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Hotfix/mcfgen #84

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merged 4 commits into from
Aug 27, 2020
Merged

Hotfix/mcfgen #84

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75fc9bb
Restore mcfgen.py from 1.2 release tarball
rsdefever Aug 27, 2020
161ce01
Apply 'futurize' and add py2 deprecation warning
rsdefever Aug 27, 2020
94fdf45
Add warnings import
rsdefever Aug 27, 2020
b44037d
Update example MCF and FF files in MCF Generation directory
rsdefever Aug 27, 2020
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3 changes: 3 additions & 0 deletions Scripts/MCF_Generation/CML/benzene_ua.cml.ff → Scripts/MCF_Generation/CML/benzene_ua.ff
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Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,10 @@ begin atom-atomtype
6 CH2
end atom-atomtype

vdwtype LJ
dihedraltype OPLS
scaling_1_4_vdw 0.0
scaling_1_4_charge 0.0

nonbonded
CH2
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27 changes: 18 additions & 9 deletions ...pts/MCF_Generation/CML/benzene_ua.cml.mcf → Scripts/MCF_Generation/CML/benzene_ua.mcf
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Original file line number Diff line number Diff line change
@@ -1,18 +1,19 @@
!*******************************************************************************
!Molecular connectivity file for benzene_ua.cml.pdb
!Molecular connectivity file for benzene_ua.pdb
!*******************************************************************************
!Atom Format
!index type element mass charge type parameters
!type="LJ", parms=epsilon sigma
!index type element mass charge vdw_type parameters
!vdw_type="LJ", parms=epsilon sigma
!vdw_type="Mie", parms=epsilon sigma repulsion_exponent dispersion_exponent

# Atom_Info
6
1 C1 C 12.011 0.0 LJ 50.500 3.695 ring
2 C2 C 12.011 0.0 LJ 50.500 3.695 ring
3 C3 C 12.011 0.0 LJ 50.500 3.695 ring
4 C4 C 12.011 0.0 LJ 50.500 3.695 ring
5 C5 C 12.011 0.0 LJ 50.500 3.695 ring
6 C6 C 12.011 0.0 LJ 50.500 3.695 ring
1 CH2 C 12.011 0.0 LJ 50.500 3.695 ring
2 CH2 C 12.011 0.0 LJ 50.500 3.695 ring
3 CH2 C 12.011 0.0 LJ 50.500 3.695 ring
4 CH2 C 12.011 0.0 LJ 50.500 3.695 ring
5 CH2 C 12.011 0.0 LJ 50.500 3.695 ring
6 CH2 C 12.011 0.0 LJ 50.500 3.695 ring

!Bond Format
!index i j type parameters
Expand Down Expand Up @@ -60,6 +61,14 @@
# Improper_Info
0

!Intra Scaling
!vdw_scaling 1-2 1-3 1-4 1-N
!charge_scaling 1-2 1-3 1-4 1-N

# Intra_Scaling
0. 0. 0.0000 1.
0. 0. 0.0000 1.

!Fragment Format
!index number_of_atoms_in_fragment branch_point other_atoms

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3 changes: 2 additions & 1 deletion Scripts/MCF_Generation/PDB/argon.ff
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Original file line number Diff line number Diff line change
Expand Up @@ -5,12 +5,13 @@ begin atom-atomtype
1 Argon_type
end atom-atomtype

vdwtype LJ
dihedraltype none

nonbonded
Argon_type
Sigma 3.40
Epsilon 120.0
Epsilon 120.0
atom_type_charge

charge
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15 changes: 12 additions & 3 deletions Scripts/MCF_Generation/PDB/argon.mcf
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Original file line number Diff line number Diff line change
Expand Up @@ -2,12 +2,13 @@
!Molecular connectivity file for argon.pdb
!*******************************************************************************
!Atom Format
!index type element mass charge type parameters
!type="LJ", parms=epsilon sigma
!index type element mass charge vdw_type parameters
!vdw_type="LJ", parms=epsilon sigma
!vdw_type="Mie", parms=epsilon sigma repulsion_exponent dispersion_exponent

# Atom_Info
1
1 Ar1 Ar 39.948 0.0 LJ 120.000 3.400
1 Argon_type Ar 39.948 0.0 LJ 120.000 3.400

# Bond_Info
0
Expand All @@ -21,6 +22,14 @@
# Improper_Info
0

!Intra Scaling
!vdw_scaling 1-2 1-3 1-4 1-N
!charge_scaling 1-2 1-3 1-4 1-N

# Intra_Scaling
0. 0. 0.0000 1.
0. 0. 0.0000 1.

!Fragment Format
!index number_of_atoms_in_fragment branch_point other_atoms

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1 change: 1 addition & 0 deletions Scripts/MCF_Generation/PDB/c2.ff
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,7 @@ begin atom-atomtype
2 CH3
end atom-atomtype

vdwtype LJ
dihedraltype none

nonbonded
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17 changes: 13 additions & 4 deletions Scripts/MCF_Generation/PDB/c2.mcf
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Original file line number Diff line number Diff line change
Expand Up @@ -2,13 +2,14 @@
!Molecular connectivity file for c2.pdb
!*******************************************************************************
!Atom Format
!index type element mass charge type parameters
!type="LJ", parms=epsilon sigma
!index type element mass charge vdw_type parameters
!vdw_type="LJ", parms=epsilon sigma
!vdw_type="Mie", parms=epsilon sigma repulsion_exponent dispersion_exponent

# Atom_Info
2
1 C1 C 12.011 0.0 LJ 98.000 3.750
2 C2 C 12.011 0.0 LJ 98.000 3.750
1 CH3 C 12.011 0.0 LJ 98.000 3.750
2 CH3 C 12.011 0.0 LJ 98.000 3.750

!Bond Format
!index i j type parameters
Expand All @@ -27,6 +28,14 @@
# Improper_Info
0

!Intra Scaling
!vdw_scaling 1-2 1-3 1-4 1-N
!charge_scaling 1-2 1-3 1-4 1-N

# Intra_Scaling
0. 0. 0.0000 1.
0. 0. 0.0000 1.

!Fragment Format
!index number_of_atoms_in_fragment branch_point other_atoms

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3 changes: 3 additions & 0 deletions Scripts/MCF_Generation/PDB/c4.ff
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,10 @@ begin atom-atomtype
4 CH3
end atom-atomtype

vdwtype LJ
dihedraltype OPLS
scaling_1_4_vdw 0.0
scaling_1_4_charge 0.0

nonbonded
CH3
Expand Down
21 changes: 15 additions & 6 deletions Scripts/MCF_Generation/PDB/c4.mcf
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Original file line number Diff line number Diff line change
Expand Up @@ -2,15 +2,16 @@
!Molecular connectivity file for c4.pdb
!*******************************************************************************
!Atom Format
!index type element mass charge type parameters
!type="LJ", parms=epsilon sigma
!index type element mass charge vdw_type parameters
!vdw_type="LJ", parms=epsilon sigma
!vdw_type="Mie", parms=epsilon sigma repulsion_exponent dispersion_exponent

# Atom_Info
4
1 C1 C 12.011 0.0 LJ 98.000 3.750
2 C2 C 12.011 0.0 LJ 46.000 3.950
3 C3 C 12.011 0.0 LJ 46.000 3.950
4 C4 C 12.011 0.0 LJ 98.000 3.750
1 CH3 C 12.011 0.0 LJ 98.000 3.750
2 CH2 C 12.011 0.0 LJ 46.000 3.950
3 CH2 C 12.011 0.0 LJ 46.000 3.950
4 CH3 C 12.011 0.0 LJ 98.000 3.750

!Bond Format
!index i j type parameters
Expand Down Expand Up @@ -46,6 +47,14 @@
# Improper_Info
0

!Intra Scaling
!vdw_scaling 1-2 1-3 1-4 1-N
!charge_scaling 1-2 1-3 1-4 1-N

# Intra_Scaling
0. 0. 0.0000 1.
0. 0. 0.0000 1.

!Fragment Format
!index number_of_atoms_in_fragment branch_point other_atoms

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3 changes: 3 additions & 0 deletions Scripts/MCF_Generation/PDB/pentane.ff
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,10 @@ begin atom-atomtype
5 CH3
end atom-atomtype

vdwtype LJ
dihedraltype OPLS
scaling_1_4_vdw 0.0
scaling_1_4_charge 0.0

nonbonded
CH3
Expand Down
23 changes: 16 additions & 7 deletions Scripts/MCF_Generation/PDB/pentane.mcf
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Original file line number Diff line number Diff line change
Expand Up @@ -2,16 +2,17 @@
!Molecular connectivity file for pentane.pdb
!*******************************************************************************
!Atom Format
!index type element mass charge type parameters
!type="LJ", parms=epsilon sigma
!index type element mass charge vdw_type parameters
!vdw_type="LJ", parms=epsilon sigma
!vdw_type="Mie", parms=epsilon sigma repulsion_exponent dispersion_exponent

# Atom_Info
5
1 C1 C 12.011 0.0 LJ 98.000 3.750
2 C2 C 12.011 0.0 LJ 46.000 3.950
3 C3 C 12.011 0.0 LJ 46.000 3.950
4 C4 C 12.011 0.0 LJ 46.000 3.950
5 C5 C 12.011 0.0 LJ 98.000 3.750
1 CH3 C 12.011 0.0 LJ 98.000 3.750
2 CH2 C 12.011 0.0 LJ 46.000 3.950
3 CH2 C 12.011 0.0 LJ 46.000 3.950
4 CH2 C 12.011 0.0 LJ 46.000 3.950
5 CH3 C 12.011 0.0 LJ 98.000 3.750

!Bond Format
!index i j type parameters
Expand Down Expand Up @@ -50,6 +51,14 @@
# Improper_Info
0

!Intra Scaling
!vdw_scaling 1-2 1-3 1-4 1-N
!charge_scaling 1-2 1-3 1-4 1-N

# Intra_Scaling
0. 0. 0.0000 1.
0. 0. 0.0000 1.

!Fragment Format
!index number_of_atoms_in_fragment branch_point other_atoms

Expand Down
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