Merge pull request #60 from rbharath/travis (24c3a66f) · Commits · 钟慕尧 / deepchem

.travis.yml

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		language: python
		python:
		# We don't actually use the Travis Python, but this keeps it organized.
		- "2.7"
		install:
		- sudo apt-get update
		- wget http://repo.continuum.io/archive/Anaconda2-2.4.1-Linux-x86_64.sh -O anaconda.sh;
		- bash anaconda.sh -b -p $HOME/anaconda
		- export PATH="$HOME/anaconda/bin:$PATH"
		- hash -r
		- conda config --set always_yes yes --set changeps1 no
		- conda update -q conda
		# Useful for debugging any issues with conda
		- conda info -a

		# Replace dep1 dep2 ... with your dependencies
		#- conda create -q -n test-environment python=$TRAVIS_PYTHON_VERSION dep1 dep2 ...
		- conda install -c omnia rdkit
		- conda install -c omnia openbabel
		- conda install joblib
		- pip install --upgrade --no-deps git+git://github.com/Theano/Theano.git
		- pushd .
		- cd ~/
		- git clone https://github.com/pandegroup/keras.git
		- cd keras/
		- python setup.py install
		- popd
		- python setup.py develop

		script:
		- nosetests -v deepchem

README.md

+0 −12

Original line number	Diff line number	Diff line
		@@ -9,7 +9,6 @@ Requirements
		* [sklearn](https://github.com/scikit-learn/scikit-learn.git)
		* [numpy](https://store.continuum.io/cshop/anaconda/)
		* [keras](keras.io)
		* [vs-utils] (https://github.com/pandegroup/vs-utils.git)

		Linux (64-bit) Installation
		------------------
		@@ -46,17 +45,6 @@ Cd into the keras directory and execute
		python setup.py install
		```

		###vs_utils
		Clone the vs_utils git repository
		```bash
		git clone https://github.com/pandegroup/vs-utils.git
		```

		Cd into the vs-utils directory and execute
		```bash
		python setup.py develop
		```

		###deepchem
		Clone the deep_chem git repository
		```bash

deepchem/featurizers/coulomb_matrices.py

+138 −138

Original line number	Diff line number	Diff line
		@@ -13,7 +13,7 @@ import numpy as np
		from rdkit import Chem

		from deepchem.featurizers import Featurizer
		from vs_utils.utils import pad_array
		from deepchem.utils import pad_array


		class CoulombMatrix(Featurizer):

deepchem/featurizers/featurize.py

+4 −7

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		@@ -15,7 +15,7 @@ from deepchem.featurizers.basic import SimpleDescriptors
		from deepchem.utils.save import save_to_disk
		from deepchem.utils.save import load_from_disk
		from deepchem.utils.save import load_pandas_from_disk
		from vs_utils.utils import ScaffoldGenerator
		from deepchem.utils import ScaffoldGenerator
		from deepchem.featurizers.nnscore import NNScoreComplexFeaturizer
		import multiprocessing as mp
		from functools import partial
		@@ -137,19 +137,17 @@ class DataFeaturizer(object):
		"""Featurize provided file and write to specified location."""
		input_type = _get_input_type(input_file)

		print("Loading raw samples now.")
		raw_df = load_pandas_from_disk(input_file)
		fields = raw_df.keys()
		print("Loaded raw data frame from file.")
		def process_raw_sample_helper(row, fields, input_type):
		return self._process_raw_sample(input_type, row, fields)
		process_raw_sample_helper_partial = partial(process_raw_sample_helper,
		fields=fields,
		input_type=input_type)

		processed_rows = raw_df.apply(process_raw_sample_helper_partial, axis=1)
		print("finished processing rows")
		raw_df = pd.DataFrame.from_records(processed_rows)
		#processed_rows = raw_df.apply(process_raw_sample_helper_partial, axis=1)
		raw_df = raw_df.apply(process_raw_sample_helper_partial, axis=1, reduce=False)
		#raw_df = pd.DataFrame.from_records(processed_rows)

		nb_sample = raw_df.shape[0]
		interval_points = np.linspace(
		@@ -174,7 +172,6 @@ class DataFeaturizer(object):
		if input_type == "csv":
		for ind, field in enumerate(fields):
		data[field] = _process_field(row[ind])
		return data
		elif input_type in ["pandas-pickle", "pandas-joblib"]:
		for field in fields:
		data[field] = _process_field(row[field])

deepchem/featurizers/tests/data/3bwf_ligand_hyd.pdb

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+71 −0

Original line number	Diff line number	Diff line
		COMPND 3bwf ligand
		AUTHOR GENERATED BY OPEN BABEL 2.3.90
		ATOM 1 O9 DWC A 1 21.431 -40.526 0.720 1.00 0.00 O
		ATOM 2 C1 DWC A 1 20.612 -39.592 0.816 1.00 0.00 C
		ATOM 3 C2 DWC A 1 20.061 -38.848 -0.214 1.00 0.00 C
		ATOM 4 C3 DWC A 1 20.231 -38.935 -1.628 1.00 0.00 C
		ATOM 5 C4 DWC A 1 21.064 -39.820 -2.345 1.00 0.00 C
		ATOM 6 C5 DWC A 1 21.120 -39.762 -3.756 1.00 0.00 C
		ATOM 7 C6 DWC A 1 20.335 -38.834 -4.470 1.00 0.00 C
		ATOM 8 C7 DWC A 1 19.504 -38.047 -2.409 1.00 0.00 C
		ATOM 9 N21 DWC A 1 19.551 -37.958 -3.803 1.00 0.00 N1+
		ATOM 10 C22 DWC A 1 18.649 -37.145 -1.784 1.00 0.00 C
		ATOM 11 N19 DWC A 1 17.939 -36.271 -2.545 1.00 0.00 N
		ATOM 12 C17 DWC A 1 16.057 -36.612 -4.980 1.00 0.00 C
		ATOM 13 C16 DWC A 1 16.639 -37.866 -5.401 1.00 0.00 C
		ATOM 14 C14 DWC A 1 17.577 -37.591 -6.456 1.00 0.00 C
		ATOM 15 C13 DWC A 1 17.573 -36.175 -6.677 1.00 0.00 C
		ATOM 16 C12 DWC A 1 16.641 -35.570 -5.768 1.00 0.00 C
		ATOM 17 C10 DWC A 1 19.500 -35.179 -4.711 1.00 0.00 C
		ATOM 18 O11 DWC A 1 20.260 -34.371 -4.788 1.00 0.00 O
		ATOM 19 N20 DWC A 1 20.115 -39.153 2.031 1.00 0.00 N
		ATOM 20 C31 DWC A 1 19.232 -38.135 1.781 1.00 0.00 C
		ATOM 21 O8 DWC A 1 18.639 -37.550 2.679 1.00 0.00 O
		ATOM 22 C30 DWC A 1 19.172 -37.914 0.402 1.00 0.00 C
		ATOM 23 C29 DWC A 1 18.446 -37.006 -0.417 1.00 0.00 C
		ATOM 24 C28 DWC A 1 17.527 -35.968 -0.291 1.00 0.00 C
		ATOM 25 C23 DWC A 1 17.214 -35.545 -1.610 1.00 0.00 C
		ATOM 26 C24 DWC A 1 16.282 -34.531 -1.835 1.00 0.00 C
		ATOM 27 C25 DWC A 1 15.704 -33.894 -0.738 1.00 0.00 C
		ATOM 28 C26 DWC A 1 15.988 -34.299 0.589 1.00 0.00 C
		ATOM 29 O15 DWC A 1 15.362 -33.685 1.644 1.00 0.00 O
		ATOM 30 C27 DWC A 1 16.897 -35.365 0.812 1.00 0.00 C
		ATOM 31 OS DWC A 1 18.233 -36.554 -4.619 1.00 0.00 Os
		ATOM 32 H DWC A 1 20.353 -39.509 2.917 1.00 0.00 H
		ATOM 33 H DWC A 1 14.763 -32.982 1.488 1.00 0.00 H
		CONECT 1 2
		CONECT 2 1 3 19
		CONECT 3 2 4 22
		CONECT 4 3 5 8
		CONECT 5 4 6
		CONECT 6 5 7
		CONECT 7 6 9
		CONECT 8 4 9 10
		CONECT 9 7 8 31
		CONECT 10 8 11 23
		CONECT 11 10 25 31
		CONECT 12 13 16 31
		CONECT 13 12 14 31
		CONECT 14 13 15 31
		CONECT 15 14 16 31
		CONECT 16 12 15 31
		CONECT 17 18 31
		CONECT 18 17
		CONECT 19 2 20 32
		CONECT 20 19 21 22
		CONECT 21 20
		CONECT 22 3 20 23
		CONECT 23 10 22 24
		CONECT 24 23 25 30
		CONECT 25 11 24 26
		CONECT 26 25 27
		CONECT 27 26 28
		CONECT 28 27 29 30
		CONECT 29 28 33
		CONECT 30 24 28
		CONECT 31 9 11 12 13
		CONECT 31 14 15 16 17
		CONECT 32 19
		CONECT 33 29
		MASTER 0 0 0 0 0 0 0 0 33 0 33 0
		END

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