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202310003 Tamiflu total synthesis, relocation of ring bond, and refin…
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…ement of crossover
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@renan991995
renan991995 committed Oct 3, 2023
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4,478 changes: 0 additions & 4,478 deletions LOG_FILES/an-1gen.txt
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8,026 changes: 0 additions & 8,026 deletions LOG_FILES/cat-1gen.txt
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18 changes: 9 additions & 9 deletions README.md
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Expand Up @@ -25,7 +25,7 @@ MARS+ is based on MARS [3], with various improvements:
1-1. Group-like elements are allowed.
1-2. Cationic cores and anionic cores are included.
1-3. The library is not hard-coded.
It can be appended easily. (See the instructions in INPUTS/ELEMENT_LISTS/element_list.txt)
It can be appended easily. (See the instructions in inputs/element_lists/element_list.txt)


2. **The generalization of MDS**
Expand Down Expand Up @@ -106,28 +106,28 @@ Please refer to the repository of [MARS+ Windows version](https://github.com/ren

## Usage

There are 3 input files for MARS+: (see `INPUTS/`)
There are 3 input files for MARS+: (see `inputs/`)

INPUTS/control.in : controls the input, output, and calculation options.
INPUTS/ELEMENT_LISTS/element_list.txt : a list that defines base element library.
INPUTS/INPUT_CHEMICALS/IL4.txt : the starting chemicals.
inputs/control.in : controls the input, output, and calculation options.
inputs/element_lists/element_list.txt : a list that defines base element library.
inputs/INPUT_CHEMICALS/IL4.txt : the starting chemicals.

Please read the instructions in `INPUTS/control.in` and `INPUTS/ELEMENT_LISTS/element_list.txt`.
Please read the instructions in `inputs/control.in` and `inputs/element_lists/element_list.txt`.
Make sure you have properly set the parameters, and then launch the MARS+.


### For Linux users:

cd src/
./MARS-PLUS ../INPUTS/control.in
./MARS-PLUS ../inputs/control.in

Alternatively, you may use the PBS scheduler. A PBS template `src/job.sh` is provided.

cd src/
qsub ./job.sh

The results for each of the operations will be outputted to `LOG_FILES/`.
For instance, the generated chemicals by applying bond change operation to an IL will be written to `LOG_FILES/change_bnd_IL.txt`.
The results for each of the operations will be outputted to `logs/`.
For instance, the generated chemicals by applying bond change operation to an IL will be written to `logs/change_bnd_IL.txt`.


### For Windows users:
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18 changes: 9 additions & 9 deletions INPUTS/control.in → inputs/control.in
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Expand Up @@ -40,11 +40,11 @@

#Directory
PROGRAM_DIR ./ # default: MARS-PLUS/src/
MDS_DIR ../LOG_FILES/mds/ # default: MARS-PLUS/LOG_FILES/mds/
LOG_DIR ../LOG_FILES/ # default: MARS-PLUS/LOG_FILES/
MDS_DIR ../logs/mds/ # default: MARS-PLUS/LOG_FILES/mds/
LOG_DIR ../logs/ # default: MARS-PLUS/LOG_FILES/

#Element definition
ELEMENT_LIST ../INPUTS/ELEMENT_LISTS/element_list.txt
ELEMENT_LIST ../inputs/element_lists/element_list.txt
#ELEMENT_LIST none #default

#Appearance of ions
Expand Down Expand Up @@ -80,12 +80,12 @@


#Initial guess molecules/ILs
#CHEMICAL_IUPUTLIST ../INPUTS/INPUT_CHEMICALS/IL.txt
#CHEMICAL_IUPUTLIST ../INPUTS/INPUT_CHEMICALS/IL1.txt
#CHEMICAL_IUPUTLIST ../INPUTS/INPUT_CHEMICALS/IL2.txt
#CHEMICAL_IUPUTLIST ../INPUTS/INPUT_CHEMICALS/IL3.txt
CHEMICAL_IUPUTLIST ../INPUTS/INPUT_CHEMICALS/IL4.txt
#CHEMICAL_IUPUTLIST ../INPUTS/INPUT_CHEMICALS/IL5.txt
#CHEMICAL_IUPUTLIST ../inputs/input_chemicals/IL.txt
#CHEMICAL_IUPUTLIST ../inputs/input_chemicals/IL1.txt
#CHEMICAL_IUPUTLIST ../inputs/input_chemicals/IL2.txt
#CHEMICAL_IUPUTLIST ../inputs/input_chemicals/IL3.txt
CHEMICAL_IUPUTLIST ../inputs/input_chemicals/IL4.txt
#CHEMICAL_IUPUTLIST ../inputs/input_chemicals/IL5.txt

#Set REDU_DUPLICATES to be 1 if you do not count duplicates
#REDU_DUPLICATES 1
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0 INPUTS/ELEMENT_LISTS/element_list.txt → inputs/element_lists/element_list.txt
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0 INPUTS/INPUT_CHEMICALS/IL1.txt → inputs/input_chemicals/IL1.txt
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0 INPUTS/INPUT_CHEMICALS/IL2.txt → inputs/input_chemicals/IL2.txt
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0 INPUTS/INPUT_CHEMICALS/IL3.txt → inputs/input_chemicals/IL3.txt
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0 INPUTS/INPUT_CHEMICALS/IL4.txt → inputs/input_chemicals/IL4.txt
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0 INPUTS/INPUT_CHEMICALS/IL5.txt → inputs/input_chemicals/IL5.txt
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74 changes: 74 additions & 0 deletions logs/Tamiflu_Corey.txt
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@@ -0,0 +1,74 @@
C=CC=C.C=CC(=O)OCC(F)(F)F Initialization
CCC(=O)OCC(F)(F)F B.change_bnd(1,1,1,1)
C=C/C=C\CCC(=O)OCC(F)(F)F A.combination(B,0,0,1)
C=CCCCCC(=O)OCC(F)(F)F A.change_bnd(1,1,2,1)
CCCCCCC(=O)OCC(F)(F)F A.change_ele(3,1,1,0)
O=C(C1CCCCC1)OCC(F)(F)F A.cyclization(3,5,1)
O=C([C@H]1CCC=CC1)OCC(F)(F)F A.change_bnd(2,2,2,2)
O=C([C@H]1CCC=CC1)OCC(F)(F)F 1st step
FC(COC(=O)[C@H]1CCC=CC1)F A.subtraction(13,0)
FCCOC(=O)[C@H]1CCC=CC1 A.subtraction(12,0)
CCOC(=O)[C@H]1CCC=CC1 A.subtraction(11,0)
COC(=O)[C@H]1CCC=CC1 A.subtraction(10,0)
OC(=O)[C@H]1CCC=CC1 A.subtraction(9,0)
NC(=O)[C@H]1CCC=CC1 A.change_ele(8,7,1,0)
NC(=O)[C@H]1CCC=CC1 2nd step
NC(=O)C1CCCCC1 A.change_bnd(2,1,1,1)
I[C@@H]1CC[C@H](CC1)C(=O)N A.addition(1,14,1)
I[C@H]1CC[C@H]2C[C@@H]1NC2=O A.cyclization(2,8,1)
I[C@H]1CC[C@H]2C[C@@H]1NC2=O 3rd step
O=C1N[C@H]2C[C@@H]1CCC2 A.subtraction(9,0)
O=C1N[C@H]2C[C@@H]1CC=C2 A.change_bnd(1,2,2,2)
O=C1[C@H]2CC=C[C@@H](N1C)C2 A.addition(8,2,1)
C1[C@H]2C=CC[C@@H]1C(=O)N2C=O A.addition(9,6,2)
OC(=O)N1[C@H]2C[C@@H](C1=O)CC=C2 A.addition(9,5,1)
COC(=O)N1[C@@H]2C=CC[C@H](C1=O)C2 A.addition(11,1,1)
CCOC(=O)N1[C@H]2C[C@@H](C1=O)CC=C2 A.addition(12,1,1)
CC(OC(=O)N1[C@@H]2C=CC[C@H](C1=O)C2)C A.addition(12,1,1)
O=C(N1[C@@H]2C=CC[C@H](C1=O)C2)OC(C)(C)C A.addition(12,1,1)
O=C(N1[C@@H]2C=CC[C@H](C1=O)C2)OC(C)(C)C 4th step
O=C(N1[C@@H]2CCC[C@H](C1=O)C2)OC(C)(C)C A.change_bnd(1,2,1,1)
Br[C@H]1CC[C@H]2C[C@@H]1N(C(=O)OC(C)(C)C)C2=O A.addition(1,13,1)
Br[C@H]1C=C[C@H]2C[C@@H]1N(C(=O)OC(C)(C)C)C2=O A.change_bnd(4,2,2,2)
Br[C@H]1C=C[C@H]2C[C@@H]1N(C(=O)OC(C)(C)C)C2=O 5th step
O=C(N1[C@@H]2CC=C[C@H](C1=O)C2)OC(C)(C)C A.subtraction(16,0)
O=C(N1[C@@H]2CC=C[C@H](C1=O)C2)OC(C)(C)C A.cycbnd_relocate(2)
O=C[C@H]1C=CC[C@@H](C1)NC(=O)OC(C)(C)C A.decyclization(2)
O=C[C@H]1CCC[C@@H](C1)NC(=O)OC(C)(C)C A.change_bnd(4,2,2,1)
O=C[C@H]1CC=C[C@@H](C1)NC(=O)OC(C)(C)C A.change_bnd(1,2,2,2)
O=CC1=CC=C[C@@H](C1)NC(=O)OC(C)(C)C A.change_bnd(5,2,2,2)
O=C(OC(C)(C)C)N[C@H]1C=CC=C(C1)C(=O)O A.addition(6,5,1)
COC(=O)C1=CC=C[C@@H](C1)NC(=O)OC(C)(C)C A.addition(16,1,1)
CCOC(=O)C1=CC=C[C@@H](C1)NC(=O)OC(C)(C)C A.addition(17,1,1)
CCOC(=O)C1=CC=C[C@H](C1)NC(=O)OC(C)(C)C A.change_chirality(2,1)
CCOC(=O)C1=CC=C[C@H](C1)NC(=O)OC(C)(C)C 6th step
CCOC(=O)C1=CCC[C@H](C1)NC(=O)OC(C)(C)C A.change_bnd(1,1,1,1)
CCOC(=O)C1=CC[C@@H]([C@H](C1)NC(=O)OC(C)(C)C)Br A.addition(1,13,1)
CCOC(=O)C1=C[C@@H]([C@@H]([C@H](C1)NC(=O)OC(C)(C)C)Br)N A.addition(0,7,1)
CCOC(=O)C1=C[C@@H]([C@@H]([C@H](C1)NC(=O)OC(C)(C)C)Br)NC A.addition(20,2,1)
O=CN[C@H]1C=C(C[C@@H]([C@H]1Br)NC(=O)OC(C)(C)C)C(=O)OCC A.addition(21,6,2)
CCOC(=O)C1=C[C@@H]([C@@H]([C@H](C1)NC(=O)OC(C)(C)C)Br)NC(=O)C A.addition(21,1,1)
CCOC(=O)C1=C[C@@H]([C@H]([C@H](C1)NC(=O)OC(C)(C)C)Br)NC(=O)C A.change_chirality(1,1)
CCOC(=O)C1=C[C@@H]([C@H]([C@H](C1)NC(=O)OC(C)(C)C)Br)NC(=O)C 7th step
CCOC(=O)C1=C[C@@H](C[C@H](C1)NC(=O)OC(C)(C)C)NC(=O)C A.subtraction(19,0)
CCOC(=O)C1=C[C@H]2[C@@H]([C@H](C1)NC(=O)OC(C)(C)C)N2C(=O)C A.cyclization(1,19,1)
CCOC(=O)C1=C[C@H]2[C@@H]([C@H](C1)NC(=O)OC(C)(C)C)N2C(=O)C 8th step
CCOC(=O)C1=C[C@H]2[C@@H]([C@H](C1)NC(=O)OC(C)(C)C)N2C(=O)C A.cycbnd_relocate(2)
CCOC(=O)C1=CC[C@H]([C@H](C1)NC(=O)OC(C)(C)C)NC(=O)C A.decyclization(2)
CCOC(=O)C1=CC[C@@H]([C@H](C1)NC(=O)OC(C)(C)C)NC(=O)C A.change_chirality(1,2)
CCOC(=O)C1=CC[C@@H]([C@H](C1)NC(=O)OC(C)(C)C)NC(=O)C A.change_chirality(0,1)
CCOC(=O)C1=C[C@H]([C@@H]([C@H](C1)NC(=O)OC(C)(C)C)NC(=O)C)O A.addition(0,5,1)
CCOC(=O)C1=C[C@H]([C@@H]([C@H](C1)NC(=O)OC(C)(C)C)NC(=O)C)OC A.addition(23,1,1)
CCO[C@@H]1C=C(C[C@@H]([C@H]1NC(=O)C)NC(=O)OC(C)(C)C)C(=O)OCC A.addition(24,1,1)
CCCO[C@@H]1C=C(C[C@@H]([C@H]1NC(=O)C)NC(=O)OC(C)(C)C)C(=O)OCC A.addition(25,1,1)
CCOC(=O)C1=C[C@H]([C@@H]([C@H](C1)NC(=O)OC(C)(C)C)NC(=O)C)O[C@@H](CC)C A.addition(24,1,1)
CCOC(=O)C1=C[C@H]([C@@H]([C@H](C1)NC(=O)OC(C)(C)C)NC(=O)C)OC(CC)CC A.addition(27,1,1)
CCOC(=O)C1=C[C@H]([C@@H]([C@H](C1)NC(=O)OC(C)(C)C)NC(=O)C)OC(CC)CC 9th step
CCOC(=O)C1=C[C@H]([C@@H]([C@H](C1)NC(=O)OC(C)C)NC(=O)C)OC(CC)CC A.subtraction(15,0)
CCOC(=O)N[C@H]1CC(=C[C@H]([C@@H]1NC(=O)C)OC(CC)CC)C(=O)OCC A.subtraction(14,0)
CCOC(=O)C1=C[C@H]([C@@H]([C@H](C1)NC(=O)OC)NC(=O)C)OC(CC)CC A.subtraction(13,0)
CCOC(=O)C1=C[C@H]([C@@H]([C@H](C1)NC(=O)O)NC(=O)C)OC(CC)CC A.subtraction(12,0)
O=CN[C@H]1CC(=C[C@H]([C@@H]1NC(=O)C)OC(CC)CC)C(=O)OCC A.subtraction(11,0)
CCOC(=O)C1=C[C@H]([C@@H]([C@H](C1)NC)NC(=O)C)OC(CC)CC A.subtraction(10,0)
CCOC(=O)C1=C[C@H]([C@@H]([C@H](C1)N)NC(=O)C)OC(CC)CC A.subtraction(9,0)
CCOC(=O)C1=C[C@H]([C@@H]([C@H](C1)N)NC(=O)C)OC(CC)CC 10th step
0 LOG_FILES/addition_IL.txt → logs/addition_IL.txt
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