#include "babelconfig.h"
#include <math.h>
#include <algorithm>
#include <vector>
#include <string>
#include <map>
#include <iostream>
#include <fstream>
#include "base.h"
#include "data.h"
#include "chains.h"
#include "math/vector3.h"
#include "bitvec.h"
#include "ring.h"
#include "generic.h"
#include "typer.h"
#include "oberror.h"
#include "obiter.h"
#include "reaction.h"
Go to the source code of this file.
Namespaces | |
| namespace | OpenBabel |
Classes | |
| class | OBResidue |
| Residue information. More... | |
| class | OBAtom |
| Atom class. More... | |
| class | OBBond |
| Bond class. More... | |
| class | OBMol |
| Molecule Class. More... | |
| class | OBInternalCoord |
| Used to transform from z-matrix to cartesian coordinates. More... | |
Defines | |
| #define | OB_4RING_ATOM (1<<1) |
| Atom is in a 4-membered ring. | |
| #define | OB_3RING_ATOM (1<<2) |
| Atom is in a 3-membered ring. | |
| #define | OB_AROMATIC_ATOM (1<<3) |
| Atom is aromatic. | |
| #define | OB_RING_ATOM (1<<4) |
| Atom is in a ring. | |
| #define | OB_CSTEREO_ATOM (1<<5) |
| Atom has clockwise SMILES chiral stereochemistry (i.e., "@@"). | |
| #define | OB_ACSTEREO_ATOM (1<<6) |
| Atom has anticlockwise SMILES chiral stereochemistry (i.e., "@"). | |
| #define | OB_DONOR_ATOM (1<<7) |
| Atom is an electron donor. | |
| #define | OB_ACCEPTOR_ATOM (1<<8) |
| Atom is an electron acceptor. | |
| #define | OB_CHIRAL_ATOM (1<<9) |
| Atom is chiral. | |
| #define | OB_POS_CHIRAL_ATOM (1<<10) |
| Atom has + chiral volume. | |
| #define | OB_NEG_CHIRAL_ATOM (1<<11) |
| Atom has - chiral volume. | |
| #define | OB_AROMATIC_BOND (1<<1) |
| An aromatic bond (regardless of bond order). | |
| #define | OB_WEDGE_BOND (1<<2) |
| A solid black wedge in 2D representations -- i.e., "up" from the 2D plane. | |
| #define | OB_HASH_BOND (1<<3) |
| A dashed "hash" bond in 2D representations -- i.e., "down" from the 2D plane. | |
| #define | OB_RING_BOND (1<<4) |
| A bond in a ring. | |
| #define | OB_TORUP_BOND (1<<5) |
| The "upper" bond in a double bond cis/trans isomer (i.e., "/" in SMILES). | |
| #define | OB_TORDOWN_BOND (1<<6) |
| The "down" bond in a double bond cis/trans isomer (i.e., "\" in SMILES). | |
| #define | OB_KSINGLE_BOND (1<<7) |
| A Kekule single bond. | |
| #define | OB_KDOUBLE_BOND (1<<8) |
| A Kekule double bond. | |
| #define | OB_KTRIPLE_BOND (1<<9) |
| A Kekule triple bond. | |
| #define | OB_CLOSURE_BOND (1<<10) |
| #define | OB_SSSR_MOL (1<<1) |
| #define | OB_RINGFLAGS_MOL (1<<2) |
| #define | OB_AROMATIC_MOL (1<<3) |
| #define | OB_ATOMTYPES_MOL (1<<4) |
| #define | OB_CHIRALITY_MOL (1<<5) |
| #define | OB_PCHARGE_MOL (1<<6) |
| #define | OB_HYBRID_MOL (1<<8) |
| #define | OB_IMPVAL_MOL (1<<9) |
| #define | OB_KEKULE_MOL (1<<10) |
| #define | OB_CLOSURE_MOL (1<<11) |
| #define | OB_H_ADDED_MOL (1<<12) |
| #define | OB_PH_CORRECTED_MOL (1<<13) |
| #define | OB_AROM_CORRECTED_MOL (1<<14) |
| #define | OB_CHAINS_MOL (1<<15) |
| #define | OB_TCHARGE_MOL (1<<16) |
| #define | OB_TSPIN_MOL (1<<17) |
| #define | OB_CURRENT_CONFORMER -1 |
| #define | BUFF_SIZE 32768 |
| #define | EQ(a, b) (!strcmp((a), (b))) |
| #define | EQn(a, b, n) (!strncmp((a), (b), (n))) |
| #define | SQUARE(x) ((x)*(x)) |
| #define | IsUnsatType(x) (EQ(x,"Car") || EQ(x,"C2") || EQ(x,"Sox") || EQ(x,"Sac") || EQ(x,"Pac") || EQ(x,"So2")) |
Functions | |
| bool | tokenize (vector< string > &, const char *, const char *) |
| bool | tokenize (std::vector< std::string > &, std::string &, const char *delimstr=" \t\n", int limit=-1) |
| void | Trim (std::string &txt) |
| remove leading and trailing whitespace from a string | |
| void | ThrowError (char *str) |
| void | ThrowError (std::string &str) |
| void | CartesianToInternal (std::vector< OBInternalCoord * > &, OBMol &) |
| void | InternalToCartesian (std::vector< OBInternalCoord * > &, OBMol &) |
| std::string | NewExtension (string &src, char *ext) |
| Utility function: replace the last extension in string &src with new extension char *ext. | |
| void | get_rmat (double *, double *, double *, int) |
| void | ob_make_rmat (double mat[3][3], double rmat[9]) |
| void | qtrfit (double *r, double *f, int size, double u[3][3]) |
| double | superimpose (double *, double *, int) |
Variables | |
| OBElementTable | etab |
| Global OBElementTable for element properties. | |
| OBTypeTable | ttab |
| OBIsotopeTable | isotab |
| Global OBIsotopeTable for isotope properties. | |
| OBAromaticTyper | aromtyper |
| Global OBAromaticTyper for detecting aromatic atoms and bonds. | |
| OBAtomTyper | atomtyper |
| OBChainsParser | chainsparser |
| Global OBChainsParser for detecting macromolecular chains and residues. | |
| OBMessageHandler | obErrorLog |
| Global OBMessageHandler error handler. | |
| OBResidueData | resdat |
| Global OBResidueData biomolecule residue database. | |
| #define OB_4RING_ATOM (1<<1) |
Atom is in a 4-membered ring.
| #define OB_3RING_ATOM (1<<2) |
Atom is in a 3-membered ring.
| #define OB_AROMATIC_ATOM (1<<3) |
Atom is aromatic.
| #define OB_RING_ATOM (1<<4) |
Atom is in a ring.
| #define OB_CSTEREO_ATOM (1<<5) |
Atom has clockwise SMILES chiral stereochemistry (i.e., "@@").
| #define OB_ACSTEREO_ATOM (1<<6) |
Atom has anticlockwise SMILES chiral stereochemistry (i.e., "@").
| #define OB_DONOR_ATOM (1<<7) |
Atom is an electron donor.
| #define OB_ACCEPTOR_ATOM (1<<8) |
Atom is an electron acceptor.
| #define OB_CHIRAL_ATOM (1<<9) |
Atom is chiral.
| #define OB_POS_CHIRAL_ATOM (1<<10) |
Atom has + chiral volume.
| #define OB_NEG_CHIRAL_ATOM (1<<11) |
Atom has - chiral volume.
| #define OB_AROMATIC_BOND (1<<1) |
An aromatic bond (regardless of bond order).
| #define OB_WEDGE_BOND (1<<2) |
A solid black wedge in 2D representations -- i.e., "up" from the 2D plane.
| #define OB_HASH_BOND (1<<3) |
A dashed "hash" bond in 2D representations -- i.e., "down" from the 2D plane.
| #define OB_RING_BOND (1<<4) |
A bond in a ring.
| #define OB_TORUP_BOND (1<<5) |
The "upper" bond in a double bond cis/trans isomer (i.e., "/" in SMILES).
| #define OB_TORDOWN_BOND (1<<6) |
The "down" bond in a double bond cis/trans isomer (i.e., "\" in SMILES).
| #define OB_KSINGLE_BOND (1<<7) |
A Kekule single bond.
| #define OB_KDOUBLE_BOND (1<<8) |
A Kekule double bond.
| #define OB_KTRIPLE_BOND (1<<9) |
A Kekule triple bond.
| #define OB_CLOSURE_BOND (1<<10) |
| #define OB_SSSR_MOL (1<<1) |
| #define OB_RINGFLAGS_MOL (1<<2) |
| #define OB_AROMATIC_MOL (1<<3) |
| #define OB_ATOMTYPES_MOL (1<<4) |
| #define OB_CHIRALITY_MOL (1<<5) |
| #define OB_PCHARGE_MOL (1<<6) |
| #define OB_HYBRID_MOL (1<<8) |
| #define OB_IMPVAL_MOL (1<<9) |
| #define OB_KEKULE_MOL (1<<10) |
| #define OB_CLOSURE_MOL (1<<11) |
| #define OB_H_ADDED_MOL (1<<12) |
| #define OB_PH_CORRECTED_MOL (1<<13) |
| #define OB_AROM_CORRECTED_MOL (1<<14) |
| #define OB_CHAINS_MOL (1<<15) |
| #define OB_TCHARGE_MOL (1<<16) |
| #define OB_TSPIN_MOL (1<<17) |
| #define OB_CURRENT_CONFORMER -1 |
| #define BUFF_SIZE 32768 |
| #define EQ | ( | a, | |||
| b | ) | (!strcmp((a), (b))) |
| #define EQn | ( | a, | |||
| b, | |||||
| n | ) | (!strncmp((a), (b), (n))) |
| #define SQUARE | ( | x | ) | ((x)*(x)) |
| #define IsUnsatType | ( | x | ) | (EQ(x,"Car") || EQ(x,"C2") || EQ(x,"Sox") || EQ(x,"Sac") || EQ(x,"Pac") || EQ(x,"So2")) |
This file is part of the documentation for Open Babel, version 2.0.2.
1.5.1.