From a19eadd80f4fb74ba2c03ed518d14fe033354892 Mon Sep 17 00:00:00 2001 From: Francois Berenger Date: Thu, 26 Sep 2024 17:44:32 +0900 Subject: [PATCH 1/4] new file: packages/molenc/molenc.17.0.1/opam some more python scripts are installed --- packages/molenc/molenc.17.0.1/opam | 99 ++++++++++++++++++++++++++++++ 1 file changed, 99 insertions(+) create mode 100644 packages/molenc/molenc.17.0.1/opam diff --git a/packages/molenc/molenc.17.0.1/opam b/packages/molenc/molenc.17.0.1/opam new file mode 100644 index 00000000000..e576222b151 --- /dev/null +++ b/packages/molenc/molenc.17.0.1/opam @@ -0,0 +1,99 @@ +opam-version: "2.0" +authors: "Francois Berenger" +maintainer: "unixjunkie@sdf.org" +homepage: "https://github.com/UnixJunkie/molenc" +bug-reports: "https://github.com/UnixJunkie/molenc/issues" +dev-repo: "git+https://github.com/UnixJunkie/molenc.git" +license: "BSD-3-Clause" +build: ["dune" "build" "-p" name "-j" jobs] +install: [ + ["cp" "bin/molenc_diam.py" "%{bin}%/molenc_diam.py"] + ["cp" "bin/molenc_ph4.py" "%{bin}%/molenc_ph4.py"] + ["cp" "bin/molenc.sh" "%{bin}%/molenc.sh"] + ["cp" "bin/molenc_ligprep.sh" "%{bin}%/molenc_ligprep.sh"] + ["cp" "bin/molenc_common.py" "%{bin}%/molenc_common.py"] + ["cp" "bin/molenc_lean.py" "%{bin}%/molenc_lean.py"] + ["cp" "bin/molenc_lizard.py" "%{bin}%/molenc_lizard.py"] + ["cp" "bin/molenc_scan.py" "%{bin}%/molenc_scan.py"] + ["cp" "bin/molenc_scan.sh" "%{bin}%/molenc_scan.sh"] + ["cp" "bin/molenc_type_atoms.py" "%{bin}%/molenc_type_atoms.py"] + ["cp" "bin/smi2png.py" "%{bin}%/molenc_smi2png.py"] + ["cp" "bin/molenc_smisur.py" "%{bin}%/molenc_smisur.py"] + ["cp" "bin/molenc_panascan.py" "%{bin}%/molenc_panascan.py"] + ["cp" "bin/molenc_scaffold.py" "%{bin}%/molenc_scaffold.py"] + ["cp" "bin/molenc_deepsmi.py" "%{bin}%/molenc_deepsmi.py"] + ["cp" "bin/molenc_lead.py" "%{bin}%/molenc_lead.py"] + ["cp" "bin/molenc_drug.py" "%{bin}%/molenc_drug.py"] + ["cp" "bin/molenc_smi2cansmi.py" "%{bin}%/molenc_smi2cansmi.py"] + ["cp" "bin/molenc_std.py" "%{bin}%/molenc_std.py"] + ["cp" "bin/molenc_padel.py" "%{bin}%/molenc_padel.py"] + ["cp" "bin/molenc_rotbond.py" "%{bin}%/molenc_rotbond.py"] + ["cp" "bin/molenc_mview.py" "%{bin}%/molenc_mview.py"] + ["cp" "bin/molenc_HA.py" "%{bin}%/molenc_HA.py"] + ["cp" "bin/molenc_sdf2smi.py" "%{bin}%/molenc_sdf2smi.py"] + ["cp" "bin/molenc_atoms_filter.py" "%{bin}%/molenc_atoms_filter.py"] + ["cp" "bin/molenc_gpr.py" "%{bin}%/molenc_gpr.py"] + ["cp" "bin/molenc_stable.py" "%{bin}%/molenc_stable.py"] + ["cp" "bin/molenc_thash.py" "%{bin}%/molenc_thash.py"] + ["cp" "bin/molenc_SA.py" "%{bin}%/molenc_SA.py"] + ["cp" "bin/fpscores.pkl.gz" "%{bin}%/fpscores.pkl.gz"] # molenc_SA.py's data +] +depends: [ + "batteries" {>= "3.5.0"} + "bst" {>= "2.0.0"} + "conf-graphviz" + "conf-python-3" + "conf-rdkit" + "cpm" {>= "9.0.0"} + "dokeysto" + "dolog" {>= "5.0.0"} + "dune" {>= "1.11"} + "line_oriented" {>= "1.2.0"} + "minicli" {>= "5.0.0"} + "ocaml" {>= "5.1.0"} + "ocamlgraph" + "parany" {>= "12.1.1"} + "vector3" + "pyml" {>= "20211015"} +] +available: arch != "arm32" & arch != "x86_32" +synopsis: "Molecular encoder/featurizer using rdkit and OCaml" +description: """Chemical fingerprints are lossy encodings of molecules. +molenc allows to encode molecules using unfolded-counted fingerprints +(i.e. a potentially very long but sparse vector of positive integers). + +Currently, Faulon fingerprints and atom pairs are supported. + +Currently, atom types are the quadruplet +(#pi-electrons, element symbol, #HA neighbors, formal charge). +In the future, pharmacophore features might be supported (a more abstract/fuzzy +atom typing scheme). + +Bibliography: +============= + +Faulon, J. L., Visco, D. P., & Pophale, R. S. (2003). +The signature molecular descriptor. +1. Using extended valence sequences in QSAR and QSPR studies. +Journal of chemical information and computer sciences, 43(3), 707-720. + +Carhart, R. E., Smith, D. H., & Venkataraghavan, R. (1985). +Atom pairs as molecular features in structure-activity studies: +definition and applications. +Journal of Chemical Information and Computer Sciences, 25(2), 64-73. + +Kearsley, S. K., Sallamack, S., Fluder, E. M., Andose, J. D., Mosley, R. T., & +Sheridan, R. P. (1996). +Chemical similarity using physiochemical property descriptors. +Journal of Chemical Information and Computer Sciences, 36(1), 118-127. + +OpenSMILES specification. Craig A. James et. al. v1.0 2016-05-15. +http://opensmiles.org/opensmiles.html +""" +url { + src: + "https://github.com/UnixJunkie/molenc/archive/refs/tags/v17.0.1.tar.gz" + checksum: [ + "sha256=dee16015c4088cc4a690bfeb5afc4fe4869540bf7e2a998ae3ca8094023728ae" + ] +} From 2ce590ec84cbc1e57d0d79f724540b93518608e1 Mon Sep 17 00:00:00 2001 From: Chet Murthy Date: Tue, 1 Oct 2024 22:16:31 -0700 Subject: [PATCH 2/4] Camlp5 release to support upcoming Ocaml 5.3.0 --- packages/camlp5/camlp5.8.03.01/opam | 67 +++++++++++++++++++++++++++++ 1 file changed, 67 insertions(+) create mode 100644 packages/camlp5/camlp5.8.03.01/opam diff --git a/packages/camlp5/camlp5.8.03.01/opam b/packages/camlp5/camlp5.8.03.01/opam new file mode 100644 index 00000000000..380c0945d65 --- /dev/null +++ b/packages/camlp5/camlp5.8.03.01/opam @@ -0,0 +1,67 @@ + +opam-version: "2.0" +synopsis: "Preprocessor-pretty-printer of OCaml" +description: """ +Camlp5 is a preprocessor and pretty-printer for OCaml programs. It also provides parsing and printing tools. + +As a preprocessor, it allows to: + +extend the syntax of OCaml, +redefine the whole syntax of the language. +As a pretty printer, it allows to: + +display OCaml programs in an elegant way, +convert from one syntax to another, +check the results of syntax extensions. +Camlp5 also provides some parsing and pretty printing tools: + +extensible grammars +extensible printers +stream parsers and lexers +pretty print module +It works as a shell command and can also be used in the OCaml toplevel.""" +maintainer: "https://github.com/ocaml/opam-repository/issues" +authors: ["Daniel de Rauglaudre" "Chet Murthy"] +license: "BSD-3-Clause" +homepage: "https://camlp5.github.io" +doc: "https://camlp5.github.io/doc/html" +bug-reports: "https://github.com/camlp5/camlp5/issues" +depends: [ + "ocaml" {>= "4.10" & < "5.04.0" } + "ocamlfind" + "camlp-streams" { >= "5.0" } + "conf-perl" + "conf-bash" { with-test } + "camlp5-buildscripts" { >= "0.02" } + "conf-diffutils" { with-test & (os-distribution = "alpine" | os-distribution = "freebsd" | os-family = "opensuse") } + "re" { >= "1.11.0" } + "ounit2" { with-test } + "pcre2" { with-test } + "rresult" + "bos" + "fmt" +] +build: [ + ["./configure" "--prefix" prefix "-libdir" lib "-mandir" man] + [make "-j%{jobs}%" "DEBUG=-g" "world.opt"] + [make "-j%{jobs}%" "DEBUG=-g" "all"] + [make "-C" "testsuite" "clean" "all-tests"] { with-test } + [make "-C" "test" "clean" "all"] { with-test & os != "macos" } +# [make "-C" "scripts" "clean" "test"] { with-test } +] +install: [make "install"] +conflicts: [ + "ocaml-option-bytecode-only" + "pa_ppx" { < "0.15" } + "p5scm" { <= "0.3.1" } + "matita" { <= "0.99.5" } + "lablgl" { <= "1.07" } +] +x-ci-accept-failures: [ "opensuse-tumbleweed" ] +dev-repo: "git+https://github.com/camlp5/camlp5.git" +url { + src: "https://github.com/camlp5/camlp5/archive/refs/tags/8.03.01.tar.gz" + checksum: [ + "sha512=bb8b664e1d5d27b7136cac3c54418abdce5c4e21eba8e1e1830c5f74058767870f0e256c1d8e92bb8a49a3a90bd6d89bede79fc399015eb22c9b5698242c10f0" + ] +} From ca19258a37a91934bcab11078719d610b6288523 Mon Sep 17 00:00:00 2001 From: Chet Murthy Date: Tue, 1 Oct 2024 22:29:13 -0700 Subject: [PATCH 3/4] fixed opam file maintainer email --- packages/camlp5/camlp5.8.03.01/opam | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/packages/camlp5/camlp5.8.03.01/opam b/packages/camlp5/camlp5.8.03.01/opam index 380c0945d65..5f65d2876f4 100644 --- a/packages/camlp5/camlp5.8.03.01/opam +++ b/packages/camlp5/camlp5.8.03.01/opam @@ -20,7 +20,7 @@ extensible printers stream parsers and lexers pretty print module It works as a shell command and can also be used in the OCaml toplevel.""" -maintainer: "https://github.com/ocaml/opam-repository/issues" +maintainer: ["Chet Murthy "] authors: ["Daniel de Rauglaudre" "Chet Murthy"] license: "BSD-3-Clause" homepage: "https://camlp5.github.io" From 43f5e22908514b06587d3cf54c695a951747f314 Mon Sep 17 00:00:00 2001 From: Chet Murthy Date: Tue, 1 Oct 2024 23:05:05 -0700 Subject: [PATCH 4/4] conflicts --- packages/camlp5/camlp5.8.03.01/opam | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/packages/camlp5/camlp5.8.03.01/opam b/packages/camlp5/camlp5.8.03.01/opam index 5f65d2876f4..548bcbe621e 100644 --- a/packages/camlp5/camlp5.8.03.01/opam +++ b/packages/camlp5/camlp5.8.03.01/opam @@ -52,7 +52,7 @@ build: [ install: [make "install"] conflicts: [ "ocaml-option-bytecode-only" - "pa_ppx" { < "0.15" } + "pa_ppx" { < "0.16" } "p5scm" { <= "0.3.1" } "matita" { <= "0.99.5" } "lablgl" { <= "1.07" } @@ -62,6 +62,6 @@ dev-repo: "git+https://github.com/camlp5/camlp5.git" url { src: "https://github.com/camlp5/camlp5/archive/refs/tags/8.03.01.tar.gz" checksum: [ - "sha512=bb8b664e1d5d27b7136cac3c54418abdce5c4e21eba8e1e1830c5f74058767870f0e256c1d8e92bb8a49a3a90bd6d89bede79fc399015eb22c9b5698242c10f0" + "sha512=144ab15e18673fa485d08cf37c6ba69146db7db4be9e7031e202e0747d922e223396b83881b1d65cf27bedb2115d91e5eb62b5a22e2d57dda838013ebd398ff2" ] }