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@dprada
dprada committed May 3, 2024
1 parent c29d492 commit babff37
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Showing 18 changed files with 12,032 additions and 223 deletions.
4 changes: 2 additions & 2 deletions molsysmt/build/add_missing_bonds.py
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Expand Up @@ -4,7 +4,7 @@

@digest()
def add_missing_bonds(molecular_system, threshold='2 angstroms', selection='all',
structure_indices=0, syntax='MolSysMT', engine='MolSysMT',
structure_index=0, syntax='MolSysMT', engine='MolSysMT',
in_place=True, skip_digestion=False):
"""
To be written soon...
Expand All @@ -16,7 +16,7 @@ def add_missing_bonds(molecular_system, threshold='2 angstroms', selection='all'
from molsysmt.build import add_bonds

bonds = get_missing_bonds(molecular_system, threshold=threshold, selection=selection,
structure_indices=structure_indices, syntax=syntax,
structure_index=structure_index, syntax=syntax,
skip_digestion=True)

return add_bonds(molecular_system, bonds, in_place=in_place, skip_digestion=True)
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2 changes: 1 addition & 1 deletion molsysmt/build/build_peptide.py
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Expand Up @@ -14,7 +14,7 @@ def build_peptide (molecular_system, to_form='molsysmt.MolSys', engine='LEaP'):
from molsysmt._private.files_and_directories import temp_directory, temp_filename
from shutil import rmtree, copyfile

sequence = convert(molecular_system, to_form='string:aminoacids3')
sequence = convert(molecular_system, to_form='string:amino_acids_3')
sequence = sequence.upper()
sequence = ' '.join([sequence[ii:ii+3] for ii in range(0, len(sequence), 3)])

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7 changes: 7 additions & 0 deletions molsysmt/data/_make/make_all.sh
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Expand Up @@ -24,3 +24,10 @@ echo -n "TcTIM.py "
python TcTIM.py
echo "DONE"

echo -n "met_enkephalin.py "
python met_enkephalin.py
echo "DONE"

echo -n "trp-cage.py "
python trp-cage.py
echo "DONE"
28 changes: 28 additions & 0 deletions molsysmt/data/_make/met_enkephalin.py
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import molsysmt as msm
import numpy as np
from pathlib import Path
import os
import shutil

data_dir = Path('../.')

# Purge

files_to_be_purged = [
'h5msm/met_enkephalin.h5msm',
'pdb/met_enkephalin.pdb',
]

for filename in files_to_be_purged:
filepath = Path(data_dir, filename)
if os.path.isfile(filepath):
os.remove(filepath)

# Make

molsys = msm.build.build_peptide('TyrGlyGlyPheMet')
_ = msm.convert(molsys, to_form='met_enkephalin.h5msm')
shutil.move('met_enkephalin.h5msm', Path(data_dir, 'h5msm/met_enkephalin.h5msm'))
_ = msm.convert(molsys, to_form='met_enkephalin.pdb')
shutil.move('met_enkephalin.pdb', Path(data_dir, 'pdb/met_enkephalin.pdb'))

29 changes: 29 additions & 0 deletions molsysmt/data/_make/trp-cage.py
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import molsysmt as msm
import os
import shutil
from pathlib import Path


data_dir = Path('../.')

# purge

files_to_be_purged = [
'h5msm/1l2y.h5msm',
'pdb/1l2y.pdb',
]

for filename in files_to_be_purged:
filepath = Path(data_dir, filename)
if os.path.isfile(filepath):
os.remove(filepath)


# 1tcd pdb, mmtf and msmpk files
print('Protein Data Bank files...')
_ = msm.convert('pdb_id:1l2y', to_form='1l2y.pdb')
shutil.move('1l2y.pdb', Path(data_dir, 'pdb/1l2y.pdb'))
_ = msm.convert('pdb_id:1l2y', to_form='1l2y.h5msm')
shutil.move('1l2y.h5msm', Path(data_dir, 'h5msm/1l2y.h5msm'))


Binary file added molsysmt/data/h5msm/met_enkephalin.h5msm
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1 change: 1 addition & 0 deletions molsysmt/data/pdb/1l2y.pdb
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Expand Up @@ -13,6 +13,7 @@ KEYWDS MINIPROTEIN, TWO-STATE FOLDING, TRP-CAGE, DE NOVO PROTEIN
EXPDTA SOLUTION NMR
NUMMDL 38
AUTHOR J.W.NEIDIGH,R.M.FESINMEYER,N.H.ANDERSEN
REVDAT 4 14-JUN-23 1L2Y 1 REMARK
REVDAT 3 05-FEB-20 1L2Y 1 REMARK
REVDAT 2 24-FEB-09 1L2Y 1 VERSN
REVDAT 1 29-MAY-02 1L2Y 0
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148 changes: 74 additions & 74 deletions molsysmt/data/pdb/met_enkephalin.pdb
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@@ -1,75 +1,75 @@
REMARK 1 CREATED WITH OPENMM 8.0 BY MOLSYSMT 0.7.3+30.gee5851a2.dirty, 2023-03-17
ATOM 1 N TYR 1 1 3.326 1.548 -0.000 1.00 0.00 N
ATOM 2 H TYR 1 1 3.909 0.724 -0.000 1.00 0.00 H
ATOM 3 CA TYR 1 1 3.970 2.846 -0.000 1.00 0.00 C
ATOM 4 HA TYR 1 1 3.672 3.400 -0.890 1.00 0.00 H
ATOM 5 CB TYR 1 1 3.577 3.654 1.232 1.00 0.00 C
ATOM 6 HB2 TYR 1 1 2.497 3.801 1.241 1.00 0.00 H
ATOM 7 HB3 TYR 1 1 3.877 3.116 2.131 1.00 0.00 H
ATOM 8 CG TYR 1 1 4.267 4.996 1.195 1.00 0.00 C
ATOM 9 CD1 TYR 1 1 4.060 5.919 2.227 1.00 0.00 C
ATOM 10 HD1 TYR 1 1 3.400 5.668 3.058 1.00 0.00 H
ATOM 11 CE1 TYR 1 1 4.700 7.164 2.193 1.00 0.00 C
ATOM 12 HE1 TYR 1 1 4.539 7.882 2.997 1.00 0.00 H
ATOM 13 CZ TYR 1 1 5.547 7.486 1.126 1.00 0.00 C
ATOM 14 OH TYR 1 1 6.169 8.695 1.092 1.00 0.00 O
ATOM 15 HH TYR 1 1 5.956 9.247 1.848 1.00 0.00 H
ATOM 16 CE2 TYR 1 1 5.755 6.563 0.094 1.00 0.00 C
ATOM 17 HE2 TYR 1 1 6.415 6.814 -0.737 1.00 0.00 H
ATOM 18 CD2 TYR 1 1 5.115 5.318 0.128 1.00 0.00 C
ATOM 19 HD2 TYR 1 1 5.276 4.600 -0.676 1.00 0.00 H
ATOM 20 C TYR 1 1 5.486 2.705 -0.000 1.00 0.00 C
ATOM 21 O TYR 1 1 6.009 1.593 -0.000 1.00 0.00 O
ATOM 22 N GLY 1 2 6.191 3.839 -0.000 1.00 0.00 N
ATOM 23 H GLY 1 2 5.715 4.730 -0.000 1.00 0.00 H
ATOM 24 CA GLY 1 2 7.640 3.839 -0.000 1.00 0.00 C
ATOM 25 HA2 GLY 1 2 8.004 3.325 0.890 1.00 0.00 H
ATOM 26 HA3 GLY 1 2 8.004 3.325 -0.890 1.00 0.00 H
ATOM 27 C GLY 1 2 8.171 5.265 -0.000 1.00 0.00 C
ATOM 28 O GLY 1 2 7.395 6.219 0.000 1.00 0.00 O
ATOM 29 N GLY 1 3 9.498 5.409 -0.000 1.00 0.00 N
ATOM 30 H GLY 1 3 10.094 4.594 -0.000 1.00 0.00 H
ATOM 31 CA GLY 1 3 10.126 6.715 0.000 1.00 0.00 C
ATOM 32 HA2 GLY 1 3 9.821 7.266 -0.890 1.00 0.00 H
ATOM 33 HA3 GLY 1 3 9.821 7.266 0.890 1.00 0.00 H
ATOM 34 C GLY 1 3 11.642 6.574 -0.000 1.00 0.00 C
ATOM 35 O GLY 1 3 12.165 5.462 -0.000 1.00 0.00 O
ATOM 36 N PHE 1 4 12.347 7.708 -0.000 1.00 0.00 N
ATOM 37 H PHE 1 4 11.871 8.599 0.000 1.00 0.00 H
ATOM 38 CA PHE 1 4 13.796 7.708 -0.000 1.00 0.00 C
ATOM 39 HA PHE 1 4 14.160 7.194 0.890 1.00 0.00 H
ATOM 40 CB PHE 1 4 14.345 6.996 -1.232 1.00 0.00 C
ATOM 41 HB2 PHE 1 4 13.997 5.964 -1.241 1.00 0.00 H
ATOM 42 HB3 PHE 1 4 13.997 7.505 -2.131 1.00 0.00 H
ATOM 43 CG PHE 1 4 15.852 6.945 -1.321 1.00 0.00 C
ATOM 44 CD1 PHE 1 4 16.467 6.316 -2.410 1.00 0.00 C
ATOM 45 HD1 PHE 1 4 15.860 5.864 -3.193 1.00 0.00 H
ATOM 46 CE1 PHE 1 4 17.864 6.269 -2.492 1.00 0.00 C
ATOM 47 HE1 PHE 1 4 18.344 5.779 -3.340 1.00 0.00 H
ATOM 48 CZ PHE 1 4 18.645 6.850 -1.486 1.00 0.00 C
ATOM 49 HZ PHE 1 4 19.733 6.813 -1.550 1.00 0.00 H
ATOM 50 CE2 PHE 1 4 18.029 7.478 -0.397 1.00 0.00 C
ATOM 51 HE2 PHE 1 4 18.637 7.931 0.386 1.00 0.00 H
ATOM 52 CD2 PHE 1 4 16.632 7.526 -0.315 1.00 0.00 C
ATOM 53 HD2 PHE 1 4 16.153 8.015 0.533 1.00 0.00 H
ATOM 54 C PHE 1 4 14.344 9.128 -0.000 1.00 0.00 C
ATOM 55 O PHE 1 4 13.581 10.091 0.000 1.00 0.00 O
ATOM 56 N MET 1 5 15.673 9.256 -0.000 1.00 0.00 N
ATOM 57 H MET 1 5 16.259 8.433 -0.000 1.00 0.00 H
ATOM 58 CA MET 1 5 16.317 10.554 0.000 1.00 0.00 C
ATOM 59 HA MET 1 5 16.019 11.108 -0.890 1.00 0.00 H
ATOM 60 CB MET 1 5 15.924 11.362 1.232 1.00 0.00 C
ATOM 61 HB2 MET 1 5 14.844 11.509 1.241 1.00 0.00 H
ATOM 62 HB3 MET 1 5 16.225 10.824 2.131 1.00 0.00 H
ATOM 63 CG MET 1 5 16.621 12.717 1.195 1.00 0.00 C
ATOM 64 HG2 MET 1 5 17.701 12.571 1.186 1.00 0.00 H
ATOM 65 HG3 MET 1 5 16.321 13.256 0.296 1.00 0.00 H
ATOM 66 SD MET 1 5 16.164 13.689 2.652 1.00 0.00 S
ATOM 67 CE MET 1 5 17.100 15.171 2.341 1.00 0.00 C
ATOM 68 HE1 MET 1 5 16.781 15.612 1.397 1.00 0.00 H
ATOM 69 HE2 MET 1 5 16.933 15.883 3.149 1.00 0.00 H
ATOM 70 HE3 MET 1 5 18.161 14.927 2.287 1.00 0.00 H
ATOM 71 C MET 1 5 17.833 10.413 -0.000 1.00 0.00 C
ATOM 72 O MET 1 5 18.356 9.301 -0.000 1.00 0.00 O
TER 73 MET 1 5
HEADER MOLECULAR SYSTEM 03-MAY-24
REMARK 1 Created by MolSysMT version 1.0 on 03-MAY-2024 at 15:04:56
ATOM 1 N TYR 1 1 3.326 1.548 -0.000 0.00 0.00 N
ATOM 2 H TYR 1 1 3.909 0.724 -0.000 0.00 0.00 H
ATOM 3 CA TYR 1 1 3.970 2.846 -0.000 0.00 0.00 C
ATOM 4 HA TYR 1 1 3.672 3.400 -0.890 0.00 0.00 H
ATOM 5 CB TYR 1 1 3.577 3.654 1.232 0.00 0.00 C
ATOM 6 HB2 TYR 1 1 2.497 3.801 1.241 0.00 0.00 H
ATOM 7 HB3 TYR 1 1 3.877 3.116 2.131 0.00 0.00 H
ATOM 8 CG TYR 1 1 4.267 4.996 1.195 0.00 0.00 C
ATOM 9 CD1 TYR 1 1 4.060 5.919 2.227 0.00 0.00 C
ATOM 10 HD1 TYR 1 1 3.400 5.668 3.058 0.00 0.00 H
ATOM 11 CE1 TYR 1 1 4.700 7.164 2.193 0.00 0.00 C
ATOM 12 HE1 TYR 1 1 4.539 7.882 2.997 0.00 0.00 H
ATOM 13 CZ TYR 1 1 5.547 7.486 1.126 0.00 0.00 C
ATOM 14 OH TYR 1 1 6.169 8.695 1.092 0.00 0.00 O
ATOM 15 HH TYR 1 1 5.956 9.247 1.848 0.00 0.00 H
ATOM 16 CE2 TYR 1 1 5.755 6.563 0.094 0.00 0.00 C
ATOM 17 HE2 TYR 1 1 6.415 6.814 -0.737 0.00 0.00 H
ATOM 18 CD2 TYR 1 1 5.115 5.318 0.128 0.00 0.00 C
ATOM 19 HD2 TYR 1 1 5.276 4.600 -0.676 0.00 0.00 H
ATOM 20 C TYR 1 1 5.486 2.705 -0.000 0.00 0.00 C
ATOM 21 O TYR 1 1 6.009 1.593 -0.000 0.00 0.00 O
ATOM 22 N GLY 1 2 6.191 3.839 -0.000 0.00 0.00 N
ATOM 23 H GLY 1 2 5.715 4.730 -0.000 0.00 0.00 H
ATOM 24 CA GLY 1 2 7.640 3.839 -0.000 0.00 0.00 C
ATOM 25 HA2 GLY 1 2 8.004 3.325 0.890 0.00 0.00 H
ATOM 26 HA3 GLY 1 2 8.004 3.325 -0.890 0.00 0.00 H
ATOM 27 C GLY 1 2 8.171 5.265 -0.000 0.00 0.00 C
ATOM 28 O GLY 1 2 7.395 6.219 0.000 0.00 0.00 O
ATOM 29 N GLY 1 3 9.498 5.409 -0.000 0.00 0.00 N
ATOM 30 H GLY 1 3 10.094 4.594 -0.000 0.00 0.00 H
ATOM 31 CA GLY 1 3 10.126 6.715 0.000 0.00 0.00 C
ATOM 32 HA2 GLY 1 3 9.821 7.266 -0.890 0.00 0.00 H
ATOM 33 HA3 GLY 1 3 9.821 7.266 0.890 0.00 0.00 H
ATOM 34 C GLY 1 3 11.642 6.574 -0.000 0.00 0.00 C
ATOM 35 O GLY 1 3 12.165 5.462 -0.000 0.00 0.00 O
ATOM 36 N PHE 1 4 12.347 7.708 -0.000 0.00 0.00 N
ATOM 37 H PHE 1 4 11.871 8.599 0.000 0.00 0.00 H
ATOM 38 CA PHE 1 4 13.796 7.708 -0.000 0.00 0.00 C
ATOM 39 HA PHE 1 4 14.160 7.194 0.890 0.00 0.00 H
ATOM 40 CB PHE 1 4 14.345 6.996 -1.232 0.00 0.00 C
ATOM 41 HB2 PHE 1 4 13.997 5.964 -1.241 0.00 0.00 H
ATOM 42 HB3 PHE 1 4 13.997 7.505 -2.131 0.00 0.00 H
ATOM 43 CG PHE 1 4 15.852 6.945 -1.321 0.00 0.00 C
ATOM 44 CD1 PHE 1 4 16.467 6.316 -2.410 0.00 0.00 C
ATOM 45 HD1 PHE 1 4 15.860 5.864 -3.193 0.00 0.00 H
ATOM 46 CE1 PHE 1 4 17.864 6.269 -2.492 0.00 0.00 C
ATOM 47 HE1 PHE 1 4 18.344 5.779 -3.340 0.00 0.00 H
ATOM 48 CZ PHE 1 4 18.645 6.850 -1.486 0.00 0.00 C
ATOM 49 HZ PHE 1 4 19.733 6.813 -1.550 0.00 0.00 H
ATOM 50 CE2 PHE 1 4 18.029 7.478 -0.397 0.00 0.00 C
ATOM 51 HE2 PHE 1 4 18.637 7.931 0.386 0.00 0.00 H
ATOM 52 CD2 PHE 1 4 16.632 7.526 -0.315 0.00 0.00 C
ATOM 53 HD2 PHE 1 4 16.153 8.015 0.533 0.00 0.00 H
ATOM 54 C PHE 1 4 14.344 9.128 -0.000 0.00 0.00 C
ATOM 55 O PHE 1 4 13.581 10.091 0.000 0.00 0.00 O
ATOM 56 N MET 1 5 15.673 9.256 -0.000 0.00 0.00 N
ATOM 57 H MET 1 5 16.259 8.433 -0.000 0.00 0.00 H
ATOM 58 CA MET 1 5 16.317 10.554 0.000 0.00 0.00 C
ATOM 59 HA MET 1 5 16.019 11.108 -0.890 0.00 0.00 H
ATOM 60 CB MET 1 5 15.924 11.362 1.232 0.00 0.00 C
ATOM 61 HB2 MET 1 5 14.844 11.509 1.241 0.00 0.00 H
ATOM 62 HB3 MET 1 5 16.225 10.824 2.131 0.00 0.00 H
ATOM 63 CG MET 1 5 16.621 12.717 1.195 0.00 0.00 C
ATOM 64 HG2 MET 1 5 17.701 12.571 1.186 0.00 0.00 H
ATOM 65 HG3 MET 1 5 16.321 13.256 0.296 0.00 0.00 H
ATOM 66 SD MET 1 5 16.164 13.689 2.652 0.00 0.00 S
ATOM 67 CE MET 1 5 17.100 15.171 2.341 0.00 0.00 C
ATOM 68 HE1 MET 1 5 16.781 15.612 1.397 0.00 0.00 H
ATOM 69 HE2 MET 1 5 16.933 15.883 3.149 0.00 0.00 H
ATOM 70 HE3 MET 1 5 18.161 14.927 2.287 0.00 0.00 H
ATOM 71 C MET 1 5 17.833 10.413 -0.000 0.00 0.00 C
ATOM 72 O MET 1 5 18.356 9.301 -0.000 0.00 0.00 O
END
2 changes: 2 additions & 0 deletions molsysmt/form/molsysmt_MolSys/__init__.py
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Expand Up @@ -41,6 +41,7 @@
from .to_pdbfixer_PDBFixer import to_pdbfixer_PDBFixer
from .to_file_msmpk import to_file_msmpk
from .to_file_h5msm import to_file_h5msm
from .to_file_pdb import to_file_pdb
from .to_string_pdb_text import to_string_pdb_text

_convert_to={
Expand All @@ -60,6 +61,7 @@
'string:pdb_text': to_string_pdb_text,
'file:msmpk': to_file_msmpk,
'file:h5msm': to_file_h5msm,
'file:pdb': to_file_pdb,
}


13 changes: 13 additions & 0 deletions molsysmt/form/molsysmt_MolSys/to_file_pdb.py
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@@ -0,0 +1,13 @@
from molsysmt._private.digestion import *

@digest(form='molsysmt.MolSys')
def to_file_pdb(item, atom_indices='all', structure_indices='all', output_filename=None, skip_digestion=False):

from . import to_string_pdb_text

tmp_item = to_string_pdb_text(item, atom_indices=atom_indices, structure_indices=structure_indices, skip_digestion=True)
with open(output_filename, "w") as fff:
fff.write(tmp_item)

return output_filename

18 changes: 0 additions & 18 deletions molsysmt/old_systems/make/met_enkephalin.py
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22 changes: 0 additions & 22 deletions molsysmt/old_systems/make/trp-cage.py
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8 changes: 4 additions & 4 deletions molsysmt/systems.py
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Expand Up @@ -115,14 +115,14 @@ def path(package, file):

systems['Trp-Cage'] = {}
systems['Trp-Cage']['1l2y.pdb'] = path('molsysmt.data.pdb', '1l2y.pdb')
systems['Trp-Cage']['1l2y.mmtf'] = path('molsysmt.data.mmtf', '1l2y.mmtf')
systems['Trp-Cage']['1l2y.h5msm'] = path('molsysmt.data.h5msm', '1l2y.h5msm')


# Metenkephalin

#systems['Met-enkephalin'] = {}
#systems['Met-enkephalin']['met_enkephalin.pdb'] = path('molsysmt.data.pdb', 'met_enkephalin.pdb')
#systems['Met-enkephalin']['met_enkephalin.msmpk'] = path('molsysmt.data.msmpk', 'met_enkephalin.msmpk')
systems['Met-enkephalin'] = {}
systems['Met-enkephalin']['met_enkephalin.pdb'] = path('molsysmt.data.pdb', 'met_enkephalin.pdb')
systems['Met-enkephalin']['met_enkephalin.h5msm'] = path('molsysmt.data.h5msm', 'met_enkephalin.h5msm')


# Two LJ particles
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4 changes: 2 additions & 2 deletions molsysmt/tests/build/add_missing_hydrogens/test_add_missing_hydrogens_molsysmt_MolSys.py
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Expand Up @@ -5,13 +5,13 @@

# Import package, test suite, and other packages as needed
import molsysmt as msm
from molsysmt.systems import tests as tests_systems
from molsysmt import systems
import numpy as np

# Distance between atoms in space and time

def test_add_hydrogens_molsysmt_MolSys_1():
molsys = msm.convert(tests_systems['Met-enkephalin']['met_enkephalin.pdb'], to_form='molsysmt.MolSys')
molsys = msm.convert(systems['Met-enkephalin']['met_enkephalin.pdb'], to_form='molsysmt.MolSys')
molsys = msm.remove(molsys, selection='atom_type=="H"')
output_before = msm.contains(molsys, selection='atom_type=="H"')
molsys = msm.build.add_missing_hydrogens(molsys)
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