Moved tests, changed travis script, changed setup for setuptools

cbouy · Apr 30, 2018 · bab8349 · bab8349
1 parent d0076ec
commit bab8349
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Showing 26 changed files with 10,120 additions and 2,872 deletions.
diff --git a/.gitignore b/.gitignore
@@ -103,5 +103,3 @@ venv.bak/
 
 
 # End of https://www.gitignore.io/api/python
-
-.ipynb
diff --git a/.travis.yml b/.travis.yml
@@ -18,11 +18,14 @@ install:
   - source activate test-environment
   - pip install coveralls
   - pip install coverage
-script:
   # Install prolif
-  - python setup.py install
+  - pip install -e .
+script:
+  - prolif --help
+  - prolif --version
+  - prolif --log INFO --protein examples/protein.mol2 --reference examples/ligand.mol2 --ligand examples/ligand.mol2
+after_success:
   # Run tests with coverage
   - coverage run setup.py test
-after_success:
   # Create report for coveralls
   - coveralls
diff --git a/MANIFEST.in b/MANIFEST.in
@@ -1,2 +1,12 @@
-include README.md LICENSE prolif/parameters.json
-recursive-include prolif *.mol2
+
+# README
+include README.md
+
+# License
+include LICENSE
+
+# Parameters file
+recursive-include prolif *.json
+
+# Files for tests
+recursive-include examples *.mol2
diff --git a/README.md b/README.md
@@ -3,6 +3,7 @@
 [![PyPI - Status](https://img.shields.io/pypi/status/prolif.svg)](https://pypi.org/project/prolif/)
 [![Build Status](https://travis-ci.org/cbouy/ProLIF.svg?branch=master)](https://travis-ci.org/cbouy/ProLIF)
 [![Coveralls github branch](https://img.shields.io/coveralls/github/cbouy/ProLIF/master.svg)](https://coveralls.io/github/cbouy/ProLIF?branch=master)
+[![Say Thanks!](https://img.shields.io/badge/Say%20Thanks-!-1EAEDB.svg)](https://saythanks.io/to/cbouy)
 
 # ProLIF
 Protein-Ligand Interaction Fingerprints

diff --git a/examples/ligand.mol2 b/examples/ligand.mol2
@@ -0,0 +1,105 @@
+@<TRIPOS>MOLECULE
+1b38_ligand
+47 49 1
+SMALL
+USER_CHARGES
+@<TRIPOS>ATOM
+1	P1    -2.8080    25.0870    11.6450	P	1	noname	0.0686
+2	P2    -1.5390    24.1240    14.0510	P	1	noname	0.1090
+3	P3    -3.9040    24.9710    15.4350	P	1	noname	0.0637
+4	C1    -1.3230    24.0470     9.7560	C.3	1	noname	0.0915
+5	O1    -1.5280    25.1160    10.7000	O.3	1	noname	-0.1455
+6	C2     0.1470    24.2240     9.3530	C.3	1	noname	0.1130
+7	O2     0.2670    25.3240     8.4430	O.3	1	noname	-0.3483
+8	C3     1.0020    24.5810    10.5740	C.3	1	noname	0.1127
+9	O3     2.2980    23.9790    10.3950	O.3	1	noname	-0.3873
+10	C4     1.1570    26.1370    10.4540	C.3	1	noname	0.1258
+11	O4     2.5240    26.4140    10.8540	O.3	1	noname	-0.3857
+12	C5     1.1040    26.3300     8.9230	C.3	1	noname	0.1590
+13	N1     1.4530    31.0030     6.6910	N.2	1	noname	-0.2575
+14	O5    -3.9180    24.4130    10.8710	O.3	1	noname	-0.1575
+15	O6    -1.0190    25.5070    14.0070	O.3	1	noname	-0.1517
+16	O7    -4.4430    24.7710    16.7730	O.3	1	noname	-0.1584
+17	C6     2.1200    29.8590     6.3980	C.2	1	noname	0.0503
+18	O8    -3.0730    26.4080    12.1520	O.2	1	noname	-0.1855
+19	O9    -0.5640    23.0450    14.1360	O.2	1	noname	-0.1763
+20	O10    -3.5100    26.3670    15.1110	O.3	1	noname	-0.1584
+21	N2     1.9780    28.6720     6.9310	N.2	1	noname	-0.2441
+22	O11    -2.4940    23.9450    12.7710	O.3	1	noname	-0.0201
+23	O12    -2.7130    23.9850    15.1190	O.3	1	noname	-0.0210
+24	O13    -5.0210    24.5800    14.4860	O.2	1	noname	-0.1869
+25	C7     0.9630    28.6570     7.8040	C.2	1	noname	0.1238
+26	C8     0.2000    29.7400     8.1750	C.2	1	noname	0.0254
+27	C9     0.4350    30.9830     7.5800	C.2	1	noname	0.0729
+28	N3    -0.1950    32.1280     7.7750	N.3	1	noname	-0.1031
+29	N4    -0.7080    29.3770     9.0570	N.2	1	noname	-0.2172
+30	C10    -0.5280    28.1410     9.2580	C.2	1	noname	-0.0362
+31	N5     0.4810    27.5940     8.5420	N.2	1	noname	0.0257
+32	H1    -1.9563    24.2527     8.8930	H	1	noname	0.0605
+33	H2    -1.4326    23.1096    10.3013	H	1	noname	0.0605
+34	H3     0.4958    23.3221     8.8499	H	1	noname	0.0657
+35	H4     0.6283    24.2067    11.5271	H	1	noname	0.0657
+36	H5     2.6880    23.7978    11.2533	H	1	noname	0.2106
+37	H6     0.4860    26.7657    11.0393	H	1	noname	0.0674
+38	H7     2.5809    26.4255    11.8122	H	1	noname	0.2107
+39	H8     2.0873    26.2846     8.4548	H	1	noname	0.0853
+40	H9    -4.5490    24.0298    11.4846	H	1	noname	0.2283
+41	H10    -0.8969    25.8316    14.9022	H	1	noname	0.2283
+42	H11    -4.5150    23.8305    16.9517	H	1	noname	0.2283
+43	H12     2.8822    29.8995     5.6198	H	1	noname	0.1062
+44	H13    -3.3716    26.8575    15.9246	H	1	noname	0.2283
+45	H14     0.3306    32.9873     7.8495	H	1	noname	0.1258
+46	H15    -1.2021    32.1439     7.8495	H	1	noname	0.1258
+47	H16    -1.1665    27.6103     9.9643	H	1	noname	0.1016
+@<TRIPOS>BOND
+1	1	5	1
+2	1	14	1
+3	1	18	2
+4	1	22	1
+5	2	15	1
+6	2	19	2
+7	2	22	1
+8	2	23	1
+9	3	16	1
+10	3	20	1
+11	3	23	1
+12	3	24	2
+13	4	6	1
+14	4	5	1
+15	6	7	1
+16	6	8	1
+17	7	12	1
+18	8	9	1
+19	8	10	1
+20	10	11	1
+21	10	12	1
+22	12	31	1
+23	13	17	ar
+24	17	21	ar
+25	21	25	ar
+26	25	26	ar
+27	26	27	ar
+28	13	27	ar
+29	27	28	1
+30	26	29	ar
+31	29	30	ar
+32	25	31	ar
+33	30	31	ar
+34	4	32	1
+35	4	33	1
+36	6	34	1
+37	8	35	1
+38	9	36	1
+39	10	37	1
+40	11	38	1
+41	12	39	1
+42	14	40	1
+43	15	41	1
+44	16	42	1
+45	17	43	1
+46	20	44	1
+47	28	45	1
+48	28	46	1
+49	30	47	1
+@<TRIPOS>SUBSTRUCTURE
+1	noname	1