keyword stringclasses 7
values | repo_name stringlengths 8 98 | file_path stringlengths 4 244 | file_extension stringclasses 29
values | file_size int64 0 84.1M | line_count int64 0 1.6M | content stringlengths 1 84.1M ⌀ | language stringclasses 14
values |
|---|---|---|---|---|---|---|---|
3D | Aswendt-Lab/AIDAmri | ARA/AllenBrainAPI-master/getAllenStructureList.m | .m | 10,526 | 284 | function [ARA_table,tableRowInds] = getAllenStructureList(varargin)
% Download the list of adult mouse structures from the Allen API.
%
% function ARA_table = getAllenStructureList('param1',val1,...)
%
%
% Purpose
% Make an API query to read in the Allen Reference Atlas (ARA) brain area
% list. All areas and data are ... | MATLAB |
3D | Aswendt-Lab/AIDAmri | ARA/AllenBrainAPI-master/examples/thalamus.m | .m | 3,201 | 77 | function thalamus
% make a projection density plot
%
% This is the MATLAB version of the R example found at
% http://api.brain-map.org/examples/doc/thalamus/thalamus.R.html
%
% We have some more robust MATLAB functions that encapsulate
% some operations that were performed in-line in the R example.
% These standalon... | MATLAB |
3D | zhengfj1994/PPGB_MS2 | smiles_create_dataset.py | .py | 3,732 | 103 | import os
import torch
import math
import pickle
import random
import functools
import multiprocessing
import numpy as np
import os.path as osp
from torch import Tensor
from joblib import Parallel, delayed
from torch_geometric.data import Dataset
from torch_geometric.data import Batch
from utils import pickle_load
from... | Python |
3D | zhengfj1994/PPGB_MS2 | utils3_ms2_matching.py | .py | 1,875 | 49 | import os
import pickle
import pandas as pd
from tqdm.notebook import tqdm
from joblib import Parallel, delayed
from pandas.core.frame import DataFrame
def batch_ms2_matching(MSMSFilePath, step2FilePath, step3FilePath, n_jobs = -1):
if not os.path.exists(step3FilePath): os.makedirs(step3FilePath)
rawCsvData =... | Python |
3D | zhengfj1994/PPGB_MS2 | utils5_pyg_graph.py | .py | 10,592 | 192 | import os
import copy
import torch
import pickle
import numpy as np
import networkx as nx
from rdkit import Chem
from torch import Tensor
from utils import pickle_load
from itertools import product
from tqdm.notebook import tqdm
from collections import defaultdict
from joblib import Parallel, delayed
from torch_geometr... | Python |
3D | zhengfj1994/PPGB_MS2 | utils4_graph_augmentation.py | .py | 2,217 | 50 | import os
import copy
import pickle
import numpy as np
import networkx as nx
from itertools import product
from tqdm.notebook import tqdm
from joblib import Parallel, delayed
# networkx
def graph_augmentation(raw_Graph, repeat = 2, augmentation_ratio = 0.6, with_raw_Graph = True):
copyed_Graph = copy.deepcopy(raw... | Python |
3D | zhengfj1994/PPGB_MS2 | smiles_augmentation.py | .py | 2,560 | 52 | import os
import copy
import math
import random
import pickle
import numpy as np
import networkx as nx
from itertools import product
from itertools import combinations
from tqdm.notebook import tqdm
from joblib import Parallel, delayed
def smiles_augmentation(raw_smiles, repeat, augmentation_ratio, max_augmentation_ti... | Python |
3D | zhengfj1994/PPGB_MS2 | utils6_loss.py | .py | 5,138 | 144 | import torch
from torch import nn
import torch.nn.functional as F
from torch.nn.modules.loss import _Loss
from torch.distributions import MultivariateNormal as MVN
class WeightedFocalLoss(nn.Module):
"Non weighted version of Focal Loss"
def __init__(self, alpha=.25, gamma=2):
super(WeightedFoc... | Python |
3D | zhengfj1994/PPGB_MS2 | smiles_ms2_matching.py | .py | 2,970 | 64 | import os
import pickle
import pandas as pd
from tqdm.notebook import tqdm
from joblib import Parallel, delayed
from pandas.core.frame import DataFrame
def batch_ms2_matching(MSMSFilePath, step2FilePath, step3FilePath, int_threshold, MS2_mz_tolerance, n_jobs = -1):
if not os.path.exists(step3FilePath): os.makedirs... | Python |
3D | zhengfj1994/PPGB_MS2 | utils1_fragmentation.py | .py | 10,794 | 210 | import copy
import pandas as pd
import networkx as nx
from rdkit import Chem
from rdkit.Chem import Descriptors
adduct_dict = {'[M+H]+' : {'mz': 1.00727646677, 'smiles':'.[H+]', 'charge_mz': -0.00054857990924, 'charge_smiles': '.[+]', 'ion_mode':'positive'},
'[H+]' : {'mz': 1.00727646677, 'smiles... | Python |
3D | zhengfj1994/PPGB_MS2 | utils.py | .py | 4,542 | 107 | import os
import math
import glob
import copy
import random
import shutil
import pickle
import numpy as np
import pandas as pd
from collections import Counter
from scipy.ndimage import convolve1d
from scipy.signal.windows import triang
from scipy.ndimage import gaussian_filter1d
import matplotlib.pyplot as plt
import m... | Python |
3D | zhengfj1994/PPGB_MS2 | utils6_training_evaluation.py | .py | 9,075 | 191 | import torch
import pandas as pd
from IPython import display
from matplotlib import pyplot as plt
from matplotlib_inline import backend_inline
from utils6_loss import WeightedFocalLoss
from sklearn.metrics import accuracy_score, precision_score, recall_score, f1_score, confusion_matrix
from sklearn.metrics import mean_... | Python |
3D | zhengfj1994/PPGB_MS2 | smiles_grouping.py | .py | 4,653 | 71 | import os
import pickle
import pandas as pd
from rdkit import Chem
from rdkit.Chem import Descriptors
from tqdm.notebook import tqdm
from joblib import Parallel, delayed
adduct_dict = {'[M+H]+' : {'mz': 1.00727646677, 'smiles':'.[H+]', 'charge_mz': -0.00054857990924, 'charge_smiles': '.[+]', 'ion_mode':'positive'... | Python |
3D | zhengfj1994/PPGB_MS2 | utils2_graph_grouping.py | .py | 4,908 | 93 | import os
import pickle
import itertools
import pandas as pd
import networkx as nx
from tqdm.notebook import tqdm
from joblib import Parallel, delayed
def disjoint_all_graph(GraphList, MSMS, argumentation = False):
if argumentation:
disjointed_graph_list = []
sub_GraphLists = []
for i in ... | Python |
3D | zhengfj1994/PPGB_MS2 | utils6_model.py | .py | 3,975 | 86 | import torch
from torch import nn
from torch.nn import init
import torch.nn.functional as F
from pydantic.dataclasses import dataclass
from torch_geometric.nn import RGCNConv, TransformerConv
from torch_geometric.nn import global_max_pool
from torch_geometric.nn import global_add_pool
from torch_geometric.nn import gl... | Python |
3D | zhengfj1994/PPGB_MS2 | smiles_to_pyg_graph.py | .py | 8,935 | 217 | import os
import torch
import pickle
import torch_geometric
from utils import pickle_load
from tqdm.notebook import tqdm
from rdkit import Chem, RDLogger
from joblib import Parallel, delayed
from torch_geometric.data import Data
def one_hot_k_encode(x, permitted_list):
if x not in permitted_list: x = permitted_l... | Python |
3D | zhengfj1994/PPGB_MS2 | smiles_fragmentation.py | .py | 15,013 | 236 | import os
import pickle
import pandas as pd
from rdkit import Chem
from itertools import chain
from tqdm.notebook import tqdm
from rdkit.Chem import AllChem
from rdkit.Chem import Descriptors
from joblib import Parallel, delayed
########################################## fragmentation reaction
crf1_0 = AllChem.Reactio... | Python |
3D | Parmeggiani-Lab/elfin | theories_and_assumptions.md | .md | 5,111 | 59 | # elfin theories and assumptions
[D] is a definition
[T] is a given truths or unproven theories derived from given truths
[A] is an assumption we use to bound the problem that elfin attempts to solve
[S] is a speculation
## Protein Database
- [D] A "module" is a protein that has two or more uncapped termini (inte... | Markdown |
3D | Parmeggiani-Lab/elfin | pymol_scripts/extensions/extrude_single_at_single_n.py | .py | 2,355 | 73 | #!/usr/bin/env python3
#
# A PyMol extension script to test extrusion of a single module from a single
# module's n-term
#
def main():
"""main"""
raise RuntimeError('This module should not be executed as a script')
if __name__ =='__main__':
main()
in_pymol = False
try:
import pymol
in_pymol = T... | Python |
3D | Parmeggiani-Lab/elfin | pymol_scripts/extensions/extension_template.py | .py | 403 | 24 | #!/usr/bin/env python3
#
# A PyMol extension script template
#
def main():
"""main"""
raise RuntimeError('This module should not be executed as a script')
if __name__ =='__main__':
main()
in_pymol = False
try:
import pymol
in_pymol = True
except ImportError as ie:
main()
if in_pymol:
f... | Python |
3D | Parmeggiani-Lab/elfin | pymol_scripts/extensions/draw_lines.py | .py | 5,465 | 185 | #!/usr/bin/env python3
#
# A PyMol extension script for drawing lines.
#
def main():
"""main"""
raise RuntimeError('This module should not be executed as a script')
if __name__ =='__main__':
main()
in_pymol = False
try:
import pymol
in_pymol = True
except ImportError as ie:
main()
if in_py... | Python |
3D | Parmeggiani-Lab/elfin | pymol_scripts/extensions/extrude_hub_at_single_n.py | .py | 2,736 | 82 | #!/usr/bin/env python3
#
# A PyMol extension script to test extrusion of a hub from a single module's
# n-term
#
def main():
"""main"""
raise RuntimeError('This module should not be executed as a script')
if __name__ =='__main__':
main()
in_pymol = False
try:
import pymol
in_pymol = True
except... | Python |
3D | Parmeggiani-Lab/elfin | pymol_scripts/extensions/__init__.py | .py | 0 | 0 | null | Python |
3D | Parmeggiani-Lab/elfin | pymol_scripts/extensions/load_all_extensions.py | .py | 870 | 39 | #!/usr/bin/env python2
#
# This is a PyMol extension script to load all PyMol extensions in the same
# directory.
#
def main():
"""main"""
raise RuntimeError('This module should not be executed as a script')
if __name__ =='__main__':
main()
in_pymol = False
try:
import pymol
in_pymol = True
exc... | Python |
3D | Parmeggiani-Lab/elfin | pymol_scripts/extensions/extrude_hub_at_single_c.py | .py | 2,172 | 68 | #!/usr/bin/env python3
#
# A PyMol extension script to test extrusion of a hub from a single module's
# c-term
#
def main():
"""main"""
raise RuntimeError('This module should not be executed as a script')
if __name__ =='__main__':
main()
in_pymol = False
try:
import pymol
in_pymol = True
except... | Python |
3D | Parmeggiani-Lab/elfin | pymol_scripts/extensions/transform_helper.py | .py | 1,855 | 65 | #!/usr/bin/env python3
#
# A PyMol extension script to shorten the transform_selection() command and
# accept python lists as argument.
#
def main():
"""main"""
raise RuntimeError('This module should not be executed as a script')
if __name__ =='__main__':
main()
in_pymol = False
try:
import pymol
... | Python |
3D | Parmeggiani-Lab/elfin | pymol_scripts/extensions/extrude_single_at_single_c.py | .py | 2,269 | 74 | #!/usr/bin/env python3
#
# A PyMol extension script to test extrusion of a single module from a single
# module's c-term
#
def main():
"""main"""
raise RuntimeError('This module should not be executed as a script')
if __name__ =='__main__':
main()
in_pymol = False
try:
import pymol
in_pymol = T... | Python |
3D | Parmeggiani-Lab/elfin | pymol_scripts/extensions/batch_convert.py | .py | 2,221 | 76 | #!/usr/bin/env python3
#
# A PyMol extension script for batch converting objects (originally intended
# to convert into .obj models).
#
def main():
"""main"""
raise RuntimeError('This module should not be executed as a script')
if __name__ =='__main__':
main()
in_pymol = False
try:
import pymol
... | Python |
3D | Parmeggiani-Lab/elfin | pymol_scripts/extensions/deprecated/color_by_restype.py | .py | 2,636 | 117 | # Copyright (c) 2004 Robert L. Campbell
import colorsys,sys
from pymol import cmd
aa_1_3 = {
'A': 'ALA',
'C': 'CYS',
'D': 'ASP',
'E': 'GLU',
'F': 'PHE',
'G': 'GLY',
'H': 'HIS',
'I': 'ILE',
'K': 'LYS',
'L': 'LEU',
'M': 'MET',
'N': 'ASN',
'P': 'PRO',
'... | Python |
3D | Parmeggiani-Lab/elfin | pymol_scripts/extensions/deprecated/center_of_mass.py | .py | 2,243 | 87 | """
See more here: http://www.pymolwiki.org/index.php/center_of_mass
DESCRIPTION
Places a pseudoatom at the center of mass
Author: Sean Law
Michigan State University
slaw (at) msu . edu
SEE ALSO
pseudoatom, get_com
"""
from __future__ import print_function
from pymol import cmd
def com(... | Python |
3D | Parmeggiani-Lab/elfin | pymol_scripts/extensions/deprecated/compare_solutions.py | .py | 1,798 | 67 | #!/usr/bin/env python3
#
# A PyMol extension script to compare Elfin solution against specification.
#
# *Needs to be re-implemented to deal with new spec and solution format.
#
from pymol import cmd
import numpy as np
import elfinpy
def compare_solutions(spec_file=None, sol_csv_file=None):
"""
Compares s... | Python |
3D | Parmeggiani-Lab/elfin | misc/get_omp_version.cpp | .cpp | 307 | 11 | #include <unordered_map>
#include <cstdio>
#include <omp.h>
int main(int argc, char *argv[])
{
std::unordered_map<unsigned,std::string> map{
{200505,"2.5"},{200805,"3.0"},{201107,"3.1"},{201307,"4.0"},{201511,"4.5"}};
printf("Available OpenMP version: %s\n", map.at(_OPENMP).c_str());
return 0;
} | C++ |
3D | Parmeggiani-Lab/elfin | elfinpy/template.py | .py | 566 | 20 | #!/usr/bin/env python3
import argparse, sys
from utilities import *
def parse_args(args):
"""Parse command line arguments."""
parser = argparse.ArgumentParser(description='Template Elfin Python script')
parser.add_argument('input') # Absence of dash denotes mandatory argument
return parser.parse_args(... | Python |
3D | Parmeggiani-Lab/elfin | elfinpy/utilities.py | .py | 10,406 | 336 | """
Elfin data processing utilities module
"""
import inspect
import os
import sys
import code
import traceback as traceback_module
import json
import csv
import re
import numpy as np
RADII_TYPES = ['average_all', 'max_ca_dist', 'max_heavy_dist']
INF = float('inf')
TERM_TYPES = {'n', 'c'}
MOD_TYPES = {'single', 'hub'... | Python |
3D | Parmeggiani-Lab/elfin | elfinpy/stat_xdb.py | .py | 2,667 | 103 | #!/usr/bin/env python3
import argparse, sys
import warnings
warnings.filterwarnings("ignore")
import matplotlib.pyplot as plt
import matplotlib
import networkx as nx
matplotlib.use('Agg')
plt.ioff()
from utilities import *
def parse_args(args):
parser = argparse.ArgumentParser(description='Prints module radii... | Python |
3D | Parmeggiani-Lab/elfin | elfinpy/dbgen.py | .py | 24,008 | 660 | #!/usr/bin/env python3
import glob
import numpy as np
import codecs
import json
import argparse
import shutil
from collections import defaultdict
from collections import OrderedDict
import Bio.PDB
from utilities import *
from pdb_utilities import *
nested_dict = lambda: defaultdict(nested_dict)
def parse_args(args)... | Python |
3D | Parmeggiani-Lab/elfin | elfinpy/elfin_node.py | .py | 1,926 | 53 | import numpy as np
import warnings
class ElfinNode(object):
"""
A single module instance and stores info about connectivity
"""
def __init__(
self,
**kwargs
):
self.id = kwargs.pop('id')
self.name = kwargs.pop('name')
self.trim = kwargs.pop('trim', {'n': Fal... | Python |
3D | Parmeggiani-Lab/elfin | elfinpy/v1_design_convert.py | .py | 2,830 | 92 | #!/usr/bin/env python3
import argparse, sys
import copy
try:
from elfin_graph import ElfinGraph
from elfin_node import ElfinNode
from utilities import *
except ImportError as e:
from .elfin_graph import ElfinGraph
from .elfin_node import ElfinNode
from .utilities import *
def compute_old_grap... | Python |
3D | Parmeggiani-Lab/elfin | elfinpy/pdb_utilities.py | .py | 3,134 | 101 | import Bio.PDB
DIRTY_ATOMS = {'1H', '2H', '3H', 'OXT'}
BACKBONE_NAMES = {'N', 'CA', 'C', 'O', 'H', 'HA'}
def get_pdb_residue_count(pdb):
"""Returns the residue count of a Bio.PDB.Structure.Structure."""
return sum([len(c.child_list) for c in pdb.child_list[0].child_list])
def get_chain_residue_count(struct, ... | Python |
3D | Parmeggiani-Lab/elfin | elfinpy/preprocess.py | .py | 8,078 | 213 | #!/usr/bin/env python3
import argparse, sys
import subprocess, glob
from utilities import *
from pdb_utilities import *
def merge_chains(pdb):
"""Merge all chains in a PDB structure and re-number the residue IDs
accordingly
Args:
- pdb - Bio.PDB.Structure.Structure
Returns:
Bio.PDB.Structure... | Python |
3D | Parmeggiani-Lab/elfin | elfinpy/__init__.py | .py | 0 | 0 | null | Python |
3D | Parmeggiani-Lab/elfin | elfinpy/extract_solution.py | .py | 4,164 | 115 | #!/usr/bin/env python3
# This script takes a solver output JSON and exports a specific solution
import sys
import argparse
try:
from utilities import *
except ImportError as e:
from .utilities import *
def parse_args(args):
desc = 'Exports a specific solution from a solver output JSON.'
parser = arg... | Python |
3D | Parmeggiani-Lab/elfin | elfinpy/kabsch.py | .py | 4,082 | 161 | #!/usr/bin/env python3
"""
Calculate RMSD between two XYZ files
by: Jimmy Charnley Kromann <jimmy@charnley.dk> and Lars Andersen Bratholm <larsbratholm@gmail.com>
project: https://github.com/charnley/rmsd
license: https://github.com/charnley/rmsd/blob/master/LICENSE
"""
import numpy as np
import re
def kabsch_rms... | Python |
3D | Parmeggiani-Lab/elfin | elfinpy/elfin_graph.py | .py | 622 | 24 | class ElfinGraph(object):
"""
A network of nodes that are connected either by doubles or through hubs.
Might be multi-chain.
"""
def __init__(self, name='', nodes=[]):
self.name = name
self.nodes = nodes
def __repr__(self):
return 'ElfinGraph: {{\n{}\n}}\n'.format(
... | Python |
3D | Parmeggiani-Lab/elfin | elfinpy/hubinfo_convert.py | .py | 1,446 | 42 | #!/usr/bin/env python3
import argparse, sys
from collections import OrderedDict
from utilities import *
def parse_args(args):
"""Parse command line arguments."""
parser = argparse.ArgumentParser(
description='Converts hub info metadata from csv to json.')
parser.add_argument('input') # Absence of... | Python |
3D | Parmeggiani-Lab/elfin | elfinpy/job_dispatcher.py | .py | 1,014 | 36 | #!/usr/bin/env python3
import argparse, sys
import multiprocessing
import subprocess
from utilities import *
def dispatch(*cmd_and_arg):
"""Dispatches a process to run cmd with given arguments."""
subprocess.check_call(*cmd_and_arg)
def parse_args(args):
"""Parse command line arguments."""
parser = ... | Python |
3D | Parmeggiani-Lab/elfin | elfinpy/stitch.py | .py | 26,251 | 747 | #!/usr/bin/env python3
#
# This script creates the CIF atom model from a design solution exported from
# elfin-ui in JSON format.
#
from collections import deque
from collections import namedtuple
import sys
import argparse
import numpy as np
import Bio.PDB
import Bio.SubsMat.MatrixInfo
import Bio.PDB.StructureBuild... | Python |
3D | Parmeggiani-Lab/elfin | elfinpy/rmsd.py | .py | 3,891 | 106 | #!/usr/bin/env python3
import argparse, sys
from utilities import *
def parse_args(args):
parser = argparse.ArgumentParser(description='Sliding-window RMSD calculator')
parser.add_argument('solution_dir') # Absence of dash denotes mandatory argument
parser.add_argument('minimised_dir')
parser.add_argu... | Python |
3D | Parmeggiani-Lab/elfin | elfinpy/obsolete/PlotPerf.py | .py | 4,274 | 183 | #!/usr/bin/env python
import ElfinUtils
import numpy as np
import matplotlib
matplotlib.use('TkAgg')
import matplotlib.pyplot as plt
from matplotlib.pyplot import cm
def main():
# Note: inf length ~22
machines = [
'IvyBridge\nZoo\n24-core\n2.7Ghz',
'KNL\nZoo\n64-core\n1.3Ghz',
'JetsonTX1\nZoo\n4-core\n1.9G... | Python |
3D | Parmeggiani-Lab/elfin | elfinpy/obsolete/RMSDStatRosetta.py | .py | 718 | 27 | #!/usr/bin/env python
import glob, sys
from ElfinUtils import *
### Rosetta overall score based... deprecated in favour of windowed RMSD (RMSDStat.py)
if(len(sys.argv) < 2):
print './RMSDStat.py <scoreDir>'
exit()
scoreDir = sys.argv[1]
files = glob.glob(scoreDir + '/*_comp.sc')
nFiles = len(files)
rmsds = [... | Python |
3D | Parmeggiani-Lab/elfin | elfinpy/obsolete/AnalyseComplexity.py | .py | 1,664 | 70 | #!/usr/bin/env python
import ElfinUtils
import json
import argparse
import numpy as np
from decimal import Decimal
import matplotlib
matplotlib.use('TkAgg')
import matplotlib.pyplot as plt
def main():
ap = argparse.ArgumentParser(description='Compute the number of combinations for a given MMC protein length');
ap.... | Python |
3D | Parmeggiani-Lab/elfin | elfinpy/obsolete/GenBench.py | .py | 6,343 | 192 | #!/usr/bin/env python
import Bio.PDB, json
import numpy, random, string, math, codecs
from collections import OrderedDict
from time import gmtime, strftime
import sys, os
import argparse
haveCmd = False
try:
from pymol import cmd
cmd.reinitialize()
haveCmd = True
except ImportError:
print 'Could not i... | Python |
3D | Parmeggiani-Lab/elfin | elfinpy/obsolete/Json2Csv.py | .py | 679 | 31 | #!/usr/bin/env python
import glob, json, sys
from utilities import *
### Converts spec JSON files into pure CoMs in CSV form ###
if len(sys.argv) < 2:
print './Json2Csv.py <sourceDir> <outDir=sourceDir>'
exit()
sourceDir = sys.argv[1]
outDir = sourceDir
if len(sys.argv) >= 3:
outDir = sys.argv[2]
jsonFiles... | Python |
3D | Parmeggiani-Lab/elfin | elfinpy/obsolete/GridSearchParams.py | .py | 2,642 | 93 | # This file contains versioned grid search parameter data
def getGSParams(gsVersion):
if gsVersion == 1:
return getGSParamsV1()
if gsVersion == 2:
return getGSParamsV2()
print 'Unknown Grid Search version: {}'.format(gsVersion)
def getGSParamsV2():
# Define the grid
chromoLenDevs = [0.2]
gaPopSizes = ... | Python |
3D | Parmeggiani-Lab/elfin | elfinpy/obsolete/pymol_helpers/gen_transform.py | .py | 1,025 | 43 | #!/usr/bin/env python
import argparse, sys
import numpy as np
from utilities import *
def main():
ap = argparse.ArgumentParser(description='Generate Pymol Transform');
ap.add_argument('double_name')
ap.add_argument('--xdb_path', default='./resources/xdb.json')
ap.add_argument('--double_dir', default='./resources/... | Python |
3D | Parmeggiani-Lab/elfin | elfinpy/obsolete/pymol_helpers/gen_spec_sol_rot.py | .py | 1,130 | 41 | #!/usr/bin/env python
import argparse, sys
import numpy as np
import kabsch
from utilities import *
def get_spec_sol_rot(spec_file, sol_csv):
if spec_file.rfind('.csv') != -1:
spec_pts = read_csv_points(spec_file)
elif spec_file.rfind('.json') != -1:
with open(spec_file, 'r') as file:
... | Python |
3D | Parmeggiani-Lab/elfin | tests/__init__.py | .py | 0 | 0 | null | Python |
3D | Parmeggiani-Lab/elfin | tests/helper.py | .py | 1,304 | 41 | #!/usr/bin/env python3
import pytest
import importlib
from functools import partial
def _test(module_name=None, error_type=None, module_test_callback=None, assert_callback=None, package_name=None):
if module_name is None or \
error_type is None or \
module_test_callback is None or \
assert_callback is ... | Python |
3D | Parmeggiani-Lab/elfin | tests/test_pymol_extensions/__init__.py | .py | 135 | 4 | import sys, os
curr_dir = os.getcwd()
sys.path.append(os.path.realpath(os.path.join(curr_dir, 'pymol_scripts'))) # for test scripts | Python |
3D | Parmeggiani-Lab/elfin | tests/test_pymol_extensions/test_mains.py | .py | 744 | 21 | import pytest
import importlib
from functools import partial
from tests import helper
test_package_name = 'extensions'
script_main_test = partial(helper._test_script_main, package_name=test_package_name)
non_executable_test = partial(helper._test_non_executable, package_name=test_package_name)
def test_mains():
n... | Python |
3D | Parmeggiani-Lab/elfin | tests/test_elfinpy/__init__.py | .py | 129 | 4 | import sys, os
curr_dir = os.getcwd()
sys.path.append(os.path.realpath(os.path.join(curr_dir, 'elfinpy'))) # for test scripts | Python |
3D | Parmeggiani-Lab/elfin | tests/test_elfinpy/test_mains.py | .py | 744 | 27 | import pytest
import importlib
from functools import partial
from tests import helper
test_package_name = 'elfinpy'
script_main_test = partial(helper._test_script_main, package_name=test_package_name)
non_executable_test = partial(helper._test_non_executable, package_name=test_package_name)
def test_mains():
# Te... | Python |
3D | OpenMS/OpenMS | AGENTS.md | .md | 28,824 | 700 | # OpenMS Agent Notes
This file provides context and instructions for AI coding agents working on OpenMS. It follows the [AGENTS.md](https://agents.md) standard.
## Critical Constraints
**NEVER do these things:**
- Build the project unless explicitly asked (extremely resource-intensive)
- Modify files in `src/openms/... | Markdown |
3D | OpenMS/OpenMS | CONTRIBUTING.md | .md | 3,337 | 43 | Help us to make OpenMS better and become part of the OpenMS open-source community.
This document is displayed because you either opened an issue or you want to provide your code as a pull request for inclusion into OpenMS. Please take a look at the appropriate section below to find some details on how we handle this p... | Markdown |
3D | OpenMS/OpenMS | ARCHITECTURE.MD | .MD | 15,270 | 319 | # OpenMS Architecture Documentation
## Introduction
OpenMS is an open‐source software framework dedicated to mass spectrometry data analysis in proteomics, metabolomics, and related fields. It provides a robust, flexible, and extensible platform that supports rapid algorithm development, data processing, and the crea... | Markdown |
3D | OpenMS/OpenMS | CODE_OF_CONDUCT.md | .md | 6,242 | 74 | ### OpenMS Code of Conduct
#### Code of Conduct (Summary View)
Below is a summary of the OpenMS Code of Conduct.
We are dedicated to providing a welcoming and supportive environment for all people, regardless of background or identity. By participating in this community, participants accept to abide by OpenMS' Code ... | Markdown |
3D | OpenMS/OpenMS | PULL_REQUEST_TEMPLATE.md | .md | 1,765 | 35 | ## Description
<!-- Please include a summary of the change and which issue is fixed here. -->
## Checklist
- [ ] Make sure that you are listed in the AUTHORS file
- [ ] Add relevant changes and new features to the CHANGELOG file
- [ ] I have commented my code, particularly in hard-to-understand areas
- [ ] New and ex... | Markdown |
3D | OpenMS/OpenMS | LICENSE.md | .md | 1,609 | 30 | BSD 3-Clause License
Copyright (c) 2002-present, OpenMS Inc. -- Eberhard Karls University Tuebingen, ETH Zurich, and Freie Universitaet Berlin
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
1. Redistr... | Markdown |
3D | OpenMS/OpenMS | tools/changelog_helper.sh | .sh | 5,984 | 172 | #!/bin/bash
# Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
# SPDX-License-Identifier: BSD-3-Clause
#
# --------------------------------------------------------------------------
# $Maintainer: Johannes Veit $
# $Authors: Johannes Veit $
# -----------------------------------------... | Shell |
3D | OpenMS/OpenMS | tools/PythonExtensionChecker.py | .py | 52,975 | 1,278 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
# Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
# SPDX-License-Identifier: BSD-3-Clause
#
# --------------------------------------------------------------------------
# $Maintainer: Hannes Roest$
# $Authors: Hannes Roest$
# ------... | Python |
3D | OpenMS/OpenMS | tools/rest_server_update_helper.sh | .sh | 1,442 | 44 | #!/bin/bash
# Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
# SPDX-License-Identifier: BSD-3-Clause
#
# --------------------------------------------------------------------------
# $Maintainer: Timo Sachsenberg $
# $Authors: Timo Sachsenberg $
# ------------------------------------... | Shell |
3D | OpenMS/OpenMS | tools/quickbuild.sh | .sh | 790 | 38 | #!/bin/sh
set -e
# first argument used for number of jobs
if [ ! -z "$1" ]
then
numberOfJobs=$1
else
numberOfJobs=1
fi
###################################
# 1. download and build contrib (if not present already)
git submodule update --init contrib
# set contrib absolute path for configure
CONTRIB_PATH=`pwd`/co... | Shell |
3D | OpenMS/OpenMS | tools/quickbuild-osx.sh | .sh | 876 | 38 | #!/bin/sh
set -e
# first argument used for number of jobs
if [ ! -z "$1" ]
then
numberOfJobs=$1
else
numberOfJobs=1
fi
###################################
# 1. download and build contrib (if not present already)
git submodule update --init contrib
# set contrib absolute path for configure
CONTRIB_PATH=`pwd`/cont... | Shell |
3D | OpenMS/OpenMS | tools/update_ini_files_OpenMS_version.sh | .sh | 330 | 4 | #DEPRECATED. Functionality has been merged into update_version_numbers.yml
TOOL_DIR_PATH="./src/tests/topp/"
find $TOOL_DIR_PATH -type f -iname '*.ini' -exec grep -q '<ITEM name="version".*Version of the tool' {} \; -exec sed -i '' -e 's/name="version" value=".*" type="string"/name="version" value="3.2.0" type="string"... | Shell |
3D | OpenMS/OpenMS | tools/load_vcvarsall.sh | .sh | 2,294 | 69 | # This is a script for creating a "Visual Studio Command Line" in (git) bash on Windows
# It basically invokes the corresponding vcvarsall.bat (that is also called when opening a VS Command Line)
# and copies all the environment variables from it.
# You can source it or add this function to your ~/.bashrc for example
... | Shell |
3D | OpenMS/OpenMS | tools/update_version_numbers.sh | .sh | 3,565 | 102 | #!/usr/bin/env bash
################################################################################
set -eu
set -o pipefail
################################################################################
usage() {
cat <<EOF
Usage: $(basename "$0") [options] major minor patch
-h This message
Update the Op... | Shell |
3D | OpenMS/OpenMS | tools/PythonCheckerLib.py | .py | 3,859 | 107 | from __future__ import print_function
def parse_pxd_file(path):
import os
from Cython.Compiler.CmdLine import parse_command_line
from Cython.Compiler.Main import create_default_resultobj, CompilationSource
from Cython.Compiler import Pipeline
from Cython.Compiler.Scanning import FileSourceDescrip... | Python |
3D | OpenMS/OpenMS | tools/update_header_dates.sh | .sh | 362 | 4 | #find . -type f | xargs sed -i 's/and Freie Universitaet Berlin 2002-present.and Freie Universitaet Berlin 2002-present.g'
## For all files and on MacOS:
find . -type f ! -path "./.git/*" -exec grep -q "Freie Universitaet Berlin 2002-20" {} \; -exec sed -i '' -e 's/and Freie Universitaet Berlin 2002-present.and Freie ... | Shell |
3D | OpenMS/OpenMS | tools/overwriteTOPPTestFiles.sh | .sh | 541 | 12 | #!/bin/bash
# Use in your build folder with the test regex (as for ctest -R) as argument like: ../tools/overwriteTOPPTestFiles.sh TOPP_OpenSwathAnalyzer
# Runs the tests with ctest, checks for failed ones and copies the (temporary) result file from the test OVER the
# expected file from the OpenMS test sources.
ctest -... | Shell |
3D | OpenMS/OpenMS | tools/ci/deps-macos.sh | .sh | 1,228 | 62 | #!/usr/bin/env bash
set -eu
set -o pipefail
# Unfortunately GitHub's macOS runner already has Python installed so
# we need to tell brew to overwrite the existing links. The following
# function will be called when the brew commands below are executed.
# It then calls the real brew command.
function brew() {
local... | Shell |
3D | OpenMS/OpenMS | tools/ci/capture-env.sh | .sh | 3,162 | 141 | #!/usr/bin/env bash
################################################################################
set -eu
set -o pipefail
################################################################################
vars_to_cache=(
"ADDRESS_SANITIZER"
"CC"
"CXX"
"CMAKE_CXX_COMPILER"
"CMAKE_CXX_COMPILER_LAUNCHER"
"C... | Shell |
3D | OpenMS/OpenMS | tools/ci/deps-ubuntu.sh | .sh | 1,481 | 64 | #!/usr/bin/env bash
set -eu
set -o pipefail
# Code between the following doxygen markers are included in the
# public-facing OpenMS installation instructions.
# [installation_documentation]
# Add "universe" and update:
sudo add-apt-repository universe
sudo apt update
# Required dependencies:
sudo apt-get -qq instal... | Shell |
3D | OpenMS/OpenMS | tools/scripts/create_im_with_swathIm.py | .py | 7,952 | 230 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
SPDX-License-Identifier: BSD-3-Clause
--------------------------------------------------------------------------
$Maintainer: Hannes Roest, Joshua Charkow $
$Authors: Hannes Roest, Josh... | Python |
3D | OpenMS/OpenMS | tools/scripts/git_showdiff.sh | .sh | 396 | 16 |
echo "Usage: git_showdiff.sh REV1 REV2"
git diff $1 $2 --name-only \
| grep -v '^src/tests/topp/' \
| grep -v '^share/OpenMS' \
| grep -v '^src/tests/class_tests/openms/data/' \
| grep -v '^cmake/modules/' \
| grep -v '^cmake/' \
| grep -v '^src/openswathalgo/thirdparty' \
| grep -v '^src/openms/third... | Shell |
3D | OpenMS/OpenMS | tools/scripts/check_for_unused_testdata.py | .py | 3,765 | 96 | import os
import subprocess
import glob
# script that lists all test files in the topp folder that are:
# 1. tracked by git
# 2. not referenced in the topp tests (CMakeList.txt)
# after careful check these potentially can be removed
def list_files_in_directory(start_path):
""" Returns a list of all files in a dir... | Python |
3D | OpenMS/OpenMS | tools/scripts/create_testdata_flqt.py | .py | 1,133 | 34 |
import pyopenms
"""
Producing the test data for TOPP_FeatureLinkerUnlabeledQT_5 and TOPP_FeatureLinkerUnlabeledQT_6
"""
fmaps = [ pyopenms.FeatureMap() for i in range(3)]
pepids = []
pepseq = ["PEPTIDEA", "PEPTIDEK", "PEPTIDER"]
for s in pepseq:
pepid = pyopenms.PeptideIdentification()
hit = pyopenms.PeptideH... | Python |
3D | OpenMS/OpenMS | tools/scripts/create_im.py | .py | 4,192 | 147 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
# Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
# SPDX-License-Identifier: BSD-3-Clause
#
# --------------------------------------------------------------------------
# $Maintainer: Hannes Roest $
# $Authors: Hannes Roest $
# ----... | Python |
3D | OpenMS/OpenMS | doc/code_examples/Tutorial_SavitzkyGolayFilter.cpp | .cpp | 1,143 | 39 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
#include <OpenMS/PROCESSING/SMOOTHING/SavitzkyGolayFilter.h>
#include <OpenMS/PROCESSING/RESAMPLING/LinearResampler.h>
#include <OpenMS/FORMAT/FileHandler.h>
#include <OpenMS/KERNEL/Standa... | C++ |
3D | OpenMS/OpenMS | doc/code_examples/Tutorial_FileIO.cpp | .cpp | 2,339 | 54 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
#include <OpenMS/FORMAT/FileHandler.h>
#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/KERNEL/FeatureMap.h>
#include <OpenMS/SYSTEM/File.h>
#include <OpenMS/openms_data_path.h> //... | C++ |
3D | OpenMS/OpenMS | doc/code_examples/Tutorial_MetaInfo.cpp | .cpp | 709 | 28 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/METADATA/MetaInfoInterface.h>
#include <iostream>
using namespace OpenMS;
using namespace std;
Int main()
{
MetaInfoInterface... | C++ |
3D | OpenMS/OpenMS | doc/code_examples/Tutorial_GUI_Plot1D.cpp | .cpp | 1,404 | 39 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
#include <OpenMS/FORMAT/FileHandler.h>
#include <OpenMS/KERNEL/OnDiscMSExperiment.h>
#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/VISUAL/LayerDataBase.h>
#include <OpenMS/VISU... | C++ |
3D | OpenMS/OpenMS | doc/code_examples/Tutorial_GUI_ParamEditor.cpp | .cpp | 929 | 37 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
#include <OpenMS/VISUAL/ParamEditor.h>
#include <OpenMS/DATASTRUCTURES/Param.h>
#include <OpenMS/FORMAT/ParamXMLFile.h>
#include <OpenMS/SYSTEM/File.h>
#include <OpenMS/openms_data_path.h>... | C++ |
3D | OpenMS/OpenMS | doc/code_examples/Tutorial_Unlabeled.cpp | .cpp | 1,313 | 40 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/ANALYSIS/MAPMATCHING/FeatureGroupingAlgorithmUnlabeled.h>
#include <OpenMS/FORMAT/FileHandler.h>
#include <OpenMS/openms_data_path.h> //... | C++ |
3D | OpenMS/OpenMS | doc/code_examples/Tutorial_DPosition.cpp | .cpp | 837 | 36 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
#include <OpenMS/DATASTRUCTURES/DPosition.h>
#include <iostream>
using namespace OpenMS;
Int main()
{
DPosition<2> pos {-8.15, 47.11};
static_assert(pos.size() == 2);
std::cout <<... | C++ |
3D | OpenMS/OpenMS | doc/code_examples/Tutorial_Template.cpp | .cpp | 2,318 | 93 | //! [doxygen_snippet_Template]
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
// --------------------------------------------------------------------------
// $Maintainer: Maintainer $
// $Authors: Author1, Author2 $
// -------------------... | C++ |
3D | OpenMS/OpenMS | doc/code_examples/Tutorial_FeatureMap.cpp | .cpp | 1,033 | 41 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
//! [doxygen_snippet_FeatureMap]
#include <OpenMS/KERNEL/FeatureMap.h>
#include <iostream>
using namespace OpenMS;
using namespace std;
int main()
{
// Insert of two features into a m... | C++ |
3D | OpenMS/OpenMS | doc/code_examples/Tutorial_MapAlignment.cpp | .cpp | 1,279 | 40 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
#include <OpenMS/ANALYSIS/MAPMATCHING/MapAlignmentAlgorithmPoseClustering.h>
#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/FORMAT/FileHandler.h>
#include <OpenMS/openms_data_path.h> /... | C++ |
3D | OpenMS/OpenMS | doc/code_examples/Tutorial_MSExperiment.cpp | .cpp | 3,212 | 90 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
//! [doxygen_snippet_MSExperiment]
#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/FORMAT/FileHandler.h>
#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/SYSTEM/File.h>
#includ... | C++ |
3D | OpenMS/OpenMS | doc/code_examples/Tutorial_Precursor.cpp | .cpp | 2,054 | 58 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//! [doxygen_snippet_Precursor]
#include <OpenMS/CONCEPT/Exception.h>
#include <OpenMS/FORMAT/FileHandler.h>
#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/METADATA/Precursor.h>
#i... | C++ |
3D | OpenMS/OpenMS | doc/code_examples/Tutorial_ResidueModification.cpp | .cpp | 1,636 | 46 | //! [doxygen_snippet_ResidueModification]
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
#include <OpenMS/CHEMISTRY/AASequence.h>
#include <OpenMS/CHEMISTRY/ResidueModification.h>
#include <OpenMS/CHEMISTRY/ModificationsDB.h>
#include <io... | C++ |
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