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   #  If mo_path is not nil, then clear existing mo info and load from mo_path
 784   def sub_load_janpa_log(inppath, mo_path = nil)
 785     begin
 786       if mo_path
 787         fp = File.open(mo_path, "rt") rescue fp = nil
 788         if fp == nil
 789           hide_progress_panel  #  Close if it is open
 790           message_box("Cannot open MO molden file #{mo_path}: " + $!.to_s)
 791           return false
 792         end
 793         @lineno = 0
 794         type = get_mo_info(:type)
 795         alpha = get_mo_info(:alpha)
 796         beta = get_mo_info(:beta)
 797         clear_basis_set
 798         set_mo_info(:type=>type, :alpha=>alpha, :beta=>beta)
 799         #  mol.@hf_type should be set before calling sub_load_molden
 800         @hf_type = type
 801         sub_load_molden(fp)
 802         fp.close
 803       end
 804       fp = File.open(inppath + ".janpa.log", "rt") rescue fp = nil
 805       if fp == nil
 806         hide_progress_panel  #  Close if it is open
 807         message_box("Cannot open JANPA log file #{inppath + '.janpa.log'}: " + $!.to_s)
 808         return false
 809       end
 810       print("Importing #{inppath}.janpa.log.\n")
 811       lineno = 0
 812       getline = lambda { lineno += 1; return fp.gets }
 813       h = Hash.new
 814       mfiles = Hash.new
 815       h["software"] = "JANPA"
 816       nao_num = nil  #  Set later
 817       nao_infos = [] #  index=atom_index, value=Hash with key "s", "px", "py" etc.
 818       #  nao_infos[index][key]: array of [nao_num, occupancy], in the reverse order of appearance
 819       while line = getline.call
 820         if line =~ /^NAO \#/
 821           h["NAO"] = []
 822           while line = getline.call
 823             break if line !~ /^\s*[1-9]/
 824             num = Integer(line[0, 5])
 825             name = line[5, 21]
 826             occ = Float(line[26, 11])
 827             #  like A1*: R1*s(0)
 828             #  atom_number, occupied?, group_number, orb_sym, angular_number
 829             name =~ /\s*[A-Z]+([0-9]+)(\*?):\s* R([0-9]+)\*([a-z]+)\(([-0-9]+)\)/
 830             anum = Integer($1)
 831             occupied = $2
 832             group_num = Integer($3)
 833             orb_sym = $4
 834             ang_num = Integer($5)
 835             orb_desc = orb_sym
 836             if orb_desc == "p"
 837               orb_desc += ["z", "x", "y"][ang_num + 1]
 838             elsif orb_desc == "d"
 839             #  TODO: handle d, f, g orbitals
 840             end
 841             h["NAO"].push([num, anum, occupied, group_num, orb_desc, occ])
 842             nao_num = h["NAO"].length
 843             ((nao_infos[anum - 1] ||= Hash.new)[orb_desc] ||= []).unshift([nao_num, occ])
 844           end
 845           #  Create labels
 846           h["NAO_L"] = []
 847           nao_infos.each_with_index { |value, atom_index|
 848             aname = self.atoms[atom_index].name
 849             value.each { |orb_desc, ar|
 850               ar.each_with_index { |v, group_index|
 851                 if v[1] > 1.9
 852                   label = "core"
 853                 elsif v[1] > 0.01
 854                   label = "val"
 855                 else
 856                   label = "ryd"
 857                 end
 858                 principle = group_index + 1
 859                 orb_sym = orb_desc[0]
 860                 if orb_sym == "p"
 861                   principle += 1
 862                 elsif orb_sym == "d"
 863                   principle += 2
 864                 elsif orb_sym == "f"
 865                   principle += 3
 866                 elsif orb_sym == "g"
 867                   principle += 4
 868                 end
 869                 h["NAO_L"][v[0] - 1] = "#{aname} (#{principle}#{orb_desc}) (#{label})"
 870               }
 871             }
 872           }
 873         elsif line =~ /^\s*(C?)LPO\s+D e s c r i p t i o n\s+Occupancy\s+Composition/
 874           if $1 == "C"
 875             key = "CLPO"
 876           else
 877             key = "LPO"
 878           end
 879           h[key] = []
 880           while line = getline.call
 881             break if line =~ /^\s*$/
 882             num = Integer(line[0, 5])
 883             label1 = line[5, 6].strip
 884             desc = line[11, 30].strip
 885             occ = line[41, 11].strip
 886             comp = line[52, 1000].strip
 887             desc =~ /\s*([-A-Za-z0-9]+)(,\s*(.*$))?/
 888             desc1 = $1
 889             desc2 = ($3 || "")
 890             if desc2 =~ /^(.*)*\(NB\)\s*$/ && label1 == ""
 891               label1 = "(NB)"
 892               desc2 = $1.strip
 893             end
 894             atoms = desc1.scan(/[A-Za-z]+(\d+)/)   # "C1-H3" -> [["1"], ["3"]]
 895             atoms = atoms.map { |a| Integer(a[0]) }  # [1, 3]
 896             hybrids_a = comp.scan(/h(\d+)@[A-Za-z]+(\d+)/)  #  "h8@C1...h13@H3" -> "[["8", "1"], ["13", "3"]]
 897             hybrids = []
 898             hybrids_a.each { |a|
 899               i = atoms.find_index(Integer(a[1]))
 900               if i != nil
 901                 hybrids[i] = Integer(a[0])
 902               end
 903             } # [8, 13]
 904             #  like ["(BD)", [1, 3], "Io = 0.2237", occ, [8, 13]]
 905             #  1, 3 are the atom indices (1-based)
 906             #  8, 13 are the number of hybrid orbitals (1-based)
 907             h[key][num - 1] = [label1, atoms, desc2, Float(occ), hybrids]
 908           end
 909           h[key + "_L"] = []
 910           if key == "CLPO"
 911             #  Also register labels of "LHO"
 912             h["LHO_L"] = [""] * nao_num
 913           end
 914           nao_num.times { |i|
 915             val = h[key][i]
 916             if val == nil
 917               label = ""  #  The labels for Rydberg orbitals may be replaced later
 918             else
 919               aname1 = self.atoms[val[1][0] - 1].name rescue aname1 = ""
 920               aname2 = self.atoms[val[1][1] - 1].name rescue aname2 = ""
 921               if aname2 == ""
 922                 label = "#{aname1} #{val[0]}"
 923               else
 924                 label = "#{aname1}(#{aname2}) #{val[0]}"
 925               end
 926             end
 927             h[key + "_L"][i] = label
 928             if key == "CLPO" && val != nil && val[0] != "(NB)"
 929               hybrids = val[4]
 930               kind = (val[0] == "(BD)" ? "(val)" : "(lp)")
 931               if aname2 == ""
 932                 label = "#{aname1} #{kind}"
 933               else
 934                 label = "#{aname1}(#{aname2}) #{kind}"
 935               end
 936               h["LHO_L"][hybrids[0] - 1] = label
 937               if hybrids[1] != nil
 938                 #  aname2 should be non-empty
 939                 label = "#{aname2}(#{aname1}) #{kind}"
 940                 h["LHO_L"][hybrids[1] - 1] = label
 941               end
 942             end
 943           }
 944         elsif line =~ /^ -NAO_Molden_File: (\S*)/
 945           mfiles["NAO"] = $1
 946         elsif line =~ /^ -LHO_Molden_File: (\S*)/
 947           mfiles["LHO"] = $1
 948         elsif line =~ /^ -CLPO_Molden_File: (\S*)/
 949           mfiles["CLPO"] = $1
 950         elsif line =~ /^ -PNAO_Molden_File: (\S*)/
 951           mfiles["PNAO"] = $1
 952         elsif line =~ /^ -AHO_Molden_File: (\S*)/
 953           mfiles["AHO"] = $1
 954         elsif line =~ /^ -LPO_Molden_File: (\S*)/
 955           mfiles["LPO"] = $1
 956         end
 957       end
 958       fp.close
 959       #  Read molden files
 960       mfiles.each { |key, value|
 961         fp = Kernel.open(value, "rt") rescue fp = nil
 962         if fp
 963           print("Importing #{value}.\n")
 964           res = sub_load_molden(fp, key)
 965           if res
 966             #  Some kind of orbital based on AO
 967             h["AO/#{key}"] = LAMatrix.new(res[:mo])
 968           end
 969           fp.close
 970           if key == "CLPO" || key == "LPO" || key == "LHO"
 971             #  Set the label of Rydberg orbitals if possible
 972             if h[key + "_L"] != nil
 973               a = h["AO/#{key}"]
 974               nao_num.times { |i|
 975                 label = h[key + "_L"][i]
 976                 if label == ""
 977                   max_idx = nil
 978                   max_val = -1.0
 979                   nao_infos.each_with_index { |inf, atom_index|
 980                     atomic_contrib = 0.0
 981                     inf.each { |k, v| # k is "s", "px" etc, v is array of [nao_num, occupancy]
 982                       #  Sum for all naos belonging to this atom
 983                       v.each { |num_occ|
 984                         atomic_contrib += a[i, num_occ[0] - 1] ** 2
 985                       }
 986                     }
 987                     if atomic_contrib > max_val
 988                       max_val = atomic_contrib
 989                       max_idx = atom_index
 990                     end
 991                   }
 992                   label = self.atoms[max_idx].name + " (ry)"
 993                   h[key + "_L"][i] = label
 994                 end
 995               }
 996             end
 997           end
 998         end
 999       }
1000       @nbo = h
1001       if @nbo["AO/NAO"] && @nbo["AO/LHO"] && @nbo["AO/PNAO"]
1002         #  Generate PLHO from PNAO, NAO, LHO
1003         #  This protocol was suggested by the JANPA author in a private commnunication.
1004         begin
1005           nao2lho = @nbo["AO/NAO"].inverse * @nbo["AO/LHO"]
1006           nao2pnao = @nbo["AO/NAO"].inverse * @nbo["AO/PNAO"]
1007           sign = LAMatrix.diagonal((0...nao2pnao.column_size).map { |i| (nao2pnao[i, i] < 0 ? -1 : 1)})
1008           @nbo["AO/PLHO"] = @nbo["AO/PNAO"] * sign * nao2lho
1009         rescue
1010           @nbo["AO/PLHO"] = nil
1011         end
1012       end
1013       return true
1014     rescue => e
1015       $stderr.write(e.message + "\n")
1016       $stderr.write(e.backtrace.inspect + "\n")
1017     end
1018   end
1019
1020   def loadout(filename)
1021   retval = false
1022   fp = open(filename, "rb")
1023   @lineno = 0
1024   begin
1025     while s = fp.gets
1026       @lineno += 1
1027       if s =~ /Gaussian/
1028         retval = sub_load_gaussian_log(fp)
1029         break
1030       elsif s =~ /GAMESS/
1031         retval = sub_load_gamess_log(fp)
1032         break
1033       elsif s =~ /Psi4/
1034         retval = sub_load_psi4_log(fp)
1035         if retval
1036           #  If .molden file exists, then try to read it
1037           namepath = filename.gsub(/\.\w*$/, "")
1038           mname = "#{namepath}.molden"
1039           if File.exists?(mname)
1040             fp2 = open(mname, "rb")
1041             if fp2
1042               flag = sub_load_molden(fp2)
1043               fp2.close
1044               status = (flag ? 0 : -1)
1045             end
1046           end
1047           if File.exists?("#{namepath}.janpa.log")
1048             flag = sub_load_janpa_log(namepath)
1049             status = (flag ? 0 : -1)
1050           end
1051         end
1052         break
1053       end
1054     end
1055   rescue
1056     hide_progress_panel
1057     raise
1058   end
1059         fp.close
1060         return retval
1061   end
1062
1063   alias :loadlog :loadout
1064
1065   def loadxyz(filename)
1066         fp = open(filename, "rb")
1067         n = 0
1068         coords = []
1069         names = []
1070         cell = nil
1071         while 1
1072           line = fp.gets
1073           if line == nil
1074                 fp.close
1075                 break
1076           end
1077           line.chomp
1078           toks = line.split
1079           if coords.length == 0
1080             #  Allow "number of atoms" line or "number of atoms and crystallographic cell parameter"
1081                 #  (Chem3D xyz format)
1082                 next if toks.length == 1
1083                 if toks.length == 7
1084                   cell = toks[1..6].map { |s| Float(s.sub(/\(\d+\)/, "")) }  #  Remove (xx) and convert to float
1085                   next
1086                 end
1087           end
1088           name, x, y, z = line.split
1089           next if z == nil
1090           x = Float(x.sub(/\(\d+\)/, ""))
1091           y = Float(y.sub(/\(\d+\)/, ""))
1092           z = Float(z.sub(/\(\d+\)/, ""))
1093           r = Vector3D[x, y, z]
1094           coords.push(r)
1095           names.push(name)
1096           n += 1
1097         end
1098         celltr = nil
1099         if cell
1100           self.cell = cell
1101           celltr = self.cell_transform
1102         end
1103         names.each_index { |i|
1104           ap = add_atom(names[i])
1105           names[i] =~ /^([A-Za-z]{1,2})/
1106           element = $1.capitalize
1107           ap.element = element
1108           ap.atom_type = element
1109           if celltr
1110             ap.r = celltr * coords[i]
1111           else
1112             ap.r = coords[i]
1113           end
1114         }
1115         guess_bonds
1116         #  Find bonds
1117 #       atoms.each { |ap|
1118 #         j = ap.index
1119 #         (j + 1 ... natoms).each { |k|
1120 #               if calc_bond(j, k) < 1.7
1121 #               #  create_bond(j, k)
1122 #               end
1123 #         }
1124 #       }
1125 #       self.undo_enabled = save_undo_enabled
1126         (n > 0 ? true : false)
1127   end
1128
1129   def savexyz(filename)
1130     open(filename, "wb") { |fp|
1131           fp.printf "%d\n", self.natoms
1132           each_atom { |ap|
1133             fp.printf "%s %.5f %.5f %.5f\n", ap.element, ap.x, ap.y, ap.z
1134           }
1135         }
1136         return true
1137   end
1138
1139   def loadzmat(filename)
1140     self.remove(All)
1141         open(filename, "rb") { |fp|
1142           while (line = fp.gets)
1143             line.chomp!
1144                 a = line.split
1145                 an = Molecule.guess_atomic_number_from_name(a[0])
1146                 elm = Parameter.builtin.elements[an].name
1147                 base1 = a[1].to_i - 1
1148                 base2 = a[3].to_i - 1
1149                 base3 = a[5].to_i - 1
1150                 base1 = nil if base1 < 0
1151                 base2 = nil if base2 < 0
1152                 base3 = nil if base3 < 0
1153                 add_atom(a[0], elm, elm, a[2].to_f, base1, a[4].to_f, base2, a[6].to_f, base3)
1154           end
1155         }
1156         return true
1157   end
1158
1159   def savezmat(filename)
1160   end
1161
1162   def loadcom(filename)
1163 #       save_undo_enabled = self.undo_enabled?
1164 #       self.undo_enabled = false
1165         self.remove(All)
1166         fp = open(filename, "rb")
1167         section = 0
1168         while (line = fp.gets)
1169           line.chomp!
1170           if section == 0
1171             section = 1 if line =~ /^\#/
1172                 next
1173           elsif section == 1 || section == 2
1174             section += 1 if line =~ /^\s*$/
1175                 next
1176           else
1177             #  The first line is skipped (charge and multiplicity)
1178                 while (line = fp.gets)
1179                   line.chomp!
1180                   break if line =~ /^\s*$/
1181                   a = line.split(/\s*[ \t,\/]\s*/)
1182                   r = Vector3D[Float(a[1]), Float(a[2]), Float(a[3])]
1183                   ap = add_atom(a[0])
1184                   a[0] =~ /^([A-Za-z]{1,2})/
1185                   element = $1.capitalize
1186               ap.element = element
1187               ap.atom_type = element
1188               ap.r = r
1189                 end
1190                 break
1191           end
1192         end
1193         fp.close
1194         guess_bonds
1195 #       self.undo_enabled = save_undo_enabled
1196         return true
1197   end
1198
1199   def loadinp(filename)
1200 #       save_undo_enabled = self.undo_enabled?
1201 #       self.undo_enabled = false
1202         self.remove(All)
1203         fp = open(filename, "rb")
1204         section = 0
1205         has_basis = false
1206         while (line = fp.gets)
1207           if line =~ /\A \$BASIS/
1208             has_basis = true
1209                 next
1210           end
1211           next if line !~ /\A \$DATA/
1212           line = fp.gets   #  Title line
1213           line = fp.gets   #  Symmetry line
1214           while (line = fp.gets)
1215 #           puts line
1216             line.chomp!
1217                 break if line =~ /\$END/
1218                 a = line.split
1219                 ap = add_atom(a[0])
1220                 ap.atomic_number = Integer(a[1])
1221                 ap.atom_type = ap.element
1222                 r = Vector3D[Float(a[2]), Float(a[3]), Float(a[4])]
1223                 ap.r = r;
1224                 if !has_basis
1225                   #  Skip until one blank line is detected
1226                   while (line = fp.gets) && line =~ /\S/
1227                   end
1228                 end
1229       end
1230           break
1231         end
1232         fp.close
1233         guess_bonds
1234 #       self.undo_enabled = save_undo_enabled
1235         return true
1236   end
1237
1238   def saveinp(filename)
1239     if natoms == 0
1240       raise MolbyError, "cannot save GAMESS input; the molecule is empty"
1241     end
1242     fp = open(filename, "wb")
1243         now = Time.now.to_s
1244         fp.print <<end_of_header
1245 !  GAMESS input
1246 !  Generated by Molby at #{now}
1247  $CONTRL COORD=UNIQUE EXETYP=RUN ICHARG=0
1248          ICUT=20 INTTYP=HONDO ITOL=30
1249          MAXIT=200 MOLPLT=.T. MPLEVL=0
1250          MULT=1 QMTTOL=1e-08 RUNTYP=OPTIMIZE
1251          SCFTYP=RHF UNITS=ANGS                  $END
1252  $SCF    CONV=1.0E-06 DIRSCF=.T.                $END
1253  $STATPT NSTEP=400 OPTTOL=1.0E-06               $END
1254  $SYSTEM MEMDDI=0 MWORDS=16 TIMLIM=50000        $END
1255  $BASIS  GBASIS=N31 NDFUNC=1 NGAUSS=6           $END
1256  $GUESS  GUESS=HUCKEL                           $END
1257 !
1258  $DATA
1259  #{name}
1260  C1
1261 end_of_header
1262         each_atom { |ap|
1263                 next if ap.atomic_number == 0
1264                 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
1265         }
1266         fp.print " $END\n"
1267         fp.close
1268         return true
1269   end
1270
1271   def savecom(filename)
1272     if natoms == 0
1273       raise MolbyError, "cannot save Gaussian input; the molecule is empty"
1274     end
1275     fp = open(filename, "wb")
1276         base = File.basename(filename, ".*")
1277         fp.print <<end_of_header
1278 %Chk=#{base}.chk
1279 \# PM3 Opt
1280
1281  #{name}; created by Molby at #{Time.now.to_s}
1282
1283  0 1
1284 end_of_header
1285         each_atom { |ap|
1286             next if ap.atomic_number == 0
1287                 fp.printf "%-6s %10.6f %10.6f %10.6f\n", ap.element, ap.r.x, ap.r.y, ap.r.z
1288         }
1289         fp.print "\n"
1290         fp.close
1291         return true
1292   end
1293
1294   alias :loadgjf :loadcom
1295   alias :savegjf :savecom
1296
1297   def loadcif(filename)
1298     mol = self
1299     def getciftoken(fp)
1300           while @tokens.length == 0
1301             line = fp.gets
1302             return nil if !line
1303                 if line[0] == ?;
1304                   s = line
1305                   while line = fp.gets
1306                     break if line[0] == ?;
1307                     s += line
1308                   end
1309                   return s if !line
1310                   s += ";"
1311                   @tokens.push(s)
1312                   line = line[1...line.length]
1313                 end
1314             line.strip!
1315             line.scan(/'[^\']*'|"[^\"]*"|[^#\s]+|#.*/) do |s|
1316               next if s[0] == ?#
1317                   if s =~ /^data_|loop_|global_|save_|stop_/i
1318                     s = "#" + s    #  Label for reserved words
1319                   end
1320                   @tokens.push(s)
1321             end
1322           end
1323           return @tokens.shift
1324         end
1325         def float_strip_rms(str)
1326           str =~ /^(-?)(\d*)(\.(\d*))?(\((\d+)\))?$/
1327           sgn, i, frac, rms = $1, $2, $4, $6
1328           i = i.to_f
1329           if frac
1330                 base = 0.1 ** frac.length
1331                 i = i + frac.to_f * base
1332           else
1333             base = 1.0
1334           end
1335           if rms
1336             rms = rms.to_f * base
1337           else
1338             rms = 0.0
1339           end
1340           if sgn == "-"
1341             i = -i
1342           end
1343           return i, rms
1344         end
1345         def parse_symmetry_operation(str)
1346           if str == "."
1347             sym = nil
1348           elsif (str =~ /(\d+)_(\d)(\d)(\d)/) || (str =~ /(\d+) +(\d)(\d)(\d)/)
1349             sym = [Integer($1) - 1, Integer($2) - 5, Integer($3) - 5, Integer($4) - 5]
1350           elsif (str =~ /^(\d+)$/)
1351             sym = [Integer($1) - 1, 0, 0, 0]
1352           end
1353           if sym && (sym[0] == 0 && sym[1] == 0 && sym[2] == 0 && sym[3] == 0)
1354             sym = nil
1355           end
1356           sym
1357         end
1358         def find_atom_by_name(mol, name)
1359           name = name.delete(" ()")
1360           ap = mol.atoms[name] rescue ap = nil
1361           return ap
1362         end
1363         selfname = self.name
1364         fp = open(filename, "rb")
1365         data_identifier = nil
1366         @tokens = []
1367         count_up = 1
1368         while true
1369           warn_message = ""
1370           verbose = nil
1371           bond_defined = false
1372           special_positions = []
1373           mol.remove(All)
1374           cell = []
1375           cell_trans = cell_trans_inv = Transform.identity
1376           token = getciftoken(fp)
1377           pardigits_re = /\(\d+\)/
1378           calculated_atoms = []
1379           while token != nil
1380             if token =~ /^\#data_/i
1381                   if data_identifier == nil || mol.natoms == 0
1382                     #  First block or no atoms yet
1383             #  Continue processing of this molecule
1384                     data_identifier = token
1385                         token = getciftoken(fp)
1386                         next
1387                   else
1388                     #  Description of another molecule begins here
1389                         data_identifier = token
1390                         break
1391                   end
1392             elsif token =~ /^_cell/
1393                   val = getciftoken(fp)
1394                   if token == "_cell_length_a"
1395                     cell[0], cell[6] = float_strip_rms(val)
1396                   elsif token == "_cell_length_b"
1397                     cell[1], cell[7] = float_strip_rms(val)
1398                   elsif token == "_cell_length_c"
1399                     cell[2], cell[8] = float_strip_rms(val)
1400                   elsif token == "_cell_angle_alpha"
1401                     cell[3], cell[9] = float_strip_rms(val)
1402                   elsif token == "_cell_angle_beta"
1403                     cell[4], cell[10] = float_strip_rms(val)
1404                   elsif token == "_cell_angle_gamma"
1405                     cell[5], cell[11] = float_strip_rms(val)
1406                   end
1407                   if cell.length == 12 && cell.all?
1408                     mol.cell = cell
1409             puts "Unit cell is set to #{mol.cell.inspect}." if verbose
1410                     cell = []
1411                     cell_trans = mol.cell_transform
1412                     cell_trans_inv = cell_trans.inverse
1413                   end
1414                   token = getciftoken(fp)
1415                   next
1416         elsif token.casecmp("#loop_") == 0
1417               labels = []
1418                   while (token = getciftoken(fp)) && token[0] == ?_
1419                     labels.push(token)
1420                   end
1421                   if labels[0] =~ /symmetry_equiv_pos|space_group_symop|atom_site_label|atom_site_aniso_label|geom_bond/
1422                     hlabel = Hash.new(-10000000)
1423                     labels.each_with_index { |lb, i|
1424                           hlabel[lb] = i
1425                     }
1426                     data = []
1427                     n = labels.length
1428                     a = []
1429                     while true
1430                           break if token == nil || token[0] == ?_ || token[0] == ?#
1431                           a.push(token)
1432                           if a.length == n
1433                             data.push(a)
1434                             a = []
1435                           end
1436                           token = getciftoken(fp)
1437                     end
1438                     if labels[0] =~ /^_symmetry_equiv_pos/ || labels[0] =~ /^_space_group_symop/
1439                       data.each { |d|
1440                             symstr = d[hlabel["_symmetry_equiv_pos_as_xyz"]] || d[hlabel["_space_group_symop_operation_xyz"]]
1441                             symstr.delete("\"\'")
1442                             exps = symstr.split(/,/)
1443                             sym = [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
1444                             exps.each_with_index { |s, i|
1445                               terms = s.scan(/([-+]?)(([.0-9]+)(\/([0-9]+))?([xXyYzZ])?|([xXyYzZ]))/)
1446                                   terms.each { |a|
1447                                     #  a[0]: sign, a[2]: numerator, a[4]: denometer
1448                                     if a[4] != nil
1449                                       #  The number part is a[2]/a[4]
1450                                       num = Float(a[2])/Float(a[4])
1451                                     elsif a[2] != nil
1452                                       #  The number part is either integer or a floating point
1453                                       num = Float(a[2])
1454                                     else
1455                                       num = 1.0
1456                                     end
1457                                     num = -num if a[0][0] == ?-
1458                                     xyz = (a[5] || a[6])
1459                                     if xyz == "x" || xyz == "X"
1460                                       sym[i] = num
1461                                     elsif xyz == "y" || xyz == "Y"
1462                                       sym[i + 3] = num
1463                                     elsif xyz == "z" || xyz == "Z"
1464                                       sym[i + 6] = num
1465                                     else
1466                                       sym[9 + i] = num
1467                                     end
1468                                   }
1469                             }
1470                             puts "symmetry operation #{sym.inspect}" if verbose
1471                             mol.add_symmetry(Transform.new(sym))
1472                           }
1473                           puts "#{mol.nsymmetries} symmetry operations are added" if verbose
1474                     elsif labels[0] =~ /^_atom_site_label/
1475                           #  Create atoms
1476                           data.each { |d|
1477                             name = d[hlabel["_atom_site_label"]]
1478                             elem = d[hlabel["_atom_site_type_symbol"]]
1479                             fx = d[hlabel["_atom_site_fract_x"]]
1480                             fy = d[hlabel["_atom_site_fract_y"]]
1481                             fz = d[hlabel["_atom_site_fract_z"]]
1482                             uiso = d[hlabel["_atom_site_U_iso_or_equiv"]]
1483                             biso = d[hlabel["_atom_site_B_iso_or_equiv"]]
1484                             occ = d[hlabel["_atom_site_occupancy"]]
1485                             calc = d[hlabel["_atom_site_calc_flag"]]
1486                             name = name.delete(" ()")
1487                             if elem == nil || elem == ""
1488                               if name =~ /[A-Za-z]{1,2}/
1489                                     elem = $&.capitalize
1490                                   else
1491                                     elem = "Du"
1492                                   end
1493                             end
1494                             ap = mol.add_atom(name, elem, elem)
1495                             ap.fract_x, ap.sigma_x = float_strip_rms(fx)
1496                             ap.fract_y, ap.sigma_y = float_strip_rms(fy)
1497                             ap.fract_z, ap.sigma_z = float_strip_rms(fz)
1498                             if biso
1499                               ap.temp_factor, sig = float_strip_rms(biso)
1500                             elsif uiso
1501                               ap.temp_factor, sig = float_strip_rms(uiso)
1502                                   ap.temp_factor *= 78.9568352087149          #  8*pi*pi
1503                             end
1504                             ap.occupancy, sig = float_strip_rms(occ)
1505                             if calc == "c" || calc == "calc"
1506                               calculated_atoms.push(ap.index)
1507                         end
1508                             #  Guess special positions
1509                             (1...mol.nsymmetries).each { |isym|
1510                               sr = ap.fract_r
1511                               sr = (mol.transform_for_symop(isym) * sr) - sr;
1512                                   nx = (sr.x + 0.5).floor
1513                                   ny = (sr.y + 0.5).floor
1514                                   nz = (sr.z + 0.5).floor
1515                                   if (Vector3D[sr.x - nx, sr.y - ny, sr.z - nz].length2 < 1e-6)
1516                                     #  [isym, -nx, -ny, -nz] transforms this atom to itself
1517                                     #  The following line is equivalent to:
1518                                     #    if special_positions[ap.index] == nil; special_positions[ap.index] = []; end;
1519                                     #    special_positions[ap.index].push(...)
1520                                     (special_positions[ap.index] ||= []).push([isym, -nx, -ny, -nz])
1521                                   end
1522                             }
1523                             if verbose && special_positions[ap.index]
1524                               puts "#{name} is on the special position: #{special_positions[ap.index].inspect}"
1525                             end
1526                           }
1527                           puts "#{mol.natoms} atoms are created." if verbose
1528                     elsif labels[0] =~ /^_atom_site_aniso_label/
1529                       #  Set anisotropic parameters
1530                           c = 0
1531                           data.each { |d|
1532                             name = d[hlabel["_atom_site_aniso_label"]]
1533                             ap = find_atom_by_name(mol, name)
1534                             next if !ap
1535                             u11 = d[hlabel["_atom_site_aniso_U_11"]]
1536                             if u11
1537                               usig = []
1538                               u11, usig[0] = float_strip_rms(u11)
1539                               u22, usig[1] = float_strip_rms(d[hlabel["_atom_site_aniso_U_22"]])
1540                               u33, usig[2] = float_strip_rms(d[hlabel["_atom_site_aniso_U_33"]])
1541                               u12, usig[3] = float_strip_rms(d[hlabel["_atom_site_aniso_U_12"]])
1542                               u13, usig[4] = float_strip_rms(d[hlabel["_atom_site_aniso_U_13"]])
1543                               u23, usig[5] = float_strip_rms(d[hlabel["_atom_site_aniso_U_23"]])
1544                               ap.aniso = [u11, u22, u33, u12, u13, u23, 8] + usig
1545                                   c += 1
1546                             end
1547                           }
1548                           puts "#{c} anisotropic parameters are set." if verbose
1549                     elsif labels[0] =~ /^_geom_bond/
1550                       #  Create bonds
1551                           exbonds = []
1552                           data.each { |d|
1553                             n1 = d[hlabel["_geom_bond_atom_site_label_1"]]
1554                             n2 = d[hlabel["_geom_bond_atom_site_label_2"]]
1555                             sym1 = d[hlabel["_geom_bond_site_symmetry_1"]] || "."
1556                             sym2 = d[hlabel["_geom_bond_site_symmetry_2"]] || "."
1557                             n1 = find_atom_by_name(mol, n1)
1558                             n2 = find_atom_by_name(mol, n2)
1559                             next if n1 == nil || n2 == nil
1560                         n1 = n1.index
1561                             n2 = n2.index
1562                             sym1 = parse_symmetry_operation(sym1)
1563                             sym2 = parse_symmetry_operation(sym2)
1564                             if sym1 || sym2
1565                               exbonds.push([n1, n2, sym1, sym2])
1566                             else
1567                               mol.create_bond(n1, n2)
1568                             end
1569                             tr1 = (sym1 ? mol.transform_for_symop(sym1) : Transform.identity)
1570                             tr2 = (sym2 ? mol.transform_for_symop(sym2) : Transform.identity)
1571                             if special_positions[n1]
1572                                   #  Add extra bonds for equivalent positions of n1
1573                                   special_positions[n1].each { |symop|
1574                                     sym2x = mol.symop_for_transform(tr1 * mol.transform_for_symop(symop) * tr1.inverse * tr2)
1575                                     exbonds.push([n1, n2, sym1, sym2x])
1576                                   }
1577                             end
1578                             if special_positions[n2]
1579                                   #  Add extra bonds n2-n1.symop, where symop transforms n2 to self
1580                                   tr = (sym1 ? mol.transform_for_symop(sym1) : Transform.identity)
1581                                   special_positions[n2].each { |symop|
1582                                     sym1x = mol.symop_for_transform(tr2 * mol.transform_for_symop(symop) * tr2.inverse * tr1)
1583                                     exbonds.push([n2, n1, sym2, sym1x])
1584                                   }
1585                             end
1586                       }
1587               if mol.nbonds > 0
1588                 bond_defined = true
1589               end
1590                           puts "#{mol.nbonds} bonds are created." if verbose
1591                           if calculated_atoms.length > 0
1592                             #  Guess bonds for calculated hydrogen atoms
1593                             n1 = 0
1594                             calculated_atoms.each { |ai|
1595                               if mol.atoms[ai].connects.length == 0
1596                                     as = mol.find_close_atoms(ai)
1597                                     as.each { |aj|
1598                                       mol.create_bond(ai, aj)
1599                                           n1 += 1
1600                                     }
1601                                   end
1602                             }
1603                             puts "#{n1} bonds are guessed." if verbose
1604                           end
1605                           if exbonds.length > 0
1606                             h = Dialog.run("CIF Import: Symmetry Expansion") {
1607                               layout(1,
1608                                     item(:text, :title=>"There are bonds including symmetry related atoms.\nWhat do you want to do?"),
1609                                     item(:radio, :title=>"Expand only atoms that are included in those extra bonds.", :tag=>"atoms_only"),
1610                                     item(:radio, :title=>"Expand fragments having atoms included in the extra bonds.", :tag=>"fragment", :value=>1),
1611                                     item(:radio, :title=>"Ignore these extra bonds.", :tag=>"ignore")
1612                                   )
1613                                   radio_group("atoms_only", "fragment", "ignore")
1614                             }
1615                             if h[:status] == 0 && h["ignore"] == 0
1616                               atoms_only = (h["atoms_only"] != 0)
1617                                   if !atoms_only
1618                                     fragments = []
1619                                     mol.each_fragment { |f| fragments.push(f) }
1620                                   end
1621                                   debug = nil
1622                                   exbonds.each { |ex|
1623                                     if debug; puts "extra bond #{ex[0]}(#{ex[2].inspect}) - #{ex[1]}(#{ex[3].inspect})"; end
1624                                     ex0 = ex.dup
1625                                     (2..3).each { |i|
1626                                       symop = ex[i]
1627                                           if symop == nil
1628                                             ex[i + 2] = ex[i - 2]
1629                                           else
1630                                             if debug; puts "  symop = #{symop.inspect}"; end
1631                                             #  Expand the atom or the fragment including the atom
1632                                             if atoms_only
1633                                                   ig = IntGroup[ex[i - 2]]
1634                                                   idx = 0
1635                                             else
1636                                                   ig = fragments.find { |f| f.include?(ex[i - 2]) }
1637                                                   ig.each_with_index { |n, ii| if n == ex[i - 2]; idx = ii; break; end }
1638                                             end
1639                                             symop[4] = ex[i - 2]  #  Base atom
1640                                             if debug; puts "  expanding #{ig} by #{symop.inspect}"; end
1641                                             a = mol.expand_by_symmetry(ig, symop[0], symop[1], symop[2], symop[3])
1642                                             ex[i + 2] = a[idx]   #  Index of the expanded atom
1643                                           end
1644                                     }
1645                                     if ex[4] && ex[5] && ex[4] != ex[5]
1646                                       if debug; puts "  creating bond #{ex[4]} - #{ex[5]}"; end
1647                                       mol.create_bond(ex[4], ex[5])
1648                                     end
1649                                   }
1650                             end
1651                           end
1652                           puts "#{mol.nbonds} bonds are created." if verbose
1653                     end
1654                     next
1655                   else
1656                   #  puts "Loop beginning with #{labels[0]} is skipped"
1657                   end
1658             else
1659               #  Skip this token
1660                   token = getciftoken(fp)
1661             end
1662             #  Skip tokens until next tag or reserved word is detected
1663             while token != nil && token[0] != ?_ && token[0] != ?#
1664                   token = getciftoken(fp)
1665             end
1666             next
1667           end
1668       if !bond_defined
1669                 mol.guess_bonds
1670           end
1671           if token != nil && token == data_identifier
1672             #  Process next molecule: open a new molecule and start adding atom on that
1673                 mol = Molecule.new
1674                 count_up += 1
1675                 (@aux_mols ||= []).push(mol)
1676                 next
1677           end
1678           break
1679         end
1680         fp.close
1681 #       self.undo_enabled = save_undo_enabled
1682         return true
1683   end
1684
1685   def dump(group = nil)
1686     def quote(str)
1687           if str == ""
1688             str = "\"\""
1689           else
1690             str = str.gsub(/%/, "%%")
1691                 str.gsub!(/ /, "%20")
1692                 str.gsub!(/\t/, "%09")
1693           end
1694           str
1695         end
1696         group = atom_group(group ? group : 0...natoms)
1697         s = ""
1698         group.each { |i|
1699           ap = atoms[i]
1700           s += sprintf("%4d %-7s %-4s %-4s %-2s %7.3f %7.3f %7.3f %6.3f [%s]\n",
1701                 ap.index, sprintf("%3s.%d", ap.res_name, ap.res_seq),
1702                 quote(ap.name), quote(ap.atom_type), quote(ap.element),
1703                 ap.r.x, ap.r.y, ap.r.z, ap.charge,
1704                 ap.connects.join(","))
1705         }
1706         print s
1707   end
1708
1709   def from_dump(arg)
1710     if natoms > 0
1711           raise "Molecule must be empty"
1712         end
1713     format = "index residue name atom_type element rx ry rz charge connects"
1714         keys = []
1715         resAtoms = Hash.new
1716         newBonds = []
1717         #  arg can be either a String or an array of String.
1718         #  Iterates for each line in the string or each member of the array.
1719         if arg.is_a?(String)
1720           arg = arg.split("\n")
1721         end
1722     arg.each { |line|
1723           if line =~ /^\#/
1724             format = line[1..-1]
1725                 keys = []
1726           end
1727           if keys.length == 0
1728             keys = format.split(" ").collect { |key| key.to_sym }
1729           end
1730           values = line.chomp.split(" ")
1731           next if values == nil || values.length == 0
1732           ap = create_atom(sprintf("X%03d", natoms))
1733           r = Vector3D[0, 0, 0]
1734           keys.each_index { |i|
1735             break if (value = values[i]) == nil
1736                 if value == "\"\""
1737                   value = ""
1738                 else
1739                   value.gsub(/%09/, "\t")
1740                   value.gsub(/%20/, " ")
1741                   value.gsub(/%%/, "%")
1742                 end
1743                 key = keys[i]
1744                 if key == :residue
1745                   if resAtoms[value] == nil
1746                     resAtoms[value] = []
1747                   end
1748                   resAtoms[value].push(ap.index)
1749                 elsif key == :rx
1750                   r.x = value.to_f
1751                 elsif key == :ry
1752                   r.y = value.to_f
1753                 elsif key == :rz
1754                   r.z = value.to_f
1755                 elsif key == :connects
1756                   value.scan(/\d+/).each { |i|
1757                     i = i.to_i
1758                     if ap.index < i
1759                           newBonds.push(ap.index)
1760                           newBonds.push(i)
1761                         end
1762                   }
1763                 elsif key == :index
1764                   next
1765                 else
1766                   ap.set_attr(key, value)
1767                 end
1768           }
1769           ap.r = r
1770         }
1771         resAtoms.each_key { |key|
1772           assign_residue(atom_group(resAtoms[key]), key)
1773         }
1774         create_bond(*newBonds)
1775         self
1776   end
1777
1778   #  Plug-in for loading mbsf
1779   def loadmbsf_plugin(s, lineno)
1780     ""
1781   end
1782
1783   #  Plug-in for saving mbsf
1784   def savembsf_plugin
1785     ""
1786   end
1787
1788 end