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empty lines in mol2 (#140)
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* empty lines in mol2

Some mol2 files have empty lines between blocks. We need to remove them from the block content of the previous one.

* Update CHANGELOG.md

* corrected the logic

* test case
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@Ruibin-Liu
Ruibin-Liu authored Sep 19, 2023
1 parent 1eb121e commit bf53321
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Showing 4 changed files with 141 additions and 2 deletions.
2 changes: 1 addition & 1 deletion biopandas/mol2/pandas_mol2.py
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Original file line number Diff line number Diff line change
Expand Up @@ -180,7 +180,7 @@ def _get_atomsection(mol2_lst):
if s.startswith("@<TRIPOS>ATOM"):
first_idx = idx + 1
started = True
elif started and s.startswith("@<TRIPOS>"):
elif started and (s.startswith("@<TRIPOS>") or not s.strip()):
last_idx_plus1 = idx
break
if first_idx is None:
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134 changes: 134 additions & 0 deletions biopandas/mol2/tests/data/empty_line.mol2
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Original file line number Diff line number Diff line change
@@ -0,0 +1,134 @@
###
### Created by X-TOOL on Mon Sep 10 21:13:02 2018
###

@<TRIPOS>MOLECULE
KEGG_DURG-00000915-01
59 62 0 0 0
SMALL
USER_CHARGES

@<TRIPOS>ATOM
1 C1 13.6130 -13.2290 0.5400 C.3 1 UNK -0.0641
2 C2 13.6610 -14.6640 -0.0280 C.3 1 UNK -0.1181
3 H1 13.5640 -14.6060 -1.1140 H 1 UNK 0.0751
4 C3 14.9450 -12.6420 -0.0330 C.3 1 UNK 0.0713
5 C4 12.2940 -12.5990 0.0140 C.3 1 UNK -0.1283
6 H4 12.1950 -11.5780 0.3820 H 1 UNK 0.1073
7 H5 12.3260 -12.5380 -1.0730 H 1 UNK 0.1073
8 C5 13.6650 -13.1760 2.1030 C.3 1 UNK -0.1903
9 H6 12.9190 -13.8150 2.5630 H 1 UNK 0.0759
10 H7 13.4830 -12.1610 2.4520 H 1 UNK 0.0759
11 H8 14.6310 -13.4920 2.4920 H 1 UNK 0.0759
12 C6 12.5050 -15.5710 0.4610 C.3 1 UNK -0.0772
13 H2 12.5780 -15.7040 1.5370 H 1 UNK 0.0964
14 C7 15.1040 -15.1140 0.2500 C.3 1 UNK -0.1650
15 H9 15.1810 -15.5500 1.2450 H 1 UNK 0.0719
16 H10 15.4370 -15.8400 -0.4910 H 1 UNK 0.0719
17 C8 15.9400 -13.8200 0.1740 C.3 1 UNK -0.1775
18 H11 16.6600 -13.8750 -0.6430 H 1 UNK 0.1311
19 H12 16.4900 -13.7230 1.1080 H 1 UNK 0.1311
20 C9 15.3500 -11.2870 0.5690 C.2 1 UNK 0.2576
21 O1 14.8390 -12.4040 -1.4490 O.3 1 UNK -0.2914
22 H13 14.6770 -13.2350 -1.9010 H 1 UNK 0.1808
23 C10 11.0220 -13.4010 0.3830 C.3 1 UNK 0.0519
24 H14 10.2200 -12.9980 -0.2360 H 1 UNK 0.0475
25 C11 11.1300 -14.9350 0.0800 C.3 1 UNK -0.1158
26 H3 11.1240 -14.9650 -1.0110 H 1 UNK 0.0831
27 C12 12.6340 -16.9590 -0.2080 C.3 1 UNK -0.1553
28 H15 12.6060 -16.8550 -1.2930 H 1 UNK 0.0891
29 H16 13.5810 -17.4220 0.0640 H 1 UNK 0.0891
30 C13 16.8260 -11.0440 0.8340 C.3 1 UNK 0.0393
31 H17 17.1600 -11.7490 1.5930 H 1 UNK 0.0811
32 H18 16.9170 -10.0260 1.2140 H 1 UNK 0.0811
33 O2 14.5050 -10.3750 0.7910 O.2 1 UNK -0.3530
34 O3 10.6600 -13.1060 1.7360 O.3 1 UNK -0.3271
35 H19 9.7760 -13.4360 1.9080 H 1 UNK 0.1813
36 C14 9.9080 -15.8370 0.5080 C.3 1 UNK -0.0198
37 C15 11.4970 -17.8860 0.2330 C.3 1 UNK -0.1375
38 H20 11.5910 -18.8340 -0.2960 H 1 UNK 0.0883
39 H21 11.6230 -18.0880 1.2960 H 1 UNK 0.0883
40 O4 17.6110 -11.1790 -0.3690 O.3 1 UNK -0.7221
41 C16 10.1250 -17.2710 0.0120 C.2 1 UNK -0.0019
42 C17 8.6370 -15.2160 -0.1430 C.3 1 UNK -0.1517
43 H22 8.3730 -14.2770 0.3430 H 1 UNK 0.0896
44 H23 8.8340 -15.0010 -1.1940 H 1 UNK 0.0896
45 C18 9.6870 -15.9140 2.0440 C.3 1 UNK -0.1960
46 H24 9.0260 -16.7450 2.2870 H 1 UNK 0.0767
47 H25 9.2190 -15.0140 2.4360 H 1 UNK 0.0767
48 H26 10.6250 -16.0800 2.5700 H 1 UNK 0.0767
49 P1 19.1650 -10.8930 -0.3570 P.3 1 UNK 2.4858
50 C19 9.1550 -17.9940 -0.5410 C.2 1 UNK -0.2577
51 H27 9.3730 -18.9970 -0.8790 H 1 UNK 0.1428
52 C20 7.4270 -16.1570 -0.0830 C.3 1 UNK -0.1970
53 H28 7.1160 -16.2980 0.9510 H 1 UNK 0.1046
54 H29 6.5980 -15.7140 -0.6340 H 1 UNK 0.1046
55 C21 7.7690 -17.5030 -0.6830 C.2 1 UNK 0.2584
56 O5 6.9100 -18.2110 -1.2760 O.2 1 UNK -0.3304
57 O6 19.7370 -11.4000 -1.6580 O.co2 1 UNK -1.2593
58 O7 19.7870 -11.6320 0.8040 O.co2 1 UNK -1.2593
59 O8 19.3700 -9.4020 -0.2290 O.co2 1 UNK -1.2593

@<TRIPOS>BOND
1 1 2 1
2 1 4 1
3 1 5 1
4 1 8 1
5 2 12 1
6 2 14 1
7 4 17 1
8 4 20 1
9 4 21 1
10 5 23 1
11 12 25 1
12 12 27 1
13 20 30 1
14 20 33 2
15 23 34 1
16 25 36 1
17 27 37 1
18 30 40 1
19 36 41 1
20 36 42 1
21 36 45 1
22 40 49 1
23 41 50 2
24 42 52 1
25 50 55 1
26 55 56 2
27 14 17 1
28 23 25 1
29 37 41 1
30 52 55 1
31 2 3 1
32 12 13 1
33 25 26 1
34 49 57 1
35 49 58 1
36 49 59 2
37 5 6 1
38 5 7 1
39 8 9 1
40 8 10 1
41 8 11 1
42 14 15 1
43 14 16 1
44 17 18 1
45 17 19 1
46 21 22 1
47 23 24 1
48 27 28 1
49 27 29 1
50 30 31 1
51 30 32 1
52 34 35 1
53 37 38 1
54 37 39 1
55 42 43 1
56 42 44 1
57 45 46 1
58 45 47 1
59 45 48 1
60 50 51 1
61 52 53 1
62 52 54 1
4 changes: 4 additions & 0 deletions biopandas/mol2/tests/test_pandas_mol2.py
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Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,7 @@ def test_read_mol2():

data_path_1 = os.path.join(this_dir, "data", "40_mol2_files.mol2")
data_path_2 = os.path.join(this_dir, "data", "40_mol2_files.mol2.gz")
data_path_3 = os.path.join(this_dir, "data", "empty_line.mol2")

for data_path in (data_path_1, data_path_2):
pdmol = PandasMol2().read_mol2(data_path)
Expand All @@ -38,6 +39,9 @@ def test_read_mol2():
assert len(pdmol.mol2_text) == 6469
assert pdmol.mol2_path == data_path

pdmol = PandasMol2().read_mol2(data_path_3)
assert pdmol.df.shape == (59, 9)


def test_read_mol2_from_list():

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3 changes: 2 additions & 1 deletion docs/CHANGELOG.md
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Original file line number Diff line number Diff line change
@@ -1,4 +1,5 @@
# Release Notes ![](img/logos/3eiy_120.png)
- Supports `mol` files that have empty lines between blocks, (Via [Ruibin Liu](https://github.com/Ruibin-Liu) PR #[140](https://github.com/BioPandas/biopandas/pull/140#))

The CHANGELOG for the current development version is available at
[https://github.com/rasbt/biopandas/blob/main/docs/sources/CHANGELOG.md](https://github.com/rasbt/biopandas/blob/main/docs/sources/CHANGELOG.md).
Expand Down Expand Up @@ -353,4 +354,4 @@ The CHANGELOG for the current development version is available at

### 0.1.2 (2015-11-23)

- First Release.
- First Release.

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