Commit 0ab924b9 authored by Akdel's avatar Akdel
Browse files

Merge remote-tracking branch 'origin/master'

parents e5196843 c99376b6
......@@ -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>
......
......@@ -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/"),
......
......@@ -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
......
......@@ -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",
......
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