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22
Dockerfile
Normal file
22
Dockerfile
Normal file
@@ -0,0 +1,22 @@
|
||||
FROM debian:bookworm-slim
|
||||
RUN groupadd -r fpocket && useradd --no-log-init -r -g fpocket fpocket
|
||||
RUN apt update -y && apt install -y gcc g++ make libnetcdf-dev && rm -rf /var/lib/apt/lists/*
|
||||
|
||||
# all of this mess is essentially to have a minimalistic build at the end
|
||||
COPY makefile /opt/fpocket/
|
||||
COPY src /opt/fpocket/src
|
||||
COPY man /opt/fpocket/man
|
||||
COPY headers /opt/fpocket/headers
|
||||
COPY obj /opt/fpocket/obj
|
||||
COPY scripts /opt/fpocket/scripts
|
||||
COPY bin /opt/fpocket/bin
|
||||
COPY plugins/LINUXAMD64 /opt/fpocket/plugins/LINUXAMD64
|
||||
COPY plugins/include /opt/fpocket/plugins/include
|
||||
COPY plugins/noarch /opt/fpocket/plugins/noarch
|
||||
|
||||
WORKDIR /opt/fpocket
|
||||
|
||||
RUN make && make install && make clean
|
||||
USER fpocket
|
||||
WORKDIR /tmp
|
||||
CMD ["fpocket"]
|
||||
@@ -81,10 +81,10 @@ docker build -t fpocket/fpocket .
|
||||
This will build fpocket into your local fpocket/fpocket image. You can then run fpocket/mdpocket etc using:
|
||||
|
||||
```bash
|
||||
docker run -v `pwd`:/WORKDIR fpocket/fpocket fpocket -f data/sample/1UYD.pdb
|
||||
docker run -v `pwd`:/workdir fpocket/fpocket fpocket -f /workdir/yourfile.pdb
|
||||
```
|
||||
|
||||
Here you mount your current directory with your input files into the preconfigured `/WORKDIR` in the docker container and then run fpocket on a file in that mounted folder.
|
||||
Here you mount your current directory with your input files into the preconfigured `/workdir` in the docker container and then run fpocket on a file in that mounted folder. Make sure that the folder is writeable to others if you run it through docker.
|
||||
|
||||
### Installing
|
||||
|
||||
@@ -107,6 +107,11 @@ make ARCH=MACOSXX86_64
|
||||
sudo make install
|
||||
```
|
||||
|
||||
For M1 and M2, use the MACOSXARM64 architecture:
|
||||
```
|
||||
ARCH=MACOSXARM64 make
|
||||
```
|
||||
|
||||
#### Using conda
|
||||
|
||||
There's also a conda package of fpocket available thanks to Simon Bray. You can install fpocket using conda with:
|
||||
|
||||
9565
data/sample/123abc.cif
Normal file
9565
data/sample/123abc.cif
Normal file
File diff suppressed because it is too large
Load Diff
10785
data/sample/6a5k.cif
Normal file
10785
data/sample/6a5k.cif
Normal file
File diff suppressed because it is too large
Load Diff
13962
data/sample/7z9t.cif
Normal file
13962
data/sample/7z9t.cif
Normal file
File diff suppressed because it is too large
Load Diff
@@ -37,12 +37,14 @@ typedef struct s_atm
|
||||
char name[5], /**< Atom name */
|
||||
type[7], /**< Atom type */
|
||||
chain[16], /**< Chain name */
|
||||
label_asym_id[16],
|
||||
symbol[3], /**< Chemical symbol of the atom */
|
||||
res_name[8]; /**< Atom residue name */
|
||||
|
||||
int id, /**< Atom id */
|
||||
seen, /**< Say if we have seen this atom during a neighbor search */
|
||||
res_id, /**< Atom residue ID */
|
||||
label_seq_id, /**<MMCIF label seq ID*/
|
||||
atype,
|
||||
charge, /**< Atom charge */
|
||||
abpa; /**< 1 if atom is an abpa, 0 otherwise*/
|
||||
|
||||
@@ -81,8 +81,8 @@ typedef struct s_desc
|
||||
characterChain2, /**< 0 if protein, 1 if nucl acid pocket, 2 if HETATM pocket*/
|
||||
numResChain1, /**<number of resdiues on chain 1*/
|
||||
numResChain2; /**<number of res on chain 2*/
|
||||
char nameChain1[2], /**<name of the first chain in contact with the pocket*/
|
||||
nameChain2[2]; /**<name of the second chain in contact with the pocket, if there is*/
|
||||
char nameChain1[255], /**<name of the first chain in contact with the pocket*/
|
||||
nameChain2[255]; /**<name of the second chain in contact with the pocket, if there is*/
|
||||
char ligTag[8]; /**<het atom tag of ligands situated in the pocket*/
|
||||
|
||||
} s_desc ;
|
||||
|
||||
@@ -33,7 +33,7 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI
|
||||
|
||||
/* ------------------------------- PUBLIC MACROS ---------------------------- */
|
||||
|
||||
#define M_MAX_PDB_NAME_LEN 200 /**< maximum pdb filename length*/
|
||||
#define M_MAX_PDB_NAME_LEN 2000 /**< maximum pdb filename length*/
|
||||
#define M_MAX_CUSTOM_POCKET_LEN 8000 /** maximum length for a custom pocket string*/
|
||||
#define M_SIGN 1
|
||||
#define M_NO_SIGN 0
|
||||
|
||||
@@ -28,6 +28,6 @@ void write_pqr_atom_line(FILE *f, const char *rec_name, int id, const char *atom
|
||||
|
||||
void write_mmcif_atom_line(FILE *f, const char rec_name[], int id, const char atom_name[],
|
||||
char alt_loc, const char res_name[], const char chain[],
|
||||
int res_id, const char insert, float x, float y, float z, float occ,
|
||||
int res_id, const char label_asym_id[],int label_seq_id, const char insert, float x, float y, float z, float occ,
|
||||
float bfactor, int abpa, const char *symbol, int charge,float abpa_prob) ;
|
||||
#endif
|
||||
|
||||
@@ -40,6 +40,7 @@ void write_pdb_atoms(FILE *f, s_atm *atoms, int natoms) ;
|
||||
void write_each_pocket_for_DB(const char out_path[], c_lst_pockets *pockets,s_pdb *pdb);
|
||||
void write_pocket_pqr_DB(const char out[], s_pocket *pocket);
|
||||
void write_pocket_pdb_DB(const char out[], s_pocket *pocket,s_pdb *pdb);
|
||||
void write_pocket_mmcif_DB(const char out[], s_pocket *pocket, s_pdb *pdb);
|
||||
|
||||
void write_mmcif_atoms(FILE *f, s_atm *atoms, int natoms);
|
||||
void write_pockets_single_mmcif(const char out[], s_pdb *pdb, c_lst_pockets *pockets);
|
||||
|
||||
2
makefile
2
makefile
@@ -1,7 +1,7 @@
|
||||
#------------------------------------------------------------
|
||||
# Makefile.
|
||||
#------------------------------------------------------------
|
||||
#ARCH = MACOSXX86_64
|
||||
# ARCH = MACOSXX86_64
|
||||
ARCH = LINUXAMD64
|
||||
export ARCH
|
||||
|
||||
|
||||
Binary file not shown.
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BIN
plugins/MACOSXARM64/molfile/abinitplugin.so
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BIN
plugins/MACOSXARM64/molfile/abinitplugin.so
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plugins/MACOSXARM64/molfile/amiraplugin.so
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plugins/MACOSXARM64/molfile/amiraplugin.so
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plugins/MACOSXARM64/molfile/avsplugin.so
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plugins/MACOSXARM64/molfile/avsplugin.so
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plugins/MACOSXARM64/molfile/babelplugin.so
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plugins/MACOSXARM64/molfile/babelplugin.so
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plugins/MACOSXARM64/molfile/basissetplugin.so
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plugins/MACOSXARM64/molfile/basissetplugin.so
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plugins/MACOSXARM64/molfile/bgfplugin.so
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plugins/MACOSXARM64/molfile/bgfplugin.so
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plugins/MACOSXARM64/molfile/binposplugin.so
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plugins/MACOSXARM64/molfile/binposplugin.so
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plugins/MACOSXARM64/molfile/biomoccaplugin.so
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plugins/MACOSXARM64/molfile/biomoccaplugin.so
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plugins/MACOSXARM64/molfile/brixplugin.so
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plugins/MACOSXARM64/molfile/brixplugin.so
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plugins/MACOSXARM64/molfile/carplugin.so
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plugins/MACOSXARM64/molfile/carplugin.so
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plugins/MACOSXARM64/molfile/ccp4plugin.so
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plugins/MACOSXARM64/molfile/ccp4plugin.so
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plugins/MACOSXARM64/molfile/corplugin.so
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plugins/MACOSXARM64/molfile/corplugin.so
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plugins/MACOSXARM64/molfile/cpmdplugin.so
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plugins/MACOSXARM64/molfile/cpmdplugin.so
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plugins/MACOSXARM64/molfile/crdplugin.so
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plugins/MACOSXARM64/molfile/crdplugin.so
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plugins/MACOSXARM64/molfile/cubeplugin.so
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plugins/MACOSXARM64/molfile/cubeplugin.so
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plugins/MACOSXARM64/molfile/dcdplugin.so
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plugins/MACOSXARM64/molfile/dcdplugin.so
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plugins/MACOSXARM64/molfile/dlpolyplugin.so
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plugins/MACOSXARM64/molfile/dlpolyplugin.so
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BIN
plugins/MACOSXARM64/molfile/dsn6plugin.so
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plugins/MACOSXARM64/molfile/dsn6plugin.so
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plugins/MACOSXARM64/molfile/dtrplugin.so
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plugins/MACOSXARM64/molfile/dtrplugin.so
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BIN
plugins/MACOSXARM64/molfile/dxplugin.so
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plugins/MACOSXARM64/molfile/dxplugin.so
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BIN
plugins/MACOSXARM64/molfile/edmplugin.so
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plugins/MACOSXARM64/molfile/edmplugin.so
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BIN
plugins/MACOSXARM64/molfile/fs4plugin.so
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BIN
plugins/MACOSXARM64/molfile/fs4plugin.so
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BIN
plugins/MACOSXARM64/molfile/gamessplugin.so
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BIN
plugins/MACOSXARM64/molfile/gamessplugin.so
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BIN
plugins/MACOSXARM64/molfile/graspplugin.so
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BIN
plugins/MACOSXARM64/molfile/graspplugin.so
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BIN
plugins/MACOSXARM64/molfile/grdplugin.so
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BIN
plugins/MACOSXARM64/molfile/grdplugin.so
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BIN
plugins/MACOSXARM64/molfile/gridplugin.so
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BIN
plugins/MACOSXARM64/molfile/gridplugin.so
Executable file
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BIN
plugins/MACOSXARM64/molfile/gromacsplugin.so
Executable file
BIN
plugins/MACOSXARM64/molfile/gromacsplugin.so
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BIN
plugins/MACOSXARM64/molfile/jsplugin.so
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BIN
plugins/MACOSXARM64/molfile/jsplugin.so
Executable file
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BIN
plugins/MACOSXARM64/molfile/lammpsplugin.so
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BIN
plugins/MACOSXARM64/molfile/lammpsplugin.so
Executable file
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BIN
plugins/MACOSXARM64/molfile/libmolfile_plugin.a
Normal file
BIN
plugins/MACOSXARM64/molfile/libmolfile_plugin.a
Normal file
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415
plugins/MACOSXARM64/molfile/libmolfile_plugin.h
Normal file
415
plugins/MACOSXARM64/molfile/libmolfile_plugin.h
Normal file
@@ -0,0 +1,415 @@
|
||||
#ifndef LIBMOLFILE_PLUGIN_H
|
||||
#define LIBMOLFILE_PLUGIN_H
|
||||
#include "vmdplugin.h"
|
||||
|
||||
#ifdef __cplusplus
|
||||
extern "C" {
|
||||
#endif
|
||||
|
||||
extern int molfile_abinitplugin_init(void);
|
||||
extern int molfile_abinitplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_abinitplugin_fini(void);
|
||||
extern int molfile_amiraplugin_init(void);
|
||||
extern int molfile_amiraplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_amiraplugin_fini(void);
|
||||
extern int molfile_avsplugin_init(void);
|
||||
extern int molfile_avsplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_avsplugin_fini(void);
|
||||
extern int molfile_babelplugin_init(void);
|
||||
extern int molfile_babelplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_babelplugin_fini(void);
|
||||
extern int molfile_basissetplugin_init(void);
|
||||
extern int molfile_basissetplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_basissetplugin_fini(void);
|
||||
extern int molfile_bgfplugin_init(void);
|
||||
extern int molfile_bgfplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_bgfplugin_fini(void);
|
||||
extern int molfile_binposplugin_init(void);
|
||||
extern int molfile_binposplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_binposplugin_fini(void);
|
||||
extern int molfile_biomoccaplugin_init(void);
|
||||
extern int molfile_biomoccaplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_biomoccaplugin_fini(void);
|
||||
extern int molfile_brixplugin_init(void);
|
||||
extern int molfile_brixplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_brixplugin_fini(void);
|
||||
extern int molfile_carplugin_init(void);
|
||||
extern int molfile_carplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_carplugin_fini(void);
|
||||
extern int molfile_ccp4plugin_init(void);
|
||||
extern int molfile_ccp4plugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_ccp4plugin_fini(void);
|
||||
extern int molfile_corplugin_init(void);
|
||||
extern int molfile_corplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_corplugin_fini(void);
|
||||
extern int molfile_cpmdplugin_init(void);
|
||||
extern int molfile_cpmdplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_cpmdplugin_fini(void);
|
||||
extern int molfile_crdplugin_init(void);
|
||||
extern int molfile_crdplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_crdplugin_fini(void);
|
||||
extern int molfile_cubeplugin_init(void);
|
||||
extern int molfile_cubeplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_cubeplugin_fini(void);
|
||||
extern int molfile_dcdplugin_init(void);
|
||||
extern int molfile_dcdplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_dcdplugin_fini(void);
|
||||
extern int molfile_dlpolyplugin_init(void);
|
||||
extern int molfile_dlpolyplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_dlpolyplugin_fini(void);
|
||||
extern int molfile_dsn6plugin_init(void);
|
||||
extern int molfile_dsn6plugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_dsn6plugin_fini(void);
|
||||
extern int molfile_dxplugin_init(void);
|
||||
extern int molfile_dxplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_dxplugin_fini(void);
|
||||
extern int molfile_edmplugin_init(void);
|
||||
extern int molfile_edmplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_edmplugin_fini(void);
|
||||
extern int molfile_fs4plugin_init(void);
|
||||
extern int molfile_fs4plugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_fs4plugin_fini(void);
|
||||
extern int molfile_gamessplugin_init(void);
|
||||
extern int molfile_gamessplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_gamessplugin_fini(void);
|
||||
extern int molfile_graspplugin_init(void);
|
||||
extern int molfile_graspplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_graspplugin_fini(void);
|
||||
extern int molfile_grdplugin_init(void);
|
||||
extern int molfile_grdplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_grdplugin_fini(void);
|
||||
extern int molfile_gridplugin_init(void);
|
||||
extern int molfile_gridplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_gridplugin_fini(void);
|
||||
extern int molfile_gromacsplugin_init(void);
|
||||
extern int molfile_gromacsplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_gromacsplugin_fini(void);
|
||||
extern int molfile_jsplugin_init(void);
|
||||
extern int molfile_jsplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_jsplugin_fini(void);
|
||||
extern int molfile_lammpsplugin_init(void);
|
||||
extern int molfile_lammpsplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_lammpsplugin_fini(void);
|
||||
extern int molfile_mapplugin_init(void);
|
||||
extern int molfile_mapplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_mapplugin_fini(void);
|
||||
extern int molfile_mdfplugin_init(void);
|
||||
extern int molfile_mdfplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_mdfplugin_fini(void);
|
||||
extern int molfile_mol2plugin_init(void);
|
||||
extern int molfile_mol2plugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_mol2plugin_fini(void);
|
||||
extern int molfile_moldenplugin_init(void);
|
||||
extern int molfile_moldenplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_moldenplugin_fini(void);
|
||||
extern int molfile_molemeshplugin_init(void);
|
||||
extern int molfile_molemeshplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_molemeshplugin_fini(void);
|
||||
extern int molfile_msmsplugin_init(void);
|
||||
extern int molfile_msmsplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_msmsplugin_fini(void);
|
||||
extern int molfile_namdbinplugin_init(void);
|
||||
extern int molfile_namdbinplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_namdbinplugin_fini(void);
|
||||
extern int molfile_offplugin_init(void);
|
||||
extern int molfile_offplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_offplugin_fini(void);
|
||||
extern int molfile_parm7plugin_init(void);
|
||||
extern int molfile_parm7plugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_parm7plugin_fini(void);
|
||||
extern int molfile_parmplugin_init(void);
|
||||
extern int molfile_parmplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_parmplugin_fini(void);
|
||||
extern int molfile_pbeqplugin_init(void);
|
||||
extern int molfile_pbeqplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_pbeqplugin_fini(void);
|
||||
extern int molfile_pdbplugin_init(void);
|
||||
extern int molfile_pdbplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_pdbplugin_fini(void);
|
||||
extern int molfile_pdbxplugin_init(void);
|
||||
extern int molfile_pdbxplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_pdbxplugin_fini(void);
|
||||
extern int molfile_phiplugin_init(void);
|
||||
extern int molfile_phiplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_phiplugin_fini(void);
|
||||
extern int molfile_pltplugin_init(void);
|
||||
extern int molfile_pltplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_pltplugin_fini(void);
|
||||
extern int molfile_plyplugin_init(void);
|
||||
extern int molfile_plyplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_plyplugin_fini(void);
|
||||
extern int molfile_pqrplugin_init(void);
|
||||
extern int molfile_pqrplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_pqrplugin_fini(void);
|
||||
extern int molfile_psfplugin_init(void);
|
||||
extern int molfile_psfplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_psfplugin_fini(void);
|
||||
extern int molfile_raster3dplugin_init(void);
|
||||
extern int molfile_raster3dplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_raster3dplugin_fini(void);
|
||||
extern int molfile_rst7plugin_init(void);
|
||||
extern int molfile_rst7plugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_rst7plugin_fini(void);
|
||||
extern int molfile_situsplugin_init(void);
|
||||
extern int molfile_situsplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_situsplugin_fini(void);
|
||||
extern int molfile_spiderplugin_init(void);
|
||||
extern int molfile_spiderplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_spiderplugin_fini(void);
|
||||
extern int molfile_stlplugin_init(void);
|
||||
extern int molfile_stlplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_stlplugin_fini(void);
|
||||
extern int molfile_tinkerplugin_init(void);
|
||||
extern int molfile_tinkerplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_tinkerplugin_fini(void);
|
||||
extern int molfile_uhbdplugin_init(void);
|
||||
extern int molfile_uhbdplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_uhbdplugin_fini(void);
|
||||
extern int molfile_vaspchgcarplugin_init(void);
|
||||
extern int molfile_vaspchgcarplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_vaspchgcarplugin_fini(void);
|
||||
extern int molfile_vaspoutcarplugin_init(void);
|
||||
extern int molfile_vaspoutcarplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_vaspoutcarplugin_fini(void);
|
||||
extern int molfile_vaspparchgplugin_init(void);
|
||||
extern int molfile_vaspparchgplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_vaspparchgplugin_fini(void);
|
||||
extern int molfile_vaspposcarplugin_init(void);
|
||||
extern int molfile_vaspposcarplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_vaspposcarplugin_fini(void);
|
||||
extern int molfile_vasp5xdatcarplugin_init(void);
|
||||
extern int molfile_vasp5xdatcarplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_vasp5xdatcarplugin_fini(void);
|
||||
extern int molfile_vaspxdatcarplugin_init(void);
|
||||
extern int molfile_vaspxdatcarplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_vaspxdatcarplugin_fini(void);
|
||||
extern int molfile_vaspxmlplugin_init(void);
|
||||
extern int molfile_vaspxmlplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_vaspxmlplugin_fini(void);
|
||||
extern int molfile_vtkplugin_init(void);
|
||||
extern int molfile_vtkplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_vtkplugin_fini(void);
|
||||
extern int molfile_xbgfplugin_init(void);
|
||||
extern int molfile_xbgfplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_xbgfplugin_fini(void);
|
||||
extern int molfile_xsfplugin_init(void);
|
||||
extern int molfile_xsfplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_xsfplugin_fini(void);
|
||||
extern int molfile_xyzplugin_init(void);
|
||||
extern int molfile_xyzplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_xyzplugin_fini(void);
|
||||
extern int molfile_dtrplugin_init(void);
|
||||
extern int molfile_dtrplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_dtrplugin_fini(void);
|
||||
extern int molfile_maeffplugin_init(void);
|
||||
extern int molfile_maeffplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_maeffplugin_fini(void);
|
||||
|
||||
#define MOLFILE_INIT_ALL \
|
||||
molfile_abinitplugin_init(); \
|
||||
molfile_amiraplugin_init(); \
|
||||
molfile_avsplugin_init(); \
|
||||
molfile_babelplugin_init(); \
|
||||
molfile_basissetplugin_init(); \
|
||||
molfile_bgfplugin_init(); \
|
||||
molfile_binposplugin_init(); \
|
||||
molfile_biomoccaplugin_init(); \
|
||||
molfile_brixplugin_init(); \
|
||||
molfile_carplugin_init(); \
|
||||
molfile_ccp4plugin_init(); \
|
||||
molfile_corplugin_init(); \
|
||||
molfile_cpmdplugin_init(); \
|
||||
molfile_crdplugin_init(); \
|
||||
molfile_cubeplugin_init(); \
|
||||
molfile_dcdplugin_init(); \
|
||||
molfile_dlpolyplugin_init(); \
|
||||
molfile_dsn6plugin_init(); \
|
||||
molfile_dxplugin_init(); \
|
||||
molfile_edmplugin_init(); \
|
||||
molfile_fs4plugin_init(); \
|
||||
molfile_gamessplugin_init(); \
|
||||
molfile_graspplugin_init(); \
|
||||
molfile_grdplugin_init(); \
|
||||
molfile_gridplugin_init(); \
|
||||
molfile_gromacsplugin_init(); \
|
||||
molfile_jsplugin_init(); \
|
||||
molfile_lammpsplugin_init(); \
|
||||
molfile_mapplugin_init(); \
|
||||
molfile_mdfplugin_init(); \
|
||||
molfile_mol2plugin_init(); \
|
||||
molfile_moldenplugin_init(); \
|
||||
molfile_molemeshplugin_init(); \
|
||||
molfile_msmsplugin_init(); \
|
||||
molfile_namdbinplugin_init(); \
|
||||
molfile_offplugin_init(); \
|
||||
molfile_parm7plugin_init(); \
|
||||
molfile_parmplugin_init(); \
|
||||
molfile_pbeqplugin_init(); \
|
||||
molfile_pdbplugin_init(); \
|
||||
molfile_pdbxplugin_init(); \
|
||||
molfile_phiplugin_init(); \
|
||||
molfile_pltplugin_init(); \
|
||||
molfile_plyplugin_init(); \
|
||||
molfile_pqrplugin_init(); \
|
||||
molfile_psfplugin_init(); \
|
||||
molfile_raster3dplugin_init(); \
|
||||
molfile_rst7plugin_init(); \
|
||||
molfile_situsplugin_init(); \
|
||||
molfile_spiderplugin_init(); \
|
||||
molfile_stlplugin_init(); \
|
||||
molfile_tinkerplugin_init(); \
|
||||
molfile_uhbdplugin_init(); \
|
||||
molfile_vaspchgcarplugin_init(); \
|
||||
molfile_vaspoutcarplugin_init(); \
|
||||
molfile_vaspparchgplugin_init(); \
|
||||
molfile_vaspposcarplugin_init(); \
|
||||
molfile_vasp5xdatcarplugin_init(); \
|
||||
molfile_vaspxdatcarplugin_init(); \
|
||||
molfile_vaspxmlplugin_init(); \
|
||||
molfile_vtkplugin_init(); \
|
||||
molfile_xbgfplugin_init(); \
|
||||
molfile_xsfplugin_init(); \
|
||||
molfile_xyzplugin_init(); \
|
||||
molfile_dtrplugin_init(); \
|
||||
molfile_maeffplugin_init(); \
|
||||
|
||||
#define MOLFILE_REGISTER_ALL(v, cb) \
|
||||
molfile_abinitplugin_register(v, cb); \
|
||||
molfile_amiraplugin_register(v, cb); \
|
||||
molfile_avsplugin_register(v, cb); \
|
||||
molfile_babelplugin_register(v, cb); \
|
||||
molfile_basissetplugin_register(v, cb); \
|
||||
molfile_bgfplugin_register(v, cb); \
|
||||
molfile_binposplugin_register(v, cb); \
|
||||
molfile_biomoccaplugin_register(v, cb); \
|
||||
molfile_brixplugin_register(v, cb); \
|
||||
molfile_carplugin_register(v, cb); \
|
||||
molfile_ccp4plugin_register(v, cb); \
|
||||
molfile_corplugin_register(v, cb); \
|
||||
molfile_cpmdplugin_register(v, cb); \
|
||||
molfile_crdplugin_register(v, cb); \
|
||||
molfile_cubeplugin_register(v, cb); \
|
||||
molfile_dcdplugin_register(v, cb); \
|
||||
molfile_dlpolyplugin_register(v, cb); \
|
||||
molfile_dsn6plugin_register(v, cb); \
|
||||
molfile_dxplugin_register(v, cb); \
|
||||
molfile_edmplugin_register(v, cb); \
|
||||
molfile_fs4plugin_register(v, cb); \
|
||||
molfile_gamessplugin_register(v, cb); \
|
||||
molfile_graspplugin_register(v, cb); \
|
||||
molfile_grdplugin_register(v, cb); \
|
||||
molfile_gridplugin_register(v, cb); \
|
||||
molfile_gromacsplugin_register(v, cb); \
|
||||
molfile_jsplugin_register(v, cb); \
|
||||
molfile_lammpsplugin_register(v, cb); \
|
||||
molfile_mapplugin_register(v, cb); \
|
||||
molfile_mdfplugin_register(v, cb); \
|
||||
molfile_mol2plugin_register(v, cb); \
|
||||
molfile_moldenplugin_register(v, cb); \
|
||||
molfile_molemeshplugin_register(v, cb); \
|
||||
molfile_msmsplugin_register(v, cb); \
|
||||
molfile_namdbinplugin_register(v, cb); \
|
||||
molfile_offplugin_register(v, cb); \
|
||||
molfile_parm7plugin_register(v, cb); \
|
||||
molfile_parmplugin_register(v, cb); \
|
||||
molfile_pbeqplugin_register(v, cb); \
|
||||
molfile_pdbplugin_register(v, cb); \
|
||||
molfile_pdbxplugin_register(v, cb); \
|
||||
molfile_phiplugin_register(v, cb); \
|
||||
molfile_pltplugin_register(v, cb); \
|
||||
molfile_plyplugin_register(v, cb); \
|
||||
molfile_pqrplugin_register(v, cb); \
|
||||
molfile_psfplugin_register(v, cb); \
|
||||
molfile_raster3dplugin_register(v, cb); \
|
||||
molfile_rst7plugin_register(v, cb); \
|
||||
molfile_situsplugin_register(v, cb); \
|
||||
molfile_spiderplugin_register(v, cb); \
|
||||
molfile_stlplugin_register(v, cb); \
|
||||
molfile_tinkerplugin_register(v, cb); \
|
||||
molfile_uhbdplugin_register(v, cb); \
|
||||
molfile_vaspchgcarplugin_register(v, cb); \
|
||||
molfile_vaspoutcarplugin_register(v, cb); \
|
||||
molfile_vaspparchgplugin_register(v, cb); \
|
||||
molfile_vaspposcarplugin_register(v, cb); \
|
||||
molfile_vasp5xdatcarplugin_register(v, cb); \
|
||||
molfile_vaspxdatcarplugin_register(v, cb); \
|
||||
molfile_vaspxmlplugin_register(v, cb); \
|
||||
molfile_vtkplugin_register(v, cb); \
|
||||
molfile_xbgfplugin_register(v, cb); \
|
||||
molfile_xsfplugin_register(v, cb); \
|
||||
molfile_xyzplugin_register(v, cb); \
|
||||
molfile_dtrplugin_register(v, cb); \
|
||||
molfile_maeffplugin_register(v, cb); \
|
||||
|
||||
#define MOLFILE_FINI_ALL \
|
||||
molfile_abinitplugin_fini(); \
|
||||
molfile_amiraplugin_fini(); \
|
||||
molfile_avsplugin_fini(); \
|
||||
molfile_babelplugin_fini(); \
|
||||
molfile_basissetplugin_fini(); \
|
||||
molfile_bgfplugin_fini(); \
|
||||
molfile_binposplugin_fini(); \
|
||||
molfile_biomoccaplugin_fini(); \
|
||||
molfile_brixplugin_fini(); \
|
||||
molfile_carplugin_fini(); \
|
||||
molfile_ccp4plugin_fini(); \
|
||||
molfile_corplugin_fini(); \
|
||||
molfile_cpmdplugin_fini(); \
|
||||
molfile_crdplugin_fini(); \
|
||||
molfile_cubeplugin_fini(); \
|
||||
molfile_dcdplugin_fini(); \
|
||||
molfile_dlpolyplugin_fini(); \
|
||||
molfile_dsn6plugin_fini(); \
|
||||
molfile_dxplugin_fini(); \
|
||||
molfile_edmplugin_fini(); \
|
||||
molfile_fs4plugin_fini(); \
|
||||
molfile_gamessplugin_fini(); \
|
||||
molfile_graspplugin_fini(); \
|
||||
molfile_grdplugin_fini(); \
|
||||
molfile_gridplugin_fini(); \
|
||||
molfile_gromacsplugin_fini(); \
|
||||
molfile_jsplugin_fini(); \
|
||||
molfile_lammpsplugin_fini(); \
|
||||
molfile_mapplugin_fini(); \
|
||||
molfile_mdfplugin_fini(); \
|
||||
molfile_mol2plugin_fini(); \
|
||||
molfile_moldenplugin_fini(); \
|
||||
molfile_molemeshplugin_fini(); \
|
||||
molfile_msmsplugin_fini(); \
|
||||
molfile_namdbinplugin_fini(); \
|
||||
molfile_offplugin_fini(); \
|
||||
molfile_parm7plugin_fini(); \
|
||||
molfile_parmplugin_fini(); \
|
||||
molfile_pbeqplugin_fini(); \
|
||||
molfile_pdbplugin_fini(); \
|
||||
molfile_pdbxplugin_fini(); \
|
||||
molfile_phiplugin_fini(); \
|
||||
molfile_pltplugin_fini(); \
|
||||
molfile_plyplugin_fini(); \
|
||||
molfile_pqrplugin_fini(); \
|
||||
molfile_psfplugin_fini(); \
|
||||
molfile_raster3dplugin_fini(); \
|
||||
molfile_rst7plugin_fini(); \
|
||||
molfile_situsplugin_fini(); \
|
||||
molfile_spiderplugin_fini(); \
|
||||
molfile_stlplugin_fini(); \
|
||||
molfile_tinkerplugin_fini(); \
|
||||
molfile_uhbdplugin_fini(); \
|
||||
molfile_vaspchgcarplugin_fini(); \
|
||||
molfile_vaspoutcarplugin_fini(); \
|
||||
molfile_vaspparchgplugin_fini(); \
|
||||
molfile_vaspposcarplugin_fini(); \
|
||||
molfile_vasp5xdatcarplugin_fini(); \
|
||||
molfile_vaspxdatcarplugin_fini(); \
|
||||
molfile_vaspxmlplugin_fini(); \
|
||||
molfile_vtkplugin_fini(); \
|
||||
molfile_xbgfplugin_fini(); \
|
||||
molfile_xsfplugin_fini(); \
|
||||
molfile_xyzplugin_fini(); \
|
||||
molfile_dtrplugin_fini(); \
|
||||
molfile_maeffplugin_fini(); \
|
||||
|
||||
#ifdef __cplusplus
|
||||
}
|
||||
#endif
|
||||
#endif
|
||||
BIN
plugins/MACOSXARM64/molfile/maeffplugin.so
Executable file
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plugins/MACOSXARM64/molfile/maeffplugin.so
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plugins/MACOSXARM64/molfile/mapplugin.so
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plugins/MACOSXARM64/molfile/mapplugin.so
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plugins/MACOSXARM64/molfile/mdfplugin.so
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plugins/MACOSXARM64/molfile/mdfplugin.so
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plugins/MACOSXARM64/molfile/mol2plugin.so
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plugins/MACOSXARM64/molfile/mol2plugin.so
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plugins/MACOSXARM64/molfile/moldenplugin.so
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plugins/MACOSXARM64/molfile/moldenplugin.so
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plugins/MACOSXARM64/molfile/molemeshplugin.so
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plugins/MACOSXARM64/molfile/molemeshplugin.so
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plugins/MACOSXARM64/molfile/msmsplugin.so
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plugins/MACOSXARM64/molfile/msmsplugin.so
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plugins/MACOSXARM64/molfile/namdbinplugin.so
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plugins/MACOSXARM64/molfile/namdbinplugin.so
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plugins/MACOSXARM64/molfile/offplugin.so
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plugins/MACOSXARM64/molfile/offplugin.so
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plugins/MACOSXARM64/molfile/parm7plugin.so
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plugins/MACOSXARM64/molfile/parm7plugin.so
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plugins/MACOSXARM64/molfile/parmplugin.so
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plugins/MACOSXARM64/molfile/parmplugin.so
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plugins/MACOSXARM64/molfile/pbeqplugin.so
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plugins/MACOSXARM64/molfile/pbeqplugin.so
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plugins/MACOSXARM64/molfile/pdbplugin.so
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plugins/MACOSXARM64/molfile/pdbplugin.so
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plugins/MACOSXARM64/molfile/pdbxplugin.so
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plugins/MACOSXARM64/molfile/pdbxplugin.so
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plugins/MACOSXARM64/molfile/phiplugin.so
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plugins/MACOSXARM64/molfile/phiplugin.so
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plugins/MACOSXARM64/molfile/pltplugin.so
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plugins/MACOSXARM64/molfile/pltplugin.so
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plugins/MACOSXARM64/molfile/plyplugin.so
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plugins/MACOSXARM64/molfile/plyplugin.so
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plugins/MACOSXARM64/molfile/pqrplugin.so
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plugins/MACOSXARM64/molfile/pqrplugin.so
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plugins/MACOSXARM64/molfile/psfplugin.so
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plugins/MACOSXARM64/molfile/psfplugin.so
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plugins/MACOSXARM64/molfile/raster3dplugin.so
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plugins/MACOSXARM64/molfile/raster3dplugin.so
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plugins/MACOSXARM64/molfile/rst7plugin.so
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plugins/MACOSXARM64/molfile/rst7plugin.so
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plugins/MACOSXARM64/molfile/situsplugin.so
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plugins/MACOSXARM64/molfile/situsplugin.so
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plugins/MACOSXARM64/molfile/spiderplugin.so
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plugins/MACOSXARM64/molfile/spiderplugin.so
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plugins/MACOSXARM64/molfile/stlplugin.so
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plugins/MACOSXARM64/molfile/stlplugin.so
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plugins/MACOSXARM64/molfile/tinkerplugin.so
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plugins/MACOSXARM64/molfile/tinkerplugin.so
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plugins/MACOSXARM64/molfile/uhbdplugin.so
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plugins/MACOSXARM64/molfile/uhbdplugin.so
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plugins/MACOSXARM64/molfile/vasp5xdatcarplugin.so
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plugins/MACOSXARM64/molfile/vasp5xdatcarplugin.so
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plugins/MACOSXARM64/molfile/vaspchgcarplugin.so
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plugins/MACOSXARM64/molfile/vaspchgcarplugin.so
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plugins/MACOSXARM64/molfile/vaspoutcarplugin.so
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plugins/MACOSXARM64/molfile/vaspoutcarplugin.so
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plugins/MACOSXARM64/molfile/vaspparchgplugin.so
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plugins/MACOSXARM64/molfile/vaspparchgplugin.so
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plugins/MACOSXARM64/molfile/vaspposcarplugin.so
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plugins/MACOSXARM64/molfile/vaspposcarplugin.so
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plugins/MACOSXARM64/molfile/vaspxdatcarplugin.so
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plugins/MACOSXARM64/molfile/vaspxdatcarplugin.so
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plugins/MACOSXARM64/molfile/vaspxmlplugin.so
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plugins/MACOSXARM64/molfile/vaspxmlplugin.so
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plugins/MACOSXARM64/molfile/vtkplugin.so
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plugins/MACOSXARM64/molfile/vtkplugin.so
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plugins/MACOSXARM64/molfile/xbgfplugin.so
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plugins/MACOSXARM64/molfile/xbgfplugin.so
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plugins/MACOSXARM64/molfile/xsfplugin.so
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plugins/MACOSXARM64/molfile/xsfplugin.so
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plugins/MACOSXARM64/molfile/xyzplugin.so
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plugins/MACOSXARM64/molfile/xyzplugin.so
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@@ -65,7 +65,6 @@ s_desc* allocate_s_desc(void)
|
||||
s_desc *desc = (s_desc*)my_malloc(sizeof(s_desc)) ;
|
||||
|
||||
reset_desc(desc) ;
|
||||
|
||||
return desc ;
|
||||
}
|
||||
|
||||
@@ -364,7 +363,7 @@ void set_atom_based_descriptors(s_atm **atoms, int natoms, s_desc *desc,s_atm *a
|
||||
nb_res_ids = 0 ; /* Current number of residus */
|
||||
|
||||
int nb_polar_atm = 0 ;
|
||||
char curChainName[2];
|
||||
char *curChainName = (char*)my_malloc(255*sizeof(char));
|
||||
|
||||
if(atoms && natoms>1){
|
||||
firstatom=atoms[0];
|
||||
@@ -373,8 +372,8 @@ void set_atom_based_descriptors(s_atm **atoms, int natoms, s_desc *desc,s_atm *a
|
||||
if(element_in_std_res(firstatom->res_name)) desc->characterChain1=0;
|
||||
else if(element_in_nucl_acid(firstatom->res_name)) desc->characterChain1=1;
|
||||
else if(element_in_kept_res(firstatom->res_name)) desc->characterChain1=2;
|
||||
strncpy(desc->nameChain1,firstatom->chain,2);
|
||||
strncpy(curChainName,firstatom->chain,2);
|
||||
strcpy(desc->nameChain1,firstatom->chain);
|
||||
strcpy(curChainName,firstatom->chain);
|
||||
desc->numResChain1 = countResidues(all_atoms,all_natoms,firstatom->chain);
|
||||
|
||||
for(i = 0 ; i < natoms ; i++) {
|
||||
@@ -384,7 +383,7 @@ void set_atom_based_descriptors(s_atm **atoms, int natoms, s_desc *desc,s_atm *a
|
||||
desc->interChain = 1;
|
||||
if(!desc->numResChain2){
|
||||
desc->numResChain2 = countResidues(all_atoms,all_natoms,curatom->chain);
|
||||
strncpy(curChainName,curatom->chain,1);
|
||||
strcpy(curChainName,curatom->chain);
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
@@ -260,11 +260,13 @@ float pte_get_enegativity(const char *symbol)
|
||||
*/
|
||||
char *pte_get_element_from_number(int atomicnumber)
|
||||
{
|
||||
|
||||
char *tmp=malloc(sizeof(char)*3) ;
|
||||
if(atomicnumber>0 && atomicnumber<112){
|
||||
|
||||
tmp[0] = ST_pte_symbol[atomicnumber][0] ;
|
||||
tmp[1] = ST_pte_symbol[atomicnumber][1] ;
|
||||
tmp[2]='\0';
|
||||
return tmp;
|
||||
} else {
|
||||
tmp[0]='-';
|
||||
|
||||
@@ -63,7 +63,7 @@ s_pdb *open_mmcif(char *fpath, const char *ligan, const int keep_lig, int model_
|
||||
void *h_in;
|
||||
molfile_timestep_t ts_in;
|
||||
molfile_atom_t *at_in;
|
||||
int optflags = 0x0040;
|
||||
int optflags[] = {0x0001,0x0040};
|
||||
int rc;
|
||||
int rc2;
|
||||
int j;
|
||||
@@ -75,7 +75,7 @@ s_pdb *open_mmcif(char *fpath, const char *ligan, const int keep_lig, int model_
|
||||
}
|
||||
at_in = (molfile_atom_t *)malloc(inatoms * sizeof(molfile_atom_t));
|
||||
ts_in.coords = (float *)malloc(3 * inatoms * sizeof(float)); /*allocating space for the coords*/
|
||||
rc2 = api->read_structure(h_in, &optflags, at_in);
|
||||
rc2 = api->read_structure(h_in, optflags, at_in);
|
||||
rc = api->read_next_timestep(h_in, inatoms, &ts_in);
|
||||
if (!model_number)
|
||||
model_number = 1;
|
||||
@@ -124,9 +124,13 @@ s_pdb *open_mmcif(char *fpath, const char *ligan, const int keep_lig, int model_
|
||||
if (par->xlig_resnumber > -1)
|
||||
{
|
||||
|
||||
if (((is_ligand(par->chain_as_ligand, at_in[i].chain_auth,par->n_chains_as_ligand)) || (par->xlig_chain_code !=NULL && at_in[i].chain_auth[0] == par->xlig_chain_code[0] && at_in[i].resid == par->xlig_resnumber && par->xlig_resname[0] == at_in[i].resname[0] && par->xlig_resname[1] == at_in[i].resname[1] && par->xlig_resname[2] == at_in[i].resname[2]) || (par->xlig_chain_code!=NULL && at_in[i].chain_auth[0] == par->xlig_chain_code[0] && at_in[i].resid_auth == par->xlig_resnumber && par->xlig_resname[0] == at_in[i].resname[0] && par->xlig_resname[1] == at_in[i].resname[1] && par->xlig_resname[2] == at_in[i].resname[2])))
|
||||
// if (((is_ligand(par->chain_as_ligand, at_in[i].chain_auth,par->n_chains_as_ligand)) || (par->xlig_chain_code !=NULL && at_in[i].chain_auth[0] == par->xlig_chain_code[0] && at_in[i].resid_auth == par->xlig_resnumber && par->xlig_resname[0] == at_in[i].resname[0] && par->xlig_resname[1] == at_in[i].resname[1] && par->xlig_resname[2] == at_in[i].resname[2]) || (par->xlig_chain_code!=NULL && at_in[i].chain_auth[0] == par->xlig_chain_code[0] && at_in[i].resid_auth == par->xlig_resnumber && par->xlig_resname[0] == at_in[i].resname[0] && par->xlig_resname[1] == at_in[i].resname[1] && par->xlig_resname[2] == at_in[i].resname[2])))
|
||||
if (((is_ligand(par->chain_as_ligand, at_in[i].chain_auth,par->n_chains_as_ligand)) || (par->xlig_chain_code !=NULL && strcmp(at_in[i].chain_auth,par->xlig_chain_code)==0 && at_in[i].resid_auth == par->xlig_resnumber && par->xlig_resname[0] == at_in[i].resname[0] && par->xlig_resname[1] == at_in[i].resname[1] && par->xlig_resname[2] == at_in[i].resname[2]) || (par->xlig_chain_code!=NULL && at_in[i].chain_auth[0] == par->xlig_chain_code[0] && at_in[i].resid_auth == par->xlig_resnumber && par->xlig_resname[0] == at_in[i].resname[0] && par->xlig_resname[1] == at_in[i].resname[1] && par->xlig_resname[2] == at_in[i].resname[2])))
|
||||
|
||||
{
|
||||
|
||||
pdb->n_xlig_atoms++;
|
||||
|
||||
}
|
||||
}
|
||||
}
|
||||
@@ -179,7 +183,7 @@ s_pdb *open_mmcif(char *fpath, const char *ligan, const int keep_lig, int model_
|
||||
}
|
||||
if (par->xlig_resnumber > -1)
|
||||
{
|
||||
if ((is_ligand(par->chain_as_ligand, at_in[i].chain_auth,par->n_chains_as_ligand)) || (par->xlig_chain_code !=NULL && !strcmp(at_in[i].chain_auth,par->xlig_chain_code) && (at_in[i].resid == par->xlig_resnumber) && (par->xlig_resname[0] == at_in[i].resname[0]) && (par->xlig_resname[1] == at_in[i].resname[1]) && (par->xlig_resname[2] == at_in[i].resname[2])) || (par->xlig_chain_code!=NULL && !strcmp(at_in[i].chain_auth, par->xlig_chain_code) && at_in[i].resid_auth == par->xlig_resnumber && par->xlig_resname[0] == at_in[i].resname[0] && par->xlig_resname[1] == at_in[i].resname[1] && par->xlig_resname[2] == at_in[i].resname[2]))
|
||||
if ((is_ligand(par->chain_as_ligand, at_in[i].chain_auth,par->n_chains_as_ligand)) || (par->xlig_chain_code !=NULL && !strcmp(at_in[i].chain_auth,par->xlig_chain_code) && (at_in[i].resid_auth == par->xlig_resnumber) && (par->xlig_resname[0] == at_in[i].resname[0]) && (par->xlig_resname[1] == at_in[i].resname[1]) && (par->xlig_resname[2] == at_in[i].resname[2])) || (par->xlig_chain_code!=NULL && !strcmp(at_in[i].chain_auth, par->xlig_chain_code) && at_in[i].resid_auth == par->xlig_resnumber && par->xlig_resname[0] == at_in[i].resname[0] && par->xlig_resname[1] == at_in[i].resname[1] && par->xlig_resname[2] == at_in[i].resname[2]))
|
||||
{
|
||||
pdb->n_xlig_atoms++;
|
||||
}
|
||||
@@ -313,8 +317,10 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
|
||||
strcpy(atom->name, at_in[i].type);
|
||||
atom->pdb_aloc = at_in[i].altloc[0];
|
||||
strcpy(atom->res_name, at_in[i].resname);
|
||||
strncpy(atom->chain, at_in[i].chain, 2);
|
||||
atom->res_id = at_in[i].resid;
|
||||
strcpy(atom->chain, at_in[i].chain_auth);
|
||||
strcpy(atom->label_asym_id, at_in[i].chain);
|
||||
atom->res_id = at_in[i].resid_auth;
|
||||
atom->label_seq_id=at_in[i].resid;
|
||||
atom->pdb_insert = at_in[i].insertion[0];
|
||||
atom->x = ts_in.coords[(3 * i)];
|
||||
atom->y = ts_in.coords[(3 * i) + 1];
|
||||
@@ -350,8 +356,10 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
|
||||
strcpy(atom->name, at_in[i].type);
|
||||
atom->pdb_aloc = at_in[i].altloc[0];
|
||||
strcpy(atom->res_name, at_in[i].resname);
|
||||
strncpy(atom->chain, at_in[i].chain, 2);
|
||||
atom->res_id = at_in[i].resid;
|
||||
strcpy(atom->chain, at_in[i].chain_auth);
|
||||
strcpy(atom->label_asym_id, at_in[i].chain);
|
||||
atom->res_id = at_in[i].resid_auth;
|
||||
atom->label_seq_id=at_in[i].resid;
|
||||
atom->pdb_insert = at_in[i].insertion[0];
|
||||
atom->x = ts_in.coords[(3 * i)];
|
||||
atom->y = ts_in.coords[(3 * i) + 1];
|
||||
@@ -395,8 +403,11 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
|
||||
atom->pdb_aloc = at_in[i].altloc[0];
|
||||
strcpy(atom->res_name, at_in[i].resname);
|
||||
|
||||
strncpy(atom->chain, at_in[i].chain, 2);
|
||||
atom->res_id = at_in[i].resid;
|
||||
strcpy(atom->chain, at_in[i].chain_auth);
|
||||
strcpy(atom->label_asym_id, at_in[i].chain);
|
||||
|
||||
atom->res_id = at_in[i].resid_auth;
|
||||
atom->label_seq_id=at_in[i].resid;
|
||||
atom->pdb_insert = at_in[i].insertion[0];
|
||||
|
||||
atom->x = ts_in.coords[(3 * i)];
|
||||
@@ -429,7 +440,7 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
|
||||
{
|
||||
unsigned short is_chain_ligand=(is_ligand(params->chain_as_ligand, at_in[i].chain_auth,params->n_chains_as_ligand) && strncmp(at_in[i].resname, "HOH", 3) && strncmp(at_in[i].resname, "WAT", 3) && strncmp(at_in[i].resname, "TIP", 3));
|
||||
|
||||
if (is_chain_ligand || (params->xlig_chain_code !=NULL && at_in[i].chain_auth[0] == params->xlig_chain_code[0] && at_in[i].resid == params->xlig_resnumber && params->xlig_resname[0] == at_in[i].resname[0] && params->xlig_resname[1] == at_in[i].resname[1] && params->xlig_resname[2] == at_in[i].resname[2]))
|
||||
if (is_chain_ligand || (params->xlig_chain_code !=NULL && at_in[i].chain_auth[0] == params->xlig_chain_code[0] && at_in[i].resid_auth == params->xlig_resnumber && params->xlig_resname[0] == at_in[i].resname[0] && params->xlig_resname[1] == at_in[i].resname[1] && params->xlig_resname[2] == at_in[i].resname[2]))
|
||||
{
|
||||
*(pdb->xlig_x + i_explicit_ligand_atom) = ts_in.coords[3 * i];
|
||||
*(pdb->xlig_y + i_explicit_ligand_atom) = ts_in.coords[(3 * i) + 1];
|
||||
@@ -465,9 +476,12 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
|
||||
strcpy(atom->name, at_in[i].type);
|
||||
atom->pdb_aloc = at_in[i].altloc[0];
|
||||
strcpy(atom->res_name, at_in[i].resname);
|
||||
strncpy(atom->chain, at_in[i].chain, 2);
|
||||
atom->res_id = at_in[i].resid;
|
||||
strcpy(atom->chain, at_in[i].chain_auth);
|
||||
strcpy(atom->label_asym_id, at_in[i].chain);
|
||||
atom->res_id = at_in[i].resid_auth;
|
||||
atom->label_seq_id=at_in[i].resid;
|
||||
atom->pdb_insert = at_in[i].insertion[0];
|
||||
|
||||
atom->x = ts_in.coords[(3 * i)];
|
||||
atom->y = ts_in.coords[(3 * i) + 1];
|
||||
atom->z = ts_in.coords[(3 * i) + 2];
|
||||
@@ -502,8 +516,10 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
|
||||
strcpy(atom->name, at_in[i].type);
|
||||
atom->pdb_aloc = at_in[i].altloc[0];
|
||||
strcpy(atom->res_name, at_in[i].resname);
|
||||
strncpy(atom->chain, at_in[i].chain, 2);
|
||||
atom->res_id = at_in[i].resid;
|
||||
strcpy(atom->chain, at_in[i].chain_auth);
|
||||
strcpy(atom->label_asym_id, at_in[i].chain);
|
||||
atom->res_id = at_in[i].resid_auth;
|
||||
atom->label_seq_id=at_in[i].resid;
|
||||
atom->pdb_insert = at_in[i].insertion[0];
|
||||
atom->x = ts_in.coords[(3 * i)];
|
||||
atom->y = ts_in.coords[(3 * i) + 1];
|
||||
@@ -540,9 +556,12 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
|
||||
strcpy(atom->name, at_in[i].type);
|
||||
atom->pdb_aloc = at_in[i].altloc[0];
|
||||
strcpy(atom->res_name, at_in[i].resname);
|
||||
strncpy(atom->chain, at_in[i].chain, 2);
|
||||
atom->res_id = at_in[i].resid;
|
||||
strcpy(atom->chain, at_in[i].chain_auth);
|
||||
strcpy(atom->label_asym_id, at_in[i].chain);
|
||||
atom->res_id = at_in[i].resid_auth;
|
||||
atom->label_seq_id=at_in[i].resid;
|
||||
atom->pdb_insert = at_in[i].insertion[0];
|
||||
|
||||
atom->x = ts_in.coords[(3 * i)];
|
||||
atom->y = ts_in.coords[(3 * i) + 1];
|
||||
atom->z = ts_in.coords[(3 * i) + 2];
|
||||
@@ -578,8 +597,10 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
|
||||
strcpy(atom->name, at_in[i].type);
|
||||
atom->pdb_aloc = at_in[i].altloc[0];
|
||||
strcpy(atom->res_name, at_in[i].resname);
|
||||
strncpy(atom->chain, at_in[i].chain, 2);
|
||||
atom->res_id = at_in[i].resid;
|
||||
strcpy(atom->chain, at_in[i].chain_auth);
|
||||
strcpy(atom->label_asym_id, at_in[i].chain);
|
||||
atom->res_id = at_in[i].resid_auth;
|
||||
atom->label_seq_id=at_in[i].resid;
|
||||
atom->pdb_insert = at_in[i].insertion[0];
|
||||
atom->x = ts_in.coords[(3 * i)];
|
||||
atom->y = ts_in.coords[(3 * i) + 1];
|
||||
@@ -607,15 +628,14 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
if (pdb->n_xlig_atoms)
|
||||
{
|
||||
|
||||
unsigned short is_chain_ligand=(is_ligand(params->chain_as_ligand, at_in[i].chain_auth,params->n_chains_as_ligand) && strncmp(at_in[i].resname, "HOH", 3) && strncmp(at_in[i].resname, "WAT", 3) && strncmp(at_in[i].resname, "TIP", 3));
|
||||
|
||||
if (is_chain_ligand || (params->xlig_chain_code !=NULL && at_in[i].chain_auth[0] == params->xlig_chain_code[0] && at_in[i].resid == params->xlig_resnumber && params->xlig_resname[0] == at_in[i].resname[0] && params->xlig_resname[1] == at_in[i].resname[1] && params->xlig_resname[2] == at_in[i].resname[2]) || (params->xlig_chain_code!=NULL && at_in[i].chain_auth[0] == params->xlig_chain_code[0] && at_in[i].resid_auth == params->xlig_resnumber && params->xlig_resname[0] == at_in[i].resname[0] && params->xlig_resname[1] == at_in[i].resname[1] && params->xlig_resname[2] == at_in[i].resname[2]))
|
||||
{
|
||||
|
||||
if (is_chain_ligand || (params->xlig_chain_code !=NULL && strcmp(at_in[i].chain_auth, params->xlig_chain_code)==0 && at_in[i].resid_auth == params->xlig_resnumber && params->xlig_resname[0] == at_in[i].resname[0] && params->xlig_resname[1] == at_in[i].resname[1] && params->xlig_resname[2] == at_in[i].resname[2]) || (params->xlig_chain_code!=NULL && strcmp(at_in[i].chain_auth, params->xlig_chain_code)==0 && at_in[i].resid_auth == params->xlig_resnumber && params->xlig_resname[0] == at_in[i].resname[0] && params->xlig_resname[1] == at_in[i].resname[1] && params->xlig_resname[2] == at_in[i].resname[2]))
|
||||
{
|
||||
*(pdb->xlig_x + i_explicit_ligand_atom) = ts_in.coords[3 * i];
|
||||
*(pdb->xlig_y + i_explicit_ligand_atom) = ts_in.coords[(3 * i) + 1];
|
||||
*(pdb->xlig_z + i_explicit_ligand_atom) = ts_in.coords[(3 * i) + 2];
|
||||
|
||||
26
src/rpdb.c
26
src/rpdb.c
@@ -1161,6 +1161,9 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
|
||||
atom->radius = pte_get_vdw_ray(atom->symbol);
|
||||
atom->electroneg = pte_get_enegativity(atom->symbol);
|
||||
atom->sort_x = -1;
|
||||
atom->label_seq_id=atom->res_id;
|
||||
strcpy(atom->label_asym_id, atom->chain);
|
||||
|
||||
|
||||
atoms_p[iatoms] = atom;
|
||||
iatoms++;
|
||||
@@ -1189,7 +1192,9 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
|
||||
atom->radius = pte_get_vdw_ray(atom->symbol);
|
||||
atom->electroneg = pte_get_enegativity(atom->symbol);
|
||||
atom->sort_x = -1;
|
||||
|
||||
atom->label_seq_id=atom->res_id;
|
||||
strcpy(atom->label_asym_id, atom->chain);
|
||||
|
||||
atoms_p[iatoms] = atom;
|
||||
iatoms++;
|
||||
|
||||
@@ -1215,6 +1220,9 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
|
||||
atom->radius = pte_get_vdw_ray(atom->symbol);
|
||||
atom->electroneg = pte_get_enegativity(atom->symbol);
|
||||
atom->sort_x = -1;
|
||||
atom->label_seq_id=atom->res_id;
|
||||
strcpy(atom->label_asym_id, atom->chain);
|
||||
|
||||
// printf("type : %s, id : %d, name : %s, aloc : %c, res_name : %s, chain : %s, res_id : %d, pdb_insert : %c, occupancy : %f, b_factor : %f, symbol : %s, charge : %d\n",
|
||||
// atom->type, atom->id,atom->name ,atom->pdb_aloc,atom->res_name,atom->chain,atom->res_id,atom->pdb_insert,atom->occupancy,atom->bfactor, atom->symbol,atom->charge);
|
||||
// printf("electroneg : %s\n",atom->symbol);
|
||||
@@ -1284,7 +1292,9 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
|
||||
atom->radius = pte_get_vdw_ray(atom->symbol);
|
||||
atom->electroneg = pte_get_enegativity(atom->symbol);
|
||||
atom->sort_x = -1;
|
||||
|
||||
atom->label_seq_id=atom->res_id;
|
||||
strcpy(atom->label_asym_id, atom->chain);
|
||||
|
||||
atoms_p[iatoms] = atom;
|
||||
atm_lig[iatm_lig] = atom;
|
||||
|
||||
@@ -1310,7 +1320,9 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
|
||||
atom->radius = pte_get_vdw_ray(atom->symbol);
|
||||
atom->electroneg = pte_get_enegativity(atom->symbol);
|
||||
atom->sort_x = -1;
|
||||
|
||||
atom->label_seq_id=atom->res_id;
|
||||
strcpy(atom->label_asym_id, atom->chain);
|
||||
|
||||
atoms_p[iatoms] = atom;
|
||||
atm_lig[iatm_lig] = atom;
|
||||
|
||||
@@ -1338,7 +1350,9 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
|
||||
atom->radius = pte_get_vdw_ray(atom->symbol);
|
||||
atom->electroneg = pte_get_enegativity(atom->symbol);
|
||||
atom->sort_x = -1;
|
||||
|
||||
atom->label_seq_id=atom->res_id;
|
||||
strcpy(atom->label_asym_id, atom->chain);
|
||||
|
||||
atoms_p[iatoms] = atom;
|
||||
pdb->lhetatm[ihetatm] = atom;
|
||||
ihetatm++;
|
||||
@@ -1366,7 +1380,9 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
|
||||
atom->radius = pte_get_vdw_ray(atom->symbol);
|
||||
atom->electroneg = pte_get_enegativity(atom->symbol);
|
||||
atom->sort_x = -1;
|
||||
|
||||
atom->label_seq_id=atom->res_id;
|
||||
strcpy(atom->label_asym_id, atom->chain);
|
||||
|
||||
atoms_p[iatoms] = atom;
|
||||
pdb->lhetatm[ihetatm] = atom;
|
||||
ihetatm++;
|
||||
|
||||
@@ -1488,23 +1488,23 @@ void write_mmcif_vert(FILE *f, s_vvertice *v, int i)
|
||||
if (v->electrostatic_energy <= -0.05)
|
||||
{
|
||||
|
||||
write_mmcif_atom_line(f, "HETATM", i, " POL",
|
||||
' ', "ACC", "O", v->resid, ' ',
|
||||
write_mmcif_atom_line(f, "HETATM", i, "POL",
|
||||
'.', "ACC", "O", v->resid, "O",v->resid,'.',
|
||||
v->x, v->y, v->z, 0.0, 0.0, 0,
|
||||
"V", -1, 0.0);
|
||||
}
|
||||
else if (v->electrostatic_energy >= 0.05)
|
||||
{
|
||||
|
||||
write_mmcif_atom_line(f, "HETATM", i, " POL", ' ', "DON", "N",
|
||||
v->resid, ' ', v->x, v->y, v->z, 0.0, 0.0, 0,
|
||||
write_mmcif_atom_line(f, "HETATM", i, "POL", '.', "DON", "N",
|
||||
v->resid, "N",v->resid,'.', v->x, v->y, v->z, 0.0, 0.0, 0,
|
||||
"V", -1, 0.0);
|
||||
}
|
||||
else
|
||||
{
|
||||
|
||||
write_mmcif_atom_line(f, "HETATM", i, "APOL", ' ', "STP", "C",
|
||||
v->resid, ' ', v->x, v->y, v->z, 0.0, 0.0, 0,
|
||||
write_mmcif_atom_line(f, "HETATM", i, "APOL", '.', "STP", "C",
|
||||
v->resid, "C", v->resid,'.', v->x, v->y, v->z, 0.0, 0.0, 0,
|
||||
"V", -1, 0.0);
|
||||
}
|
||||
}
|
||||
|
||||
@@ -206,7 +206,7 @@ void write_pqr_atom_line(FILE *f, const char *rec_name, int id, const char *atom
|
||||
|
||||
void write_mmcif_atom_line(FILE *f, const char rec_name[], int id, const char atom_name[],
|
||||
char alt_loc, const char res_name[], const char chain[],
|
||||
int res_id, const char insert, float x, float y, float z, float occ,
|
||||
int res_id, const char label_asym_id[],int label_seq_id, char insert, float x, float y, float z, float occ,
|
||||
float bfactor, int abpa, const char *symbol, int charge, float abpa_prob)
|
||||
{
|
||||
int status = 0;
|
||||
@@ -214,19 +214,13 @@ void write_mmcif_atom_line(FILE *f, const char rec_name[], int id, const char at
|
||||
res_id_buf[5] = "****",
|
||||
charge_buf[3] = " \0";
|
||||
|
||||
if (id < 100000)
|
||||
sprintf(id_buf, "%5d", id);
|
||||
else
|
||||
sprintf(id_buf, "%05x", id);
|
||||
|
||||
sprintf(id_buf, "%d", id);
|
||||
|
||||
sprintf(res_id_buf, "%d", res_id);
|
||||
|
||||
if (res_id < 10000)
|
||||
sprintf(res_id_buf, "%4d", res_id);
|
||||
else if (res_id < 65536)
|
||||
sprintf(res_id_buf, "%04x", res_id);
|
||||
else
|
||||
sprintf(res_id_buf, "****");
|
||||
|
||||
alt_loc = (alt_loc == '\0') ? ' ' : alt_loc;
|
||||
alt_loc = (alt_loc == '\0' || (alt_loc == ' ')) ? '?' : alt_loc;
|
||||
insert = (insert == '\0' || insert==' ') ? '?' : insert;
|
||||
|
||||
if (charge == -1)
|
||||
sprintf(charge_buf, " 0");
|
||||
@@ -237,14 +231,8 @@ void write_mmcif_atom_line(FILE *f, const char rec_name[], int id, const char at
|
||||
if (abpa)
|
||||
finalabpa = abpa_prob;
|
||||
|
||||
//status = fprintf(f, "%-7s %6s %3s %4s . %4s %3s . %s ? %8.3f%8.3f%8.3f%6.2f %2s %4s %4s %2s %4s\n",
|
||||
// rec_name, id_buf, symbol, atom_name, res_name, chain, res_id_buf, x, y, z, occ, charge_buf, res_id_buf, res_name, chain, atom_name);
|
||||
status = fprintf(f, "%-7s %-6s %3s %4s %c %4s %6s %d %c %8.3f %8.3f %8.3f %6.2f %2s %d %s\n",
|
||||
rec_name, id_buf, symbol, atom_name,alt_loc, res_name, label_asym_id, label_seq_id,insert, x, y, z, occ, charge_buf, res_id,chain);
|
||||
|
||||
status = fprintf(f, "%-7s %-6s %3s %4s . %4s %3s . %s ? %8.3f%8.3f%8.3f%6.2f %2s %2s\n",
|
||||
rec_name, id_buf, symbol, atom_name, res_name, chain, res_id_buf, x, y, z, occ, charge_buf, chain);
|
||||
}
|
||||
|
||||
/*"ATOM %d %s %s . %s %s . %d ? %f %f %f %f %f %s\n",
|
||||
i + 1, atoms[i].name, atoms[i].type, atoms[i].resname, atoms[i].chain,
|
||||
atoms[i].resid, *x, *y, *z, atoms[i].occupancy,
|
||||
atoms[i].charge, atoms[i].chain);*/
|
||||
}
|
||||
@@ -44,7 +44,6 @@ static const char atomSiteHeader[] =
|
||||
"_atom_site.label_alt_id\n"
|
||||
"_atom_site.label_comp_id\n"
|
||||
"_atom_site.label_asym_id\n"
|
||||
"_atom_site.label_entity_id\n"
|
||||
"_atom_site.label_seq_id\n"
|
||||
"_atom_site.pdbx_PDB_ins_code\n"
|
||||
"_atom_site.Cartn_x\n"
|
||||
@@ -52,6 +51,7 @@ static const char atomSiteHeader[] =
|
||||
"_atom_site.Cartn_z\n"
|
||||
"_atom_site.occupancy\n"
|
||||
"_atom_site.pdbx_formal_charge\n"
|
||||
"_atom_site.auth_seq_id\n"
|
||||
"_atom_site.auth_asym_id\n";
|
||||
|
||||
/*static const char atomSiteHeader[] =
|
||||
@@ -79,11 +79,10 @@ static const char atomSiteHeader[] =
|
||||
|
||||
void write_each_pocket_for_DB(const char out_path[], c_lst_pockets *pockets, s_pdb *pdb) {
|
||||
int out_len = strlen(out_path);
|
||||
char out[out_len + 20];
|
||||
char out[out_len + 40];
|
||||
out[0] = '\0';
|
||||
|
||||
node_pocket *pcur;
|
||||
|
||||
int i = 0;
|
||||
if (pockets) {
|
||||
pcur = pockets->first;
|
||||
@@ -92,13 +91,26 @@ void write_each_pocket_for_DB(const char out_path[], c_lst_pockets *pockets, s_p
|
||||
sprintf(out, "%s/pocket%d_vert.pqr", out_path, i + 1);
|
||||
write_pocket_pqr_DB(out, pcur->pocket);
|
||||
|
||||
sprintf(out, "%s/pocket%d_env_atm.pdb", out_path, i + 1);
|
||||
write_pocket_pdb_DB(out, pcur->pocket, pdb);
|
||||
|
||||
|
||||
if(write_mode[0] == 'p' || write_mode[0] == 'b'){
|
||||
|
||||
sprintf(out, "%s/pocket%d_atm.pdb", out_path, i + 1);
|
||||
write_pocket_pdb(out, pcur->pocket);
|
||||
|
||||
sprintf(out, "%s/pocket%d_env_atm.pdb", out_path, i + 1);
|
||||
write_pocket_pdb_DB(out, pcur->pocket, pdb);
|
||||
// sprintf(out, "%s/pocket%d_atm.pdb", out_path, i+1);
|
||||
// write_pocket_pdb_DB(out, pcur->pocket);
|
||||
}
|
||||
|
||||
if(write_mode[0] == 'm' || write_mode[0] == 'b'){
|
||||
sprintf(out, "%s/pocket%d_atm.cif", out_path, i + 1);
|
||||
write_pocket_mmcif(out, pcur->pocket);
|
||||
|
||||
sprintf(out, "%s/pocket%d_env_atm.cif", out_path, i+1);
|
||||
write_pocket_mmcif_DB(out, pcur->pocket,pdb);
|
||||
}
|
||||
|
||||
|
||||
pcur = pcur->next;
|
||||
i++;
|
||||
}
|
||||
@@ -144,14 +156,7 @@ void write_pocket_pdb_DB(const char out[], s_pocket *pocket, s_pdb *pdb) {
|
||||
|
||||
node_vertice *nvcur = pocket->v_lst->first;
|
||||
|
||||
/*
|
||||
fprintf(stdout, "A Pocket:\n") ;
|
||||
*/
|
||||
while (nvcur) {
|
||||
/*
|
||||
fprintf(stdout, "Vertice %d: %p %d %f\n", i, nvcur->vertice, nvcur->vertice->id, nvcur->vertice->ray) ;
|
||||
fprintf(stdout, "Atom %s\n", nvcur->vertice->neigh[0]->name) ;
|
||||
*/
|
||||
|
||||
tab_vert[nvert] = nvcur->vertice;
|
||||
nvcur = nvcur->next;
|
||||
@@ -159,7 +164,6 @@ void write_pocket_pdb_DB(const char out[], s_pocket *pocket, s_pdb *pdb) {
|
||||
}
|
||||
sa = (int *) get_surrounding_atoms_idx(tab_vert, nvert, pdb, &n_sa);
|
||||
for (i = 0; i < n_sa; i++) {
|
||||
//atom = pocket->sou_atoms[i] ;
|
||||
atom = pdb->latoms_p[sa[i]];
|
||||
write_pdb_atom_line(f, atom->type, atom->id, atom->name, atom->pdb_aloc,
|
||||
atom->res_name, atom->chain, atom->res_id,
|
||||
@@ -167,36 +171,7 @@ void write_pocket_pdb_DB(const char out[], s_pocket *pocket, s_pdb *pdb) {
|
||||
atom->dA, atom->a0, atom->abpa, atom->symbol,
|
||||
atom->charge, atom->abpa_sourrounding_prob);
|
||||
}
|
||||
/*
|
||||
vcur = pocket->v_lst->first ;
|
||||
|
||||
while(vcur){
|
||||
for(i = 0 ; i < 4 ; i++) {
|
||||
if(!is_in_lst_atm(atms, cur_size, vcur->vertice->neigh[i]->id)) {
|
||||
if(cur_size >= cur_allocated-1) {
|
||||
cur_allocated *= 2 ;
|
||||
atms = (s_atm**) my_realloc(atms, sizeof(s_atm)*cur_allocated) ;
|
||||
}
|
||||
atms[cur_size] = vcur->vertice->neigh[i] ;
|
||||
cur_size ++ ;
|
||||
}
|
||||
|
||||
}
|
||||
vcur = vcur->next ;
|
||||
}
|
||||
*/
|
||||
// Then write atoms...
|
||||
/*
|
||||
for(i = 0 ; i < cur_size ; i++) {
|
||||
atom = atms[i] ;
|
||||
|
||||
write_pdb_atom_line(f, atom->type, atom->id, atom->name, atom->pdb_aloc,
|
||||
atom->res_name, atom->chain, atom->res_id,
|
||||
atom->pdb_insert, atom->x, atom->y, atom->z,
|
||||
atom->occupancy, atom->bfactor, atom->symbol,
|
||||
atom->charge);
|
||||
}
|
||||
*/
|
||||
|
||||
fprintf(f, "TER\nEND\n");
|
||||
fclose(f);
|
||||
} else {
|
||||
@@ -207,6 +182,56 @@ void write_pocket_pdb_DB(const char out[], s_pocket *pocket, s_pdb *pdb) {
|
||||
my_free(atms);
|
||||
}
|
||||
|
||||
|
||||
|
||||
void write_pocket_mmcif_DB(const char out[], s_pocket *pocket, s_pdb *pdb) {
|
||||
int i = 0, nvert = 0;
|
||||
s_atm **atms = (s_atm **) my_malloc(sizeof (s_atm*)*10);
|
||||
s_atm *atom = NULL;
|
||||
int n_sa = 0;
|
||||
int *sa = NULL; /*surrounding atoms container*/
|
||||
s_vvertice **tab_vert = NULL;
|
||||
char tmp[250];
|
||||
strcpy(tmp,out);
|
||||
remove_ext(tmp);
|
||||
remove_path(tmp);
|
||||
FILE *f = fopen(out, "w");
|
||||
fprintf(f,"data_%s\n# \n",tmp);
|
||||
fprintf(f,"%s",atomSiteHeader);/*print the header*/
|
||||
if (f && pocket) {
|
||||
// First get the list of atoms
|
||||
tab_vert = (s_vvertice **) my_malloc(pocket->v_lst->n_vertices * sizeof (s_vvertice*));
|
||||
|
||||
node_vertice *nvcur = pocket->v_lst->first;
|
||||
|
||||
while (nvcur) {
|
||||
|
||||
tab_vert[nvert] = nvcur->vertice;
|
||||
nvcur = nvcur->next;
|
||||
nvert++;
|
||||
}
|
||||
sa = (int *) get_surrounding_atoms_idx(tab_vert, nvert, pdb, &n_sa);
|
||||
for (i = 0; i < n_sa; i++) {
|
||||
atom = pdb->latoms_p[sa[i]];
|
||||
write_mmcif_atom_line(f, atom->type, atom->id, atom->name, atom->pdb_aloc,
|
||||
atom->res_name, atom->chain, atom->res_id,atom->label_asym_id,atom->label_seq_id,
|
||||
atom->pdb_insert, atom->x, atom->y, atom->z,
|
||||
atom->dA, atom->a0, atom->abpa, atom->symbol,
|
||||
atom->charge, atom->abpa_sourrounding_prob);
|
||||
}
|
||||
|
||||
fprintf(f, "#\n");
|
||||
fclose(f);
|
||||
} else {
|
||||
if (!f) fprintf(stderr, "! The file %s could not be opened!\n", out);
|
||||
else fprintf(stderr, "! Invalid pocket to write in write_pocket_pqr !\n");
|
||||
}
|
||||
|
||||
my_free(atms);
|
||||
}
|
||||
|
||||
|
||||
|
||||
/**
|
||||
## FUNCTION:
|
||||
write_single_pdb
|
||||
@@ -350,9 +375,9 @@ void write_mmcif_atoms(FILE *f, s_atm *atoms, int natoms) {
|
||||
for (i = 0; i < natoms; i++) {
|
||||
atom = atoms + i;
|
||||
//atom->chain[1]='\0';
|
||||
//printf("%d:%s|symb:%s\t",i,atom->chain,atom->symbol);
|
||||
// printf("%d:%s vs %s\n",i,atom->chain,atom->label_asym_id);
|
||||
write_mmcif_atom_line(f, atom->type, atom->id, atom->name, atom->pdb_aloc,
|
||||
atom->res_name, atom->chain, atom->res_id,
|
||||
atom->res_name, atom->chain,atom->res_id,atom->label_asym_id,atom->label_seq_id,
|
||||
atom->pdb_insert, atom->x, atom->y, atom->z,
|
||||
atom->dA, atom->a0, atom->abpa, atom->symbol,
|
||||
atom->charge, atom->abpa_sourrounding_prob);
|
||||
@@ -475,7 +500,7 @@ void write_mdpockets_concat_pqr(FILE *f, c_lst_pockets *pockets) {
|
||||
*/
|
||||
void write_each_pocket(const char out_path[], c_lst_pockets *pockets) {
|
||||
int out_len = strlen(out_path);
|
||||
char out[out_len + 20];
|
||||
char out[out_len + 40];
|
||||
out[0] = '\0';
|
||||
|
||||
node_pocket *pcur;
|
||||
@@ -483,7 +508,7 @@ void write_each_pocket(const char out_path[], c_lst_pockets *pockets) {
|
||||
int i = 1;
|
||||
if (pockets) {
|
||||
pcur = pockets->first;
|
||||
|
||||
|
||||
while (pcur) {
|
||||
sprintf(out, "%s/pocket%d_vert.pqr", out_path, i);
|
||||
|
||||
@@ -717,7 +742,7 @@ void write_pocket_mmcif(const char out[], s_pocket *pocket) {
|
||||
atom = atms[i];
|
||||
|
||||
write_mmcif_atom_line(f, atom->type, atom->id, atom->name, atom->pdb_aloc,
|
||||
atom->res_name, atom->chain, atom->res_id,
|
||||
atom->res_name, atom->chain, atom->res_id,atom->label_asym_id,atom->label_seq_id,
|
||||
atom->pdb_insert, atom->x, atom->y, atom->z,
|
||||
atom->dA, atom->a0, atom->abpa, atom->symbol,
|
||||
atom->charge, atom->abpa_sourrounding_prob);
|
||||
|
||||
76
tests/reference_output/123abc_out/pocket10_atm.cif
Normal file
76
tests/reference_output/123abc_out/pocket10_atm.cif
Normal file
@@ -0,0 +1,76 @@
|
||||
data_pocket10_atm
|
||||
#
|
||||
loop_
|
||||
_struct.pdbx_descriptor
|
||||
This is a mmcif format file writen by the programm fpocket.
|
||||
It represents the atoms contacted by the voronoi vertices of the pocket.
|
||||
|
||||
Information about the pocket 10:
|
||||
0 - Pocket Score : 0.0405
|
||||
1 - Drug Score : 0.0230
|
||||
2 - Number of alpha spheres : 57
|
||||
3 - Mean alpha-sphere radius : 3.8604
|
||||
4 - Mean alpha-sphere Solvent Acc. : 0.4592
|
||||
5 - Mean B-factor of pocket residues : 0.2769
|
||||
6 - Hydrophobicity Score : 40.0769
|
||||
7 - Polarity Score : 6
|
||||
8 - Amino Acid based volume Score : 3.6154
|
||||
9 - Pocket volume (Monte Carlo) : 433.1334
|
||||
10 -Pocket volume (convex hull) : 76.0139
|
||||
11 - Charge Score : 1
|
||||
12 - Local hydrophobic density Score : 32.4571
|
||||
13 - Number of apolar alpha sphere : 35
|
||||
14 - Proportion of apolar alpha sphere : 0.6140
|
||||
#
|
||||
loop_
|
||||
_atom_site.group_PDB
|
||||
_atom_site.id
|
||||
_atom_site.type_symbol
|
||||
_atom_site.label_atom_id
|
||||
_atom_site.label_alt_id
|
||||
_atom_site.label_comp_id
|
||||
_atom_site.label_asym_id
|
||||
_atom_site.label_seq_id
|
||||
_atom_site.pdbx_PDB_ins_code
|
||||
_atom_site.Cartn_x
|
||||
_atom_site.Cartn_y
|
||||
_atom_site.Cartn_z
|
||||
_atom_site.occupancy
|
||||
_atom_site.pdbx_formal_charge
|
||||
_atom_site.auth_seq_id
|
||||
_atom_site.auth_asym_id
|
||||
ATOM 3335 C CG2 ? THR Bxp 167 ? 23.611 41.302 32.855 0.00 0 394 B
|
||||
ATOM 3339 O O ? ALA Bxp 168 ? 21.154 41.582 30.397 0.00 0 395 B
|
||||
ATOM 1238 O O ? ALA Axp 168 ? 20.773 34.081 30.515 0.00 0 395 A
|
||||
ATOM 3399 C CD1 ? ILE Bxp 176 ? 22.413 39.457 35.570 0.00 0 403 B
|
||||
ATOM 3397 C CG1 ? ILE Bxp 176 ? 21.483 40.079 36.568 0.00 0 403 B
|
||||
ATOM 3345 C CB ? HIS Bxp 169 ? 17.804 41.919 30.765 0.00 0 396 B
|
||||
ATOM 3378 C CB ? PHE Bxp 174 ? 18.390 43.943 35.478 0.00 0 401 B
|
||||
ATOM 3332 O O ? THR Bxp 167 ? 21.633 44.211 32.694 -1.07 0 394 B
|
||||
ATOM 3735 C CA ? SER Bxp 219 ? 24.536 33.701 35.059 0.00 0 446 B
|
||||
ATOM 3729 O O ? LEU Bxp 218 ? 23.720 35.415 36.830 0.00 0 445 B
|
||||
ATOM 1239 C CB ? ALA Axp 168 ? 21.952 31.542 32.252 0.00 0 395 A
|
||||
ATOM 3454 O O ? SER Bxp 183 ? 12.618 40.049 35.823 -1.07 0 410 B
|
||||
ATOM 3488 O OD1 ? ASN Bxp 187 ? 12.383 40.631 32.241 -1.07 0 414 B
|
||||
ATOM 3380 C CD1 ? PHE Bxp 174 ? 16.492 43.534 33.887 0.00 0 401 B
|
||||
ATOM 3460 O O ? LEU Bxp 184 ? 14.089 37.175 34.255 -3.21 0 411 B
|
||||
ATOM 3458 C CA ? LEU Bxp 184 ? 14.473 38.083 36.400 0.00 0 411 B
|
||||
ATOM 3348 C CD2 ? HIS Bxp 169 ? 16.267 39.878 30.268 0.00 0 396 B
|
||||
ATOM 1241 C CA ? HIS Axp 169 ? 18.086 33.603 31.255 0.00 0 396 A
|
||||
ATOM 3760 C CB ? TYR Bxp 222 ? 18.259 32.959 38.062 0.00 0 449 B
|
||||
ATOM 3756 N N ? TYR Bxp 222 ? 20.251 33.164 39.466 -1.09 0 449 B
|
||||
ATOM 3398 C CG2 ? ILE Bxp 176 ? 21.928 38.594 38.565 0.00 0 403 B
|
||||
ATOM 3463 C CD1 ? LEU Bxp 184 ? 17.369 37.208 38.932 0.00 0 411 B
|
||||
ATOM 3737 O O ? SER Bxp 219 ? 23.395 31.686 35.276 -1.07 0 446 B
|
||||
ATOM 3728 C C ? LEU Bxp 218 ? 24.912 35.395 36.613 0.00 0 445 B
|
||||
ATOM 3730 C CB ? LEU Bxp 218 ? 25.994 37.693 36.437 0.00 0 445 B
|
||||
ATOM 3738 C CB ? SER Bxp 219 ? 25.152 33.376 33.704 0.00 0 446 B
|
||||
ATOM 3346 C CG ? HIS Bxp 169 ? 16.549 41.202 30.364 0.00 0 396 B
|
||||
ATOM 3464 C CD2 ? LEU Bxp 184 ? 17.512 38.953 37.066 0.00 0 411 B
|
||||
ATOM 3734 N N ? SER Bxp 219 ? 25.438 34.466 35.848 -1.09 0 446 B
|
||||
ATOM 1247 C CD2 ? HIS Axp 169 ? 15.907 36.141 30.193 0.00 0 396 A
|
||||
ATOM 3461 C CB ? LEU Bxp 184 ? 15.552 37.271 37.155 0.00 0 411 B
|
||||
ATOM 1250 N N ? ALA Axp 170 ? 17.224 33.325 33.516 -4.79 0 397 A
|
||||
ATOM 1255 N N ? GLY Axp 171 ? 17.151 30.558 34.884 -1.09 0 398 A
|
||||
ATOM 1237 C C ? ALA Axp 168 ? 20.392 32.949 30.818 0.00 0 395 A
|
||||
#
|
||||
91
tests/reference_output/123abc_out/pocket10_env_atm.cif
Normal file
91
tests/reference_output/123abc_out/pocket10_env_atm.cif
Normal file
@@ -0,0 +1,91 @@
|
||||
data_pocket10_env_atm
|
||||
#
|
||||
loop_
|
||||
_atom_site.group_PDB
|
||||
_atom_site.id
|
||||
_atom_site.type_symbol
|
||||
_atom_site.label_atom_id
|
||||
_atom_site.label_alt_id
|
||||
_atom_site.label_comp_id
|
||||
_atom_site.label_asym_id
|
||||
_atom_site.label_seq_id
|
||||
_atom_site.pdbx_PDB_ins_code
|
||||
_atom_site.Cartn_x
|
||||
_atom_site.Cartn_y
|
||||
_atom_site.Cartn_z
|
||||
_atom_site.occupancy
|
||||
_atom_site.pdbx_formal_charge
|
||||
_atom_site.auth_seq_id
|
||||
_atom_site.auth_asym_id
|
||||
ATOM 1236 C CA ? ALA Axp 168 ? 21.345 31.742 30.855 0.00 0 395 A
|
||||
ATOM 1237 C C ? ALA Axp 168 ? 20.392 32.949 30.818 0.00 0 395 A
|
||||
ATOM 1238 O O ? ALA Axp 168 ? 20.773 34.081 30.515 0.00 0 395 A
|
||||
ATOM 1239 C CB ? ALA Axp 168 ? 21.952 31.542 32.252 0.00 0 395 A
|
||||
ATOM 1240 N N ? HIS Axp 169 ? 19.130 32.633 31.043 0.00 0 396 A
|
||||
ATOM 1241 C CA ? HIS Axp 169 ? 18.086 33.603 31.255 0.00 0 396 A
|
||||
ATOM 1242 C C ? HIS Axp 169 ? 17.124 32.937 32.241 0.00 0 396 A
|
||||
ATOM 1244 C CB ? HIS Axp 169 ? 17.333 33.968 29.971 0.00 0 396 A
|
||||
ATOM 1245 C CG ? HIS Axp 169 ? 16.104 34.797 30.229 0.00 0 396 A
|
||||
ATOM 1247 C CD2 ? HIS Axp 169 ? 15.907 36.141 30.193 0.00 0 396 A
|
||||
ATOM 1249 N NE2 ? HIS Axp 169 ? 14.590 36.367 30.529 0.00 0 396 A
|
||||
ATOM 1250 N N ? ALA Axp 170 ? 17.224 33.325 33.516 -4.79 0 397 A
|
||||
ATOM 1251 C CA ? ALA Axp 170 ? 16.342 32.830 34.571 0.00 0 397 A
|
||||
ATOM 1252 C C ? ALA Axp 170 ? 16.105 31.311 34.539 0.00 0 397 A
|
||||
ATOM 1254 C CB ? ALA Axp 170 ? 15.038 33.564 34.528 0.00 0 397 A
|
||||
ATOM 1255 N N ? GLY Axp 171 ? 17.151 30.558 34.884 -1.09 0 398 A
|
||||
ATOM 3331 C C ? THR Bxp 167 ? 22.771 43.904 32.327 0.00 0 394 B
|
||||
ATOM 3332 O O ? THR Bxp 167 ? 21.633 44.211 32.694 -1.07 0 394 B
|
||||
ATOM 3333 C CB ? THR Bxp 167 ? 23.958 42.338 33.911 0.00 0 394 B
|
||||
ATOM 3335 C CG2 ? THR Bxp 167 ? 23.611 41.302 32.855 0.00 0 394 B
|
||||
ATOM 3338 C C ? ALA Bxp 168 ? 20.955 42.763 30.104 0.00 0 395 B
|
||||
ATOM 3339 O O ? ALA Bxp 168 ? 21.154 41.582 30.397 0.00 0 395 B
|
||||
ATOM 3341 N N ? HIS Bxp 169 ? 19.743 43.280 29.949 0.00 0 396 B
|
||||
ATOM 3342 C CA ? HIS Bxp 169 ? 18.586 42.470 29.578 0.00 0 396 B
|
||||
ATOM 3345 C CB ? HIS Bxp 169 ? 17.804 41.919 30.765 0.00 0 396 B
|
||||
ATOM 3346 C CG ? HIS Bxp 169 ? 16.549 41.202 30.364 0.00 0 396 B
|
||||
ATOM 3347 N ND1 ? HIS Bxp 169 ? 15.399 41.864 29.978 -2.19 0 396 B
|
||||
ATOM 3348 C CD2 ? HIS Bxp 169 ? 16.267 39.878 30.268 0.00 0 396 B
|
||||
ATOM 3349 C CE1 ? HIS Bxp 169 ? 14.459 40.980 29.690 0.00 0 396 B
|
||||
ATOM 3350 N NE2 ? HIS Bxp 169 ? 14.959 39.769 29.859 0.00 0 396 B
|
||||
ATOM 3374 N N ? PHE Bxp 174 ? 19.806 45.500 34.237 0.00 0 401 B
|
||||
ATOM 3375 C CA ? PHE Bxp 174 ? 19.360 45.109 35.564 0.00 0 401 B
|
||||
ATOM 3377 O O ? PHE Bxp 174 ? 21.500 44.304 36.088 0.00 0 401 B
|
||||
ATOM 3378 C CB ? PHE Bxp 174 ? 18.390 43.943 35.478 0.00 0 401 B
|
||||
ATOM 3379 C CG ? PHE Bxp 174 ? 17.076 44.325 34.855 0.00 0 401 B
|
||||
ATOM 3380 C CD1 ? PHE Bxp 174 ? 16.492 43.534 33.887 0.00 0 401 B
|
||||
ATOM 3382 C CE1 ? PHE Bxp 174 ? 15.273 43.909 33.319 0.00 0 401 B
|
||||
ATOM 3396 C CB ? ILE Bxp 176 ? 21.966 39.989 38.044 0.00 0 403 B
|
||||
ATOM 3397 C CG1 ? ILE Bxp 176 ? 21.483 40.079 36.568 0.00 0 403 B
|
||||
ATOM 3398 C CG2 ? ILE Bxp 176 ? 21.928 38.594 38.565 0.00 0 403 B
|
||||
ATOM 3399 C CD1 ? ILE Bxp 176 ? 22.413 39.457 35.570 0.00 0 403 B
|
||||
ATOM 3453 C C ? SER Bxp 183 ? 12.616 39.571 36.930 0.00 0 410 B
|
||||
ATOM 3454 O O ? SER Bxp 183 ? 12.618 40.049 35.823 -1.07 0 410 B
|
||||
ATOM 3457 N N ? LEU Bxp 184 ? 13.478 38.624 37.304 0.00 0 411 B
|
||||
ATOM 3458 C CA ? LEU Bxp 184 ? 14.473 38.083 36.400 0.00 0 411 B
|
||||
ATOM 3459 C C ? LEU Bxp 184 ? 13.764 37.165 35.433 0.00 0 411 B
|
||||
ATOM 3460 O O ? LEU Bxp 184 ? 14.089 37.175 34.255 -3.21 0 411 B
|
||||
ATOM 3461 C CB ? LEU Bxp 184 ? 15.552 37.271 37.155 0.00 0 411 B
|
||||
ATOM 3462 C CG ? LEU Bxp 184 ? 16.587 38.098 37.951 0.00 0 411 B
|
||||
ATOM 3463 C CD1 ? LEU Bxp 184 ? 17.369 37.208 38.932 0.00 0 411 B
|
||||
ATOM 3464 C CD2 ? LEU Bxp 184 ? 17.512 38.953 37.066 0.00 0 411 B
|
||||
ATOM 3488 O OD1 ? ASN Bxp 187 ? 12.383 40.631 32.241 -1.07 0 414 B
|
||||
ATOM 3727 C CA ? LEU Bxp 218 ? 25.851 36.423 37.264 0.00 0 445 B
|
||||
ATOM 3728 C C ? LEU Bxp 218 ? 24.912 35.395 36.613 0.00 0 445 B
|
||||
ATOM 3729 O O ? LEU Bxp 218 ? 23.720 35.415 36.830 0.00 0 445 B
|
||||
ATOM 3730 C CB ? LEU Bxp 218 ? 25.994 37.693 36.437 0.00 0 445 B
|
||||
ATOM 3734 N N ? SER Bxp 219 ? 25.438 34.466 35.848 -1.09 0 446 B
|
||||
ATOM 3735 C CA ? SER Bxp 219 ? 24.536 33.701 35.059 0.00 0 446 B
|
||||
ATOM 3736 C C ? SER Bxp 219 ? 24.150 32.474 35.811 0.00 0 446 B
|
||||
ATOM 3737 O O ? SER Bxp 219 ? 23.395 31.686 35.276 -1.07 0 446 B
|
||||
ATOM 3738 C CB ? SER Bxp 219 ? 25.152 33.376 33.704 0.00 0 446 B
|
||||
ATOM 3751 C C ? VAL Bxp 221 ? 21.031 32.982 40.538 0.00 0 448 B
|
||||
ATOM 3753 C CB ? VAL Bxp 221 ? 22.559 35.077 40.397 0.00 0 448 B
|
||||
ATOM 3756 N N ? TYR Bxp 222 ? 20.251 33.164 39.466 -1.09 0 449 B
|
||||
ATOM 3757 C CA ? TYR Bxp 222 ? 18.886 32.708 39.432 0.00 0 449 B
|
||||
ATOM 3760 C CB ? TYR Bxp 222 ? 18.259 32.959 38.062 0.00 0 449 B
|
||||
ATOM 3761 C CG ? TYR Bxp 222 ? 16.811 32.522 38.032 0.00 0 449 B
|
||||
ATOM 3762 C CD1 ? TYR Bxp 222 ? 15.795 33.459 38.329 0.00 0 449 B
|
||||
ATOM 3768 N N ? GLU Bxp 223 ? 19.652 30.471 39.123 0.00 0 450 B
|
||||
ATOM 3773 C CG ? GLU Bxp 223 ? 20.865 28.953 37.013 0.00 0 450 B
|
||||
ATOM 3776 O OE2 ? GLU Bxp 223 ? 21.549 28.266 34.820 0.00 0 450 B
|
||||
#
|
||||
59
tests/reference_output/123abc_out/pocket10_vert.pqr
Normal file
59
tests/reference_output/123abc_out/pocket10_vert.pqr
Normal file
@@ -0,0 +1,59 @@
|
||||
ATOM 1 O STP 10 21.702 37.817 31.893 0.00 4.09
|
||||
ATOM 2 C STP 10 19.673 40.504 33.491 0.00 3.60
|
||||
ATOM 3 C STP 10 19.762 41.204 33.656 0.00 3.56
|
||||
ATOM 4 O STP 10 19.774 41.436 33.555 0.00 3.45
|
||||
ATOM 5 O STP 10 19.888 41.310 33.676 0.00 3.53
|
||||
ATOM 6 O STP 10 20.810 34.601 34.374 0.00 3.89
|
||||
ATOM 7 O STP 10 22.171 36.269 33.386 0.00 3.87
|
||||
ATOM 8 O STP 10 15.383 40.306 33.837 0.00 3.41
|
||||
ATOM 9 O STP 10 15.487 40.276 33.991 0.00 3.41
|
||||
ATOM 10 O STP 10 15.519 40.241 33.611 0.00 3.44
|
||||
ATOM 11 C STP 10 19.399 38.571 32.764 0.00 4.21
|
||||
ATOM 12 O STP 10 19.631 37.930 32.444 0.00 4.45
|
||||
ATOM 13 C STP 10 19.282 37.676 32.828 0.00 4.53
|
||||
ATOM 14 O STP 10 20.160 35.844 37.073 0.00 3.59
|
||||
ATOM 15 C STP 10 20.138 35.856 37.103 0.00 3.58
|
||||
ATOM 16 C STP 10 20.119 35.880 36.964 0.00 3.63
|
||||
ATOM 17 O STP 10 20.785 34.426 34.531 0.00 3.86
|
||||
ATOM 18 C STP 10 24.048 36.964 33.366 0.00 3.71
|
||||
ATOM 19 C STP 10 23.766 36.842 33.568 0.00 3.56
|
||||
ATOM 20 C STP 10 23.470 37.040 32.145 0.00 4.32
|
||||
ATOM 21 C STP 10 22.938 36.606 32.779 0.00 4.02
|
||||
ATOM 22 C STP 10 24.363 37.273 32.697 0.00 4.10
|
||||
ATOM 23 C STP 10 24.101 36.997 33.214 0.00 3.80
|
||||
ATOM 24 C STP 10 17.002 40.176 33.584 0.00 3.41
|
||||
ATOM 25 C STP 10 17.136 40.046 33.708 0.00 3.55
|
||||
ATOM 26 C STP 10 16.167 40.018 33.979 0.00 3.53
|
||||
ATOM 27 C STP 10 16.305 39.958 33.848 0.00 3.58
|
||||
ATOM 28 C STP 10 19.086 39.525 33.553 0.00 3.89
|
||||
ATOM 29 C STP 10 19.053 38.731 33.178 0.00 4.19
|
||||
ATOM 30 C STP 10 18.646 40.617 34.047 0.00 3.63
|
||||
ATOM 31 C STP 10 18.847 40.579 34.038 0.00 3.69
|
||||
ATOM 32 C STP 10 20.140 36.950 36.141 0.00 3.43
|
||||
ATOM 33 C STP 10 20.148 36.427 35.991 0.00 3.81
|
||||
ATOM 34 C STP 10 19.995 36.133 36.373 0.00 3.82
|
||||
ATOM 35 C STP 10 19.906 35.986 36.229 0.00 3.90
|
||||
ATOM 36 C STP 10 24.433 36.790 33.463 0.00 3.48
|
||||
ATOM 37 C STP 10 24.463 36.791 33.428 0.00 3.49
|
||||
ATOM 38 C STP 10 17.930 37.771 33.253 0.00 4.01
|
||||
ATOM 39 C STP 10 19.259 37.654 32.729 0.00 4.47
|
||||
ATOM 40 C STP 10 19.138 37.660 32.994 0.00 4.54
|
||||
ATOM 41 C STP 10 19.116 37.654 33.024 0.00 4.54
|
||||
ATOM 42 C STP 10 19.115 37.662 33.021 0.00 4.54
|
||||
ATOM 43 C STP 10 18.498 35.757 35.907 0.00 3.54
|
||||
ATOM 44 O STP 10 18.041 37.280 33.428 0.00 4.04
|
||||
ATOM 45 C STP 10 18.664 37.361 33.249 0.00 4.29
|
||||
ATOM 46 O STP 10 17.586 36.737 34.326 0.00 3.53
|
||||
ATOM 47 C STP 10 18.506 35.744 35.825 0.00 3.58
|
||||
ATOM 48 C STP 10 19.301 37.188 33.471 0.00 4.39
|
||||
ATOM 49 O STP 10 19.927 36.095 35.154 0.00 4.20
|
||||
ATOM 50 O STP 10 19.807 35.859 35.537 0.00 4.14
|
||||
ATOM 51 O STP 10 19.624 36.886 33.557 0.00 4.29
|
||||
ATOM 52 O STP 10 20.418 35.977 34.266 0.00 4.22
|
||||
ATOM 53 O STP 10 20.780 34.426 34.534 0.00 3.86
|
||||
ATOM 54 O STP 10 20.507 34.155 35.241 0.00 3.80
|
||||
ATOM 55 O STP 10 20.041 32.362 35.203 0.00 3.42
|
||||
ATOM 56 O STP 10 20.690 34.424 34.197 0.00 3.70
|
||||
ATOM 57 O STP 10 20.804 34.600 34.377 0.00 3.90
|
||||
TER
|
||||
END
|
||||
63
tests/reference_output/123abc_out/pocket11_atm.cif
Normal file
63
tests/reference_output/123abc_out/pocket11_atm.cif
Normal file
@@ -0,0 +1,63 @@
|
||||
data_pocket11_atm
|
||||
#
|
||||
loop_
|
||||
_struct.pdbx_descriptor
|
||||
This is a mmcif format file writen by the programm fpocket.
|
||||
It represents the atoms contacted by the voronoi vertices of the pocket.
|
||||
|
||||
Information about the pocket 11:
|
||||
0 - Pocket Score : 0.0388
|
||||
1 - Drug Score : 0.0007
|
||||
2 - Number of alpha spheres : 30
|
||||
3 - Mean alpha-sphere radius : 3.6177
|
||||
4 - Mean alpha-sphere Solvent Acc. : 0.4151
|
||||
5 - Mean B-factor of pocket residues : 0.1046
|
||||
6 - Hydrophobicity Score : 17.4167
|
||||
7 - Polarity Score : 7
|
||||
8 - Amino Acid based volume Score : 3.8333
|
||||
9 - Pocket volume (Monte Carlo) : 157.8834
|
||||
10 -Pocket volume (convex hull) : 11.3291
|
||||
11 - Charge Score : -1
|
||||
12 - Local hydrophobic density Score : 5.0000
|
||||
13 - Number of apolar alpha sphere : 6
|
||||
14 - Proportion of apolar alpha sphere : 0.2000
|
||||
#
|
||||
loop_
|
||||
_atom_site.group_PDB
|
||||
_atom_site.id
|
||||
_atom_site.type_symbol
|
||||
_atom_site.label_atom_id
|
||||
_atom_site.label_alt_id
|
||||
_atom_site.label_comp_id
|
||||
_atom_site.label_asym_id
|
||||
_atom_site.label_seq_id
|
||||
_atom_site.pdbx_PDB_ins_code
|
||||
_atom_site.Cartn_x
|
||||
_atom_site.Cartn_y
|
||||
_atom_site.Cartn_z
|
||||
_atom_site.occupancy
|
||||
_atom_site.pdbx_formal_charge
|
||||
_atom_site.auth_seq_id
|
||||
_atom_site.auth_asym_id
|
||||
ATOM 1405 C CD2 ? PHE Axp 189 ? 10.703 31.452 22.157 0.00 0 416 A
|
||||
ATOM 1435 O O ? SER Axp 193 ? 11.879 32.960 15.552 -3.21 0 420 A
|
||||
ATOM 1407 C CE2 ? PHE Axp 189 ? 11.966 31.656 22.739 0.00 0 416 A
|
||||
ATOM 996 O O ? ARG Axp 135 ? 13.454 28.096 20.320 -4.69 0 362 A
|
||||
ATOM 1436 C CB ? SER Axp 193 ? 9.997 34.149 17.982 0.00 0 420 A
|
||||
ATOM 1329 N N ? ALA Axp 180 ? 14.229 35.929 18.757 -1.09 0 407 A
|
||||
ATOM 1327 O OG1 ? THR Axp 179 ? 17.108 33.330 21.134 -2.14 0 406 A
|
||||
ATOM 1290 C CD ? PRO Axp 175 ? 18.295 29.738 22.438 0.00 0 402 A
|
||||
ATOM 1323 C CA ? THR Axp 179 ? 16.193 34.623 19.411 0.00 0 406 A
|
||||
ATOM 1437 O OG ? SER Axp 193 ? 9.317 33.077 18.605 0.00 0 420 A
|
||||
ATOM 1289 C CG ? PRO Axp 175 ? 18.737 29.443 21.033 0.00 0 402 A
|
||||
ATOM 1312 C CB ? TRP Axp 178 ? 18.807 31.481 17.128 0.00 0 405 A
|
||||
ATOM 1005 C CA ? ASP Axp 136 ? 14.988 26.627 18.681 0.00 0 363 A
|
||||
ATOM 1311 O O ? TRP Axp 178 ? 16.495 33.261 16.896 -2.14 0 405 A
|
||||
ATOM 1471 C CB ? ALA Axp 197 ? 14.926 31.065 14.885 0.00 0 424 A
|
||||
ATOM 1355 O OG ? SER Axp 183 ? 10.954 35.267 20.964 0.00 0 410 A
|
||||
ATOM 1012 N N ? LEU Axp 137 ? 14.970 26.942 16.300 0.00 0 364 A
|
||||
ATOM 1444 O OD1 ? ASP Axp 194 ? 10.115 28.834 16.531 0.00 0 421 A
|
||||
ATOM 995 C C ? ARG Axp 135 ? 12.856 27.406 19.519 0.00 0 362 A
|
||||
ATOM 994 C CA ? ARG Axp 135 ? 11.309 27.407 19.509 0.00 0 362 A
|
||||
ATOM 1328 C CG2 ? THR Axp 179 ? 15.235 34.657 21.794 0.00 0 406 A
|
||||
#
|
||||
64
tests/reference_output/123abc_out/pocket11_env_atm.cif
Normal file
64
tests/reference_output/123abc_out/pocket11_env_atm.cif
Normal file
@@ -0,0 +1,64 @@
|
||||
data_pocket11_env_atm
|
||||
#
|
||||
loop_
|
||||
_atom_site.group_PDB
|
||||
_atom_site.id
|
||||
_atom_site.type_symbol
|
||||
_atom_site.label_atom_id
|
||||
_atom_site.label_alt_id
|
||||
_atom_site.label_comp_id
|
||||
_atom_site.label_asym_id
|
||||
_atom_site.label_seq_id
|
||||
_atom_site.pdbx_PDB_ins_code
|
||||
_atom_site.Cartn_x
|
||||
_atom_site.Cartn_y
|
||||
_atom_site.Cartn_z
|
||||
_atom_site.occupancy
|
||||
_atom_site.pdbx_formal_charge
|
||||
_atom_site.auth_seq_id
|
||||
_atom_site.auth_asym_id
|
||||
ATOM 993 N N ? ARG Axp 135 ? 10.598 26.723 18.417 0.00 0 362 A
|
||||
ATOM 994 C CA ? ARG Axp 135 ? 11.309 27.407 19.509 0.00 0 362 A
|
||||
ATOM 995 C C ? ARG Axp 135 ? 12.856 27.406 19.519 0.00 0 362 A
|
||||
ATOM 996 O O ? ARG Axp 135 ? 13.454 28.096 20.320 -4.69 0 362 A
|
||||
ATOM 997 C CB ? ARG Axp 135 ? 10.850 26.919 20.881 0.00 0 362 A
|
||||
ATOM 1004 N N ? ASP Axp 136 ? 13.515 26.641 18.666 0.00 0 363 A
|
||||
ATOM 1005 C CA ? ASP Axp 136 ? 14.988 26.627 18.681 0.00 0 363 A
|
||||
ATOM 1006 C C ? ASP Axp 136 ? 15.413 26.185 17.291 0.00 0 363 A
|
||||
ATOM 1008 C CB ? ASP Axp 136 ? 15.490 25.673 19.755 0.00 0 363 A
|
||||
ATOM 1009 C CG ? ASP Axp 136 ? 16.996 25.759 19.996 0.00 0 363 A
|
||||
ATOM 1010 O OD1 ? ASP Axp 136 ? 17.712 26.739 19.639 0.00 0 363 A
|
||||
ATOM 1012 N N ? LEU Axp 137 ? 14.970 26.942 16.300 0.00 0 364 A
|
||||
ATOM 1014 C C ? LEU Axp 137 ? 16.652 27.030 14.689 0.00 0 364 A
|
||||
ATOM 1015 O O ? LEU Axp 137 ? 16.968 28.209 14.932 0.00 0 364 A
|
||||
ATOM 1280 C CD2 ? PHE Axp 174 ? 15.409 30.643 25.623 0.00 0 401 A
|
||||
ATOM 1287 O O ? PRO Axp 175 ? 19.472 32.424 20.666 0.00 0 402 A
|
||||
ATOM 1289 C CG ? PRO Axp 175 ? 18.737 29.443 21.033 0.00 0 402 A
|
||||
ATOM 1290 C CD ? PRO Axp 175 ? 18.295 29.738 22.438 0.00 0 402 A
|
||||
ATOM 1309 C CA ? TRP Axp 178 ? 18.854 33.025 17.137 0.00 0 405 A
|
||||
ATOM 1310 C C ? TRP Axp 178 ? 17.481 33.558 17.564 0.00 0 405 A
|
||||
ATOM 1311 O O ? TRP Axp 178 ? 16.495 33.261 16.896 -2.14 0 405 A
|
||||
ATOM 1312 C CB ? TRP Axp 178 ? 18.807 31.481 17.128 0.00 0 405 A
|
||||
ATOM 1322 N N ? THR Axp 179 ? 17.421 34.347 18.657 0.00 0 406 A
|
||||
ATOM 1323 C CA ? THR Axp 179 ? 16.193 34.623 19.411 0.00 0 406 A
|
||||
ATOM 1324 C C ? THR Axp 179 ? 15.545 35.958 19.044 0.00 0 406 A
|
||||
ATOM 1326 C CB ? THR Axp 179 ? 16.508 34.581 20.893 0.00 0 406 A
|
||||
ATOM 1327 O OG1 ? THR Axp 179 ? 17.108 33.330 21.134 -2.14 0 406 A
|
||||
ATOM 1328 C CG2 ? THR Axp 179 ? 15.235 34.657 21.794 0.00 0 406 A
|
||||
ATOM 1329 N N ? ALA Axp 180 ? 14.229 35.929 18.757 -1.09 0 407 A
|
||||
ATOM 1333 C CB ? ALA Axp 180 ? 12.155 36.812 17.751 0.00 0 407 A
|
||||
ATOM 1354 C CB ? SER Axp 183 ? 11.829 35.508 22.060 0.00 0 410 A
|
||||
ATOM 1355 O OG ? SER Axp 183 ? 10.954 35.267 20.964 0.00 0 410 A
|
||||
ATOM 1405 C CD2 ? PHE Axp 189 ? 10.703 31.452 22.157 0.00 0 416 A
|
||||
ATOM 1407 C CE2 ? PHE Axp 189 ? 11.966 31.656 22.739 0.00 0 416 A
|
||||
ATOM 1408 C CZ ? PHE Axp 189 ? 12.053 32.229 24.016 0.00 0 416 A
|
||||
ATOM 1433 C CA ? SER Axp 193 ? 9.893 34.090 16.472 0.00 0 420 A
|
||||
ATOM 1434 C C ? SER Axp 193 ? 10.658 32.899 15.802 0.00 0 420 A
|
||||
ATOM 1435 O O ? SER Axp 193 ? 11.879 32.960 15.552 -3.21 0 420 A
|
||||
ATOM 1436 C CB ? SER Axp 193 ? 9.997 34.149 17.982 0.00 0 420 A
|
||||
ATOM 1437 O OG ? SER Axp 193 ? 9.317 33.077 18.605 0.00 0 420 A
|
||||
ATOM 1438 N N ? ASP Axp 194 ? 9.907 31.853 15.450 0.00 0 421 A
|
||||
ATOM 1439 C CA ? ASP Axp 194 ? 10.435 30.800 14.622 0.00 0 421 A
|
||||
ATOM 1444 O OD1 ? ASP Axp 194 ? 10.115 28.834 16.531 0.00 0 421 A
|
||||
ATOM 1471 C CB ? ALA Axp 197 ? 14.926 31.065 14.885 0.00 0 424 A
|
||||
#
|
||||
32
tests/reference_output/123abc_out/pocket11_vert.pqr
Normal file
32
tests/reference_output/123abc_out/pocket11_vert.pqr
Normal file
@@ -0,0 +1,32 @@
|
||||
ATOM 1 O STP 11 12.898 31.662 19.017 0.00 3.84
|
||||
ATOM 2 O STP 11 13.150 32.247 19.120 0.00 3.85
|
||||
ATOM 3 O STP 11 15.088 30.679 21.810 0.00 3.40
|
||||
ATOM 4 O STP 11 14.161 31.633 19.836 0.00 3.64
|
||||
ATOM 5 O STP 11 13.387 31.848 19.044 0.00 3.96
|
||||
ATOM 6 O STP 11 13.175 32.231 19.116 0.00 3.86
|
||||
ATOM 7 O STP 11 12.808 31.604 18.987 0.00 3.81
|
||||
ATOM 8 O STP 11 12.873 31.765 19.036 0.00 3.81
|
||||
ATOM 9 C STP 11 12.557 32.462 19.477 0.00 3.41
|
||||
ATOM 10 O STP 11 12.931 31.991 19.076 0.00 3.80
|
||||
ATOM 11 C STP 11 16.028 30.026 18.804 0.00 3.56
|
||||
ATOM 12 O STP 11 13.473 31.801 18.968 0.00 3.94
|
||||
ATOM 13 O STP 11 13.537 32.512 18.591 0.00 3.49
|
||||
ATOM 14 O STP 11 15.773 30.122 18.478 0.00 3.59
|
||||
ATOM 15 O STP 11 14.671 31.353 19.355 0.00 3.61
|
||||
ATOM 16 O STP 11 15.838 30.562 19.199 0.00 3.61
|
||||
ATOM 17 O STP 11 15.915 30.373 18.983 0.00 3.61
|
||||
ATOM 18 O STP 11 16.143 30.691 19.153 0.00 3.44
|
||||
ATOM 19 O STP 11 13.668 31.316 18.409 0.00 3.75
|
||||
ATOM 20 O STP 11 15.536 30.118 18.260 0.00 3.56
|
||||
ATOM 21 C STP 11 15.745 30.047 18.174 0.00 3.54
|
||||
ATOM 22 O STP 11 12.904 32.687 19.451 0.00 3.57
|
||||
ATOM 23 C STP 11 15.940 29.800 17.882 0.00 3.41
|
||||
ATOM 24 O STP 11 12.225 30.961 18.523 0.00 3.60
|
||||
ATOM 25 O STP 11 12.987 30.452 17.753 0.00 3.52
|
||||
ATOM 26 O STP 11 12.997 30.420 17.738 0.00 3.50
|
||||
ATOM 27 O STP 11 11.766 30.743 19.000 0.00 3.41
|
||||
ATOM 28 O STP 11 11.834 30.739 18.825 0.00 3.44
|
||||
ATOM 29 C STP 11 13.290 32.673 19.656 0.00 3.51
|
||||
ATOM 30 C STP 11 14.144 31.854 20.011 0.00 3.50
|
||||
TER
|
||||
END
|
||||
61
tests/reference_output/123abc_out/pocket12_atm.cif
Normal file
61
tests/reference_output/123abc_out/pocket12_atm.cif
Normal file
@@ -0,0 +1,61 @@
|
||||
data_pocket12_atm
|
||||
#
|
||||
loop_
|
||||
_struct.pdbx_descriptor
|
||||
This is a mmcif format file writen by the programm fpocket.
|
||||
It represents the atoms contacted by the voronoi vertices of the pocket.
|
||||
|
||||
Information about the pocket 12:
|
||||
0 - Pocket Score : 0.0380
|
||||
1 - Drug Score : 0.0004
|
||||
2 - Number of alpha spheres : 22
|
||||
3 - Mean alpha-sphere radius : 4.0091
|
||||
4 - Mean alpha-sphere Solvent Acc. : 0.5656
|
||||
5 - Mean B-factor of pocket residues : 0.1891
|
||||
6 - Hydrophobicity Score : 14.1667
|
||||
7 - Polarity Score : 7
|
||||
8 - Amino Acid based volume Score : 4.4167
|
||||
9 - Pocket volume (Monte Carlo) : 288.4808
|
||||
10 -Pocket volume (convex hull) : 19.5893
|
||||
11 - Charge Score : 1
|
||||
12 - Local hydrophobic density Score : 1.0000
|
||||
13 - Number of apolar alpha sphere : 2
|
||||
14 - Proportion of apolar alpha sphere : 0.0909
|
||||
#
|
||||
loop_
|
||||
_atom_site.group_PDB
|
||||
_atom_site.id
|
||||
_atom_site.type_symbol
|
||||
_atom_site.label_atom_id
|
||||
_atom_site.label_alt_id
|
||||
_atom_site.label_comp_id
|
||||
_atom_site.label_asym_id
|
||||
_atom_site.label_seq_id
|
||||
_atom_site.pdbx_PDB_ins_code
|
||||
_atom_site.Cartn_x
|
||||
_atom_site.Cartn_y
|
||||
_atom_site.Cartn_z
|
||||
_atom_site.occupancy
|
||||
_atom_site.pdbx_formal_charge
|
||||
_atom_site.auth_seq_id
|
||||
_atom_site.auth_asym_id
|
||||
ATOM 3242 O OD2 ? ASP Bxp 154 ? 14.601 55.095 40.376 -2.28 0 381 B
|
||||
ATOM 3271 O OG ? SER Bxp 158 ? 19.353 51.914 34.201 -4.02 0 385 B
|
||||
ATOM 3255 C CA ? GLY Bxp 156 ? 19.014 56.342 37.269 0.00 0 383 B
|
||||
ATOM 3241 O OD1 ? ASP Bxp 154 ? 16.754 55.332 40.331 -1.07 0 381 B
|
||||
ATOM 3383 C CE2 ? PHE Bxp 174 ? 15.221 45.900 34.664 0.00 0 401 B
|
||||
ATOM 3094 O O ? ARG Bxp 135 ? 14.784 48.309 40.445 -7.50 0 362 B
|
||||
ATOM 3097 C CD ? ARG Bxp 135 ? 10.822 49.558 37.921 0.00 0 362 B
|
||||
ATOM 3504 C CE2 ? PHE Bxp 189 ? 12.691 45.021 38.263 0.00 0 416 B
|
||||
ATOM 3368 O O ? LYS Bxp 173 ? 18.932 47.542 34.352 -3.62 0 400 B
|
||||
ATOM 3109 O OD2 ? ASP Bxp 136 ? 19.063 51.084 39.753 -0.40 0 363 B
|
||||
ATOM 3258 N N ? LEU Bxp 157 ? 20.869 54.873 37.697 0.00 0 384 B
|
||||
ATOM 3095 C CB ? ARG Bxp 135 ? 12.276 49.729 39.764 0.00 0 362 B
|
||||
ATOM 3084 O O ? HIS Bxp 134 ? 12.372 52.048 41.332 -1.07 0 361 B
|
||||
ATOM 3381 C CD2 ? PHE Bxp 174 ? 16.430 45.506 35.243 0.00 0 401 B
|
||||
ATOM 3270 C CB ? SER Bxp 158 ? 20.116 50.947 34.907 0.00 0 385 B
|
||||
ATOM 3326 C CE2 ? TYR Bxp 166 ? 21.152 49.314 38.053 0.00 0 393 B
|
||||
ATOM 3391 C CD ? PRO Bxp 175 ? 19.172 45.854 38.445 0.00 0 402 B
|
||||
ATOM 3106 C CB ? ASP Bxp 136 ? 17.005 50.806 40.933 0.00 0 363 B
|
||||
ATOM 3107 C CG ? ASP Bxp 136 ? 18.465 50.434 40.626 0.00 0 363 B
|
||||
#
|
||||
58
tests/reference_output/123abc_out/pocket12_env_atm.cif
Normal file
58
tests/reference_output/123abc_out/pocket12_env_atm.cif
Normal file
@@ -0,0 +1,58 @@
|
||||
data_pocket12_env_atm
|
||||
#
|
||||
loop_
|
||||
_atom_site.group_PDB
|
||||
_atom_site.id
|
||||
_atom_site.type_symbol
|
||||
_atom_site.label_atom_id
|
||||
_atom_site.label_alt_id
|
||||
_atom_site.label_comp_id
|
||||
_atom_site.label_asym_id
|
||||
_atom_site.label_seq_id
|
||||
_atom_site.pdbx_PDB_ins_code
|
||||
_atom_site.Cartn_x
|
||||
_atom_site.Cartn_y
|
||||
_atom_site.Cartn_z
|
||||
_atom_site.occupancy
|
||||
_atom_site.pdbx_formal_charge
|
||||
_atom_site.auth_seq_id
|
||||
_atom_site.auth_asym_id
|
||||
ATOM 3084 O O ? HIS Bxp 134 ? 12.372 52.048 41.332 -1.07 0 361 B
|
||||
ATOM 3092 C CA ? ARG Bxp 135 ? 12.705 49.230 41.141 0.00 0 362 B
|
||||
ATOM 3093 C C ? ARG Bxp 135 ? 14.235 49.115 41.170 0.00 0 362 B
|
||||
ATOM 3094 O O ? ARG Bxp 135 ? 14.784 48.309 40.445 -7.50 0 362 B
|
||||
ATOM 3095 C CB ? ARG Bxp 135 ? 12.276 49.729 39.764 0.00 0 362 B
|
||||
ATOM 3096 C CG ? ARG Bxp 135 ? 10.987 49.132 39.313 0.00 0 362 B
|
||||
ATOM 3097 C CD ? ARG Bxp 135 ? 10.822 49.558 37.921 0.00 0 362 B
|
||||
ATOM 3098 N NE ? ARG Bxp 135 ? 9.837 48.697 37.316 -3.28 0 362 B
|
||||
ATOM 3099 C CZ ? ARG Bxp 135 ? 9.680 48.564 36.008 0.00 0 362 B
|
||||
ATOM 3100 N NH1 ? ARG Bxp 135 ? 10.479 49.242 35.166 0.00 0 362 B
|
||||
ATOM 3102 N N ? ASP Bxp 136 ? 14.929 49.943 41.933 0.00 0 363 B
|
||||
ATOM 3103 C CA ? ASP Bxp 136 ? 16.383 49.878 41.974 0.00 0 363 B
|
||||
ATOM 3106 C CB ? ASP Bxp 136 ? 17.005 50.806 40.933 0.00 0 363 B
|
||||
ATOM 3107 C CG ? ASP Bxp 136 ? 18.465 50.434 40.626 0.00 0 363 B
|
||||
ATOM 3108 O OD1 ? ASP Bxp 136 ? 19.011 49.469 41.230 -2.14 0 363 B
|
||||
ATOM 3109 O OD2 ? ASP Bxp 136 ? 19.063 51.084 39.753 -0.40 0 363 B
|
||||
ATOM 3240 C CG ? ASP Bxp 154 ? 15.630 55.631 40.804 0.00 0 381 B
|
||||
ATOM 3241 O OD1 ? ASP Bxp 154 ? 16.754 55.332 40.331 -1.07 0 381 B
|
||||
ATOM 3242 O OD2 ? ASP Bxp 154 ? 14.601 55.095 40.376 -2.28 0 381 B
|
||||
ATOM 3254 N N ? GLY Bxp 156 ? 19.098 56.710 38.688 0.00 0 383 B
|
||||
ATOM 3255 C CA ? GLY Bxp 156 ? 19.014 56.342 37.269 0.00 0 383 B
|
||||
ATOM 3256 C C ? GLY Bxp 156 ? 20.360 55.778 36.866 0.00 0 383 B
|
||||
ATOM 3258 N N ? LEU Bxp 157 ? 20.869 54.873 37.697 0.00 0 384 B
|
||||
ATOM 3266 N N ? SER Bxp 158 ? 21.413 52.688 36.129 0.00 0 385 B
|
||||
ATOM 3267 C CA ? SER Bxp 158 ? 21.516 51.514 35.236 0.00 0 385 B
|
||||
ATOM 3270 C CB ? SER Bxp 158 ? 20.116 50.947 34.907 0.00 0 385 B
|
||||
ATOM 3271 O OG ? SER Bxp 158 ? 19.353 51.914 34.201 -4.02 0 385 B
|
||||
ATOM 3324 C CD2 ? TYR Bxp 166 ? 21.644 48.614 37.025 0.00 0 393 B
|
||||
ATOM 3326 C CE2 ? TYR Bxp 166 ? 21.152 49.314 38.053 0.00 0 393 B
|
||||
ATOM 3368 O O ? LYS Bxp 173 ? 18.932 47.542 34.352 -3.62 0 400 B
|
||||
ATOM 3375 C CA ? PHE Bxp 174 ? 19.360 45.109 35.564 0.00 0 401 B
|
||||
ATOM 3381 C CD2 ? PHE Bxp 174 ? 16.430 45.506 35.243 0.00 0 401 B
|
||||
ATOM 3383 C CE2 ? PHE Bxp 174 ? 15.221 45.900 34.664 0.00 0 401 B
|
||||
ATOM 3390 C CG ? PRO Bxp 175 ? 19.698 46.334 39.774 0.00 0 402 B
|
||||
ATOM 3391 C CD ? PRO Bxp 175 ? 19.172 45.854 38.445 0.00 0 402 B
|
||||
ATOM 3502 C CD2 ? PHE Bxp 189 ? 11.410 45.318 38.790 0.00 0 416 B
|
||||
ATOM 3504 C CE2 ? PHE Bxp 189 ? 12.691 45.021 38.263 0.00 0 416 B
|
||||
ATOM 3505 C CZ ? PHE Bxp 189 ? 12.791 44.477 36.970 0.00 0 416 B
|
||||
#
|
||||
24
tests/reference_output/123abc_out/pocket12_vert.pqr
Normal file
24
tests/reference_output/123abc_out/pocket12_vert.pqr
Normal file
@@ -0,0 +1,24 @@
|
||||
ATOM 1 O STP 12 15.798 53.375 36.448 0.00 4.45
|
||||
ATOM 2 C STP 12 13.890 48.091 37.059 0.00 3.51
|
||||
ATOM 3 O STP 12 15.723 50.129 36.349 0.00 4.58
|
||||
ATOM 4 O STP 12 16.096 50.102 36.606 0.00 4.44
|
||||
ATOM 5 O STP 12 15.901 52.536 36.959 0.00 4.46
|
||||
ATOM 6 O STP 12 16.813 53.016 37.079 0.00 3.99
|
||||
ATOM 7 O STP 12 18.001 53.059 37.147 0.00 3.44
|
||||
ATOM 8 C STP 12 14.176 48.608 36.866 0.00 3.64
|
||||
ATOM 9 O STP 12 12.896 52.943 37.474 0.00 3.99
|
||||
ATOM 10 O STP 12 16.135 49.273 36.737 0.00 4.06
|
||||
ATOM 11 O STP 12 17.906 49.419 37.009 0.00 3.41
|
||||
ATOM 12 O STP 12 16.145 50.097 36.607 0.00 4.40
|
||||
ATOM 13 O STP 12 17.037 48.850 37.404 0.00 3.82
|
||||
ATOM 14 O STP 12 16.872 48.623 37.320 0.00 3.77
|
||||
ATOM 15 O STP 12 17.737 48.872 37.372 0.00 3.51
|
||||
ATOM 16 O STP 12 15.994 50.263 36.624 0.00 4.46
|
||||
ATOM 17 O STP 12 15.478 50.742 36.523 0.00 4.67
|
||||
ATOM 18 O STP 12 15.879 52.513 36.955 0.00 4.47
|
||||
ATOM 19 O STP 12 14.645 52.046 38.693 0.00 3.48
|
||||
ATOM 20 O STP 12 15.903 52.532 37.000 0.00 4.43
|
||||
ATOM 21 O STP 12 16.777 49.342 37.774 0.00 3.49
|
||||
ATOM 22 O STP 12 17.097 48.804 37.592 0.00 3.71
|
||||
TER
|
||||
END
|
||||
74
tests/reference_output/123abc_out/pocket13_atm.cif
Normal file
74
tests/reference_output/123abc_out/pocket13_atm.cif
Normal file
@@ -0,0 +1,74 @@
|
||||
data_pocket13_atm
|
||||
#
|
||||
loop_
|
||||
_struct.pdbx_descriptor
|
||||
This is a mmcif format file writen by the programm fpocket.
|
||||
It represents the atoms contacted by the voronoi vertices of the pocket.
|
||||
|
||||
Information about the pocket 13:
|
||||
0 - Pocket Score : 0.0342
|
||||
1 - Drug Score : 0.3180
|
||||
2 - Number of alpha spheres : 51
|
||||
3 - Mean alpha-sphere radius : 3.7908
|
||||
4 - Mean alpha-sphere Solvent Acc. : 0.4415
|
||||
5 - Mean B-factor of pocket residues : 0.1092
|
||||
6 - Hydrophobicity Score : 59.0769
|
||||
7 - Polarity Score : 0
|
||||
8 - Amino Acid based volume Score : 3.6154
|
||||
9 - Pocket volume (Monte Carlo) : 411.4784
|
||||
10 -Pocket volume (convex hull) : 39.2787
|
||||
11 - Charge Score : 0
|
||||
12 - Local hydrophobic density Score : 37.1163
|
||||
13 - Number of apolar alpha sphere : 43
|
||||
14 - Proportion of apolar alpha sphere : 0.8431
|
||||
#
|
||||
loop_
|
||||
_atom_site.group_PDB
|
||||
_atom_site.id
|
||||
_atom_site.type_symbol
|
||||
_atom_site.label_atom_id
|
||||
_atom_site.label_alt_id
|
||||
_atom_site.label_comp_id
|
||||
_atom_site.label_asym_id
|
||||
_atom_site.label_seq_id
|
||||
_atom_site.pdbx_PDB_ins_code
|
||||
_atom_site.Cartn_x
|
||||
_atom_site.Cartn_y
|
||||
_atom_site.Cartn_z
|
||||
_atom_site.occupancy
|
||||
_atom_site.pdbx_formal_charge
|
||||
_atom_site.auth_seq_id
|
||||
_atom_site.auth_asym_id
|
||||
ATOM 7064 N N ? VAL Dxp 111 ? 48.340 24.744 22.841 0.00 0 338 D
|
||||
ATOM 7069 C CG1 ? VAL Dxp 111 ? 50.065 24.177 20.697 0.00 0 338 D
|
||||
ATOM 7068 C CB ? VAL Dxp 111 ? 49.531 23.019 21.320 0.00 0 338 D
|
||||
ATOM 7063 C CB ? ALA Dxp 110 ? 45.905 26.806 22.761 0.00 0 337 D
|
||||
ATOM 8096 C CG1 ? VAL Dxp 241 ? 40.339 21.749 29.386 0.00 0 468 D
|
||||
ATOM 7780 O O ? LEU Dxp 202 ? 42.550 24.062 33.744 0.00 0 429 D
|
||||
ATOM 7784 C CD2 ? LEU Dxp 202 ? 42.820 19.922 32.429 0.00 0 429 D
|
||||
ATOM 7814 C CG2 ? ILE Dxp 205 ? 46.612 24.182 31.921 0.00 0 432 D
|
||||
ATOM 7081 O O ? LEU Dxp 113 ? 47.597 21.725 29.219 -1.07 0 340 D
|
||||
ATOM 7086 N N ? LEU Dxp 114 ? 47.359 21.989 26.988 0.00 0 341 D
|
||||
ATOM 7087 C CA ? LEU Dxp 114 ? 46.823 20.670 26.737 0.00 0 341 D
|
||||
ATOM 7080 C C ? LEU Dxp 113 ? 47.767 22.386 28.183 0.00 0 340 D
|
||||
ATOM 7062 O O ? ALA Dxp 110 ? 47.080 24.204 24.629 -3.21 0 337 D
|
||||
ATOM 7093 C CD2 ? LEU Dxp 114 ? 45.275 20.097 23.190 0.00 0 341 D
|
||||
ATOM 8079 C CG ? PRO Dxp 238 ? 40.497 24.257 24.472 0.00 0 465 D
|
||||
ATOM 7061 C C ? ALA Dxp 110 ? 47.472 25.051 23.811 0.00 0 337 D
|
||||
ATOM 8080 C CD ? PRO Dxp 238 ? 40.408 25.135 25.676 0.00 0 465 D
|
||||
ATOM 8067 O O ? GLY Dxp 236 ? 40.728 28.470 25.473 -1.21 0 463 D
|
||||
ATOM 7060 C CA ? ALA Dxp 110 ? 46.959 26.484 23.905 0.00 0 337 D
|
||||
ATOM 7084 C CD1 ? LEU Dxp 113 ? 46.418 27.158 28.740 0.00 0 340 D
|
||||
ATOM 7817 C CA ? ALA Dxp 206 ? 43.249 27.236 31.702 0.00 0 433 D
|
||||
ATOM 7819 O O ? ALA Dxp 206 ? 43.166 29.530 31.087 -4.69 0 433 D
|
||||
ATOM 8069 C CA ? CYS Dxp 237 ? 39.173 27.291 27.413 0.00 0 464 D
|
||||
ATOM 7118 C CB ? ALA Dxp 117 ? 45.712 18.926 30.827 0.00 0 344 D
|
||||
ATOM 7820 C CB ? ALA Dxp 206 ? 41.725 26.810 31.590 0.00 0 433 D
|
||||
ATOM 8073 S SG ? CYS Dxp 237 ? 38.662 25.215 29.286 0.00 0 464 D
|
||||
ATOM 7816 N N ? ALA Dxp 206 ? 43.950 26.440 32.723 0.00 0 433 D
|
||||
ATOM 7065 C CA ? VAL Dxp 111 ? 48.863 23.360 22.717 0.00 0 338 D
|
||||
ATOM 7082 C CB ? LEU Dxp 113 ? 47.325 24.825 28.299 0.00 0 340 D
|
||||
ATOM 8097 C CG2 ? VAL Dxp 241 ? 40.590 21.066 26.854 0.00 0 468 D
|
||||
ATOM 7092 C CD1 ? LEU Dxp 114 ? 44.050 19.857 25.449 0.00 0 341 D
|
||||
ATOM 8308 C CE1 ? PHE Dxp 266 ? 42.431 17.800 28.875 0.00 0 493 D
|
||||
#
|
||||
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Reference in New Issue
Block a user