Merge remote-tracking branch 'origin/master'

README.md

@@ -8,8 +8,18 @@ The command-line tool and self-hosted web application do not have this restricti
 ## Installation
 
 ### Requirements
+#### Operating system support
+1. Linux and Mac
+* All capabilities are supported
+2. Windows
+* The external tool **msms** is not available in Windows. Due to this:
+    * Feature extraction is not available.
+    * `extract-all-features` argument in caretta-cli should be always False. 
+    * `caretta-app` is not available.
+
+#### Software
 Caretta works with Python 3.7+
-Run the following commands to install required external dependencies:
+Run the following commands to install required external dependencies (Mac and Linux only):
 ```bash
 conda install -c salilab dssp
 conda install -c bioconda msms
@@ -21,7 +31,7 @@ git clone https://git.wur.nl/durai001/caretta.git
 cd caretta
 ```
 
-### Install both the command-line interface and the web-application:
+### Install both the command-line interface and the web-application (Mac and Linux only):
 ```bash
 pip install -e ".[GUI]"
 ```
@@ -47,7 +57,7 @@ caretta-cli input_pdb_folder
 # caretta-cli -h for more options
 ```
 
-### Web-application Usage
+### Web-application Usage (Mac and Linux only)
 
 ```bash
 caretta-app <host-ip> <port> 

bin/caretta-cli

@@ -8,7 +8,7 @@ from caretta import msa_numba
 
 
 def align(input_pdb,
-          dssp_dir="caretta_tmp", num_threads=20, extract_all_features=True,
+          dssp_dir="caretta_tmp", num_threads=20, extract_all_features=False,
           gap_open_penalty=1., gap_extend_penalty=0.01, consensus_weight=1.,
           write_fasta=True, output_fasta_filename=Path("./result.fasta"),
           write_pdb=True, output_pdb_folder=Path("./result_pdb/"),

caretta/msa_numba.py

@@ -64,7 +64,7 @@ def make_pairwise_rmsd_score_matrix(coords_array, secondary_array, lengths_array
                                                                       dtw_aln_1, dtw_aln_2)
             rotation_matrix, translation_matrix = rmsd_calculations.svd_superimpose(common_coords_1[:, :3], common_coords_2[:, :3])
             common_coords_2[:, :3] = rmsd_calculations.apply_rotran(common_coords_2[:, :3], rotation_matrix, translation_matrix)
-            score = rmsd_calculations.get_rmsd(common_coords_1, common_coords_2, gamma, True)
+            score = rmsd_calculations.get_rmsd(common_coords_1, common_coords_2)
             pairwise_matrix[i, j] = score
     pairwise_matrix += pairwise_matrix.T
     return pairwise_matrix

setup.py

@@ -4,7 +4,7 @@ setup(name='caretta',
       version='1.0',
       authors=["Janani Durairaj", "Mehmet Akdel"],
       packages=["caretta"],
-      install_requires=["numpy==1.16.4", "numba==0.44.1", "scipy==1.3.0", "prody==1.10.10", "biopython==1.74", "fire==0.2.1", "pyparsing==2.4.0"],
+      install_requires=["numpy", "numba", "scipy", "prody", "biopython", "fire", "pyparsing"],
       extras_require={
           'GUI': ["dash==1.3.1", "dash-bio==0.1.4", "cryptography",
                   "dash-core-components==1.2.1", "dash-html-components==1.0.1", "dash-renderer==1.1.0",