Add Dssp

recipes/dssp/build.sh

@@ -0,0 +1,23 @@
+#!/bin/bash
+
+set -e
+
+# Link dynamically
+sed -i -e 's/\-static //' makefile
+
+echo "DEST_DIR=${PREFIX}" > make.config
+echo "MAN_DIR=${PREFIX}/share/man/man1" >> make.config
+
+echo "BOOST_INC_DIR=${BUILD_PREFIX}/include" >> make.config
+echo "BOOST_LIB_DIR=${BUILD_PREFIX}/lib" >> make.config
+# Use conda-provided cxx
+sed -i -e 's/^CXX/#CXX/' makefile
+
+# clang++ won't find std::tuple unless in C++11 mode;
+# don't compile with anything newer than C++11 since we use the removed
+# std::unary_function
+if [ `uname -s` = "Darwin" ]; then
+  CFLAGS="-std=c++11 -Wno-enum-constexpr-conversion ${CFLAGS}"
+fi
+
+make -j${CPU_COUNT} install

recipes/dssp/dssp-boost-tr1.patch

@@ -0,0 +1,87 @@
+diff -Nur dssp-3.0.0/src/dssp.cpp dssp-3.0.0-patched/src/dssp.cpp
+--- dssp-3.0.0/src/dssp.cpp	2017-09-21 02:42:09.000000000 -0700
++++ dssp-3.0.0-patched/src/dssp.cpp	2018-04-25 11:05:47.499486529 -0700
+@@ -73,7 +73,7 @@
+
+   double alpha;
+   char chirality;
+-  std::tr1::tie(alpha,chirality) = residue.Alpha();
++  std::tie(alpha,chirality) = residue.Alpha();
+
+   uint32 bp[2] = {};
+   char bridgelabel[2] = { ' ', ' ' };
+diff -Nur dssp-3.0.0/src/primitives-3d.cpp dssp-3.0.0-patched/src/primitives-3d.cpp
+--- dssp-3.0.0/src/primitives-3d.cpp	2017-09-21 02:42:09.000000000 -0700
++++ dssp-3.0.0-patched/src/primitives-3d.cpp	2018-04-25 11:05:54.642577464 -0700
+@@ -152,7 +152,7 @@
+
+ // --------------------------------------------------------------------
+
+-std::tr1::tuple<double,MPoint> QuaternionToAngleAxis(MQuaternion q)
++std::tuple<double,MPoint> QuaternionToAngleAxis(MQuaternion q)
+ {
+   if (q.R_component_1() > 1)
+     q = Normalize(q);
+@@ -168,7 +168,7 @@
+
+   MPoint axis(q.R_component_2() / s, q.R_component_3() / s, q.R_component_4() / s);
+
+-  return std::tr1::make_tuple(angle, axis);
++  return std::make_tuple(angle, axis);
+ }
+
+ MPoint CenterPoints(std::vector<MPoint>& points)
+diff -Nur dssp-3.0.0/src/primitives-3d.h dssp-3.0.0-patched/src/primitives-3d.h
+--- dssp-3.0.0/src/primitives-3d.h	2017-09-21 02:42:09.000000000 -0700
++++ dssp-3.0.0-patched/src/primitives-3d.h	2018-04-25 11:05:18.542117901 -0700
+@@ -12,7 +12,7 @@
+ #pragma once
+
+ #include <boost/math/quaternion.hpp>
+-#include <boost/tr1/tuple.hpp>
++#include <tuple>
+
+ #include <vector>
+
+@@ -71,7 +71,7 @@
+
+ MQuaternion Normalize(MQuaternion q);
+
+-std::tr1::tuple<double,MPoint> QuaternionToAngleAxis(MQuaternion q);
++std::tuple<double,MPoint> QuaternionToAngleAxis(MQuaternion q);
+ MPoint Centroid(std::vector<MPoint>& points);
+ MPoint CenterPoints(std::vector<MPoint>& points);
+ MQuaternion AlignPoints(const std::vector<MPoint>& a,
+diff -Nur dssp-3.0.0/src/structure.cpp dssp-3.0.0-patched/src/structure.cpp
+--- dssp-3.0.0/src/structure.cpp	2017-09-21 02:42:09.000000000 -0700
++++ dssp-3.0.0-patched/src/structure.cpp	2018-04-25 11:05:41.581411192 -0700
+@@ -554,7 +554,7 @@
+   return result;
+ }
+
+-std::tr1::tuple<double,char> MResidue::Alpha() const
++std::tuple<double,char> MResidue::Alpha() const
+ {
+   double alhpa = 360;
+   char chirality = ' ';
+@@ -571,7 +571,7 @@
+     else
+       chirality = '+';
+   }
+-  return std::tr1::make_tuple(alhpa, chirality);
++  return std::make_tuple(alhpa, chirality);
+ }
+
+ double MResidue::Kappa() const
+diff -Nur dssp-3.0.0/src/structure.h dssp-3.0.0-patched/src/structure.h
+--- dssp-3.0.0/src/structure.h	2017-09-21 02:42:09.000000000 -0700
++++ dssp-3.0.0-patched/src/structure.h	2018-04-25 11:05:03.233921919 -0700
+@@ -171,7 +171,7 @@
+
+   double        Phi() const;
+   double        Psi() const;
+-  std::tr1::tuple<double,char>
++  std::tuple<double,char>
+             Alpha() const;
+   double        Kappa() const;
+   double        TCO() const;

recipes/dssp/meta.yaml

@@ -0,0 +1,52 @@
+{% set version = "3.0.0" %}
+{% set name = "dssp" %}
+# This file, the patch file and build file were taken from conda salilab channel's recipes - please see https://github.com/salilab/conda-recipes for more.
+package:
+  name: {{ name }}
+  version: {{ version }}
+
+source:
+  url: https://salilab.org/dssp/dssp-{{ version }}.tgz
+  sha256: 25d39a2107767b622a59dd9fa790112c1516564b8518fc6ac0fab081d5ac3ab0
+  patches:
+    - dssp-boost-tr1.patch #Rebuild with latest gcc and boost - this was taken from the 
+
+build:
+  number: 0
+  run_exports:
+    - {{ pin_subpackage('dssp', max_pin="x.x") }}
+
+requirements:
+  build:
+    - {{ compiler('c') }}
+    - {{ compiler('cxx') }}
+    - boost-cpp
+    - zlib
+    - bzip2
+    - make
+  run:
+    - {{ pin_compatible('boost-cpp') }}
+
+about:
+  home: http://swift.cmbi.ru.nl/gv/dssp/
+  summary: 'Secondary structure assignment'
+  license: Boost
+  description: >
+    The DSSP program was designed by Wolfgang Kabsch and Chris Sander to
+    standardize secondary structure assignment. DSSP is a database of secondary
+    structure assignments (and much more) for all protein entries in the Protein
+    Data Bank (PDB). DSSP is also the program that calculates DSSP entries from
+    PDB entries. DSSP does not predict secondary structure.
+
+    Note that this is a very old version of DSSP, which we have used in the
+    past. It is kept here in the hope that others may find it useful - but
+    it may not work on newer systems (e.g. Apple Silicon Macs). We recommend
+    using the most recent version of DSSP instead.
+    See [the DSSP website](http://swift.cmbi.ru.nl/gv/dssp/) for more details.
+
+    If you have problems with this conda package, please
+    [open an issue](https://github.com/salilab/conda-recipes/issues).
+
+test:
+  commands:
+    - mkdssp --version

recipes/tamper/build.sh

@@ -0,0 +1,34 @@
+#!/bin/bash
+
+mkdir -p ${PREFIX}/bin/
+mkdir -p ${PREFIX}/share/tamper/
+mkdir -p ${PREFIX}/share/tamper/src/
+mkdir -p ${PREFIX}/share/tamper/checkpoints/trained
+cp -r src/. ${PREFIX}/share/tamper/src/
+cp -r checkpoints/trained/. ${PREFIX}/share/tamper/checkpoints/trained
+ls ${PREFIX}/share/tamper/src/
+
+#This allows src code to be executbale for user and group
+chmod -R u+x ${PREFIX}/share/tamper/src/
+chmod -R g+x ${PREFIX}/share/tamper/src/
+
+ls -lah ${PREFIX}/share/tamper/src/
+
+#Adding python executable for the script to work
+echo "#!/bin/bash" > ${PREFIX}/bin/predict_tAMPer
+echo "python ${PREFIX}/share/tamper/src/predict_tAMPer.py \"\$@\"" >> ${PREFIX}/bin/predict_tAMPer
+
+echo "#!/bin/bash" > ${PREFIX}/bin/train_tAMPer.py
+echo "python ${PREFIX}/share/tamper/src/train_tAMPer.py \"\$@\"" >> ${PREFIX}/bin/train_tAMPer
+
+#Checking if files are copied within bin
+echo "Files in ${PREFIX}/bin/:"
+ls -l ${PREFIX}/bin/
+
+chmod +x ${PREFIX}/bin/predict_tAMPer
+chmod +x ${PREFIX}/bin/train_tAMPer
+
+#Verify permissions
+echo "Permissions after chmod:"
+ls -l ${PREFIX}/share/tamper/src/
+

recipes/tamper/meta.yaml

@@ -0,0 +1,43 @@
+{% set name = "tamper" %}
+{% set version = "1.0.1" %}
+
+package:
+  name: '{{ name|lower }}'
+  version: '{{ version }}'
+
+source:
+  url: https://github.com/bcgsc/tAMPer/releases/download/v{{ version }}/tAMPer_v{{ version }}.tar.gz
+  sha256: 0c4cfc57a844b89dbc9c020084b5d12b096359a7341350552f5ea707d882486a
+
+build:
+  number: 1
+  noarch: generic
+  run_exports:
+    - {{ pin_subpackage(name, max_pin='x.x') }}
+
+requirements:
+  host:
+    - python >=3.9
+  run:
+    - biopython
+    - dssp
+    - fair-esm>=2.0.0
+    - loguru
+    - pandas
+    - python>=3.9
+    - pytorch
+    - pytorch_cluster
+    - pytorch_geometric
+    - torch-scatter
+
+test:
+  commands:
+    - train_tAMPer -h
+    - predict_tAMPer -h
+
+about:
+  home: https://github.com/bcgsc/tAMPer
+  license: GPL-3
+  license_family: GPL
+  license_file: LICENSE
+  summary: Structure-aware deep learning model for peptides toxicity prediction