ORBITALS)\s*$/
 395                                 if mo_count == 0
 396                                         clear_mo_coefficients
 397                                         set_mo_info(:type=>["UHF", "RHF", "ROHF"][rflag], :alpha=>ne_alpha, :beta=>ne_beta)
 398                                 end
 399                                 mo_count += 1
 400                                 line = fp.gets; line = fp.gets
 401                                 lineno = fp.lineno
 402                                 lines = []
 403                                 set_progress_message(mes + "\nReading MO coefficients...")
 404                                 while (line = fp.gets)
 405                                         break if line =~ /\.\.\.\.\.\./ || line =~ /----------------/
 406                                         line.chomp!
 407                                         lines.push(line)
 408                                 end
 409                                 sub_load_gamess_log_mo_coefficients(lines, lineno, ncomps)
 410                                 set_progress_message(mes)
 411                         elsif line =~ /N A T U R A L   B O N D   O R B I T A L   A N A L Y S I S/
 412                                 nbo_lines = []
 413                                 while (line = fp.gets) != nil
 414                                   break if line =~ /done with NBO analysis/
 415                                   nbo_lines.push(line)
 416                                 end
 417                                 import_nbo_log(nbo_lines)
 418                         end
 419                 end
 420         end
 421         if nframes > 0
 422           select_frame(nframes - 1)
 423         end
 424         if energy && energy != 0.0
 425           set_property("energy", energy)
 426         end
 427         hide_progress_panel
 428         self.update_enabled = true
 429         (n > 0 ? true : false)
 430   end
 431
 432   def sub_load_gaussian_log(fp)
 433
 434     if natoms == 0
 435                 new_unit = true
 436         else
 437                 new_unit = false
 438     end
 439         if nframes > 0
 440                 create_frame
 441                 frame = nframes - 1
 442         end
 443         n = 0
 444         nf = 0
 445         energy = nil
 446         use_input_orientation = false
 447         show_progress_panel("Loading Gaussian out file...")
 448         while 1
 449                 line = fp.gets
 450                 if line == nil
 451                         break
 452                 end
 453                 line.chomp!
 454                 if line =~ /(Input|Standard) orientation/
 455                         match = $1
 456                         if match == "Input"
 457                                 use_input_orientation = true if nf == 0
 458                                 next if !use_input_orientation
 459                         else
 460                                 next if use_input_orientation
 461                         end
 462                         4.times { line = fp.gets }    #  Skip four lines
 463                         n = 0
 464                         coords = []
 465                         anums = []
 466                         while (line = fp.gets) != nil
 467                                 break if line =~ /-----/
 468                                 num, charge, type, x, y, z = line.split
 469                                 coords.push(Vector3D[x, y, z])
 470                                 anums.push(charge)
 471                                 n += 1
 472                         end
 473                         if new_unit
 474                                 #  Build a new molecule
 475                                 anums.each_index { |i|
 476                                         ap = add_atom("X")
 477                                         ap.atomic_number = anums[i]
 478                                         ap.atom_type = ap.element
 479                                         ap.name = sprintf("%s%d", ap.element, i)
 480                                         ap.r = coords[i]
 481                                 }
 482                                 #  Find bonds
 483                         #       atoms.each { |ap|
 484                         #               j = ap.index
 485                         #               (j + 1 ... natoms).each { |k|
 486                         #                       if calc_bond(j, k) < 1.7
 487                         #                               create_bond(j, k)
 488                         #                       end
 489                         #               }
 490                         #       }
 491                                 guess_bonds
 492                                 new_unit = false
 493                         #       create_frame
 494                         else
 495                                 create_frame([coords])  #  Should not be (coords)
 496                         end
 497                         if energy
 498                                 # TODO: to ensure whether the energy output line comes before
 499                                 # or after the atomic coordinates.
 500                                 set_property("energy", energy)
 501                         end
 502                         nf += 1
 503                 elsif line =~ /SCF Done: *E\(\w+\) *= *([-.0-9]+)/
 504                         energy = $1.to_f
 505                 end
 506         end
 507         if energy
 508                 set_property("energy", energy)
 509         end
 510         hide_progress_panel
 511         (n > 0 ? true : false)
 512   end
 513
 514   def sub_load_psi4_log(fp)
 515     if natoms == 0
 516       new_unit = true
 517     else
 518       new_unit = false
 519     end
 520     n = 0
 521     nf = 0
 522     energy = nil
 523
 524     show_progress_panel("Loading Psi4 output file...")
 525
 526     getline = lambda { @lineno += 1; return fp.gets }
 527
 528     #  Import coordinates and energies
 529     vecs = []
 530     ats = []
 531     first_frame = nframes
 532     trans = nil
 533     hf_type = nil
 534     nalpha = nil
 535     nbeta = nil
 536     while line = getline.call
 537       if line =~ /==> Geometry <==/
 538         #  Skip until line containing "------"
 539         while line = getline.call
 540           break if line =~ /------/
 541         end
 542         vecs.clear
 543         index = 0
 544         #  Read atom positions
 545         while line = getline.call
 546           line.chomp!
 547           break if line =~ /^\s*$/
 548           tokens = line.split(' ')
 549           if natoms > 0 && first_frame == nframes
 550             if index >= natoms || tokens[0] != atoms[index].element
 551               hide_progress_panel
 552               raise MolbyError, "The atom list does not match the current structure at line #{@lineno}"
 553             end
 554           end
 555           vecs.push(Vector3D[Float(tokens[1]), Float(tokens[2]), Float(tokens[3])])
 556           if natoms == 0
 557             ats.push(tokens[0])
 558           end
 559           index += 1
 560         end
 561         if natoms == 0
 562           #  Create molecule from the initial geometry
 563           ats.each_with_index { |aname, i|
 564             #  Create atoms
 565             ap = add_atom(aname)
 566             ap.element = aname
 567             ap.atom_type = ap.element
 568             ap.name = sprintf("%s%d", aname, i)
 569             ap.r = vecs[i]
 570           }
 571           guess_bonds
 572         else
 573           if vecs.length != natoms
 574             break  #  Log file is incomplete
 575           end
 576           #  Does this geometry differ from the last one?
 577           vecs.length.times { |i|
 578             if (atoms[i].r - vecs[i]).length2 > 1.0e-14
 579               #  Create a new frame and break
 580               create_frame
 581               vecs.length.times { |j|
 582                 atoms[j].r = vecs[j]
 583               }
 584               break
 585             end
 586           }
 587         end
 588         #  end geometry
 589       elsif line =~ /Final Energy: +([-.0-9]+)/
 590         #  Energy for this geometry
 591         energy = Float($1)
 592         set_property("energy", energy)
 593         if line =~ /RHF/
 594           hf_type = "RHF"
 595         elsif line =~ /UHF/
 596           hf_type = "UHF"
 597         elsif line =~ /ROHF/
 598           hf_type = "ROHF"
 599         end
 600       elsif line =~ /^ *Nalpha *= *(\d+)/
 601         nalpha = Integer($1)
 602       elsif line =~ /^ *Nbeta *= *(\d+)/
 603         nbeta = Integer($1)
 604       end
 605     end
 606     hide_progress_panel
 607     clear_basis_set
 608     clear_mo_coefficients
 609     set_mo_info(:type => hf_type, :alpha => nalpha, :beta => nbeta)
 610     return true
 611   end
 612
 613   #  mol.set_mo_info should be set before calling this function
 614   #  Optional label is for importing JANPA output: "NAO" or "CPLO"
 615   #  If label is not nil, then returns a hash containing the following key/value pairs:
 616   #    :atoms => an array of [element_symbol, seq_num, atomic_num, x, y, z] (angstrom)
 617   #    :gto => an array of an array of [sym, [ex0, c0, ex1, c1, ...]]
 618   #    :moinfo => an array of [sym, energy, spin (0 or 1), occ]
 619   #    :mo => an array of [c0, c1, ...]
 620   def sub_load_molden(fp, label = nil)
 621     getline = lambda { @lineno += 1; return fp.gets }
 622     bohr = 0.529177210903
 623     errmsg = nil
 624     ncomps = 0  #  Number of components (AOs)
 625     occ_alpha = 0  #  Number of occupied alpha orbitals
 626     occ_beta = 0   #  Number of occupied beta orbitals
 627     if label
 628       hash = Hash.new
 629     end
 630     catch :ignore do
 631       while line = getline.call
 632         if line =~ /^\[Atoms\]/
 633           i = 0
 634           while line = getline.call
 635             if line =~ /^[A-Z]/
 636               #  element, index, atomic_number, x, y, z (in AU)
 637               a = line.split(' ')
 638               if label
 639                 (hash[:atoms] ||= []).push([a[0], Integer(a[1]), Integer(a[2]), Float(a[3]) * bohr, Float(a[4]) * bohr, Float(a[5]) * bohr])
 640               else
 641                 if atoms[i].atomic_number != Integer(a[2]) ||
 642                   (atoms[i].x - Float(a[3]) * bohr).abs > 1e-4 ||
 643                   (atoms[i].y - Float(a[4]) * bohr).abs > 1e-4 ||
 644                   (atoms[i].z - Float(a[5]) * bohr).abs > 1e-4
 645                   errmsg = "The atom list does not match the current molecule."
 646                   throw :ignore
 647                 end
 648               end
 649               i += 1
 650             else
 651               break
 652             end
 653           end
 654           redo  #  The next line will be the beginning of the next block
 655         elsif line =~ /^\[GTO\]/
 656           shell = 0
 657           atom_index = 0
 658           if label
 659             gtos = []
 660             hash[:gto] = []
 661           end
 662           while line = getline.call
 663             #  index, 0?
 664             a = line.split(' ')
 665             break if a.length != 2
 666             #  loop for shells
 667             while line = getline.call
 668               #  type, no_of_primitives, 1.00?
 669               a = line.split(' ')
 670               break if a.length != 3   #  Terminated by a blank line
 671               case a[0]
 672               when "s"
 673                 sym = 0; n = 1
 674               when "p"
 675                 sym = 1; n = 3
 676               when "d"
 677                 sym = 2; n = 6    #  TODO: handle both spherical and cartesian
 678               when "f"
 679                 sym = 3; n = 10
 680               when "g"
 681                 sym = 4; n = 15
 682               else
 683                 raise MolbyError, "Unknown gaussian shell type '#{a[0]}' at line #{@lineno} in MOLDEN file"
 684               end
 685               nprimitives = Integer(a[1])
 686               if label
 687                 gtoline = [sym, []]
 688                 gtos.push(gtoline)
 689               end
 690               nprimitives.times { |i|
 691                 line = getline.call   #  exponent, contraction
 692                 b = line.split(' ')
 693                 if label
 694                   gtoline[1].push(Float(b[0]), Float(b[1]))
 695                 end
 696                 add_gaussian_primitive_coefficients(Float(b[0]), Float(b[1]), 0.0)
 697               }
 698               #  end of one shell
 699               if label == nil
 700                 add_gaussian_orbital_shell(atom_index, sym, nprimitives)
 701               end
 702               shell += 1
 703               ncomps += n
 704             end
 705             #  end of one atom
 706             atom_index += 1
 707             if label
 708               hash[:gto].push(gtos)
 709             end
 710           end
 711           redo  #  The next line will be the beginning of the next block
 712         elsif line =~ /^\[MO\]/
 713           m = []
 714           idx_alpha = 1   #  set_mo_coefficients() accepts 1-based index of MO
 715           idx_beta = 1
 716           if label
 717             hash[:mo] = []
 718             hash[:moinfo] = []
 719           end
 720           while true
 721             #  Loop for each MO
 722             m.clear
 723             ene = nil
 724             spin = nil
 725             sym = nil   #  Not used in Molby
 726             occ = nil
 727             i = 0
 728             while line = getline.call
 729               if line =~ /^ *Sym= *(\w+)/
 730                 sym = $1
 731               elsif line =~ /^ *Ene= *([-+.0-9e]+)/
 732                 ene = Float($1)
 733               elsif line =~ /^ *Spin= *(\w+)/
 734                 spin = $1
 735               elsif line =~ /^ *Occup= *([-+.0-9e]+)/
 736                 occ = Float($1)
 737                 if occ > 0.0
 738                   if spin == "Alpha"
 739                     occ_alpha += 1
 740                   else
 741                     occ_beta += 1
 742                   end
 743                 end
 744                 if label
 745                   hash[:moinfo].push([sym, ene, (spin == "Alpha" ? 0 : 1), occ])
 746                 end
 747               elsif line =~ /^ *([0-9]+) +([-+.0-9e]+)/
 748                 m[i] = Float($2)
 749                 i += 1
 750                 if i >= ncomps
 751                   if spin == "Alpha"
 752                     idx = idx_alpha
 753                     idx_alpha += 1
 754                   else
 755                     idx = idx_beta
 756                     idx_beta += 1
 757                   end
 758                   set_mo_coefficients(idx, ene, m)
 759                   if label
 760                     hash[:mo].push(m.dup)
 761                   end
 762                   break
 763                 end
 764               else
 765                 break
 766               end
 767             end
 768             break if i < ncomps  #  no MO info was found
 769           end
 770           next
 771         end
 772       end   #  end while
 773     end     #  end catch
 774     if errmsg
 775       message_box("The MOLDEN file was found but not imported. " + errmsg, "Psi4 import info", :ok)
 776       return (label ? nil : false)
 777     end
 778     return (label ? hash : true)
 779   end
 780
 781   #  Import the JANPA log and related molden files
 782   #  Files: inppath.{NAO.molden,CLPO.molden,janpa.log}
 783   def sub_load_janpa_log(inppath)
 784     begin
 785       fp = File.open(inppath + ".janpa.log", "rt") rescue fp = nil
 786       if fp == nil
 787         message_box("Cannot open JANPA log file #{inppath + '.janpa.log'}: " + $!.to_s)
 788         return false
 789       end
 790       print("Importing #{inppath}.janpa.log.\n")
 791       lineno = 0
 792       getline = lambda { lineno += 1; return fp.gets }
 793       h = Hash.new
 794       mfiles = Hash.new
 795       while line = getline.call
 796         if line =~ /^NAO \#/
 797           h["NAO"] = []
 798           while line = getline.call
 799             break if line !~ /^\s*[1-9]/
 800             num = Integer(line[0, 5])
 801             name = line[5, 21]
 802             occ = Float(line[26, 11])
 803             #  like A1*: R1*s(0)
 804             #  atom_number, occupied?, shell_number, orb_sym, angular_number
 805             name =~ /\s*[A-Z]+([0-9]+)(\*?):\s* R([0-9]+)\*([a-z]+)\(([-0-9]+)\)/
 806             anum = Integer($1)
 807             occupied = $2
 808             shell_num = Integer($3)
 809             orb_sym = $4
 810             ang_num = Integer($5)
 811             h["NAO"].push([num, anum, occupied, shell_num, orb_sym, ang_num, occ])
 812           end
 813         elsif line =~ /^\s*CLPO\s+D e s c r i p t i o n\s+Occupancy\s+Composition/
 814           h["CLPO"] = []
 815           while line = getline.call
 816             break if line =~ /^\s*$/
 817             num = Integer(line[0, 5])
 818             label1 = line[5, 6].strip
 819             desc = line[11, 30].strip
 820             desc =~ /\s*([-A-Za-z0-9]+)(,\s*(.*$))?/
 821             desc1 = $1
 822             desc2 = ($3 || "")
 823             if desc2 =~ /^(.*)*\(NB\)\s*$/ && label1 == ""
 824               label1 = "(NB)"
 825               desc2 = $1.strip
 826             end
 827             #  like ["(BD)", "C1-H3", "Io = 0.2237"]
 828             h["CLPO"][num - 1] = [label1, desc1, desc2]
 829           end
 830         elsif line =~ /^ -NAO_Molden_File: (\S*)/
 831           mfiles["NAO"] = $1
 832         elsif line =~ /^ -LHO_Molden_File: (\S*)/
 833           mfiles["LHO"] = $1
 834         elsif line =~ /^ -CLPO_Molden_File: (\S*)/
 835           mfiles["CLPO"] = $1
 836         elsif line =~ /^ -PNAO_Molden_File: (\S*)/
 837           mfiles["PNAO"] = $1
 838         elsif line =~ /^ -AHO_Molden_File: (\S*)/
 839           mfiles["AHO"] = $1
 840         elsif line =~ /^ -LPO_Molden_File: (\S*)/
 841           mfiles["LPO"] = $1
 842         end
 843       end
 844       fp.close
 845       #  Read molden files
 846       mfiles.each { |key, value|
 847         fp = Kernel.open(value, "rt") rescue fp = nil
 848         if fp
 849           print("Importing #{value}.\n")
 850           res = sub_load_molden(fp, key)
 851           if res
 852             #  Some kind of orbital based on AO
 853             h["AO/#{key}"] = LAMatrix.new(res[:mo])
 854           end
 855           fp.close
 856         end
 857       }
 858       @nbo = h
 859       return true
 860     rescue => e
 861       $stderr.write(e.message + "\n")
 862       $stderr.write(e.backtrace.inspect + "\n")
 863     end
 864   end
 865
 866   def loadout(filename)
 867   retval = false
 868   fp = open(filename, "rb")
 869   @lineno = 0
 870   begin
 871     while s = fp.gets
 872       @lineno += 1
 873       if s =~ /Gaussian/
 874         retval = sub_load_gaussian_log(fp)
 875         break
 876       elsif s =~ /GAMESS/
 877         retval = sub_load_gamess_log(fp)
 878         break
 879       elsif s =~ /Psi4/
 880         retval = sub_load_psi4_log(fp)
 881         if retval
 882           #  If .molden file exists, then try to read it
 883           namepath = filename.gsub(/\.\w*$/, "")
 884           mname = "#{namepath}.molden"
 885           if File.exists?(mname)
 886             fp2 = open(mname, "rb")
 887             if fp2
 888               flag = sub_load_molden(fp2)
 889               fp2.close
 890               status = (flag ? 0 : -1)
 891             end
 892           end
 893           if File.exists?("#{namepath}.janpa.log")
 894             flag = sub_load_janpa_log(namepath)
 895             status = (flag ? 0 : -1)
 896           end
 897         end
 898         break
 899       end
 900     end
 901   rescue
 902     hide_progress_panel
 903     raise
 904   end
 905         fp.close
 906         return retval
 907   end
 908
 909   alias :loadlog :loadout
 910
 911   def loadxyz(filename)
 912         fp = open(filename, "rb")
 913         n = 0
 914         coords = []
 915         names = []
 916         cell = nil
 917         while 1
 918           line = fp.gets
 919           if line == nil
 920                 fp.close
 921                 break
 922           end
 923           line.chomp
 924           toks = line.split
 925           if coords.length == 0
 926             #  Allow "number of atoms" line or "number of atoms and crystallographic cell parameter"
 927                 #  (Chem3D xyz format)
 928                 next if toks.length == 1
 929                 if toks.length == 7
 930                   cell = toks[1..6].map { |s| Float(s.sub(/\(\d+\)/, "")) }  #  Remove (xx) and convert to float
 931                   next
 932                 end
 933           end
 934           name, x, y, z = line.split
 935           next if z == nil
 936           x = Float(x.sub(/\(\d+\)/, ""))
 937           y = Float(y.sub(/\(\d+\)/, ""))
 938           z = Float(z.sub(/\(\d+\)/, ""))
 939           r = Vector3D[x, y, z]
 940           coords.push(r)
 941           names.push(name)
 942           n += 1
 943         end
 944         celltr = nil
 945         if cell
 946           self.cell = cell
 947           celltr = self.cell_transform
 948         end
 949         names.each_index { |i|
 950           ap = add_atom(names[i])
 951           names[i] =~ /^([A-Za-z]{1,2})/
 952           element = $1.capitalize
 953           ap.element = element
 954           ap.atom_type = element
 955           if celltr
 956             ap.r = celltr * coords[i]
 957           else
 958             ap.r = coords[i]
 959           end
 960         }
 961         guess_bonds
 962         #  Find bonds
 963 #       atoms.each { |ap|
 964 #         j = ap.index
 965 #         (j + 1 ... natoms).each { |k|
 966 #               if calc_bond(j, k) < 1.7
 967 #               #  create_bond(j, k)
 968 #               end
 969 #         }
 970 #       }
 971 #       self.undo_enabled = save_undo_enabled
 972         (n > 0 ? true : false)
 973   end
 974
 975   def savexyz(filename)
 976     open(filename, "wb") { |fp|
 977           fp.printf "%d\n", self.natoms
 978           each_atom { |ap|
 979             fp.printf "%s %.5f %.5f %.5f\n", ap.element, ap.x, ap.y, ap.z
 980           }
 981         }
 982         return true
 983   end
 984
 985   def loadzmat(filename)
 986     self.remove(All)
 987         open(filename, "rb") { |fp|
 988           while (line = fp.gets)
 989             line.chomp!
 990                 a = line.split
 991                 an = Molecule.guess_atomic_number_from_name(a[0])
 992                 elm = Parameter.builtin.elements[an].name
 993                 base1 = a[1].to_i - 1
 994                 base2 = a[3].to_i - 1
 995                 base3 = a[5].to_i - 1
 996                 base1 = nil if base1 < 0
 997                 base2 = nil if base2 < 0
 998                 base3 = nil if base3 < 0
 999                 add_atom(a[0], elm, elm, a[2].to_f, base1, a[4].to_f, base2, a[6].to_f, base3)
1000           end
1001         }
1002         return true
1003   end
1004
1005   def savezmat(filename)
1006   end
1007
1008   def loadcom(filename)
1009 #       save_undo_enabled = self.undo_enabled?
1010 #       self.undo_enabled = false
1011         self.remove(All)
1012         fp = open(filename, "rb")
1013         section = 0
1014         while (line = fp.gets)
1015           line.chomp!
1016           if section == 0
1017             section = 1 if line =~ /^\#/
1018                 next
1019           elsif section == 1 || section == 2
1020             section += 1 if line =~ /^\s*$/
1021                 next
1022           else
1023             #  The first line is skipped (charge and multiplicity)
1024                 while (line = fp.gets)
1025                   line.chomp!
1026                   break if line =~ /^\s*$/
1027                   a = line.split(/\s*[ \t,\/]\s*/)
1028                   r = Vector3D[Float(a[1]), Float(a[2]), Float(a[3])]
1029                   ap = add_atom(a[0])
1030                   a[0] =~ /^([A-Za-z]{1,2})/
1031                   element = $1.capitalize
1032               ap.element = element
1033               ap.atom_type = element
1034               ap.r = r
1035                 end
1036                 break
1037           end
1038         end
1039         fp.close
1040         guess_bonds
1041 #       self.undo_enabled = save_undo_enabled
1042         return true
1043   end
1044
1045   def loadinp(filename)
1046 #       save_undo_enabled = self.undo_enabled?
1047 #       self.undo_enabled = false
1048         self.remove(All)
1049         fp = open(filename, "rb")
1050         section = 0
1051         has_basis = false
1052         while (line = fp.gets)
1053           if line =~ /\A \$BASIS/
1054             has_basis = true
1055                 next
1056           end
1057           next if line !~ /\A \$DATA/
1058           line = fp.gets   #  Title line
1059           line = fp.gets   #  Symmetry line
1060           while (line = fp.gets)
1061 #           puts line
1062             line.chomp!
1063                 break if line =~ /\$END/
1064                 a = line.split
1065                 ap = add_atom(a[0])
1066                 ap.atomic_number = Integer(a[1])
1067                 ap.atom_type = ap.element
1068                 r = Vector3D[Float(a[2]), Float(a[3]), Float(a[4])]
1069                 ap.r = r;
1070                 if !has_basis
1071                   #  Skip until one blank line is detected
1072                   while (line = fp.gets) && line =~ /\S/
1073                   end
1074                 end
1075       end
1076           break
1077         end
1078         fp.close
1079         guess_bonds
1080 #       self.undo_enabled = save_undo_enabled
1081         return true
1082   end
1083
1084   def saveinp(filename)
1085     if natoms == 0
1086       raise MolbyError, "cannot save GAMESS input; the molecule is empty"
1087     end
1088     fp = open(filename, "wb")
1089         now = Time.now.to_s
1090         fp.print <<end_of_header
1091 !  GAMESS input
1092 !  Generated by Molby at #{now}
1093  $CONTRL COORD=UNIQUE EXETYP=RUN ICHARG=0
1094          ICUT=20 INTTYP=HONDO ITOL=30
1095          MAXIT=200 MOLPLT=.T. MPLEVL=0
1096          MULT=1 QMTTOL=1e-08 RUNTYP=OPTIMIZE
1097          SCFTYP=RHF UNITS=ANGS                  $END
1098  $SCF    CONV=1.0E-06 DIRSCF=.T.                $END
1099  $STATPT NSTEP=400 OPTTOL=1.0E-06               $END
1100  $SYSTEM MEMDDI=0 MWORDS=16 TIMLIM=50000        $END
1101  $BASIS  GBASIS=N31 NDFUNC=1 NGAUSS=6           $END
1102  $GUESS  GUESS=HUCKEL                           $END
1103 !
1104  $DATA
1105  #{name}
1106  C1
1107 end_of_header
1108         each_atom { |ap|
1109                 next if ap.atomic_number == 0
1110                 fp.printf " %-6s %4d %10.6f %10.6f %10.6f\n", ap.name, ap.atomic_number, ap.r.x, ap.r.y, ap.r.z
1111         }
1112         fp.print " $END\n"
1113         fp.close
1114         return true
1115   end
1116
1117   def savecom(filename)
1118     if natoms == 0
1119       raise MolbyError, "cannot save Gaussian input; the molecule is empty"
1120     end
1121     fp = open(filename, "wb")
1122         base = File.basename(filename, ".*")
1123         fp.print <<end_of_header
1124 %Chk=#{base}.chk
1125 \# PM3 Opt
1126
1127  #{name}; created by Molby at #{Time.now.to_s}
1128
1129  0 1
1130 end_of_header
1131         each_atom { |ap|
1132             next if ap.atomic_number == 0
1133                 fp.printf "%-6s %10.6f %10.6f %10.6f\n", ap.element, ap.r.x, ap.r.y, ap.r.z
1134         }
1135         fp.print "\n"
1136         fp.close
1137         return true
1138   end
1139
1140   alias :loadgjf :loadcom
1141   alias :savegjf :savecom
1142
1143   def loadcif(filename)
1144     mol = self
1145     def getciftoken(fp)
1146           while @tokens.length == 0
1147             line = fp.gets
1148             return nil if !line
1149                 if line[0] == ?;
1150                   s = line
1151                   while line = fp.gets
1152                     break if line[0] == ?;
1153                     s += line
1154                   end
1155                   return s if !line
1156                   s += ";"
1157                   @tokens.push(s)
1158                   line = line[1...line.length]
1159                 end
1160             line.strip!
1161             line.scan(/'[^\']*'|"[^\"]*"|[^#\s]+|#.*/) do |s|
1162               next if s[0] == ?#
1163                   if s =~ /^data_|loop_|global_|save_|stop_/i
1164                     s = "#" + s    #  Label for reserved words
1165                   end
1166                   @tokens.push(s)
1167             end
1168           end
1169           return @tokens.shift
1170         end
1171         def float_strip_rms(str)
1172           str =~ /^(-?)(\d*)(\.(\d*))?(\((\d+)\))?$/
1173           sgn, i, frac, rms = $1, $2, $4, $6
1174           i = i.to_f
1175           if frac
1176                 base = 0.1 ** frac.length
1177                 i = i + frac.to_f * base
1178           else
1179             base = 1.0
1180           end
1181           if rms
1182             rms = rms.to_f * base
1183           else
1184             rms = 0.0
1185           end
1186           if sgn == "-"
1187             i = -i
1188           end
1189           return i, rms
1190         end
1191         def parse_symmetry_operation(str)
1192           if str == "."
1193             sym = nil
1194           elsif (str =~ /(\d+)_(\d)(\d)(\d)/) || (str =~ /(\d+) +(\d)(\d)(\d)/)
1195             sym = [Integer($1) - 1, Integer($2) - 5, Integer($3) - 5, Integer($4) - 5]
1196           elsif (str =~ /^(\d+)$/)
1197             sym = [Integer($1) - 1, 0, 0, 0]
1198           end
1199           if sym && (sym[0] == 0 && sym[1] == 0 && sym[2] == 0 && sym[3] == 0)
1200             sym = nil
1201           end
1202           sym
1203         end
1204         def find_atom_by_name(mol, name)
1205           name = name.delete(" ()")
1206           ap = mol.atoms[name] rescue ap = nil
1207           return ap
1208         end
1209         selfname = self.name
1210         fp = open(filename, "rb")
1211         data_identifier = nil
1212         @tokens = []
1213         count_up = 1
1214         while true
1215           warn_message = ""
1216           verbose = nil
1217           bond_defined = false
1218           special_positions = []
1219           mol.remove(All)
1220           cell = []
1221           cell_trans = cell_trans_inv = Transform.identity
1222           token = getciftoken(fp)
1223           pardigits_re = /\(\d+\)/
1224           calculated_atoms = []
1225           while token != nil
1226             if token =~ /^\#data_/i
1227                   if data_identifier == nil || mol.natoms == 0
1228                     #  First block or no atoms yet
1229             #  Continue processing of this molecule
1230                     data_identifier = token
1231                         token = getciftoken(fp)
1232                         next
1233                   else
1234                     #  Description of another molecule begins here
1235                         data_identifier = token
1236                         break
1237                   end
1238             elsif token =~ /^_cell/
1239                   val = getciftoken(fp)
1240                   if token == "_cell_length_a"
1241                     cell[0], cell[6] = float_strip_rms(val)
1242                   elsif token == "_cell_length_b"
1243                     cell[1], cell[7] = float_strip_rms(val)
1244                   elsif token == "_cell_length_c"
1245                     cell[2], cell[8] = float_strip_rms(val)
1246                   elsif token == "_cell_angle_alpha"
1247                     cell[3], cell[9] = float_strip_rms(val)
1248                   elsif token == "_cell_angle_beta"
1249                     cell[4], cell[10] = float_strip_rms(val)
1250                   elsif token == "_cell_angle_gamma"
1251                     cell[5], cell[11] = float_strip_rms(val)
1252                   end
1253                   if cell.length == 12 && cell.all?
1254                     mol.cell = cell
1255             puts "Unit cell is set to #{mol.cell.inspect}." if verbose
1256                     cell = []
1257                     cell_trans = mol.cell_transform
1258                     cell_trans_inv = cell_trans.inverse
1259                   end
1260                   token = getciftoken(fp)
1261                   next
1262         elsif token.casecmp("#loop_") == 0
1263               labels = []
1264                   while (token = getciftoken(fp)) && token[0] == ?_
1265                     labels.push(token)
1266                   end
1267                   if labels[0] =~ /symmetry_equiv_pos|space_group_symop|atom_site_label|atom_site_aniso_label|geom_bond/
1268                     hlabel = Hash.new(-10000000)
1269                     labels.each_with_index { |lb, i|
1270                           hlabel[lb] = i
1271                     }
1272                     data = []
1273                     n = labels.length
1274                     a = []
1275                     while true
1276                           break if token == nil || token[0] == ?_ || token[0] == ?#
1277                           a.push(token)
1278                           if a.length == n
1279                             data.push(a)
1280                             a = []
1281                           end
1282                           token = getciftoken(fp)
1283                     end
1284                     if labels[0] =~ /^_symmetry_equiv_pos/ || labels[0] =~ /^_space_group_symop/
1285                       data.each { |d|
1286                             symstr = d[hlabel["_symmetry_equiv_pos_as_xyz"]] || d[hlabel["_space_group_symop_operation_xyz"]]
1287                             symstr.delete("\"\'")
1288                             exps = symstr.split(/,/)
1289                             sym = [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
1290                             exps.each_with_index { |s, i|
1291                               terms = s.scan(/([-+]?)(([.0-9]+)(\/([0-9]+))?([xXyYzZ])?|([xXyYzZ]))/)
1292                                   terms.each { |a|
1293                                     #  a[0]: sign, a[2]: numerator, a[4]: denometer
1294                                     if a[4] != nil
1295                                       #  The number part is a[2]/a[4]
1296                                       num = Float(a[2])/Float(a[4])
1297                                     elsif a[2] != nil
1298                                       #  The number part is either integer or a floating point
1299                                       num = Float(a[2])
1300                                     else
1301                                       num = 1.0
1302                                     end
1303                                     num = -num if a[0][0] == ?-
1304                                     xyz = (a[5] || a[6])
1305                                     if xyz == "x" || xyz == "X"
1306                                       sym[i] = num
1307                                     elsif xyz == "y" || xyz == "Y"
1308                                       sym[i + 3] = num
1309                                     elsif xyz == "z" || xyz == "Z"
1310                                       sym[i + 6] = num
1311                                     else
1312                                       sym[9 + i] = num
1313                                     end
1314                                   }
1315                             }
1316                             puts "symmetry operation #{sym.inspect}" if verbose
1317                             mol.add_symmetry(Transform.new(sym))
1318                           }
1319                           puts "#{mol.nsymmetries} symmetry operations are added" if verbose
1320                     elsif labels[0] =~ /^_atom_site_label/
1321                           #  Create atoms
1322                           data.each { |d|
1323                             name = d[hlabel["_atom_site_label"]]
1324                             elem = d[hlabel["_atom_site_type_symbol"]]
1325                             fx = d[hlabel["_atom_site_fract_x"]]
1326                             fy = d[hlabel["_atom_site_fract_y"]]
1327                             fz = d[hlabel["_atom_site_fract_z"]]
1328                             uiso = d[hlabel["_atom_site_U_iso_or_equiv"]]
1329                             biso = d[hlabel["_atom_site_B_iso_or_equiv"]]
1330                             occ = d[hlabel["_atom_site_occupancy"]]
1331                             calc = d[hlabel["_atom_site_calc_flag"]]
1332                             name = name.delete(" ()")
1333                             if elem == nil || elem == ""
1334                               if name =~ /[A-Za-z]{1,2}/
1335                                     elem = $&.capitalize
1336                                   else
1337                                     elem = "Du"
1338                                   end
1339                             end
1340                             ap = mol.add_atom(name, elem, elem)
1341                             ap.fract_x, ap.sigma_x = float_strip_rms(fx)
1342                             ap.fract_y, ap.sigma_y = float_strip_rms(fy)
1343                             ap.fract_z, ap.sigma_z = float_strip_rms(fz)
1344                             if biso
1345                               ap.temp_factor, sig = float_strip_rms(biso)
1346                             elsif uiso
1347                               ap.temp_factor, sig = float_strip_rms(uiso)
1348                                   ap.temp_factor *= 78.9568352087149          #  8*pi*pi
1349                             end
1350                             ap.occupancy, sig = float_strip_rms(occ)
1351                             if calc == "c" || calc == "calc"
1352                               calculated_atoms.push(ap.index)
1353                         end
1354                             #  Guess special positions
1355                             (1...mol.nsymmetries).each { |isym|
1356                               sr = ap.fract_r
1357                               sr = (mol.transform_for_symop(isym) * sr) - sr;
1358                                   nx = (sr.x + 0.5).floor
1359                                   ny = (sr.y + 0.5).floor
1360                                   nz = (sr.z + 0.5).floor
1361                                   if (Vector3D[sr.x - nx, sr.y - ny, sr.z - nz].length2 < 1e-6)
1362                                     #  [isym, -nx, -ny, -nz] transforms this atom to itself
1363                                     #  The following line is equivalent to:
1364                                     #    if special_positions[ap.index] == nil; special_positions[ap.index] = []; end;
1365                                     #    special_positions[ap.index].push(...)
1366                                     (special_positions[ap.index] ||= []).push([isym, -nx, -ny, -nz])
1367                                   end
1368                             }
1369                             if verbose && special_positions[ap.index]
1370                               puts "#{name} is on the special position: #{special_positions[ap.index].inspect}"
1371                             end
1372                           }
1373                           puts "#{mol.natoms} atoms are created." if verbose
1374                     elsif labels[0] =~ /^_atom_site_aniso_label/
1375                       #  Set anisotropic parameters
1376                           c = 0
1377                           data.each { |d|
1378                             name = d[hlabel["_atom_site_aniso_label"]]
1379                             ap = find_atom_by_name(mol, name)
1380                             next if !ap
1381                             u11 = d[hlabel["_atom_site_aniso_U_11"]]
1382                             if u11
1383                               usig = []
1384                               u11, usig[0] = float_strip_rms(u11)
1385                               u22, usig[1] = float_strip_rms(d[hlabel["_atom_site_aniso_U_22"]])
1386                               u33, usig[2] = float_strip_rms(d[hlabel["_atom_site_aniso_U_33"]])
1387                               u12, usig[3] = float_strip_rms(d[hlabel["_atom_site_aniso_U_12"]])
1388                               u13, usig[4] = float_strip_rms(d[hlabel["_atom_site_aniso_U_13"]])
1389                               u23, usig[5] = float_strip_rms(d[hlabel["_atom_site_aniso_U_23"]])
1390                               ap.aniso = [u11, u22, u33, u12, u13, u23, 8] + usig
1391                                   c += 1
1392                             end
1393                           }
1394                           puts "#{c} anisotropic parameters are set." if verbose
1395                     elsif labels[0] =~ /^_geom_bond/
1396                       #  Create bonds
1397                           exbonds = []
1398                           data.each { |d|
1399                             n1 = d[hlabel["_geom_bond_atom_site_label_1"]]
1400                             n2 = d[hlabel["_geom_bond_atom_site_label_2"]]
1401                             sym1 = d[hlabel["_geom_bond_site_symmetry_1"]] || "."
1402                             sym2 = d[hlabel["_geom_bond_site_symmetry_2"]] || "."
1403                             n1 = find_atom_by_name(mol, n1)
1404                             n2 = find_atom_by_name(mol, n2)
1405                             next if n1 == nil || n2 == nil
1406                         n1 = n1.index
1407                             n2 = n2.index
1408                             sym1 = parse_symmetry_operation(sym1)
1409                             sym2 = parse_symmetry_operation(sym2)
1410                             if sym1 || sym2
1411                               exbonds.push([n1, n2, sym1, sym2])
1412                             else
1413                               mol.create_bond(n1, n2)
1414                             end
1415                             tr1 = (sym1 ? mol.transform_for_symop(sym1) : Transform.identity)
1416                             tr2 = (sym2 ? mol.transform_for_symop(sym2) : Transform.identity)
1417                             if special_positions[n1]
1418                                   #  Add extra bonds for equivalent positions of n1
1419                                   special_positions[n1].each { |symop|
1420                                     sym2x = mol.symop_for_transform(tr1 * mol.transform_for_symop(symop) * tr1.inverse * tr2)
1421                                     exbonds.push([n1, n2, sym1, sym2x])
1422                                   }
1423                             end
1424                             if special_positions[n2]
1425                                   #  Add extra bonds n2-n1.symop, where symop transforms n2 to self
1426                                   tr = (sym1 ? mol.transform_for_symop(sym1) : Transform.identity)
1427                                   special_positions[n2].each { |symop|
1428                                     sym1x = mol.symop_for_transform(tr2 * mol.transform_for_symop(symop) * tr2.inverse * tr1)
1429                                     exbonds.push([n2, n1, sym2, sym1x])
1430                                   }
1431                             end
1432                       }
1433               if mol.nbonds > 0
1434                 bond_defined = true
1435               end
1436                           puts "#{mol.nbonds} bonds are created." if verbose
1437                           if calculated_atoms.length > 0
1438                             #  Guess bonds for calculated hydrogen atoms
1439                             n1 = 0
1440                             calculated_atoms.each { |ai|
1441                               if mol.atoms[ai].connects.length == 0
1442                                     as = mol.find_close_atoms(ai)
1443                                     as.each { |aj|
1444                                       mol.create_bond(ai, aj)
1445                                           n1 += 1
1446                                     }
1447                                   end
1448                             }
1449                             puts "#{n1} bonds are guessed." if verbose
1450                           end
1451                           if exbonds.length > 0
1452                             h = Dialog.run("CIF Import: Symmetry Expansion") {
1453                               layout(1,
1454                                     item(:text, :title=>"There are bonds including symmetry related atoms.\nWhat do you want to do?"),
1455                                     item(:radio, :title=>"Expand only atoms that are included in those extra bonds.", :tag=>"atoms_only"),
1456                                     item(:radio, :title=>"Expand fragments having atoms included in the extra bonds.", :tag=>"fragment", :value=>1),
1457                                     item(:radio, :title=>"Ignore these extra bonds.", :tag=>"ignore")
1458                                   )
1459                                   radio_group("atoms_only", "fragment", "ignore")
1460                             }
1461                             if h[:status] == 0 && h["ignore"] == 0
1462                               atoms_only = (h["atoms_only"] != 0)
1463                                   if !atoms_only
1464                                     fragments = []
1465                                     mol.each_fragment { |f| fragments.push(f) }
1466                                   end
1467                                   debug = nil
1468                                   exbonds.each { |ex|
1469                                     if debug; puts "extra bond #{ex[0]}(#{ex[2].inspect}) - #{ex[1]}(#{ex[3].inspect})"; end
1470                                     ex0 = ex.dup
1471                                     (2..3).each { |i|
1472                                       symop = ex[i]
1473                                           if symop == nil
1474                                             ex[i + 2] = ex[i - 2]
1475                                           else
1476                                             if debug; puts "  symop = #{symop.inspect}"; end
1477                                             #  Expand the atom or the fragment including the atom
1478                                             if atoms_only
1479                                                   ig = IntGroup[ex[i - 2]]
1480                                                   idx = 0
1481                                             else
1482                                                   ig = fragments.find { |f| f.include?(ex[i - 2]) }
1483                                                   ig.each_with_index { |n, ii| if n == ex[i - 2]; idx = ii; break; end }
1484                                             end
1485                                             symop[4] = ex[i - 2]  #  Base atom
1486                                             if debug; puts "  expanding #{ig} by #{symop.inspect}"; end
1487                                             a = mol.expand_by_symmetry(ig, symop[0], symop[1], symop[2], symop[3])
1488                                             ex[i + 2] = a[idx]   #  Index of the expanded atom
1489                                           end
1490                                     }
1491                                     if ex[4] && ex[5] && ex[4] != ex[5]
1492                                       if debug; puts "  creating bond #{ex[4]} - #{ex[5]}"; end
1493                                       mol.create_bond(ex[4], ex[5])
1494                                     end
1495                                   }
1496                             end
1497                           end
1498                           puts "#{mol.nbonds} bonds are created." if verbose
1499                     end
1500                     next
1501                   else
1502                   #  puts "Loop beginning with #{labels[0]} is skipped"
1503                   end
1504             else
1505               #  Skip this token
1506                   token = getciftoken(fp)
1507             end
1508             #  Skip tokens until next tag or reserved word is detected
1509             while token != nil && token[0] != ?_ && token[0] != ?#
1510                   token = getciftoken(fp)
1511             end
1512             next
1513           end
1514       if !bond_defined
1515                 mol.guess_bonds
1516           end
1517           if token != nil && token == data_identifier
1518             #  Process next molecule: open a new molecule and start adding atom on that
1519                 mol = Molecule.new
1520                 count_up += 1
1521                 (@aux_mols ||= []).push(mol)
1522                 next
1523           end
1524           break
1525         end
1526         fp.close
1527 #       self.undo_enabled = save_undo_enabled
1528         return true
1529   end
1530
1531   def dump(group = nil)
1532     def quote(str)
1533           if str == ""
1534             str = "\"\""
1535           else
1536             str = str.gsub(/%/, "%%")
1537                 str.gsub!(/ /, "%20")
1538                 str.gsub!(/\t/, "%09")
1539           end
1540           str
1541         end
1542         group = atom_group(group ? group : 0...natoms)
1543         s = ""
1544         group.each { |i|
1545           ap = atoms[i]
1546           s += sprintf("%4d %-7s %-4s %-4s %-2s %7.3f %7.3f %7.3f %6.3f [%s]\n",
1547                 ap.index, sprintf("%3s.%d", ap.res_name, ap.res_seq),
1548                 quote(ap.name), quote(ap.atom_type), quote(ap.element),
1549                 ap.r.x, ap.r.y, ap.r.z, ap.charge,
1550                 ap.connects.join(","))
1551         }
1552         print s
1553   end
1554
1555   def from_dump(arg)
1556     if natoms > 0
1557           raise "Molecule must be empty"
1558         end
1559     format = "index residue name atom_type element rx ry rz charge connects"
1560         keys = []
1561         resAtoms = Hash.new
1562         newBonds = []
1563         #  arg can be either a String or an array of String.
1564         #  Iterates for each line in the string or each member of the array.
1565         if arg.is_a?(String)
1566           arg = arg.split("\n")
1567         end
1568     arg.each { |line|
1569           if line =~ /^\#/
1570             format = line[1..-1]
1571                 keys = []
1572           end
1573           if keys.length == 0
1574             keys = format.split(" ").collect { |key| key.to_sym }
1575           end
1576           values = line.chomp.split(" ")
1577           next if values == nil || values.length == 0
1578           ap = create_atom(sprintf("X%03d", natoms))
1579           r = Vector3D[0, 0, 0]
1580           keys.each_index { |i|
1581             break if (value = values[i]) == nil
1582                 if value == "\"\""
1583                   value = ""
1584                 else
1585                   value.gsub(/%09/, "\t")
1586                   value.gsub(/%20/, " ")
1587                   value.gsub(/%%/, "%")
1588                 end
1589                 key = keys[i]
1590                 if key == :residue
1591                   if resAtoms[value] == nil
1592                     resAtoms[value] = []
1593                   end
1594                   resAtoms[value].push(ap.index)
1595                 elsif key == :rx
1596                   r.x = value.to_f
1597                 elsif key == :ry
1598                   r.y = value.to_f
1599                 elsif key == :rz
1600                   r.z = value.to_f
1601                 elsif key == :connects
1602                   value.scan(/\d+/).each { |i|
1603                     i = i.to_i
1604                     if ap.index < i
1605                           newBonds.push(ap.index)
1606                           newBonds.push(i)
1607                         end
1608                   }
1609                 elsif key == :index
1610                   next
1611                 else
1612                   ap.set_attr(key, value)
1613                 end
1614           }
1615           ap.r = r
1616         }
1617         resAtoms.each_key { |key|
1618           assign_residue(atom_group(resAtoms[key]), key)
1619         }
1620         create_bond(*newBonds)
1621         self
1622   end
1623
1624   #  Plug-in for loading mbsf
1625   def loadmbsf_plugin(s, lineno)
1626     ""
1627   end
1628
1629   #  Plug-in for saving mbsf
1630   def savembsf_plugin
1631     ""
1632   end
1633
1634 end