From 7d8bc90c442d33b692ec651d96709748fbb467bb Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Iv=C3=A1n=20Pulido?=
 <2949729+ijpulidos@users.noreply.github.com>
Date: Thu, 31 Oct 2024 09:42:36 -0400
Subject: [PATCH] Adding missing test files for expected fails

---
 feflow/tests/data/capped_AAs/GLU_capped.pdb   | 44 +++++++++++++++++++
 feflow/tests/data/capped_AAs/PRO_capped.pdb   | 43 ++++++++++++++++++
 .../data/capped_AAs/ala_to_pro_mapping.json   |  1 +
 .../data/capped_AAs/lys_to_glu_mapping.json   |  1 +
 4 files changed, 89 insertions(+)
 create mode 100644 feflow/tests/data/capped_AAs/GLU_capped.pdb
 create mode 100644 feflow/tests/data/capped_AAs/PRO_capped.pdb
 create mode 100644 feflow/tests/data/capped_AAs/ala_to_pro_mapping.json
 create mode 100644 feflow/tests/data/capped_AAs/lys_to_glu_mapping.json

diff --git a/feflow/tests/data/capped_AAs/GLU_capped.pdb b/feflow/tests/data/capped_AAs/GLU_capped.pdb
new file mode 100644
index 0000000..1e291cb
--- /dev/null
+++ b/feflow/tests/data/capped_AAs/GLU_capped.pdb
@@ -0,0 +1,44 @@
+REMARK   1 CREATED WITH OPENMM 8.1.1, 2024-10-31
+HETATM    1  H1  ACE A   1       1.328   2.173   0.000  1.00  0.00           H  
+HETATM    2  CH3 ACE A   1       2.006   1.318   0.000  1.00  0.00           C  
+HETATM    3  H2  ACE A   1       2.634   1.352   0.890  1.00  0.00           H  
+HETATM    4  H3  ACE A   1       2.634   1.352  -0.890  1.00  0.00           H  
+HETATM    5  C   ACE A   1       1.229   0.000   0.000  1.00  0.00           C  
+HETATM    6  O   ACE A   1       0.000   0.000   0.000  1.00  0.00           O  
+ATOM      7  N   GLU A   2       1.954  -1.121   0.000  1.00  0.00           N  
+ATOM      8  H   GLU A   2       3.130  -0.996  -0.122  1.00  0.00           H  
+ATOM      9  CA  GLU A   2       1.337  -2.432  -0.001  1.00  0.00           C  
+ATOM     10  HA  GLU A   2       0.639  -2.510  -0.966  1.00  0.00           H  
+ATOM     11  CB  GLU A   2       2.391  -3.535  -0.001  1.00  0.00           C  
+ATOM     12  HB2 GLU A   2       3.174  -3.442   0.897  1.00  0.00           H  
+ATOM     13  HB3 GLU A   2       1.733  -4.520   0.169  1.00  0.00           H  
+ATOM     14  C   GLU A   2       0.461  -2.626   1.229  1.00  0.00           C  
+ATOM     15  O   GLU A   2      -0.621  -3.201   1.139  1.00  0.00           O  
+ATOM     16  CG  GLU A   2       3.224  -3.837  -1.235  1.00  0.00           C  
+ATOM     17  HG2 GLU A   2       2.633  -4.297  -2.167  1.00  0.00           H  
+ATOM     18  HG3 GLU A   2       3.897  -2.967  -1.700  1.00  0.00           H  
+ATOM     19  CD  GLU A   2       4.148  -4.963  -0.767  1.00  0.00           C  
+ATOM     20  OE1 GLU A   2       3.726  -5.953  -0.125  1.00  0.00           O  
+ATOM     21  OE2 GLU A   2       5.218  -4.912  -1.414  1.00  0.00           O  
+HETATM   22  N   NME A   3       0.933  -2.143   2.381  1.00  0.00           N  
+HETATM   23  H   NME A   3       1.829  -1.678   2.404  1.00  0.00           H  
+HETATM   24  C   NME A   3       0.194  -2.264   3.621  1.00  0.00           C  
+HETATM   25  H1  NME A   3      -0.745  -2.786   3.436  1.00  0.00           H  
+HETATM   26  H2  NME A   3       0.786  -2.827   4.344  1.00  0.00           H  
+HETATM   27  H3  NME A   3      -0.014  -1.271   4.019  1.00  0.00           H  
+TER      28      NME A   3
+CONECT    1    2
+CONECT    2    5    1    3    4
+CONECT    3    2
+CONECT    4    2
+CONECT    5    2    6    7
+CONECT    6    5
+CONECT    7    5
+CONECT   14   22
+CONECT   22   14   24   23
+CONECT   23   22
+CONECT   24   25   26   27   22
+CONECT   25   24
+CONECT   26   24
+CONECT   27   24
+END
diff --git a/feflow/tests/data/capped_AAs/PRO_capped.pdb b/feflow/tests/data/capped_AAs/PRO_capped.pdb
new file mode 100644
index 0000000..9241174
--- /dev/null
+++ b/feflow/tests/data/capped_AAs/PRO_capped.pdb
@@ -0,0 +1,43 @@
+REMARK   1 CREATED WITH OPENMM 8.1.1, 2024-10-29
+HETATM    1  H1  ACE A   1       1.328   2.173   0.000  1.00  0.00           H  
+HETATM    2  CH3 ACE A   1       2.006   1.318   0.000  1.00  0.00           C  
+HETATM    3  H2  ACE A   1       2.634   1.352   0.890  1.00  0.00           H  
+HETATM    4  H3  ACE A   1       2.634   1.352  -0.890  1.00  0.00           H  
+HETATM    5  C   ACE A   1       1.229   0.000   0.000  1.00  0.00           C  
+HETATM    6  O   ACE A   1       0.000   0.000   0.000  1.00  0.00           O  
+ATOM      7  N   PRO A   2       1.954  -1.121   0.000  1.00  0.00           N  
+ATOM      8  CA  PRO A   2       1.337  -2.432  -0.001  1.00  0.00           C  
+ATOM      9  HA  PRO A   2       0.612  -2.550  -0.943  1.00  0.00           H  
+ATOM     10  CB  PRO A   2       2.391  -3.535  -0.001  1.00  0.00           C  
+ATOM     11  HB2 PRO A   2       2.914  -3.999   0.970  1.00  0.00           H  
+ATOM     12  HB3 PRO A   2       1.966  -4.516  -0.542  1.00  0.00           H  
+ATOM     13  C   PRO A   2       0.461  -2.626   1.229  1.00  0.00           C  
+ATOM     14  O   PRO A   2      -0.621  -3.201   1.139  1.00  0.00           O  
+ATOM     15  CD  PRO A   2       3.378  -1.375  -0.101  1.00  0.00           C  
+ATOM     16  HD2 PRO A   2       4.099  -1.236   0.843  1.00  0.00           H  
+ATOM     17  HD3 PRO A   2       3.939  -0.750  -0.954  1.00  0.00           H  
+ATOM     18  CG  PRO A   2       3.469  -2.740  -0.790  1.00  0.00           C  
+ATOM     19  HG2 PRO A   2       3.305  -2.861  -1.971  1.00  0.00           H  
+ATOM     20  HG3 PRO A   2       4.567  -3.189  -0.609  1.00  0.00           H  
+HETATM   21  N   NME A   3       0.933  -2.143   2.381  1.00  0.00           N  
+HETATM   22  H   NME A   3       1.829  -1.678   2.404  1.00  0.00           H  
+HETATM   23  C   NME A   3       0.194  -2.264   3.621  1.00  0.00           C  
+HETATM   24  H1  NME A   3      -0.745  -2.786   3.436  1.00  0.00           H  
+HETATM   25  H2  NME A   3       0.786  -2.827   4.344  1.00  0.00           H  
+HETATM   26  H3  NME A   3      -0.014  -1.271   4.019  1.00  0.00           H  
+TER      27      NME A   3
+CONECT    1    2
+CONECT    2    5    1    3    4
+CONECT    3    2
+CONECT    4    2
+CONECT    5    2    6    7
+CONECT    6    5
+CONECT    7    5
+CONECT   13   21
+CONECT   21   13   23   22
+CONECT   22   21
+CONECT   23   24   25   26   21
+CONECT   24   23
+CONECT   25   23
+CONECT   26   23
+END
diff --git a/feflow/tests/data/capped_AAs/ala_to_pro_mapping.json b/feflow/tests/data/capped_AAs/ala_to_pro_mapping.json
new file mode 100644
index 0000000..8907cf1
--- /dev/null
+++ b/feflow/tests/data/capped_AAs/ala_to_pro_mapping.json
@@ -0,0 +1 @@
+{"componentA": {"atoms": [[1, "1", 1, 0, " ", "H1", "ACE", 1, "N", 0], [6, "1", 2, 0, " ", "CH3", "ACE", 1, "N", 0], [1, "1", 3, 0, " ", "H2", "ACE", 1, "N", 0], [1, "1", 4, 0, " ", "H3", "ACE", 1, "N", 0], [6, "1", 5, 0, " ", "C", "ACE", 1, "N", 0], [8, "1", 6, 0, " ", "O", "ACE", 1, "N", 0], [7, "1", 7, 0, " ", "N", "ALA", 2, "N", 0], [1, "1", 8, 0, " ", "H", "ALA", 2, "N", 0], [6, "1", 9, 0, " ", "CA", "ALA", 2, "N", 0], [1, "1", 10, 0, " ", "HA", "ALA", 2, "N", 0], [6, "1", 11, 0, " ", "CB", "ALA", 2, "N", 0], [1, "1", 12, 0, " ", "HB1", "ALA", 2, "N", 0], [1, "1", 13, 0, " ", "HB2", "ALA", 2, "N", 0], [1, "1", 14, 0, " ", "HB3", "ALA", 2, "N", 0], [6, "1", 15, 0, " ", "C", "ALA", 2, "N", 0], [8, "1", 16, 0, " ", "O", "ALA", 2, "N", 0], [7, "1", 17, 0, " ", "N", "NME", 3, "N", 0], [1, "1", 18, 0, " ", "H", "NME", 3, "N", 0], [6, "1", 19, 0, " ", "C", "NME", 3, "N", 0], [1, "1", 20, 0, " ", "H1", "NME", 3, "N", 0], [1, "1", 21, 0, " ", "H2", "NME", 3, "N", 0], [1, "1", 22, 0, " ", "H3", "NME", 3, "N", 0]], "bonds": [[4, 1, "SINGLE", "N"], [4, 5, "DOUBLE", "N"], [1, 0, "SINGLE", "N"], [1, 2, "SINGLE", "N"], [1, 3, "SINGLE", "N"], [4, 6, "SINGLE", "N"], [14, 8, "SINGLE", "N"], [14, 15, "DOUBLE", "N"], [8, 10, "SINGLE", "N"], [8, 9, "SINGLE", "N"], [8, 6, "SINGLE", "N"], [10, 11, "SINGLE", "N"], [10, 12, "SINGLE", "N"], [10, 13, "SINGLE", "N"], [7, 6, "SINGLE", "N"], [14, 16, "SINGLE", "N"], [18, 19, "SINGLE", "N"], [18, 20, "SINGLE", "N"], [18, 21, "SINGLE", "N"], [18, 16, "SINGLE", "N"], [17, 16, "SINGLE", "N"]], "name": "", "conformers": ["\u0093NUMPY\u0001\u0000v\u0000{'descr': '<f8', 'fortran_order': False, 'shape': (22, 3), }                                                         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"ProteinComponent", "__module__": "gufe.components.proteincomponent", ":version:": 1}, "componentB": {"atoms": [[1, "A", 1, 0, " ", "H1", "ACE", 1, "N", 0], [6, "A", 2, 0, " ", "CH3", "ACE", 1, "N", 0], [1, "A", 3, 0, " ", "H2", "ACE", 1, "N", 0], [1, "A", 4, 0, " ", "H3", "ACE", 1, "N", 0], [6, "A", 5, 0, " ", "C", "ACE", 1, "N", 0], [8, "A", 6, 0, " ", "O", "ACE", 1, "N", 0], [7, "A", 7, 0, " ", "N", "PRO", 2, "N", 0], [6, "A", 8, 0, " ", "CA", "PRO", 2, "N", 0], [1, "A", 9, 0, " ", "HA", "PRO", 2, "N", 0], [6, "A", 10, 0, " ", "CB", "PRO", 2, "N", 0], [1, "A", 11, 0, " ", "HB2", "PRO", 2, "N", 0], [1, "A", 12, 0, " ", "HB3", "PRO", 2, "N", 0], [6, "A", 13, 0, " ", "C", "PRO", 2, "N", 0], [8, "A", 14, 0, " ", "O", "PRO", 2, "N", 0], [6, "A", 15, 0, " ", "CD", "PRO", 2, "N", 0], [1, "A", 16, 0, " ", "HD2", "PRO", 2, "N", 0], [1, "A", 17, 0, " ", "HD3", "PRO", 2, "N", 0], [6, "A", 18, 0, " ", "CG", "PRO", 2, "N", 0], [1, "A", 19, 0, " ", "HG2", "PRO", 2, "N", 0], [1, "A", 20, 0, " ", 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["\u0093NUMPY\u0001\u0000v\u0000{'descr': '<f8', 'fortran_order': False, 'shape': (26, 3), }                                                         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"__qualname__": "ProteinComponent", "__module__": "gufe.components.proteincomponent", ":version:": 1}, "componentA_to_componentB": {"17": 21, "19": 23, "20": 24, "21": 25, "14": 12, "15": 13, "16": 20, "18": 22}, "annotations": "{}", "__qualname__": "LigandAtomMapping", "__module__": "gufe.mapping.ligandatommapping", ":version:": 1}
\ No newline at end of file
diff --git a/feflow/tests/data/capped_AAs/lys_to_glu_mapping.json b/feflow/tests/data/capped_AAs/lys_to_glu_mapping.json
new file mode 100644
index 0000000..e7b7183
--- /dev/null
+++ b/feflow/tests/data/capped_AAs/lys_to_glu_mapping.json
@@ -0,0 +1 @@
+{"componentA": {"atoms": [[1, "A", 1, 0, " ", "H1", "ACE", 1, "N", 0], [6, "A", 2, 0, " ", "CH3", "ACE", 1, "N", 0], [1, "A", 3, 0, " ", "H2", "ACE", 1, "N", 0], [1, "A", 4, 0, " ", "H3", "ACE", 1, "N", 0], [6, "A", 5, 0, " ", "C", "ACE", 1, "N", 0], [8, "A", 6, 0, " ", "O", "ACE", 1, "N", 0], [7, "A", 7, 0, " ", "N", "LYS", 2, "N", 0], [1, "A", 8, 0, " ", "H", "LYS", 2, "N", 0], [6, "A", 9, 0, " ", "CA", "LYS", 2, "N", 0], [1, "A", 10, 0, " ", "HA", "LYS", 2, "N", 0], [6, "A", 11, 0, " ", "CB", "LYS", 2, "N", 0], [1, "A", 12, 0, " ", "HB2", "LYS", 2, "N", 0], [1, "A", 13, 0, " ", "HB3", "LYS", 2, "N", 0], [6, "A", 14, 0, " ", "C", "LYS", 2, "N", 0], [8, "A", 15, 0, " ", "O", "LYS", 2, "N", 0], [6, "A", 16, 0, " ", "CG", "LYS", 2, "N", 0], [1, "A", 17, 0, " ", "HG2", "LYS", 2, "N", 0], [1, "A", 18, 0, " ", "HG3", "LYS", 2, "N", 0], [6, "A", 19, 0, " ", "CD", "LYS", 2, "N", 0], [1, "A", 20, 0, " ", "HD2", "LYS", 2, "N", 0], [1, "A", 21, 0, " ", "HD3", "LYS", 2, "N", 0], [6, "A", 22, 0, 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"__qualname__": "ProteinComponent", "__module__": "gufe.components.proteincomponent", ":version:": 1}, "componentA_to_componentB": {"0": 0, "2": 2, "3": 3, "7": 7, "9": 9, "11": 12, "12": 11, "16": 16, "17": 17, "20": 19, "29": 22, "31": 24, "32": 25, "33": 26, "1": 1, "4": 4, "5": 5, "6": 6, "8": 8, "10": 10, "13": 13, "14": 14, "15": 15, "18": 18, "21": 20, "28": 21, "30": 23}, "annotations": "{}", "__qualname__": "LigandAtomMapping", "__module__": "gufe.mapping.ligandatommapping", ":version:": 1}
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