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20210615 updated
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@renan991995
renan991995 committed Jun 15, 2021
1 parent ff6f4f6 commit 4129378
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34 changes: 30 additions & 4 deletions 6set_memredu.in
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Original file line number Diff line number Diff line change
Expand Up @@ -39,14 +39,34 @@


#Appearance of ions
#ION 0
ION 1
#IF_ION 0
IF_ION 1

#SMILES enumeration
IF_ENUMERATION 0
#IF_ENUMERATION 1

#Proctection
PROTECT 0
#PROTECT 1
#IF_PROTECT 0
IF_PROTECT 1

#Molecular operations
OPERATIONS All
#OPERATIONS Crossover
#OPERATIONS Combination
#OPERATIONS Addition
#OPERATIONS Subtraction
#OPERATIONS Exchange_ele
#OPERATIONS Exchange_bnd
#OPERATIONS Cistrans_inversion
#OPERATIONS Chirality_inversion
#OPERATIONS Insertion
#OPERATIONS Cyclization
#OPERATIONS Decyclization
#OPERATIONS Component_switch

#Epoch
EPOCH 1

#Initial guess molecules/ILs
#CHEMICAL_IUPUTLIST MARIL.txt
Expand All @@ -56,6 +76,12 @@
CHEMICAL_IUPUTLIST MARIL4.txt
#CHEMICAL_IUPUTLIST MARIL5.txt

#Output Directory
OUTPUT_DIR /fileserver/tom61212/MARSIL-paper/mds/

#output mds in OUTPUT_DIR?
IF_OUTPUT_MDS 0
#IF_OUTPUT_MDS 1

#Route of Obabel executable file
OBABEL_ROUTE /home/software/programs/openbabel-openbabel-2-4-1/build/bin/obabel
104 changes: 92 additions & 12 deletions ATOM.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -47,11 +47,15 @@ void DEATOM::find_r() {
}

void POOL::set_up() {
num=70;
num=72;
int i,j,k;

a.resize(num);
for (i=0;i<num;i++) a.at(i).order.resize(6);
for (i=0;i<num;i++) {
a.at(i).order.resize(6);
//a.at(i).cybnd.resize(0);
//a.at(i).cypos.resize(0);
}
for (i=0;i<num;i++) {
a.at(i).nh=0;
for (j=0;j<6;j++) a.at(i).order.at(j)=0;
Expand Down Expand Up @@ -207,7 +211,7 @@ void POOL::set_up() {
a[8].bd[1]=1;
a[8].ang0=115.0*f;
a[8].atm="N";
a[8].probability=0.2*0.25;
a[8].probability=-1; //0.2*0.25; //-1

a[9].id=9;
a[9].name="N(#)";
Expand Down Expand Up @@ -288,7 +292,7 @@ void POOL::set_up() {
a[14].bd[0]=1;
a[14].ang0=0;
a[14].atm="I";
a[14].probability=0;
a[14].probability=0.1*0.05; //-1

a[15].id=15;
a[15].name="[NH0+](-)(-)(-)(-)";
Expand Down Expand Up @@ -578,7 +582,7 @@ void POOL::set_up() {
a[35].probability=0.005;

a[36].id=36; //GG
a[36].name="C(-)(-)(-)([N+]1C=CN(C)C=1)";
a[36].name="C(-)(-)(-)([N+]%99999C=CN(C)C=%99999)";
a[36].order[0]=a[36].order[1]=a[36].order[2]=1;
a[36].nbond=10;
a[36].norder=3;
Expand All @@ -587,12 +591,16 @@ void POOL::set_up() {
a[36].type=1;
a[36].bd[0]=3;
a[36].index=2;
//a[36].cybnd.resize(1,1);
//a[36].cypos.resize(2,vector<int>(1,0));
//a[36].cypos.at(0).at(0)=15;
//a[36].cypos.at(1).at(0)=25;
a[36].ang0=109.5*f;
a[36].atm="C";
a[36].probability=0.005;

a[37].id=37; //GG
a[37].name="C(-)(-)(-)([N+]1C=CN(C)C(C)=1)";
a[37].name="C(-)(-)(-)([N+]%99999C=CN(C)C(C)=%99999)";
a[37].order[0]=a[37].order[1]=a[37].order[2]=1;
a[37].nbond=10;
a[37].norder=3;
Expand All @@ -601,12 +609,16 @@ void POOL::set_up() {
a[37].type=1;
a[37].bd[0]=3;
a[37].index=2;
//a[37].cybnd.resize(1,1);
//a[37].cypos.resize(2,vector<int>(1,0));
//a[37].cypos.at(0).at(0)=15;
//a[37].cypos.at(1).at(0)=28;
a[37].ang0=109.5*f;
a[37].atm="C";
a[37].probability=0.005;

a[38].id=38;
a[38].name="C(-)(-)(-)(N1C=C[N+](C)=C1)";
a[38].name="C(-)(-)(-)(N%99999C=C[N+](C)=C%99999)";
a[38].order[0]=a[38].order[1]=a[38].order[2]=1;
a[38].nbond=10;
a[38].norder=3;
Expand All @@ -615,12 +627,16 @@ void POOL::set_up() {
a[38].type=1;
a[38].bd[0]=3;
a[38].index=2;
//a[38].cybnd.resize(1,1);
//a[38].cypos.resize(2,vector<int>(1,0));
//a[38].cypos.at(0).at(0)=12;
//a[38].cypos.at(1).at(0)=25;
a[38].ang0=109.5*f;
a[38].atm="C";
a[38].probability=0.005;

a[39].id=39; //GG
a[39].name="C(-)(-)(-)([N+]1=CC=CC(C)=C1)";
a[39].name="C(-)(-)(-)([N+]%99999=CC=CC(C)=C%99999)";
a[39].order[0]=a[39].order[1]=a[39].order[2]=1;
a[39].nbond=10;
a[39].norder=3;
Expand All @@ -629,12 +645,16 @@ void POOL::set_up() {
a[39].type=1;
a[39].bd[0]=3;
a[39].index=2;
//a[39].cybnd.resize(1,1);
//a[39].cypos.resize(2,vector<int>(1,0));
//a[39].cypos.at(0).at(0)=15;
//a[39].cypos.at(1).at(0)=27;
a[39].ang0=109.5*f;
a[39].atm="C";
a[39].probability=0.005;

a[40].id=40; //GG
a[40].name="C(-)(-)(-)(C1=C[N+](C)=CC=C1)";
a[40].name="C(-)(-)(-)(C%99999=C[N+](C)=CC=C%99999)";
a[40].order[0]=a[40].order[1]=a[40].order[2]=1;
a[40].nbond=10;
a[40].norder=3;
Expand All @@ -643,12 +663,16 @@ void POOL::set_up() {
a[40].type=1;
a[40].bd[0]=3;
a[40].index=2;
//a[40].cybnd.resize(1,1);
//a[40].cypos.resize(2,vector<int>(1,0));
//a[40].cypos.at(0).at(0)=12;
//a[40].cypos.at(1).at(0)=27;
a[40].ang0=109.5*f;
a[40].atm="C";
a[40].probability=0.005;

a[41].id=41;
a[41].name="C(-)(1=[NH+]C=CC=C1)";
a[41].name="C(-)(%99999=[NH+]C=CC=C%99999)";
a[41].order[0]=1;
a[41].nbond=4;
a[41].norder=1;
Expand All @@ -657,12 +681,16 @@ void POOL::set_up() {
a[41].type=3;
a[41].bd[0]=1;
a[41].index=2;
//a[41].cybnd.resize(1,1);
//a[41].cypos.resize(2,vector<int>(1,0));
//a[41].cypos.at(0).at(0)=5;
//a[41].cypos.at(1).at(0)=18;
a[41].ang0=120.0*f;
a[41].atm="C";
a[41].probability=0.005;

a[42].id=42;
a[42].name="[NH0+](-)(1=CC=CC=C1)";
a[42].name="[NH0+](-)(%99999=CC=CC=C%99999)";
a[42].order[0]=1;
a[42].nbond=9;
a[42].norder=1;
Expand All @@ -671,6 +699,10 @@ void POOL::set_up() {
a[42].type=3;
a[42].bd[0]=1;
a[42].index=7;
//a[42].cybnd.resize(1,1);
//a[42].cypos.resize(2,vector<int>(1,0));
//a[42].cypos.at(0).at(0)=10;
//a[42].cypos.at(1).at(0)=19;
a[42].ang0=120.0*f;
a[42].atm="N";
a[42].probability=0.005;
Expand Down Expand Up @@ -780,13 +812,17 @@ void POOL::set_up() {
a[50].probability=0.005;

a[51].id=51;
a[51].name="S(c(cc1)ccc1C)(=O)(=O)([O-])"; // Cc1ccc(cc1)S(=O)(=O)[O-]
a[51].name="S(c(cc%99999)ccc%99999C)(=O)(=O)([O-])"; // Cc1ccc(cc1)S(=O)(=O)[O-]
a[51].nbond=28; //1
a[51].norder=0;
a[51].chg=-1;
a[51].rb=0.82;
a[51].type=1;
a[51].index=28; //0
//a[51].cybnd.resize(1,1);
//a[51].cypos.resize(2,vector<int>(1,0));
//a[51].cypos.at(0).at(0)=6;
//a[51].cypos.at(1).at(0)=11;
a[51].ang0=109.5*f;
a[51].atm="S";
a[51].probability=0.005;
Expand Down Expand Up @@ -1030,6 +1066,50 @@ void POOL::set_up() {
a[69].atm="P";
a[69].probability=0.00001;

a[70].id=70;
a[70].name="*(-)"; //lone pair or pseudo-atom
a[70].nbond=4;
a[70].order[0]=1;
a[70].order[1]=0;
a[70].order[2]=0;
a[70].order[3]=0;
a[70].bd[0]=1;
a[70].norder=1;
a[70].rb=0.37;
a[70].ang0=0.0;
a[70].atm="Xx";
a[70].probability=-1;

a[71].id=71;
a[71].name="N(=)(-)(*)";
a[71].order[0]=2;
a[71].order[1]=1;
a[71].order[2]=a[71].order[3]=0;
a[71].nbond=7;
a[71].norder=2;
a[71].rb=0.74;
a[71].type=4;
a[71].bd[0]=1;
a[71].bd[1]=1;
a[71].ang0=115.0*f;
a[71].atm="N";
a[71].probability=0.2*0.25; //0.2*0.25;//-1;

//a[72].id=72;
//a[72].name="N(-)(-)(*)";
//a[72].order[0]=2;
//a[72].order[1]=0;
//a[72].order[2]=a[72].order[3]=0;
//a[72].nbond=7;
//a[72].norder=2;
//a[72].rb=0.74;
//a[72].type=4;
//a[72].bd[0]=1;
//a[72].bd[1]=0;
//a[72].ang0=115.0*f;
//a[72].atm="N";
//a[72].probability=-1;//0.2*0.25;//-1;


return;
}
12 changes: 9 additions & 3 deletions ATOM.h
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Original file line number Diff line number Diff line change
Expand Up @@ -39,6 +39,8 @@ class ATOM
public:
ATOM() {
order.resize(0);
//cybnd.resize(0);
//cypos.resize(0);
//order=NULL;
name=atm="";
index=2;
Expand All @@ -55,6 +57,8 @@ class ATOM
}
~ATOM() {
order.clear();
//cybnd.clear();
//cypos.clear();
//vector<int>().swap(order);
}
int id;
Expand All @@ -65,6 +69,8 @@ class ATOM
int nh;
int bd[3];
int type;
//vector<int> cybnd;
//vector< vector<int> > cypos;
int index;
double rb;
double probability;
Expand Down Expand Up @@ -113,15 +119,15 @@ class POOL
if(a.size()) {
for (int r1=0;r1<num;r1++) {
if(a.at(r1).order.size()) {
a.at(r1).order.clear();
a.at(r1).order.resize(0);
//vector<int>().swap(a.at(r1).order);
}
}
a.clear();
a.resize(0);
//vector<ATOM>().swap(a);
}

vector<ATOM>().swap(a);
//vector<ATOM>().swap(a);
}
int num;
//ATOM *a; // types of atoms
Expand Down
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