all messages for Guix-related lists mirrored at yhetil.org
 help / color / mirror / code / Atom feed
blob df96a2f5c1a7090ae4d62dfbd6f99bb2579f2894 52205 bytes (raw)
name: gnu/packages/chemistry.scm 	 # note: path name is non-authoritative(*)

   1
   2
   3
   4
   5
   6
   7
   8
   9
  10
  11
  12
  13
  14
  15
  16
  17
  18
  19
  20
  21
  22
  23
  24
  25
  26
  27
  28
  29
  30
  31
  32
  33
  34
  35
  36
  37
  38
  39
  40
  41
  42
  43
  44
  45
  46
  47
  48
  49
  50
  51
  52
  53
  54
  55
  56
  57
  58
  59
  60
  61
  62
  63
  64
  65
  66
  67
  68
  69
  70
  71
  72
  73
  74
  75
  76
  77
  78
  79
  80
  81
  82
  83
  84
  85
  86
  87
  88
  89
  90
  91
  92
  93
  94
  95
  96
  97
  98
  99
 100
 101
 102
 103
 104
 105
 106
 107
 108
 109
 110
 111
 112
 113
 114
 115
 116
 117
 118
 119
 120
 121
 122
 123
 124
 125
 126
 127
 128
 129
 130
 131
 132
 133
 134
 135
 136
 137
 138
 139
 140
 141
 142
 143
 144
 145
 146
 147
 148
 149
 150
 151
 152
 153
 154
 155
 156
 157
 158
 159
 160
 161
 162
 163
 164
 165
 166
 167
 168
 169
 170
 171
 172
 173
 174
 175
 176
 177
 178
 179
 180
 181
 182
 183
 184
 185
 186
 187
 188
 189
 190
 191
 192
 193
 194
 195
 196
 197
 198
 199
 200
 201
 202
 203
 204
 205
 206
 207
 208
 209
 210
 211
 212
 213
 214
 215
 216
 217
 218
 219
 220
 221
 222
 223
 224
 225
 226
 227
 228
 229
 230
 231
 232
 233
 234
 235
 236
 237
 238
 239
 240
 241
 242
 243
 244
 245
 246
 247
 248
 249
 250
 251
 252
 253
 254
 255
 256
 257
 258
 259
 260
 261
 262
 263
 264
 265
 266
 267
 268
 269
 270
 271
 272
 273
 274
 275
 276
 277
 278
 279
 280
 281
 282
 283
 284
 285
 286
 287
 288
 289
 290
 291
 292
 293
 294
 295
 296
 297
 298
 299
 300
 301
 302
 303
 304
 305
 306
 307
 308
 309
 310
 311
 312
 313
 314
 315
 316
 317
 318
 319
 320
 321
 322
 323
 324
 325
 326
 327
 328
 329
 330
 331
 332
 333
 334
 335
 336
 337
 338
 339
 340
 341
 342
 343
 344
 345
 346
 347
 348
 349
 350
 351
 352
 353
 354
 355
 356
 357
 358
 359
 360
 361
 362
 363
 364
 365
 366
 367
 368
 369
 370
 371
 372
 373
 374
 375
 376
 377
 378
 379
 380
 381
 382
 383
 384
 385
 386
 387
 388
 389
 390
 391
 392
 393
 394
 395
 396
 397
 398
 399
 400
 401
 402
 403
 404
 405
 406
 407
 408
 409
 410
 411
 412
 413
 414
 415
 416
 417
 418
 419
 420
 421
 422
 423
 424
 425
 426
 427
 428
 429
 430
 431
 432
 433
 434
 435
 436
 437
 438
 439
 440
 441
 442
 443
 444
 445
 446
 447
 448
 449
 450
 451
 452
 453
 454
 455
 456
 457
 458
 459
 460
 461
 462
 463
 464
 465
 466
 467
 468
 469
 470
 471
 472
 473
 474
 475
 476
 477
 478
 479
 480
 481
 482
 483
 484
 485
 486
 487
 488
 489
 490
 491
 492
 493
 494
 495
 496
 497
 498
 499
 500
 501
 502
 503
 504
 505
 506
 507
 508
 509
 510
 511
 512
 513
 514
 515
 516
 517
 518
 519
 520
 521
 522
 523
 524
 525
 526
 527
 528
 529
 530
 531
 532
 533
 534
 535
 536
 537
 538
 539
 540
 541
 542
 543
 544
 545
 546
 547
 548
 549
 550
 551
 552
 553
 554
 555
 556
 557
 558
 559
 560
 561
 562
 563
 564
 565
 566
 567
 568
 569
 570
 571
 572
 573
 574
 575
 576
 577
 578
 579
 580
 581
 582
 583
 584
 585
 586
 587
 588
 589
 590
 591
 592
 593
 594
 595
 596
 597
 598
 599
 600
 601
 602
 603
 604
 605
 606
 607
 608
 609
 610
 611
 612
 613
 614
 615
 616
 617
 618
 619
 620
 621
 622
 623
 624
 625
 626
 627
 628
 629
 630
 631
 632
 633
 634
 635
 636
 637
 638
 639
 640
 641
 642
 643
 644
 645
 646
 647
 648
 649
 650
 651
 652
 653
 654
 655
 656
 657
 658
 659
 660
 661
 662
 663
 664
 665
 666
 667
 668
 669
 670
 671
 672
 673
 674
 675
 676
 677
 678
 679
 680
 681
 682
 683
 684
 685
 686
 687
 688
 689
 690
 691
 692
 693
 694
 695
 696
 697
 698
 699
 700
 701
 702
 703
 704
 705
 706
 707
 708
 709
 710
 711
 712
 713
 714
 715
 716
 717
 718
 719
 720
 721
 722
 723
 724
 725
 726
 727
 728
 729
 730
 731
 732
 733
 734
 735
 736
 737
 738
 739
 740
 741
 742
 743
 744
 745
 746
 747
 748
 749
 750
 751
 752
 753
 754
 755
 756
 757
 758
 759
 760
 761
 762
 763
 764
 765
 766
 767
 768
 769
 770
 771
 772
 773
 774
 775
 776
 777
 778
 779
 780
 781
 782
 783
 784
 785
 786
 787
 788
 789
 790
 791
 792
 793
 794
 795
 796
 797
 798
 799
 800
 801
 802
 803
 804
 805
 806
 807
 808
 809
 810
 811
 812
 813
 814
 815
 816
 817
 818
 819
 820
 821
 822
 823
 824
 825
 826
 827
 828
 829
 830
 831
 832
 833
 834
 835
 836
 837
 838
 839
 840
 841
 842
 843
 844
 845
 846
 847
 848
 849
 850
 851
 852
 853
 854
 855
 856
 857
 858
 859
 860
 861
 862
 863
 864
 865
 866
 867
 868
 869
 870
 871
 872
 873
 874
 875
 876
 877
 878
 879
 880
 881
 882
 883
 884
 885
 886
 887
 888
 889
 890
 891
 892
 893
 894
 895
 896
 897
 898
 899
 900
 901
 902
 903
 904
 905
 906
 907
 908
 909
 910
 911
 912
 913
 914
 915
 916
 917
 918
 919
 920
 921
 922
 923
 924
 925
 926
 927
 928
 929
 930
 931
 932
 933
 934
 935
 936
 937
 938
 939
 940
 941
 942
 943
 944
 945
 946
 947
 948
 949
 950
 951
 952
 953
 954
 955
 956
 957
 958
 959
 960
 961
 962
 963
 964
 965
 966
 967
 968
 969
 970
 971
 972
 973
 974
 975
 976
 977
 978
 979
 980
 981
 982
 983
 984
 985
 986
 987
 988
 989
 990
 991
 992
 993
 994
 995
 996
 997
 998
 999
1000
1001
1002
1003
1004
1005
1006
1007
1008
1009
1010
1011
1012
1013
1014
1015
1016
1017
1018
1019
1020
1021
1022
1023
1024
1025
1026
1027
1028
1029
1030
1031
1032
1033
1034
1035
1036
1037
1038
1039
1040
1041
1042
1043
1044
1045
1046
1047
1048
1049
1050
1051
1052
1053
1054
1055
1056
1057
1058
1059
1060
1061
1062
1063
1064
1065
1066
1067
1068
1069
1070
1071
1072
1073
1074
1075
1076
1077
1078
1079
1080
1081
1082
1083
1084
1085
1086
1087
1088
1089
1090
1091
1092
1093
1094
1095
1096
1097
1098
1099
1100
1101
1102
1103
1104
1105
1106
1107
1108
1109
1110
1111
1112
1113
1114
1115
1116
1117
1118
1119
1120
1121
1122
1123
1124
1125
1126
1127
1128
1129
1130
1131
1132
1133
1134
1135
1136
1137
1138
1139
1140
1141
1142
1143
1144
1145
1146
1147
1148
1149
1150
1151
1152
1153
1154
1155
1156
1157
1158
1159
1160
1161
1162
1163
1164
1165
1166
1167
1168
1169
1170
1171
1172
1173
1174
1175
1176
1177
1178
1179
1180
1181
1182
1183
1184
1185
1186
1187
1188
1189
1190
1191
1192
1193
1194
1195
1196
1197
1198
1199
1200
1201
1202
1203
1204
1205
1206
1207
1208
1209
1210
1211
1212
1213
1214
1215
1216
1217
1218
1219
1220
1221
1222
1223
1224
1225
1226
1227
1228
1229
1230
1231
1232
1233
1234
1235
 
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2018 Konrad Hinsen <konrad.hinsen@fastmail.net>
;;; Copyright © 2018, 2021 Kei Kebreau <kkebreau@posteo.net>
;;; Copyright © 2018 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2020 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com>
;;; Copyright © 2021 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2022, 2023 David Elsing <david.elsing@posteo.net>
;;;
;;; This file is part of GNU Guix.
;;;
;;; GNU Guix is free software; you can redistribute it and/or modify it
;;; under the terms of the GNU General Public License as published by
;;; the Free Software Foundation; either version 3 of the License, or (at
;;; your option) any later version.
;;;
;;; GNU Guix is distributed in the hope that it will be useful, but
;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
;;; GNU General Public License for more details.
;;;
;;; You should have received a copy of the GNU General Public License
;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.

(define-module (gnu packages chemistry)
  #:use-module (guix packages)
  #:use-module (guix utils)
  #:use-module ((guix licenses) #:prefix license:)
  #:use-module (guix download)
  #:use-module (guix gexp)
  #:use-module (guix git-download)
  #:use-module (gnu packages)
  #:use-module (gnu packages algebra)
  #:use-module (gnu packages autotools)
  #:use-module (gnu packages backup)
  #:use-module (gnu packages base)
  #:use-module (gnu packages bison)
  #:use-module (gnu packages boost)
  #:use-module (gnu packages check)
  #:use-module (gnu packages compression)
  #:use-module (gnu packages c)
  #:use-module (gnu packages cpp)
  #:use-module (gnu packages documentation)
  #:use-module (gnu packages flex)
  #:use-module (gnu packages fonts)
  #:use-module (gnu packages fontutils)
  #:use-module (gnu packages gcc)
  #:use-module (gnu packages gl)
  #:use-module (gnu packages graphviz)
  #:use-module (gnu packages gtk)
  #:use-module (gnu packages gv)
  #:use-module (gnu packages image)
  #:use-module (gnu packages maths)
  #:use-module (gnu packages mpi)
  #:use-module (gnu packages perl)
  #:use-module (gnu packages pkg-config)
  #:use-module (gnu packages python)
  #:use-module (gnu packages python-build)
  #:use-module (gnu packages python-xyz)
  #:use-module (gnu packages qt)
  #:use-module (gnu packages serialization)
  #:use-module (gnu packages sphinx)
  #:use-module (gnu packages sqlite)
  #:use-module (gnu packages stb)
  #:use-module (gnu packages tex)
  #:use-module (gnu packages web)
  #:use-module (gnu packages xml)
  #:use-module (guix build-system cmake)
  #:use-module (guix build-system gnu)
  #:use-module (guix build-system python))

(define-public avogadrolibs
  (package
    (name "avogadrolibs")
    (version "1.93.0")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/OpenChemistry/avogadrolibs")
             (commit version)))
       (sha256
        (base32 "1xivga626n5acnmwmym8svl0pdri8hkp59czf04ri2zflnviyh39"))
       (file-name (git-file-name name version))))
    (build-system cmake-build-system)
    (native-inputs
     (list eigen
           mmtf-cpp
           googletest
           pkg-config
           pybind11))
    (inputs
     (list glew
           libarchive
           libmsym
           molequeue
           python
           spglib
           qtbase-5))
    (arguments
     '(#:configure-flags (list "-DENABLE_TESTING=ON"
                               (string-append "-DSPGLIB_INCLUDE_DIR="
                                              (assoc-ref %build-inputs "spglib")
                                              "/include"))))
    (home-page "https://www.openchemistry.org/projects/avogadro2/")
    (synopsis "Libraries for chemistry, bioinformatics, and related areas")
    (description
     "Avogadro libraries provide 3D rendering, visualization, analysis and data
processing useful in computational chemistry, molecular modeling,
bioinformatics, materials science, and related areas.")
    (license license:bsd-3)))

(define-public avogadro2
  (package
    (name "avogadro2")
    (version "1.93.0")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/OpenChemistry/avogadroapp")
             (commit version)))
       (sha256
        (base32
         "1z3pjlwja778a1dmvx9aqz2hlw5q9g3kqxhm9slz08452600jsv7"))
       (file-name (git-file-name name version))))
    (build-system cmake-build-system)
    (native-inputs
     (list eigen pkg-config))
    (inputs
     (list avogadrolibs hdf5 molequeue qtbase-5))
    ;; TODO: Enable tests with "-DENABLE_TESTING" configure flag.
    (arguments
     '(#:tests? #f))
    (home-page "https://www.openchemistry.org/projects/avogadro2/")
    (synopsis "Advanced molecule editor")
    (description
     "Avogadro 2 is an advanced molecule editor and visualizer designed for use
in computational chemistry, molecular modeling, bioinformatics, materials
science, and related areas.  It offers flexible high quality rendering and a
powerful plugin architecture.")
    (license license:bsd-3)))

(define-public inchi
  (package
    (name "inchi")
    ;; Update the inchi-doc native input when updating inchi.
    (version "1.06")
    (source (origin
              (method url-fetch)
              (uri (string-append "https://www.inchi-trust.org/download/"
                                  (string-join (string-split version #\.) "")
                                  "/INCHI-1-SRC.zip"))
              (sha256
               (base32
                "1zbygqn0443p0gxwr4kx3m1bkqaj8x9hrpch3s41py7jq08f6x28"))
              (file-name (string-append name "-" version ".zip"))))
    (build-system gnu-build-system)
    (arguments
     '(#:tests? #f ; no check target
       #:phases
       (modify-phases %standard-phases
         (delete 'configure) ; no configure script
         (add-before 'build 'chdir-to-build-directory
           (lambda _ (chdir "INCHI_EXE/inchi-1/gcc") #t))
         (add-after 'build 'build-library
           (lambda _
             (chdir "../../../INCHI_API/libinchi/gcc")
             (invoke "make")))
         (replace 'install
           (lambda* (#:key inputs outputs #:allow-other-keys)
             (let* ((out (assoc-ref outputs "out"))
                    (bin (string-append out "/bin"))
                    (doc (string-append out "/share/doc/inchi"))
                    (include-dir (string-append out "/include/inchi"))
                    (lib (string-append out "/lib/inchi"))
                    (inchi-doc (assoc-ref inputs "inchi-doc"))
                    (unzip (search-input-file inputs "/bin/unzip")))
               (chdir "../../..")
               ;; Install binary.
               (with-directory-excursion "INCHI_EXE/bin/Linux"
                 (rename-file "inchi-1" "inchi")
                 (install-file "inchi" bin))
               ;; Install libraries.
               (with-directory-excursion "INCHI_API/bin/Linux"
                 (for-each (lambda (file)
                             (install-file file lib))
                           (find-files "." "libinchi\\.so\\.1\\.*")))
               ;; Install header files.
               (with-directory-excursion "INCHI_BASE/src"
                 (for-each (lambda (file)
                             (install-file file include-dir))
                           (find-files "." "\\.h$")))
               ;; Install documentation.
               (mkdir-p doc)
               (invoke unzip "-j" "-d" doc inchi-doc)
               #t))))))
    (native-inputs
     `(("unzip" ,unzip)
       ("inchi-doc"
        ,(origin
           (method url-fetch)
           (uri (string-append "http://www.inchi-trust.org/download/"
                                  (string-join (string-split version #\.) "")
                                  "/INCHI-1-DOC.zip"))
           (sha256
            (base32
             "1kyda09i9p89xfq90ninwi7w13k1w3ljpl4gqdhpfhi5g8fgxx7f"))
           (file-name (string-append name "-" version ".zip"))))))
    (home-page "https://www.inchi-trust.org")
    (synopsis "Utility for manipulating machine-readable chemical structures")
    (description
     "The @dfn{InChI} (IUPAC International Chemical Identifier) algorithm turns
chemical structures into machine-readable strings of information.  InChIs are
unique to the compound they describe and can encode absolute stereochemistry
making chemicals and chemistry machine-readable and discoverable.  A simple
analogy is that InChI is the bar-code for chemistry and chemical structures.")
    (license (license:non-copyleft
              "file://LICENCE"
              "See LICENCE in the distribution."))))

(define-public libmsym
  (package
    (name "libmsym")
    (version "0.2.3")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/mcodev31/libmsym")
             (commit (string-append "v" version))))
       (sha256
        (base32
         "0a9j28irdsr461qpzlc9z1yjyb9kp64fh5zw7ylspc9zn3189qwk"))
       (file-name (git-file-name name version))))
    (build-system cmake-build-system)
    (arguments
     '(#:configure-flags '("-DBUILD_SHARED_LIBS=ON")
       #:tests? #f))                    ; no check target
    (home-page "https://github.com/mcodev31/libmsym")
    (synopsis "C library dealing with point group symmetry in molecules")
    (description "libmsym is a C library dealing with point group symmetry in
molecules.")
    (license license:expat)))

(define-public mmtf-cpp
  (package
    (name "mmtf-cpp")
    (version "1.1.0")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/rcsb/mmtf-cpp")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32
         "0rs2f1ppgqz663c3m22p8wsq6z839bj59zy29chci46ypfhwv6ph"))))
    (build-system cmake-build-system)
    ;; Tests require the soon-to-be-deprecated version 1 of the catch-framework.
    (arguments '(#:tests? #f))
    ;; There is no support for modern msgpack versions yet (see:
    ;; https://github.com/rcsb/mmtf-cpp/issues/44).
    (propagated-inputs (list msgpack-3)) ;included by mmtf/structure_data.hpp
    (home-page "https://mmtf.rcsb.org/")
    (synopsis "C++ API for the Macromolecular Transmission Format")
    (description "This package is a library for the
@acronym{MMTF,macromolecular transmission format}, a binary encoding of
biological structures.")
    (license license:expat)))

(define-public molequeue
  (package
    (name "molequeue")
    (version "0.9.0")
    (source
     (origin
       (method url-fetch)
       (uri (string-append "https://github.com/OpenChemistry/molequeue/"
                           "releases/download/" version "/molequeue-"
                           version ".tar.bz2"))
       (sha256
        (base32
         "1w1fgxzqrb5yxvpmnc3c9ymnvixy0z1nfafkd9whg9zw8nbgl998"))))
    (build-system cmake-build-system)
    (inputs
     (list qtbase-5))
    (arguments
     '(#:configure-flags '("-DENABLE_TESTING=ON")
       #:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'patch-tests
           (lambda _
             ;; TODO: Fix/enable the failing message and clientserver tests.
             ;; In the message test, the floating-point value "5.36893473232" on
             ;; line 165 of molequeue/app/testing/messagetest.cpp should
             ;; (apparently) be truncated, but it is not.
             (substitute* "molequeue/app/testing/messagetest.cpp"
               (("5\\.36893473232") "5.36893"))
             ;; It is unclear why the clientserver test fails, so it is
             ;; completely disabled.
             (substitute* "molequeue/app/testing/CMakeLists.txt"
               ((".*clientserver.*") ""))
             #t))
         (add-before 'check 'set-display
           (lambda _
             ;; Make Qt render "offscreen" for the sake of tests.
             (setenv "QT_QPA_PLATFORM" "offscreen")
             #t)))))
    (home-page "https://www.openchemistry.org/projects/molequeue/")
    (synopsis "Application for coordinating computational jobs")
    (description "MoleQueue is a system-tray resident desktop application for
abstracting, managing, and coordinating the execution of tasks both locally and
 on remote computational resources.  Users can set up local and remote queues
that describe where the task will be executed.  Each queue can have programs,
with templates to facilitate the execution of the program.  Input files can be
staged, and output files collected using a standard interface.")
    (license license:bsd-3)))

(define-public tng
  (package
    (name "tng")
    (version "1.8.2")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/gromacs/tng")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "1apf2n8nb34z09xarj7k4jgriq283l769sakjmj5aalpbilvai4q"))))
    (build-system cmake-build-system)
    (inputs
     (list zlib))
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'remove-bundled-zlib
           (lambda _
             (delete-file-recursively "external")
             #t))
         (replace 'check
           (lambda _
             (invoke "../build/bin/tests/tng_testing")
             #t)))))
    (home-page "https://github.com/gromacs/tng")
    (synopsis "Trajectory Next Generation binary format manipulation library")
    (description "TRAJNG (Trajectory next generation) is a program library for
handling molecular dynamics (MD) trajectories.  It can store coordinates, and
optionally velocities and the H-matrix.  Coordinates and velocities are
stored with user-specified precision.")
    (license license:bsd-3)))

(define-public gromacs
  (package
    (name "gromacs")
    (version "2022.4")
    (source (origin
              (method url-fetch)
              (uri (string-append "http://ftp.gromacs.org/pub/gromacs/gromacs-"
                                  version ".tar.gz"))
              (sha256
               (base32
                "15vjwasxjq0h18dmzacjkdim51zrvr0ni42hbc30557j5xhbw4f5"))
              ;; Our version of tinyxml2 is far newer than the bundled one and
              ;; require fixing `testutils' code. See patch header for more info
              (patches (search-patches "gromacs-tinyxml2.patch"))))
    (build-system cmake-build-system)
    (arguments
     (list #:configure-flags
           #~(list "-DGMX_DEVELOPER_BUILD=on"     ; Needed to run tests
                   ;; Unbundling
                   "-DGMX_USE_LMFIT=EXTERNAL"
                   "-DGMX_BUILD_OWN_FFTW=off"
                   "-DGMX_EXTERNAL_BLAS=on"
                   "-DGMX_EXTERNAL_LAPACK=on"
                   "-DGMX_EXTERNAL_TNG=on"
                   "-DGMX_EXTERNAL_ZLIB=on"
                   "-DGMX_EXTERNAL_TINYXML2=on"
                   (string-append "-DTinyXML2_DIR="
                                  #$(this-package-input "tinyxml2"))
                   ;; Workaround for cmake/FindSphinx.cmake version parsing that does
                   ;; not understand the guix-wrapped `sphinx-build --version' answer
                   (string-append "-DSPHINX_EXECUTABLE_VERSION="
                                  #$(package-version python-sphinx)))
           #:phases
           #~(modify-phases %standard-phases
               (add-after 'unpack 'fixes
                 (lambda* (#:key inputs #:allow-other-keys)
                   ;; Still bundled: part of gromacs, source behind registration
                   ;; but free software anyways
                   ;;(delete-file-recursively "src/external/vmd_molfile")
                   ;; Still bundled: threads-based OpenMPI-compatible fallback
                   ;; designed to be bundled like that
                   ;;(delete-file-recursively "src/external/thread_mpi")
                   ;; Unbundling
                   (delete-file-recursively "src/external/lmfit")
                   (delete-file-recursively "src/external/clFFT")
                   (delete-file-recursively "src/external/fftpack")
                   (delete-file-recursively "src/external/build-fftw")
                   (delete-file-recursively "src/external/tng_io")
                   (delete-file-recursively "src/external/tinyxml2")
                   (delete-file-recursively "src/external/googletest")
                   (copy-recursively #$(package-source googletest)
                                     "src/external/googletest")
                   ;; This test warns about the build host hardware, disable
                   (substitute* "src/gromacs/hardware/tests/hardwaretopology.cpp"
                     (("TEST\\(HardwareTopologyTest, HwlocExecute\\)")
                      "void __guix_disabled()")))))))
    (native-inputs
     (list doxygen
           graphviz
           pkg-config
           python
           python-pygments
           python-sphinx))
    (inputs
     (list fftwf
           `(,hwloc-2 "lib")
           lmfit
           openblas
           perl
           tinyxml2
           tng))
    (home-page "https://www.gromacs.org/")
    (synopsis "Molecular dynamics software package")
    (description "GROMACS is a versatile package to perform molecular dynamics,
i.e. simulate the Newtonian equations of motion for systems with hundreds to
millions of particles.  It is primarily designed for biochemical molecules like
proteins, lipids and nucleic acids that have a lot of complicated bonded
interactions, but since GROMACS is extremely fast at calculating the nonbonded
interactions (that usually dominate simulations) many groups are also using it
for research on non-biological systems, e.g. polymers.  GROMACS supports all the
usual algorithms you expect from a modern molecular dynamics implementation.")
    (license license:lgpl2.1+)
    (properties '((tunable? . #t)))))

(define-public openbabel
  (package
    (name "openbabel")
    (version "3.1.1")
    (source (origin
              (method url-fetch)
              (uri (string-append "https://github.com/openbabel/openbabel/"
                                  "releases/download/openbabel-"
                                  (string-replace-substring version "." "-")
                                  "/openbabel-" version "-source.tar.bz2"))
              (sha256
               (base32
                "0s0f4zib8vshfaywsr5bjjz55jwsg6yiz2qw4i5jm8wysn0q7v56"))))
    (build-system cmake-build-system)
    (arguments
     `(;; FIXME: Disable tests on i686 to work around
       ;; https://github.com/openbabel/openbabel/issues/2041.
       #:tests? ,(or (%current-target-system)
                     (not (string=? "i686-linux" (%current-system))))
       #:configure-flags
       (list "-DOPENBABEL_USE_SYSTEM_INCHI=ON"
             (string-append "-DINCHI_LIBRARY="
                            (assoc-ref %build-inputs "inchi")
                            "/lib/inchi/libinchi.so.1")
             (string-append "-DINCHI_INCLUDE_DIR="
                            (assoc-ref %build-inputs "inchi") "/include/inchi"))
       #:test-target "test"))
    (native-inputs
     (list pkg-config))
    (inputs
     (list eigen inchi libxml2 zlib))
    (home-page "http://openbabel.org/wiki/Main_Page")
    (synopsis "Chemistry data manipulation toolbox")
    (description
     "Open Babel is a chemical toolbox designed to speak the many languages of
chemical data.  It's a collaborative project allowing anyone to search, convert,
analyze, or store data from molecular modeling, chemistry, solid-state
materials, biochemistry, or related areas.")
    (license license:gpl2)))

(define-public spglib
  (package
    (name "spglib")
    (version "1.16.0")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/spglib/spglib")
             (commit (string-append "v" version))))
       (sha256
        (base32 "1kzc956m1pnazhz52vspqridlw72wd8x5l3dsilpdxl491aa2nws"))
       (file-name (git-file-name name version))))
    (build-system cmake-build-system)
    (arguments
     '(#:test-target "check"
       #:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'patch-header-install-dir
           (lambda _
             ;; As of the writing of this package, CMake and GNU build systems
             ;; install the header to two different location.  This patch makes
             ;; the CMake build system's choice of header directory compatible
             ;; with the GNU build system's choice and with what avogadrolibs
             ;; expects.
             ;; See https://github.com/spglib/spglib/issues/75 and the relevant
             ;; part of https://github.com/OpenChemistry/avogadroapp/issues/97.
             (substitute* "CMakeLists.txt"
               (("\\$\\{CMAKE_INSTALL_INCLUDEDIR\\}" include-dir)
                (string-append include-dir "/spglib")))
             #t)))))
    (home-page "https://spglib.github.io/spglib/index.html")
    (synopsis "Library for crystal symmetry search")
    (description "Spglib is a library for finding and handling crystal
symmetries written in C.  Spglib can be used to:

@enumerate
@item Find symmetry operations
@item Identify space-group type
@item Wyckoff position assignment
@item Refine crystal structure
@item Find a primitive cell
@item Search irreducible k-points
@end enumerate")
    (license license:bsd-3)))

(define-public python-pymol
  (package
    (name "python-pymol")
    (version "2.5.0")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/schrodinger/pymol-open-source")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32 "08zmfgclkbjkqjpq8xs1mphs1i8rpqj76mcw7m2mrhvma5qj1nr5"))))
    (build-system python-build-system)
    (arguments
     '(#:configure-flags
       (list "--glut" "--testing")
       #:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'make-reproducible
           (lambda _
             (substitute* "create_shadertext.py"
               (("time\\.time\\(\\)") "0"))))
         (add-after 'unpack 'add-include-directories
           (lambda* (#:key inputs #:allow-other-keys)
             (setenv "CPLUS_INCLUDE_PATH"
                     (string-append (assoc-ref inputs "freetype")
                                    "/include/freetype2:"
                                    (assoc-ref inputs "libxml2")
                                    "/include/libxml2:"
                                    (getenv "CPLUS_INCLUDE_PATH")))))
         ;; Prevent deleting the leading / in the __init__.py path in the
         ;; launch script.
         (add-after 'unpack 'disable-unchroot
           (lambda _
             (substitute* "setup.py"
               (("self\\.unchroot") ""))))
         ;; The setup.py script does not support one of the Python build
         ;; system's default flags, "--single-version-externally-managed".
         (replace 'install
           (lambda* (#:key outputs #:allow-other-keys)
             (invoke "python" "setup.py" "install"
                     (string-append "--prefix=" (assoc-ref outputs "out"))
                     "--root=/"))))))
    (inputs
     (list freetype
           libpng
           freeglut
           glew
           libxml2
           mmtf-cpp
           python-pyqt
           glm
           netcdf))
    (native-inputs (list catch2))
    (home-page "https://pymol.org")
    (synopsis "Molecular visualization system")
    (description "PyMOL is a capable molecular viewer and renderer.  It can be
used to prepare publication-quality figures, to share interactive results with
your colleagues, or to generate pre-rendered animations.")
    (license license:bsd-3)))

(define-public gemmi
  (package
    (name "gemmi")
    (version "0.5.7")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/project-gemmi/gemmi")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "00km5q726bslrw7xbfwb3f3mrsk19qbimfnl3hvr4wi1y3z8i18a"))
              (patches
               (search-patches "gemmi-fix-sajson-types.patch"
                               "gemmi-fix-pegtl-usage.patch"))
              (modules '((guix build utils)))
              (snippet
               '(begin
                  (delete-file-recursively "include/gemmi/third_party")
                  (delete-file-recursively "third_party")))))
    (outputs '("out" "bin" "python"))
    (build-system cmake-build-system)
    (arguments
     (list
      #:modules '((guix build cmake-build-system)
                  (guix build utils)
                  ((guix build python-build-system)
                   #:select (site-packages)))
      #:imported-modules (append %cmake-build-system-modules
                                 '((guix build python-build-system)))
      #:configure-flags
      #~(list "-DUSE_PYTHON=ON"
              (string-append "-DPYTHON_INSTALL_DIR="
                             (site-packages %build-inputs %outputs)))
      #:phases
      #~(modify-phases %standard-phases
          (add-after 'unpack 'patch-includes
            (lambda _
              (substitute* (list "include/gemmi/sprintf.hpp"
                                 "include/gemmi/dirwalk.hpp"
                                 "include/gemmi/cif.hpp"
                                 "include/gemmi/json.hpp"
                                 "python/gemmi.cpp"
                                 "include/gemmi/atof.hpp"
                                 "include/gemmi/numb.hpp"
                                 "include/gemmi/fourier.hpp")
                (("<stb/stb_sprintf.h>") "<stb_sprintf.h>")
                (("\"third_party/tinydir.h\"") "<tinydir.h>")
                (("\"third_party/tao/pegtl.hpp\"") "<tao/pegtl.hpp>")
                (("\"third_party/sajson.h\"") "<sajson.h>")
                (("\"gemmi/third_party/tao/pegtl/parse_error.hpp\"")
                 "<tao/pegtl/parse_error.hpp>")
                (("\"third_party/fast_float.h\"")
                 "<fast_float/fast_float.h>")
                (("\"third_party/pocketfft_hdronly.h\"")
                 "<pocketfft_hdronly.h>"))))
          (add-after 'unpack 'change-bin-prefix
            (lambda _
              (substitute* "CMakeLists.txt"
                (("install\\(TARGETS program DESTINATION bin\\)")
                 (string-append
                  "install(TARGETS program DESTINATION "
                  #$output:bin "/bin)")))))
          (replace 'check
            (lambda* (#:key tests? #:allow-other-keys)
              (when tests?
                (with-directory-excursion "../source"
                  (setenv "PYTHONPATH" "../build")
                  (invoke "python3" "-m" "unittest" "discover" "-v"
                          "-s" "tests"))))))))
    (inputs (list python zlib))
    (native-inputs
     (list fast-float
           optionparser
           pegtl
           pocketfft-cpp
           pybind11
           sajson-for-gemmi
           stb-sprintf
           tinydir))
    (home-page "https://gemmi.readthedocs.io/en/latest/")
    (synopsis "Macromolecular crystallography library and utilities")
    (description "GEMMI is a C++ library for macromolecular crystallography.
It can be used for working with
@enumerate
@item macromolecular models (content of PDB, PDBx/mmCIF and mmJSON files),
@item refinement restraints (CIF files),
@item reflection data (MTZ and mmCIF formats),
@item data on a 3D grid (electron density maps, masks, MRC/CCP4 format)
@item crystallographic symmetry.
@end enumerate")
    (license license:mpl2.0)))

(define-public freesasa
  (package
    (name "freesasa")
    (version "2.1.2")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/mittinatten/freesasa")
                    (commit version)))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "07wdnahf3g355ryaiqvfxd5f4rl54wv8jwxcbn0nia89fqysbv0f"))
              (modules '((guix build utils)))
              (snippet
               '(begin
                  ;; Remove C files generated by Flex and Bison
                  (for-each delete-file
                            '("src/parser.c" "src/parser.h"
                              "src/lexer.c" "src/lexer.h"))))))
    (outputs '("out" "doc"))
    (build-system gnu-build-system)
    (arguments
     (list
      #:configure-flags
      #~(list "--enable-check"
              "--enable-parser-generator"
              "CXXFLAGS=-std=c++17"
              "--enable-doxygen")
      #:phases
      #~(modify-phases %standard-phases
          (add-after 'unpack 'remove-libc++-linking
            (lambda _
              (substitute* "src/Makefile.am"
                (("-lc\\+\\+") ""))))
          (add-after 'unpack 'build-shared-library
            (lambda _
              (substitute* "src/Makefile.am"
                (("lib_LIBRARIES") "lib_LTLIBRARIES")
                (("libfreesasa\\.a") "libfreesasa.la")
                (("freesasa_LDADD \\+= libfreesasa\\.la" prev)
                 (string-append prev "\nlibfreesasa_la_LIBADD"
                                " = -ljson-c ${libxml2_LIBS}\n"))
                (("_a_SOURCES") "_la_SOURCES"))
              (substitute* "configure.ac"
                (("AC_PROG_INSTALL" inst)
                 (string-append "AM_PROG_LIBTOOL\n" inst)))
              (substitute* "tests/Makefile.am"
                (("libfreesasa\\.a") "libfreesasa.la"))))
          (add-before 'build 'build-lexer-and-parser
            (lambda _
              (with-directory-excursion "src"
                (invoke "make" "lexer.h" "parser.h"))))
          (add-after 'install 'install-doc
            (lambda _
              (copy-recursively
               "doc/html"
               (string-append #$output:doc "/share/doc/"
                              #$name "-" #$version)))))))
    (inputs (list gemmi json-c libxml2))
    (native-inputs
     (list autoconf
           automake
           bison
           check
           doxygen
           fast-float
           flex
           libtool
           pegtl
           perl
           pkg-config))
    (home-page "https://freesasa.github.io/")
    (synopsis "Calculate the solvent accessible surface area (SASA) of
molecules")
    (description "FreeSASA is a command line tool and C-library for
calculating @acronym{SASAs, solvent accessible surface areas}.  By default Lee
& Richards' algorithm is used, but Shrake & Rupley's is also available.  Both
can be parameterized to arbitrary precision, and for high resolution versions
of the algorithms, the calculations give identical results.")
    (license license:expat)))

(define-public maeparser
  (package
    (name "maeparser")
    (version "1.3.0")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/schrodinger/maeparser")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "1yv4y5hn49fhylziigsg922bb244lb57p69r7vg9q899zd3l5b7l"))))
    (build-system cmake-build-system)
    (inputs (list boost zlib))
    (home-page "https://github.com/schrodinger/maeparser")
    (synopsis "Maestro file parser")
    (description "maeparser is a parser for Schrodinger Maestro files.")
    (license license:expat)))

(define-public coordgenlibs
  (package
    (name "coordgenlibs")
    (version "3.0.1")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/schrodinger/coordgenlibs/")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "0d09x3v38i9y184bml020bq7xizdrdwng38qmdxlplzfhqkjdidv"))))
    (build-system cmake-build-system)
    (arguments
     (list
      #:configure-flags
      #~(list "-DCOORDGEN_RIGOROUS_BUILD=OFF"
              "-DCOORDGEN_USE_MAEPARSER=ON")))
    (inputs (list boost maeparser))
    (home-page "https://github.com/schrodinger/coordgenlibs/")
    (synopsis "2D molecule coordinate generation")
    (description "@code{coordgenlibs} contains algorithms to generate 2D
coordinates of molecules including macrocycles and metal complexes.  It has an
emphasis on quality rather than speed.")
    (license license:bsd-3)))

(define-public yaehmop
  (package
    (name "yaehmop")
    (version "2022.09.1")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/greglandrum/yaehmop")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "1x0d75m1hgdb411fiv7c5bwq1n4y0swrll0gigh8v5c73kjxrja0"))
              (modules '((guix build utils)))
              (snippet
               '(begin
                  ;; Separate program
                  (delete-file-recursively "viewkel")
                  ;; Remove example output (some are corrupted)
                  (for-each delete-file (find-files "examples" "\\.Z$"))
                  ;; Documentation outputs
                  (for-each delete-file (find-files "docs" "\\.(ps|pdf)$"))
                  ;; These are transpiled from Fortran to C, but we build the
                  ;; Fortran code instead
                  (delete-file-recursively "tightbind/f2c_files")
                  (with-directory-excursion "tightbind"
                    (for-each delete-file '("abfns.c"
                                            "cboris.c"
                                            "diag.c"
                                            "lovlap.c")))))))
    (build-system cmake-build-system)
    (arguments
     (list
      #:configure-flags
      #~(list
         "-DUSE_BLAS_LAPACK=ON"
         (string-append "-DPARM_FILE_LOC=" #$output
                        "/share/" #$name "-" #$version "/eht_parms.dat")
         "-DBIND_EXE_NAME=yaehmop-bind")
      #:phases
      #~(modify-phases %standard-phases
          (add-after 'unpack 'chdir
            (lambda _
              (chdir "tightbind")))
          (add-after 'chdir 'patch-fortran-functions
            (lambda _
              (substitute* '("mov.c" "prototypes.h")
                (("lovlap\\(") "lovlap_(")
                (("abfns\\(") "abfns_("))))
          (add-after 'chdir 'patch-cmake
            (lambda _
              (substitute* "CMakeLists.txt"
                (("project\\(yaehmop C\\)") "project(yaehmop C Fortran)")
                (("abfns.c") "fortran77/abfns.f")
                (("lovlap.c") "fortran77/lovlap.f")
                (("(set\\(PARM_FILE_LOC.*)\\)" all init)
                 (string-append init " CACHE STRING \"\")"))
                (("add_library\\(yaehmop_eht" lib)
                 (string-append lib " SHARED "))
                (("target_link_libraries\\(test_eht \\$\\{LAPACK_LIBRARIES\\}.*"
                  all)
                 (string-append all "\ntarget_link_libraries(yaehmop_eht "
                                "${LAPACK_LIBRARIES})\n")))))
          (add-after 'build 'build-doc
            (lambda _
              (with-directory-excursion "../docs"
                (substitute* "bind_manual.tex"
                  (("\\\\usepackage\\{bindpage\\}")
                   (string-append
                    "\\usepackage[left=2cm,right=2cm,top=4cm,bottom=2cm]"
                    "{geometry}\n"
                    "\\pdfsuppressptexinfo=-1\n")))
                (substitute* "Zmat_appendix.tex"
                  (("file=dihedral\\.eps")
                   "file=figs/dihedral.eps"))
                (setenv "FORCE_SOURCE_DATE" "1")
                (invoke "latexmk" "-pdf" "bind_manual.tex"))))
          (add-after 'install 'install-eht-parms
            (lambda _
              (install-file "../tightbind/eht_parms.dat"
                            (string-append #$output "/share/"
                                           #$name "-" #$version))))
          (add-after 'install-eht-parms 'install-doc
            (lambda _
              (install-file "../docs/bind_manual.pdf"
                            (string-append #$output "/share/doc/"
                                           #$name "-" #$version))))
          (delete 'check)
          (add-after 'install-doc 'check
            (lambda* (#:key tests? #:allow-other-keys)
              (when tests?
                (invoke "./test_eht")))))))
    (inputs (list openblas))
    (native-inputs
     (list gfortran
           (texlive-updmap.cfg
            (list texlive-epstopdf
                  texlive-latexmk))))
    (home-page "https://github.com/greglandrum/yaehmop")
    (synopsis "Perform extended Hückel calculations")
    (description "@acronym{YAeHMOP, Yet Another extended Hueckel Molecular
Orbital Package} contains a program and library for performing extended Hückel
calculations and analyzing the results.")
    (license license:bsd-2)))

(define-public avalon-toolkit
  (package
    (name "avalon-toolkit")
    (version "1.2.0")
    (source
     (origin
       (method url-fetch)
       (uri (string-append
             "mirror://sourceforge/avalontoolkit/"
             "AvalonToolkit_" (substring version 0 3) "/AvalonToolkit_"
             version ".source.tar"))
       (sha256
        (base32
         "0rnnyy6axs2da7aa4q6l30ldavbk49v6l22llj1adn74h1i67bpv"))
       (modules '((guix build utils) (ice-9 ftw)))
       (snippet
        #~(begin
            (delete-file-recursively "../SourceDistribution/java")))))
    (build-system gnu-build-system)
    (arguments
     (list
      ;; There are no intended tests
      #:tests? #f
      #:phases
      #~(let ((programs '("canonizer" "matchtest" "sketch" "smi2mol" "struchk")))
          (modify-phases %standard-phases
            (add-after 'unpack 'chdir
              (lambda _ (chdir "common")))
            (delete 'configure)
            (add-before 'build 'dont-free-static-memory
              (lambda _
                (substitute* "reaccsio.c"
                  (("MyFree\\(.*tempdir\\)" m)
                   (string-append "/* freeing memory from getenv is bad */"
                                  "// " m)))))
            ;; The makefile has incorrect compiler flags and is missing some
            ;; object files, so we build it ourselves.
            (replace 'build
              (lambda _
                (for-each
                 (lambda (part)
                   (format #t "Compiling ~a.c ~~> ~a.o~%" part part)
                   (invoke #$(cc-for-target) "-c" "-fPIC" "-O2"
                           (string-append part ".c")
                           "-o" (string-append part ".o")))
                 (list "aacheck" "casutils" "denormal" "depictutil"
                       "didepict" "fixcharges" "forio" "geometry"
                       "graph" "hashcode" "layout" "local" "pattern"
                       "perceive" "reaccsio" "rtutils" "set" "shortcut"
                       "sketch" "ssmatch" "stereo" "symbol_lists"
                       "symboltable" "utilities"))
                (display "Building libavalontoolkit.so\n")
                (apply invoke "gcc" "-fPIC" "-shared" "-lm"
                       "-o" "libavalontoolkit.so" "canonizer.c" "smi2mol.c"
                       "struchk.c" "patclean.c" (find-files "." "\\.o$"))
                ;; patclean is not built here as there is an undeclared
                ;; variable in main().
                (for-each
                 (lambda (program)
                   (display (string-append "Building " program "\n"))
                   (invoke "gcc" "-L." "-lavalontoolkit" "-lm" "-O2"
                           (string-append "-Wl,-rpath=" #$output "/lib")
                           "-DMAIN" (string-append program ".c") "-o" program))
                 programs)))
            (replace 'install
              (lambda _
                ;; Executables
                (for-each
                 (lambda (program)
                   (install-file program (string-append #$output "/bin")))
                 programs)
                (for-each
                 (lambda (name)
                   (symlink (string-append #$output "/bin/smi2mol")
                            (string-append #$output "/bin/" name)))
                 '("mol2smi" "rdf2smi" "mol2tbl" "mol2sma" "smi2rdf"))
                ;; Library
                (install-file "libavalontoolkit.so"
                              (string-append #$output "/lib"))
                (for-each
                 (lambda (file)
                   (install-file file (string-append #$output
                                                    "/include/avalontoolkit")))
                 (find-files "." "\\.h$"))
                (install-file "../license.txt"
                              (string-append #$output "/share/doc/"
                                             #$name "-" #$version "/"))))))))
    (home-page "https://sourceforge.net/projects/avalontoolkit/")
    (synopsis "Tools for SMILES and MOL files and for structure fingerprinting")
    (description "This package contains a library and programs for
canonicalization of SMILES and MOL files, molecular structure fingerprinting
and rendering molecules.")
    (license license:bsd-3)))

(define-public ringdecomposerlib
  (package
    (name "ringdecomposerlib")
    (version "1.1.3")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/rareylab/RingDecomposerLib")
                    (commit (string-append "v" version "_rdkit"))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "1rxzs2wpkkdi40wdzxc4sn0brk7dm7ivgqyfh38gf2f5c7pbg0wi"))))
    (build-system cmake-build-system)
    (arguments
     (list
      #:configure-flags
      #~(list "-DBUILD_PYTHON_WRAPPER=ON"
              "-DPYTHON_EXECUTABLE=python3"
              (string-append "-DPYTHON_FLAGS=;--prefix=" #$output ";--root=/"))
      #:imported-modules (append %cmake-build-system-modules
                                 '((guix build python-build-system)))
      #:modules '((guix build cmake-build-system)
                  (guix build utils)
                  ((guix build python-build-system)
                   #:select (add-installed-pythonpath)))
      #:phases
      #~(modify-phases %standard-phases
          (add-before 'configure 'patch-cmake
            (lambda _
              (substitute* (list "src/Test/CMakeLists.txt"
                                 "src/RingDecomposerLib/CMakeLists.txt")
                (("build_.*STATIC") "#"))
              (substitute* "test/CMakeLists.txt"
                (("STATIC_TEST") "SHARED_TEST"))
              ;; Link Python library against shared library
              (substitute* "src/python/CMakeLists.txt"
                (("RingDecomposerLibStatic") "RingDecomposerLib"))
              (substitute* "src/python/setup.py.in"
                (("static_libs =.*") "static_libs = []\n")
                (("shared_libs\\s*=.*")
                 (string-append
                  "shared_libs = ['RingDecomposerLib']"))
                (("library_dirs\\s*=\\s*\\[\\]")
                 "library_dirs = ['${CMAKE_BINARY_DIR}/src/RingDecomposerLib']")
                (("extra_objects=.*")
                 (string-append
                  "extra_link_args=['-Wl,-rpath=" #$output "/lib'],\n")))))
          (add-after 'build 'build-doc
            (lambda _
              ;; Disable redundant LaTeX documentation
              (substitute* "../source/documentation/sphinx/conf.py"
                (("^(subprocess.*latex|shutil).*") ""))
              (substitute* "../source/documentation/doxygen.cfg"
                (("GENERATE_LATEX.*YES") "GENERATE_LATEX = NO"))
              ;; Build HTML documentation
              (invoke "sphinx-build" "-b" "html"
                      "../source/documentation/sphinx" "html")))
          (add-after 'install 'install-doc
            (lambda _
              ;; Not reproducible
              (delete-file-recursively "html/.doctrees")
              (copy-recursively "html"
                                (string-append #$output "/share/doc/"
                                               #$name "-" #$version "/html"))))
          (delete 'check)
          (add-after 'install 'check
            (assoc-ref %standard-phases 'check))
          (add-before 'check 'set-pythonpath
            (lambda* (#:key inputs outputs #:allow-other-keys)
              (add-installed-pythonpath inputs outputs))))))
    (inputs (list python))
    (native-inputs (list doxygen python python-cython python-sphinx))
    (home-page "https://github.com/rareylab/RingDecomposerLib")
    (synopsis "Calculate ring topology descriptions")
    (description "RingDecomposerLib is a library for the calculation of
unique ring families, relevant cycles, the smallest set of smallest rings and
other ring topology descriptions.")
    (license license:bsd-3)))

(define-public rdkit
  (package
    (name "rdkit")
    (version "2022.03.5")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/rdkit/rdkit")
                    (commit
                     (string-append
                      "Release_" (string-replace-substring version "." "_")))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "19idgilabh04cbr1qj6zgrgsfjm248mmfz6fsr0smrd68d0xnml9"))
              (patches
               (search-patches "rdkit-unbundle-external-dependencies.patch"))
              (modules '((guix build utils)))
              (snippet
               #~(begin
                   ;; Remove pickle files (only used in tests),
                   ;; as they are compiled programs
                   (for-each
                    (lambda (name)
                      (display (string-append name "\n"))
                      (delete-file name))
                    (find-files "." "\\.pkl(\\.gz)?$"))
                   ;; Remove SQLite data files (can be generated)
                   (delete-file "Data/RDData.sqlt")
                   (delete-file "Data/RDTests.sqlt")))))
    (build-system cmake-build-system)
    (arguments
     (list
      #:imported-modules (append %cmake-build-system-modules
                                 '((guix build python-build-system)))
      #:modules '((guix build cmake-build-system)
                  (guix build utils)
                  ((guix build python-build-system)
                   #:select (add-installed-pythonpath)))
      #:configure-flags
      #~(list "-DRDK_BUILD_AVALON_SUPPORT=ON"
              "-DRDK_BUILD_CAIRO_SUPPORT=ON"
              "-DRDK_BUILD_FREESASA_SUPPORT=ON"
              "-DRDK_BUILD_INCHI_SUPPORT=ON"
              "-DRDK_BUILD_YAEHMOP_SUPPORT=ON"
              (string-append "-DCATCH_DIR="
                             (search-input-directory %build-inputs
                                                     "/include/catch2"))
              "-DRDK_INSTALL_INTREE=OFF"
              "-DRDK_INSTALL_STATIC_LIBS=OFF"
              (string-append
               "-DRDK_OPTIMIZE_POPCNT="
               #$(let ((system (or (%current-target-system)
                                   (%current-system))))
                   (cond
                    ((string-prefix? "x86_64" system) "ON")
                    ((string-prefix? "i686" system) "ON")
                    (else "OFF"))))
              "-DRDK_USE_FLEXBISON=ON"
              (string-append
               "-DCMAKE_INCLUDE_PATH="
               (search-input-directory %build-inputs "/include/avalontoolkit")))
      #:phases
      #~(modify-phases %standard-phases
          (add-after 'unpack 'copy-external-dependencies
            (lambda _
              (symlink
               (string-append
                (search-input-file
                 %build-inputs "/share/fonts/truetype/ComicNeue-Regular.ttf"))
               "Data/Fonts/ComicNeue-Regular.ttf")))
          (add-after 'unpack 'fix-inchi-include
            (lambda _
              (substitute* "Code/cmake/Modules/FindInchi.cmake"
                (("inchi_api.h.*\\)") "inchi/inchi_api.h)")
                (("INCHI_LIBRARY NAMES.*\\)")
                 "INCHI_LIBRARY NAMES inchi PATH_SUFFIXES inchi)")
                (("find_library" prev)
                 (string-append
                  "list(APPEND CMAKE_FIND_LIBRARY_SUFFIXES .so.1)\n"
                  prev)))
              (substitute* "External/INCHI-API/inchi.cpp"
                (("<inchi_api.h>") "<inchi/inchi_api.h>"))))
          (add-before 'build 'enable-bytecode-determinism
              (lambda _
                (setenv "PYTHONHASHSEED" "0")
                (setenv "PYTHONDONTWRITEBYTECODE" "1")))
          (add-after 'install 'pre-check
            (lambda* (#:key inputs outputs #:allow-other-keys)
              (with-directory-excursion "../source"
                (invoke "sqlite3" "Data/RDData.sqlt"
                        ".read rdkit/Dbase/test_data/RDData.sqlite")
                (invoke "sqlite3" "Data/RDTests.sqlt"
                        ".read rdkit/Dbase/test_data/RDTests.sqlite")
                (setenv "RDBASE" (canonicalize-path ".")))
              (add-installed-pythonpath inputs outputs)))
          (delete 'check)
          (add-after 'pre-check 'check
            (lambda* (#:key tests? parallel-tests? #:allow-other-keys)
              (when tests?
                (let ((job-count (number->string
                                  (if parallel-tests? (parallel-job-count) 1))))
                  (invoke
                   "ctest" "-j" job-count
                   "-E" (string-append
                         "("
                         (string-join
                          '(;; need pickled data
                            "pyDiscreteValueVect" "pySparseIntVect"
                            "graphmoltestPickler" "pyPartialCharges"
                            "substructLibraryTest" "pyFeatures"
                            "pythonTestDirML" "pythonTestDirChem"
                            ;; Catching Python exception fails
                            "pyRanker") "|")
                         ")")))))))))
    (inputs
     (list avalon-toolkit
           cairo
           coordgenlibs
           font-comic-neue
           freetype
           inchi
           maeparser
           python
           ringdecomposerlib
           sqlite
           yaehmop))
    (native-inputs
     (list bison
           boost
           catch2
           eigen
           flex
           freesasa
           pkg-config
           rapidjson
           tar))
    (propagated-inputs
     (list python-numpy python-cairocffi python-pillow))
    (home-page "https://rdkit.org/")
    (synopsis "Collection of cheminformatics software")
    (description "RDKit is a C++ and Python library for cheminformatics, which
includes (among other things) the analysis and modification of molecules in 2D
and 3D and descriptor generation for machine learning.")
    (license license:bsd-3)))

debug log:

solving df96a2f5c1 ...
found df96a2f5c1 in https://git.savannah.gnu.org/cgit/guix.git

(*) Git path names are given by the tree(s) the blob belongs to.
    Blobs themselves have no identifier aside from the hash of its contents.^

Code repositories for project(s) associated with this external index

	https://git.savannah.gnu.org/cgit/guix.git

This is an external index of several public inboxes,
see mirroring instructions on how to clone and mirror
all data and code used by this external index.