packmol-memgen-minimal 1.1.16__py3-none-any.whl

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Files changed (71) hide show
  1. packmol_memgen/__init__.py +2 -0
  2. packmol_memgen/__version__.py +34 -0
  3. packmol_memgen/data/LICENSE.Apache-2.0 +201 -0
  4. packmol_memgen/data/extra_solvents.lib +789 -0
  5. packmol_memgen/data/frcmod.lipid_ext +97 -0
  6. packmol_memgen/data/frcmod.solvents +129 -0
  7. packmol_memgen/data/insane_lipids.txt +138 -0
  8. packmol_memgen/data/insane_solvents.txt +45 -0
  9. packmol_memgen/data/leaprc.extra_solvents +42 -0
  10. packmol_memgen/data/leaprc.lipid_ext +48 -0
  11. packmol_memgen/data/lipid_ext.lib +12312 -0
  12. packmol_memgen/data/martini_v3.0.0.itp +356605 -0
  13. packmol_memgen/data/memgen.parm +4082 -0
  14. packmol_memgen/data/pdbs.tar.gz +0 -0
  15. packmol_memgen/data/solvent.parm +14 -0
  16. packmol_memgen/example/example.sh +31 -0
  17. packmol_memgen/lib/__init__.py +0 -0
  18. packmol_memgen/lib/amber.py +77 -0
  19. packmol_memgen/lib/charmmlipid2amber/__init__.py +0 -0
  20. packmol_memgen/lib/charmmlipid2amber/charmmlipid2amber.csv +7164 -0
  21. packmol_memgen/lib/charmmlipid2amber/charmmlipid2amber.py +225 -0
  22. packmol_memgen/lib/pdbremix/LICENSE +21 -0
  23. packmol_memgen/lib/pdbremix/__init__.py +0 -0
  24. packmol_memgen/lib/pdbremix/_version.py +1 -0
  25. packmol_memgen/lib/pdbremix/amber.py +1103 -0
  26. packmol_memgen/lib/pdbremix/asa.py +227 -0
  27. packmol_memgen/lib/pdbremix/data/aminoacid.pdb +334 -0
  28. packmol_memgen/lib/pdbremix/data/binaries.json +26 -0
  29. packmol_memgen/lib/pdbremix/data/charmm22.parameter +2250 -0
  30. packmol_memgen/lib/pdbremix/data/charmm22.topology +1635 -0
  31. packmol_memgen/lib/pdbremix/data/color_b.py +682 -0
  32. packmol_memgen/lib/pdbremix/data/hin.lib +130 -0
  33. packmol_memgen/lib/pdbremix/data/hydroxide.lib +88 -0
  34. packmol_memgen/lib/pdbremix/data/make_chi.py +92 -0
  35. packmol_memgen/lib/pdbremix/data/opls.parameter +1108 -0
  36. packmol_memgen/lib/pdbremix/data/opls.topology +1869 -0
  37. packmol_memgen/lib/pdbremix/data/phd.frcmod +82 -0
  38. packmol_memgen/lib/pdbremix/data/phd.leaprc +4 -0
  39. packmol_memgen/lib/pdbremix/data/phd.prepin +35 -0
  40. packmol_memgen/lib/pdbremix/data/template.pdb +334 -0
  41. packmol_memgen/lib/pdbremix/data/znb.frcmod +24 -0
  42. packmol_memgen/lib/pdbremix/data/znb.leaprc +7 -0
  43. packmol_memgen/lib/pdbremix/data/znb.lib +69 -0
  44. packmol_memgen/lib/pdbremix/data.py +264 -0
  45. packmol_memgen/lib/pdbremix/fetch.py +102 -0
  46. packmol_memgen/lib/pdbremix/force.py +627 -0
  47. packmol_memgen/lib/pdbremix/gromacs.py +978 -0
  48. packmol_memgen/lib/pdbremix/lib/__init__.py +0 -0
  49. packmol_memgen/lib/pdbremix/lib/docopt.py +579 -0
  50. packmol_memgen/lib/pdbremix/lib/pyqcprot.py +305 -0
  51. packmol_memgen/lib/pdbremix/namd.py +1078 -0
  52. packmol_memgen/lib/pdbremix/pdbatoms.py +543 -0
  53. packmol_memgen/lib/pdbremix/pdbtext.py +120 -0
  54. packmol_memgen/lib/pdbremix/protein.py +311 -0
  55. packmol_memgen/lib/pdbremix/pymol.py +480 -0
  56. packmol_memgen/lib/pdbremix/rmsd.py +203 -0
  57. packmol_memgen/lib/pdbremix/simulate.py +420 -0
  58. packmol_memgen/lib/pdbremix/spacehash.py +73 -0
  59. packmol_memgen/lib/pdbremix/trajectory.py +286 -0
  60. packmol_memgen/lib/pdbremix/util.py +273 -0
  61. packmol_memgen/lib/pdbremix/v3.py +16 -0
  62. packmol_memgen/lib/pdbremix/v3array.py +482 -0
  63. packmol_memgen/lib/pdbremix/v3numpy.py +350 -0
  64. packmol_memgen/lib/pdbremix/volume.py +155 -0
  65. packmol_memgen/lib/utils.py +1017 -0
  66. packmol_memgen/main.py +2827 -0
  67. packmol_memgen_minimal-1.1.16.dist-info/METADATA +664 -0
  68. packmol_memgen_minimal-1.1.16.dist-info/RECORD +71 -0
  69. packmol_memgen_minimal-1.1.16.dist-info/WHEEL +4 -0
  70. packmol_memgen_minimal-1.1.16.dist-info/entry_points.txt +2 -0
  71. packmol_memgen_minimal-1.1.16.dist-info/licenses/LICENSE +338 -0
packmol_memgen/lib/pdbremix/data/hin.lib ADDED
@@ -0,0 +1,130 @@
1
+ !!index array str
2
+ "HIN"
3
+ !entry.HIN.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
4
+ "N" "N" 0 1 131075 1 7 -0.564100
5
+ "H" "H" 0 1 131075 2 1 0.246900
6
+ "CA" "CT" 0 1 131075 3 6 0.317100
7
+ "HA" "H1" 0 1 131075 4 1 0.009600
8
+ "CB" "CT" 0 1 131075 5 6 -0.134700
9
+ "HB2" "HC" 0 1 131075 6 1 0.008300
10
+ "HB3" "HC" 0 1 131075 7 1 0.038100
11
+ "CG" "CC" 0 1 131075 8 6 0.150400
12
+ "ND1" "NA" 0 1 131075 9 7 -0.762600
13
+ "CE1" "CR" 0 1 131075 10 6 0.499400
14
+ "HE1" "H5" 0 1 131075 11 1 -0.029500
15
+ "NE2" "NB" 0 1 131075 12 7 -0.765600
16
+ "CD2" "CV" 0 1 131075 13 6 0.040500
17
+ "HD2" "H4" 0 1 131075 14 1 0.052500
18
+ "C" "C" 0 1 131075 15 6 0.458800
19
+ "O" "O" 0 1 131075 16 8 -0.565300
20
+ !entry.HIN.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
21
+ "N" "N" 0 -1 0.0
22
+ "H" "H" 0 -1 0.0
23
+ "CA" "CT" 0 -1 0.0
24
+ "HA" "H1" 0 -1 0.0
25
+ "CB" "CT" 0 -1 0.0
26
+ "HB2" "HC" 0 -1 0.0
27
+ "HB3" "HC" 0 -1 0.0
28
+ "CG" "CC" 0 -1 0.0
29
+ "ND1" "NA" 0 -1 0.0
30
+ "CE1" "CR" 0 -1 0.0
31
+ "HE1" "H5" 0 -1 0.0
32
+ "NE2" "NB" 0 -1 0.0
33
+ "CD2" "CV" 0 -1 0.0
34
+ "HD2" "H4" 0 -1 0.0
35
+ "C" "C" 0 -1 0.0
36
+ "O" "O" 0 -1 0.0
37
+ !entry.HIN.unit.boundbox array dbl
38
+ -1.000000
39
+ 0.0
40
+ 0.0
41
+ 0.0
42
+ 0.0
43
+ !entry.HIN.unit.childsequence single int
44
+ 2
45
+ !entry.HIN.unit.connect array int
46
+ 1
47
+ 15
48
+ !entry.HIN.unit.connectivity table int atom1x int atom2x int flags
49
+ 2 1 1
50
+ 3 1 1
51
+ 4 3 1
52
+ 5 3 1
53
+ 6 5 1
54
+ 7 5 1
55
+ 8 5 1
56
+ 9 8 1
57
+ 10 9 1
58
+ 11 10 1
59
+ 12 10 1
60
+ 13 12 1
61
+ 13 8 1
62
+ 14 13 1
63
+ 15 3 1
64
+ 16 15 1
65
+ !entry.HIN.unit.hierarchy table str abovetype int abovex str belowtype int belowx
66
+ "U" 0 "R" 1
67
+ "R" 1 "A" 1
68
+ "R" 1 "A" 2
69
+ "R" 1 "A" 3
70
+ "R" 1 "A" 4
71
+ "R" 1 "A" 5
72
+ "R" 1 "A" 6
73
+ "R" 1 "A" 7
74
+ "R" 1 "A" 8
75
+ "R" 1 "A" 9
76
+ "R" 1 "A" 10
77
+ "R" 1 "A" 11
78
+ "R" 1 "A" 12
79
+ "R" 1 "A" 13
80
+ "R" 1 "A" 14
81
+ "R" 1 "A" 15
82
+ "R" 1 "A" 16
83
+ !entry.HIN.unit.name single str
84
+ ""
85
+ !entry.HIN.unit.positions table dbl x dbl y dbl z
86
+ 78.631000 40.570000 45.601000
87
+ 78.239000 40.145000 44.771000
88
+ 79.741000 41.496000 45.426000
89
+ 80.576000 41.170000 46.048000
90
+ 80.188000 41.517000 43.971000
91
+ 79.313000 41.413000 43.328000
92
+ 80.665000 42.457000 43.744000
93
+ 81.161000 40.439000 43.620000
94
+ 82.408000 40.346000 44.204000
95
+ 83.069000 39.339000 43.665000
96
+ 84.076000 39.041000 43.909000
97
+ 82.297000 38.772000 42.754000
98
+ 81.098000 39.439000 42.710000
99
+ 80.259000 39.219000 42.065000
100
+ 79.319000 42.902000 45.843000
101
+ 80.131000 43.678000 46.351000
102
+ !entry.HIN.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
103
+ 0 0 0 0 0 0
104
+ !entry.HIN.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
105
+ "HIN" 1 18 1 "?" 0
106
+ !entry.HIN.unit.residuesPdbSequenceNumber array int
107
+ 1
108
+ !entry.HIN.unit.solventcap array dbl
109
+ -1.000000
110
+ 0.0
111
+ 0.0
112
+ 0.0
113
+ 0.0
114
+ !entry.HIN.unit.velocities table dbl x dbl y dbl z
115
+ 0.0 0.0 0.0
116
+ 0.0 0.0 0.0
117
+ 0.0 0.0 0.0
118
+ 0.0 0.0 0.0
119
+ 0.0 0.0 0.0
120
+ 0.0 0.0 0.0
121
+ 0.0 0.0 0.0
122
+ 0.0 0.0 0.0
123
+ 0.0 0.0 0.0
124
+ 0.0 0.0 0.0
125
+ 0.0 0.0 0.0
126
+ 0.0 0.0 0.0
127
+ 0.0 0.0 0.0
128
+ 0.0 0.0 0.0
129
+ 0.0 0.0 0.0
130
+ 0.0 0.0 0.0
packmol_memgen/lib/pdbremix/data/hydroxide.lib ADDED
@@ -0,0 +1,88 @@
1
+ !!index array str
2
+ "HO-"
3
+ !entry.HO-.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
4
+ "H1" "HO" 0 1 131075 1 1 0.204900
5
+ "O" "OH" 0 1 131075 2 8 -1.204900
6
+ !entry.HO-.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
7
+ "H1" "HO" 0 -1 0.0
8
+ "O" "OH" 0 -1 0.0
9
+ !entry.HO-.unit.boundbox array dbl
10
+ -1.000000
11
+ 0.0
12
+ 0.0
13
+ 0.0
14
+ 0.0
15
+ !entry.HO-.unit.childsequence single int
16
+ 427
17
+ !entry.HO-.unit.connect array int
18
+ 0
19
+ 0
20
+ !entry.HO-.unit.connectivity table int atom1x int atom2x int flags
21
+ 1 2 1
22
+ !entry.HO-.unit.hierarchy table str abovetype int abovex str belowtype int belowx
23
+ "U" 0 "R" 1
24
+ "R" 1 "A" 1
25
+ "R" 1 "A" 2
26
+ !entry.HO-.unit.name single str
27
+ ""
28
+ !entry.HO-.unit.positions table dbl x dbl y dbl z
29
+ 72.492000 20.788000 -76.929000
30
+ 72.210000 21.650000 -76.576000
31
+ !entry.HO-.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
32
+ 0 0 0 0 0 0
33
+ !entry.HO-.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
34
+ "HO-" 426 3 1 "?" 0
35
+ !entry.HO-.unit.residuesPdbSequenceNumber array int
36
+ 1
37
+ !entry.HO-.unit.solventcap array dbl
38
+ -1.000000
39
+ 0.0
40
+ 0.0
41
+ 0.0
42
+ 0.0
43
+ !entry.HO-.unit.velocities table dbl x dbl y dbl z
44
+ 0.0 0.0 0.0
45
+ 0.0 0.0 0.0
46
+ !entry.HO.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
47
+ "H1" "HO" 0 1 131075 1 1 0.204900
48
+ "O" "OH" 0 1 131075 2 8 -1.204900
49
+ !entry.HO.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
50
+ "H1" "HO" 0 -1 0.0
51
+ "O" "OH" 0 -1 0.0
52
+ !entry.HO.unit.boundbox array dbl
53
+ -1.000000
54
+ 0.0
55
+ 0.0
56
+ 0.0
57
+ 0.0
58
+ !entry.HO.unit.childsequence single int
59
+ 427
60
+ !entry.HO.unit.connect array int
61
+ 0
62
+ 0
63
+ !entry.HO.unit.connectivity table int atom1x int atom2x int flags
64
+ 1 2 1
65
+ !entry.HO.unit.hierarchy table str abovetype int abovex str belowtype int belowx
66
+ "U" 0 "R" 1
67
+ "R" 1 "A" 1
68
+ "R" 1 "A" 2
69
+ !entry.HO.unit.name single str
70
+ ""
71
+ !entry.HO.unit.positions table dbl x dbl y dbl z
72
+ 72.492000 20.788000 -76.929000
73
+ 72.210000 21.650000 -76.576000
74
+ !entry.HO.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
75
+ 0 0 0 0 0 0
76
+ !entry.HO.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
77
+ "HO-" 426 3 1 "?" 0
78
+ !entry.HO.unit.residuesPdbSequenceNumber array int
79
+ 1
80
+ !entry.HO.unit.solventcap array dbl
81
+ -1.000000
82
+ 0.0
83
+ 0.0
84
+ 0.0
85
+ 0.0
86
+ !entry.HO.unit.velocities table dbl x dbl y dbl z
87
+ 0.0 0.0 0.0
88
+ 0.0 0.0 0.0
packmol_memgen/lib/pdbremix/data/make_chi.py ADDED
@@ -0,0 +1,92 @@
1
+ import pprint
2
+
3
+ chi_topology_str = """
4
+ : CYS
5
+ N CA CB SG
6
+ : ASP
7
+ N CA CB CG
8
+ CA CB CG OD1
9
+ : GLU
10
+ N CA CB CG
11
+ CA CB CG CD
12
+ CB CG CD OE1
13
+ : PHE
14
+ N CA CB CG
15
+ CA CB CG CD1
16
+ : HIS
17
+ N CA CB CG
18
+ CA CB CG ND1
19
+ : ILE
20
+ N CA CB CG1
21
+ CA CB CG1 CD1
22
+ : LYS
23
+ N CA CB CG
24
+ CA CB CG CD
25
+ CB CG CD CE
26
+ CG CD CE NZ
27
+ : LYN
28
+ N CA CB CG
29
+ CA CB CG CD
30
+ CB CG CD CE
31
+ CG CD CE NZ
32
+ : LYP
33
+ N CA CB CG
34
+ CA CB CG CD
35
+ CB CG CD CE
36
+ CG CD CE NZ
37
+ : LEU
38
+ N CA CB CG
39
+ CA CB CG CD1
40
+ : MET
41
+ N CA CB CG
42
+ CA CB CG SD
43
+ CB CG SD CE
44
+ : ASN
45
+ N CA CB CG
46
+ CA CB CG OD1
47
+ : PRO
48
+ N CA CB CG
49
+ CA CB CG CD
50
+ CB CG CD N
51
+ CG CD N CA
52
+ : GLN
53
+ N CA CB CG
54
+ CA CB CG CD
55
+ CB CG CD OE1
56
+ : ARG
57
+ N CA CB CG
58
+ CA CB CG CD
59
+ CB CG CD NE
60
+ CG CD NE CZ
61
+ : SER
62
+ N CA CB OG
63
+ : THR
64
+ N CA CB OG1
65
+ : VAL
66
+ N CA CB CG1
67
+ : TRP
68
+ N CA CB CG
69
+ CA CB CG CD1
70
+ : TYR
71
+ N CA CB CG
72
+ CA CB CG CD1
73
+
74
+ : PHD
75
+ N CA CB CG
76
+ CA CB CG OD1
77
+ """
78
+
79
+ chi_topology = {}
80
+
81
+ curr_res_type = ""
82
+ for line in chi_topology_str.splitlines():
83
+ word_list = line.split()
84
+ if word_list:
85
+ if ":" in word_list[0]:
86
+ curr_res_type = word_list[1]
87
+ chi_topology[curr_res_type] = []
88
+ elif curr_res_type:
89
+ chi_topology[curr_res_type].append(word_list[0:4])
90
+
91
+ pprint.pprint(chi_topology, indent=2)
92
+