Quaternion fix and version

.travis.yml

@@ -7,7 +7,7 @@ addons:
   apt:
     sources:
       - ubuntu-toolchain-r-test
-
+      
 before_install:
   - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew install md5sha1sum; fi
 
@@ -27,10 +27,17 @@ script:
   - conda config --add channels ${ORGNAME}
   # Create a test environment
   - conda create --quiet --yes -n test python=$python
+  # Activate root environment
+  #- source activate root
   # Activate the test environment
   - source activate test
+  # Get conda info
+  - conda info 
+  # Get environment info
+  - conda list --explicit 
   # Build recipie
   - conda build devtools/conda-recipe
+  #- conda-build devtools/conda-recipe -c conda-forge/label/gcc7
   # Install locally-built package
   - conda install --yes --quiet --use-local ${PACKAGENAME}
   #- conda install --yes --quiet pip nose nose-timer
@@ -41,17 +48,16 @@ os:
   - osx
   - linux
 
-
 env:
   matrix:
     - python=2.7  CONDA_PY=27
 #    - python=3.4  CONDA_PY=34
     - python=3.5  CONDA_PY=35
     - python=3.6  CONDA_PY=36
+
   global:
-
     - PACKAGENAME="sstmap"
     - ORGNAME="solvationtools"
 
 after_success:
-  - source devtools/travis-ci/deploy_anaconda.sh
+  - source devtools/travis-ci/deploy_anaconda.sh

Makefile

@@ -1,4 +1,3 @@
-CC      = g++
 SOURCEDIR = ./sstmap
 INSTALLDIR = ~/anaconda2/bin
 bruteclust: $(SOURCEDIR)/make_clust_brute.cpp
@@ -18,4 +17,4 @@ clean:
 	rm -f kdhsa102
 	rm -f 6dimprobable
 
-test: pytest -m tests
+test: pytest -m tests

README.md

@@ -1,4 +1,4 @@
-[![Build Status](https://travis-ci.org/kamran-haider/SSTMap.svg?branch=v1.1_dev)](https://travis-ci.org/kamran-haider/SSTMap)
+[![Build Status](https://travis-ci.org/kamran-haider/SSTMap.svg?branch=master)](https://travis-ci.org/kamran-haider/SSTMap)
 [![Anaconda-Server Badge](https://anaconda.org/solvationtools/sstmap/badges/installer/conda.svg)](https://conda.anaconda.org/solvationtools)
 [![Anaconda-Server Badge](https://anaconda.org/solvationtools/sstmap/badges/downloads.svg)](https://anaconda.org/solvationtools/sstmap)
 [![DOI for Citing SSTMap](https://img.shields.io/badge/DOI-10.1021%2Fj.jctc.2017.11.021-blue.svg)](http://doi.org/10.1021/acs.jctc.7b00592)
@@ -38,8 +38,8 @@ You can also download the release package manually from GitHub, unzip it, naviga
 
 ```bash
 https://github.com/KurtzmanLab/SSTMap/archive/1.1.4.tar.gz or https://github.com/KurtzmanLab/SSTMap/archive/1.1.4.zip
-tar -xvf 1.1.4.tar.gz or unzip 1.0.0.zip
-cd SSTMap-1.0
+tar -xvf 1.1.4.tar.gz or unzip 1.1.4.zip
+cd SSTMap-1.1.4
 python setup.py install
 ```
 Or you can clone the GitHub repository, navigate into the directory, and execute the command: 
@@ -54,6 +54,7 @@ git checkout tags/1.1.4
 python setup.py install
 ```
 **For the developmental version:**
+
 ```
 python setup.py install
 ```
@@ -109,7 +110,7 @@ Principal Developer(s)
 Co-Developers
 -------------
 * Steven Ramsey <vpsramsey@gmail.com>
-* Anthony Cruz Balberdi <anthonycruzpr@gmail.com>
+* Anthony Cruz Balberdy <anthonycruzpr@gmail.com>
 * Tobias Wulsdorf <tobias.wulsdorf@pharmazie.uni-marburg.de>
 
 Principal Investigators

devtools/conda-recipe/meta.yaml

@@ -1,26 +1,30 @@
 package:
   name: sstmap
-  version: 1.1.3
+  version: 1.1.4
 
 source:
   path: ../../
 
 
 requirements:
   build:
+    - {{ compiler('c') }}
+    - {{ compiler('cxx') }}
+  host:
     - python
-    - numpy 1.14.0
-    - setuptools
-    - gcc
-    - toolchain
-    - libgcc
+    - numpy 
+    - setuptools 
+    - conda-build 
+    - toolchain3
+    - libgcc 
     - gsl 2.2.1
-    - libopenblas
-
+    - libopenblas 
+    - libgcc-ng 
+    - libstdcxx-ng 
   run:
     - python
     - libgcc
-    - numpy
+    - numpy 
     - scipy
     - mdtraj
     - parmed

setup.py

@@ -9,6 +9,7 @@
                             sources=['sstmap/_sstmap_ext.c'],
                             include_dirs=[numpy.get_include()],
                             extra_link_args=['-lgsl','-lgslcblas']))
+
 extensions.append(Extension('_sstmap_entropy',
                             sources=['sstmap/_sstmap_entropy.cpp', 'sstmap/kdhsa102.cpp'],
                             language="c++"))

sstmap/__init__.py

@@ -45,7 +45,7 @@
 __license__ = "MIT"
 __maintainer__ = "Kamran Haider"
 __email__ = "kamranhaider.mb@gmail.com"
-__version__ = "1.1.3"
+__version__ = "1.1.4"
 
 
 from sstmap import site_water_analysis, grid_water_analysis, utils

sstmap/grid_water_analysis.py

@@ -221,7 +221,7 @@ def calculate_euler_angles(self, water, coords):
 
         H_temp = np.zeros(3)
         H_temp[0] = ((w2*w2+x2*x2)-(y2*y2+z2*z2))*h1wat[0]
-        H_temp[0] = (2*(x2*y2 - w2*z2)*h1wat[1]) + H_temp[0]
+        H_temp[0] = (2*(x2*y2 + w2*z2)*h1wat[1]) + H_temp[0]
         H_temp[0] = (2*(x2*z2-w2*y2)*h1wat[2]) + H_temp[0]
 
         H_temp[1] = 2*(x2*y2 - w2*z2)* h1wat[0]
@@ -235,7 +235,7 @@ def calculate_euler_angles(self, water, coords):
         H_temp2 = np.zeros(3,)
         H_temp2[0] = ((w2*w2+x2*x2)-(y2*y2+z2*z2))*h2wat[0]
         H_temp2[0] = (2*(x2*y2 + w2*z2)*h2wat[1]) + H_temp2[0]
-        H_temp2[0] = (2*(x2*z2-w2*y2)+h2wat[2]) +H_temp2[0]
+        H_temp2[0] = (2*(x2*z2-w2*y2)*h2wat[2]) +H_temp2[0]
 
         H_temp2[1] = 2*(x2*y2 - w2*z2) *h2wat[0]
         H_temp2[1] = ((w2*w2-x2*x2+y2*y2-z2*z2)*h2wat[1]) +H_temp2[1]